diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8fd4652..533697d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -14,7 +14,7 @@ repos:
     -   id: check-added-large-files
     -   id: check-merge-conflict
 -   repo: https://github.com/psf/black
-    rev: 22.0.0
+    rev: 24.1.0
     hooks:
     -   id: black
 # We should add some linter to here at some point
diff --git a/README.md b/README.md
index d4db6f4..87407a3 100644
--- a/README.md
+++ b/README.md
@@ -39,7 +39,7 @@ Then execute the following commands in the root of the repository
 
     conda env create -f env-dev.yml
     conda activate rxn-env
-    poetry install
+    poetry install --with dev
 
 the `rxnutils` package is now installed in editable mode.
 
diff --git a/env-dev.yml b/env-dev.yml
index a4a74e4..14cef8b 100644
--- a/env-dev.yml
+++ b/env-dev.yml
@@ -3,5 +3,5 @@ channels:
   - https://conda.anaconda.org/conda-forge
   - defaults
 dependencies:
-  - python>=3.9,<3.11
-  - poetry>=1.1.4,<2.0
+  - python>=3.9,<3.13
+  - poetry>=1.2.0,<2.0
diff --git a/poetry.lock b/poetry.lock
index 5bec7cd..c0037e9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -46,48 +46,17 @@ files = [
 
 [[package]]
 name = "astroid"
-version = "2.15.8"
+version = "3.3.6"
 description = "An abstract syntax tree for Python with inference support."
 optional = false
-python-versions = ">=3.7.2"
+python-versions = ">=3.9.0"
 files = [
-    {file = "astroid-2.15.8-py3-none-any.whl", hash = "sha256:1aa149fc5c6589e3d0ece885b4491acd80af4f087baafa3fb5203b113e68cd3c"},
-    {file = "astroid-2.15.8.tar.gz", hash = "sha256:6c107453dffee9055899705de3c9ead36e74119cee151e5a9aaf7f0b0e020a6a"},
+    {file = "astroid-3.3.6-py3-none-any.whl", hash = "sha256:db676dc4f3ae6bfe31cda227dc60e03438378d7a896aec57422c95634e8d722f"},
+    {file = "astroid-3.3.6.tar.gz", hash = "sha256:6aaea045f938c735ead292204afdb977a36e989522b7833ef6fea94de743f442"},
 ]
 
 [package.dependencies]
-lazy-object-proxy = ">=1.4.0"
 typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""}
-wrapt = {version = ">=1.11,<2", markers = "python_version < \"3.11\""}
-
-[[package]]
-name = "atomicwrites"
-version = "1.4.1"
-description = "Atomic file writes."
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
-]
-
-[[package]]
-name = "attrs"
-version = "24.2.0"
-description = "Classes Without Boilerplate"
-optional = false
-python-versions = ">=3.7"
-files = [
-    {file = "attrs-24.2.0-py3-none-any.whl", hash = "sha256:81921eb96de3191c8258c199618104dd27ac608d9366f5e35d011eae1867ede2"},
-    {file = "attrs-24.2.0.tar.gz", hash = "sha256:5cfb1b9148b5b086569baec03f20d7b6bf3bcacc9a42bebf87ffaaca362f6346"},
-]
-
-[package.extras]
-benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
-tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
-tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "babel"
@@ -116,52 +85,63 @@ files = [
 
 [[package]]
 name = "black"
-version = "22.12.0"
+version = "24.10.0"
 description = "The uncompromising code formatter."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
 files = [
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-    {file = "black-22.12.0-cp310-cp310-win_amd64.whl", hash = "sha256:159a46a4947f73387b4d83e87ea006dbb2337eab6c879620a3ba52699b1f4351"},
-    {file = "black-22.12.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:d30b212bffeb1e252b31dd269dfae69dd17e06d92b87ad26e23890f3efea366f"},
-    {file = "black-22.12.0-cp311-cp311-win_amd64.whl", hash = "sha256:7412e75863aa5c5411886804678b7d083c7c28421210180d67dfd8cf1221e1f4"},
-    {file = "black-22.12.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:c116eed0efb9ff870ded8b62fe9f28dd61ef6e9ddd28d83d7d264a38417dcee2"},
-    {file = "black-22.12.0-cp37-cp37m-win_amd64.whl", hash = "sha256:1f58cbe16dfe8c12b7434e50ff889fa479072096d79f0a7f25e4ab8e94cd8350"},
-    {file = "black-22.12.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:77d86c9f3db9b1bf6761244bc0b3572a546f5fe37917a044e02f3166d5aafa7d"},
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+    {file = "black-24.10.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:e6668650ea4b685440857138e5fe40cde4d652633b1bdffc62933d0db4ed9812"},
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+    {file = "black-24.10.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:14b3502784f09ce2443830e3133dacf2c0110d45191ed470ecb04d0f5f6fcb0f"},
+    {file = "black-24.10.0-cp312-cp312-win_amd64.whl", hash = "sha256:30d2c30dc5139211dda799758559d1b049f7f14c580c409d6ad925b74a4208a8"},
+    {file = "black-24.10.0-cp313-cp313-macosx_10_13_x86_64.whl", hash = "sha256:1cbacacb19e922a1d75ef2b6ccaefcd6e93a2c05ede32f06a21386a04cedb981"},
+    {file = "black-24.10.0-cp313-cp313-macosx_11_0_arm64.whl", hash = "sha256:1f93102e0c5bb3907451063e08b9876dbeac810e7da5a8bfb7aeb5a9ef89066b"},
+    {file = "black-24.10.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:ddacb691cdcdf77b96f549cf9591701d8db36b2f19519373d60d31746068dbf2"},
+    {file = "black-24.10.0-cp313-cp313-win_amd64.whl", hash = "sha256:680359d932801c76d2e9c9068d05c6b107f2584b2a5b88831c83962eb9984c1b"},
+    {file = "black-24.10.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:17374989640fbca88b6a448129cd1745c5eb8d9547b464f281b251dd00155ccd"},
+    {file = "black-24.10.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:63f626344343083322233f175aaf372d326de8436f5928c042639a4afbbf1d3f"},
+    {file = "black-24.10.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:ccfa1d0cb6200857f1923b602f978386a3a2758a65b52e0950299ea014be6800"},
+    {file = "black-24.10.0-cp39-cp39-win_amd64.whl", hash = "sha256:2cd9c95431d94adc56600710f8813ee27eea544dd118d45896bb734e9d7a0dc7"},
+    {file = "black-24.10.0-py3-none-any.whl", hash = "sha256:3bb2b7a1f7b685f85b11fed1ef10f8a9148bceb49853e47a294a3dd963c1dd7d"},
+    {file = "black-24.10.0.tar.gz", hash = "sha256:846ea64c97afe3bc677b761787993be4991810ecc7a4a937816dd6bddedc4875"},
 ]
 
 [package.dependencies]
 click = ">=8.0.0"
 mypy-extensions = ">=0.4.3"
+packaging = ">=22.0"
 pathspec = ">=0.9.0"
 platformdirs = ">=2"
-tomli = {version = ">=1.1.0", markers = "python_full_version < \"3.11.0a7\""}
-typing-extensions = {version = ">=3.10.0.0", markers = "python_version < \"3.10\""}
+tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
+typing-extensions = {version = ">=4.0.1", markers = "python_version < \"3.11\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.7.4)"]
+d = ["aiohttp (>=3.10)"]
 jupyter = ["ipython (>=7.8.0)", "tokenize-rt (>=3.2.0)"]
 uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "boto3"
-version = "1.35.34"
+version = "1.35.81"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "boto3-1.35.34-py3-none-any.whl", hash = "sha256:291e7b97a34967ed93297e6171f1bebb8529e64633dd48426760e3fdef1cdea8"},
-    {file = "boto3-1.35.34.tar.gz", hash = "sha256:57e6ee8504e7929bc094bb2afc879943906064179a1e88c23b4812e2c6f61532"},
+    {file = "boto3-1.35.81-py3-none-any.whl", hash = "sha256:742941b2424c0223d2d94a08c3485462fa7c58d816b62ca80f08e555243acee1"},
+    {file = "boto3-1.35.81.tar.gz", hash = "sha256:d2e95fa06f095b8e0c545dd678c6269d253809b2997c30f5ce8a956c410b4e86"},
 ]
 
 [package.dependencies]
-botocore = ">=1.35.34,<1.36.0"
+botocore = ">=1.35.81,<1.36.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.10.0,<0.11.0"
 
@@ -170,13 +150,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "botocore"
-version = "1.35.34"
+version = "1.35.81"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "botocore-1.35.34-py3-none-any.whl", hash = "sha256:ccb0fe397b11b81c9abc0c87029d17298e17bf658d8db5c0c5a551a12a207e7a"},
-    {file = "botocore-1.35.34.tar.gz", hash = "sha256:789b6501a3bb4a9591c1fe10da200cc315c1fa5df5ada19c720d8ef06439b3e3"},
+    {file = "botocore-1.35.81-py3-none-any.whl", hash = "sha256:a7b13bbd959bf2d6f38f681676aab408be01974c46802ab997617b51399239f7"},
+    {file = "botocore-1.35.81.tar.gz", hash = "sha256:564c2478e50179e0b766e6a87e5e0cdd35e1bc37eb375c1cf15511f5dd13600d"},
 ]
 
 [package.dependencies]
@@ -207,6 +187,10 @@ files = [
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     {file = "Brotli-1.1.0-cp310-cp310-musllinux_1_1_ppc64le.whl", hash = "sha256:e84799f09591700a4154154cab9787452925578841a94321d5ee8fb9a9a328f0"},
     {file = "Brotli-1.1.0-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:f66b5337fa213f1da0d9000bc8dc0cb5b896b726eefd9c6046f699b169c41b9e"},
+    {file = "Brotli-1.1.0-cp310-cp310-musllinux_1_2_aarch64.whl", hash = "sha256:5dab0844f2cf82be357a0eb11a9087f70c5430b2c241493fc122bb6f2bb0917c"},
+    {file = "Brotli-1.1.0-cp310-cp310-musllinux_1_2_i686.whl", hash = "sha256:e4fe605b917c70283db7dfe5ada75e04561479075761a0b3866c081d035b01c1"},
+    {file = "Brotli-1.1.0-cp310-cp310-musllinux_1_2_ppc64le.whl", hash = "sha256:1e9a65b5736232e7a7f91ff3d02277f11d339bf34099a56cdab6a8b3410a02b2"},
+    {file = "Brotli-1.1.0-cp310-cp310-musllinux_1_2_x86_64.whl", hash = "sha256:58d4b711689366d4a03ac7957ab8c28890415e267f9b6589969e74b6e42225ec"},
     {file = "Brotli-1.1.0-cp310-cp310-win32.whl", hash = "sha256:be36e3d172dc816333f33520154d708a2657ea63762ec16b62ece02ab5e4daf2"},
     {file = "Brotli-1.1.0-cp310-cp310-win_amd64.whl", hash = "sha256:0c6244521dda65ea562d5a69b9a26120769b7a9fb3db2fe9545935ed6735b128"},
     {file = "Brotli-1.1.0-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:a3daabb76a78f829cafc365531c972016e4aa8d5b4bf60660ad8ecee19df7ccc"},
@@ -219,8 +203,14 @@ files = [
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     {file = "Brotli-1.1.0-cp311-cp311-musllinux_1_1_ppc64le.whl", hash = "sha256:510b5b1bfbe20e1a7b3baf5fed9e9451873559a976c1a78eebaa3b86c57b4265"},
     {file = "Brotli-1.1.0-cp311-cp311-musllinux_1_1_x86_64.whl", hash = "sha256:a1fd8a29719ccce974d523580987b7f8229aeace506952fa9ce1d53a033873c8"},
+    {file = "Brotli-1.1.0-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:c247dd99d39e0338a604f8c2b3bc7061d5c2e9e2ac7ba9cc1be5a69cb6cd832f"},
+    {file = "Brotli-1.1.0-cp311-cp311-musllinux_1_2_i686.whl", hash = "sha256:1b2c248cd517c222d89e74669a4adfa5577e06ab68771a529060cf5a156e9757"},
+    {file = "Brotli-1.1.0-cp311-cp311-musllinux_1_2_ppc64le.whl", hash = "sha256:2a24c50840d89ded6c9a8fdc7b6ed3692ed4e86f1c4a4a938e1e92def92933e0"},
+    {file = "Brotli-1.1.0-cp311-cp311-musllinux_1_2_x86_64.whl", hash = "sha256:f31859074d57b4639318523d6ffdca586ace54271a73ad23ad021acd807eb14b"},
     {file = "Brotli-1.1.0-cp311-cp311-win32.whl", hash = "sha256:39da8adedf6942d76dc3e46653e52df937a3c4d6d18fdc94a7c29d263b1f5b50"},
     {file = "Brotli-1.1.0-cp311-cp311-win_amd64.whl", hash = "sha256:aac0411d20e345dc0920bdec5548e438e999ff68d77564d5e9463a7ca9d3e7b1"},
+    {file = "Brotli-1.1.0-cp312-cp312-macosx_10_13_universal2.whl", hash = "sha256:32d95b80260d79926f5fab3c41701dbb818fde1c9da590e77e571eefd14abe28"},
+    {file = "Brotli-1.1.0-cp312-cp312-macosx_10_13_x86_64.whl", hash = "sha256:b760c65308ff1e462f65d69c12e4ae085cff3b332d894637f6273a12a482d09f"},
     {file = "Brotli-1.1.0-cp312-cp312-macosx_10_9_universal2.whl", hash = "sha256:316cc9b17edf613ac76b1f1f305d2a748f1b976b033b049a6ecdfd5612c70409"},
     {file = "Brotli-1.1.0-cp312-cp312-macosx_10_9_x86_64.whl", hash = "sha256:caf9ee9a5775f3111642d33b86237b05808dafcd6268faa492250e9b78046eb2"},
     {file = "Brotli-1.1.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:70051525001750221daa10907c77830bc889cb6d865cc0b813d9db7fefc21451"},
@@ -231,8 +221,24 @@ files = [
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 ]
 
 [[package]]
@@ -591,13 +628,13 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [[package]]
 name = "cloudpickle"
-version = "3.0.0"
+version = "3.1.0"
 description = "Pickler class to extend the standard pickle.Pickler functionality"
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "cloudpickle-3.0.0.tar.gz", hash = "sha256:996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882"},
+    {file = "cloudpickle-3.1.0-py3-none-any.whl", hash = "sha256:fe11acda67f61aaaec473e3afe030feb131d78a43461b718185363384f1ba12e"},
+    {file = "cloudpickle-3.1.0.tar.gz", hash = "sha256:81a929b6e3c7335c863c771d673d105f02efdb89dfaba0c90495d1c64796601b"},
 ]
 
 [[package]]
@@ -611,85 +648,92 @@ files = [
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 ]
 
+[[package]]
+name = "coloredlogs"
+version = "15.0.1"
+description = "Colored terminal output for Python's logging module"
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
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+    {file = "coloredlogs-15.0.1.tar.gz", hash = "sha256:7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0"},
+]
+
+[package.dependencies]
+humanfriendly = ">=9.1"
+
+[package.extras]
+cron = ["capturer (>=2.4)"]
+
 [[package]]
 name = "coverage"
-version = "7.6.1"
+version = "7.6.9"
 description = "Code coverage measurement for Python"
 optional = false
-python-versions = ">=3.8"
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+    {file = "coverage-7.6.9.tar.gz", hash = "sha256:4a8d8977b0c6ef5aeadcb644da9e69ae0dcfe66ec7f368c89c72e058bd71164d"},
 ]
 
 [package.dependencies]
@@ -700,35 +744,55 @@ toml = ["tomli"]
 
 [[package]]
 name = "dask"
-version = "2024.2.1"
+version = "2024.8.0"
 description = "Parallel PyData with Task Scheduling"
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "dask-2024.2.1-py3-none-any.whl", hash = "sha256:a13fcdeead3bab3576495023f83097adcffe2f03c371c241b5a1f0b232b35b38"},
-    {file = "dask-2024.2.1.tar.gz", hash = "sha256:9504a1e9f5d8e5403fae931f9f1660d41f510f48895ccefce856ec6a4c2198d8"},
+    {file = "dask-2024.8.0-py3-none-any.whl", hash = "sha256:250ea3df30d4a25958290eec4f252850091c6cfaed82d098179c3b25bba18309"},
+    {file = "dask-2024.8.0.tar.gz", hash = "sha256:f1fec39373d2f101bc045529ad4e9b30e34e6eb33b7aa0fa7073aec7b1bf9eee"},
 ]
 
 [package.dependencies]
 click = ">=8.1"
 cloudpickle = ">=1.5.0"
+dask-expr = {version = ">=1.1,<1.2", optional = true, markers = "extra == \"dataframe\""}
 fsspec = ">=2021.09.0"
-importlib-metadata = ">=4.13.0"
+importlib-metadata = {version = ">=4.13.0", markers = "python_version < \"3.12\""}
 numpy = {version = ">=1.21", optional = true, markers = "extra == \"array\""}
 packaging = ">=20.0"
-pandas = {version = ">=1.3", optional = true, markers = "extra == \"dataframe\""}
-partd = ">=1.2.0"
+pandas = {version = ">=2.0", optional = true, markers = "extra == \"dataframe\""}
+partd = ">=1.4.0"
 pyyaml = ">=5.3.1"
 toolz = ">=0.10.0"
 
 [package.extras]
 array = ["numpy (>=1.21)"]
 complete = ["dask[array,dataframe,diagnostics,distributed]", "lz4 (>=4.3.2)", "pyarrow (>=7.0)", "pyarrow-hotfix"]
-dataframe = ["dask[array]", "pandas (>=1.3)"]
+dataframe = ["dask-expr (>=1.1,<1.2)", "dask[array]", "pandas (>=2.0)"]
 diagnostics = ["bokeh (>=2.4.2)", "jinja2 (>=2.10.3)"]
-distributed = ["distributed (==2024.2.1)"]
+distributed = ["distributed (==2024.8.0)"]
 test = ["pandas[test]", "pre-commit", "pytest", "pytest-cov", "pytest-rerunfailures", "pytest-timeout", "pytest-xdist"]
 
+[[package]]
+name = "dask-expr"
+version = "1.1.10"
+description = "High Level Expressions for Dask"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "dask_expr-1.1.10-py3-none-any.whl", hash = "sha256:c6365c6fa6d3e386c5ee79bd20d4c89e566c0cf78fb6c762f74b2f04028935c6"},
+    {file = "dask_expr-1.1.10.tar.gz", hash = "sha256:3d9ac7231f41ce7a109faaf855a60d89bd4f90d304452894178a114470164014"},
+]
+
+[package.dependencies]
+dask = "2024.8.0"
+pandas = ">=2"
+pyarrow = ">=7.0.0"
+
+[package.extras]
+analyze = ["crick", "distributed"]
+
 [[package]]
 name = "decorator"
 version = "5.1.1"
@@ -742,20 +806,20 @@ files = [
 
 [[package]]
 name = "deprecated"
-version = "1.2.14"
+version = "1.2.15"
 description = "Python @deprecated decorator to deprecate old python classes, functions or methods."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7"
 files = [
-    {file = "Deprecated-1.2.14-py2.py3-none-any.whl", hash = "sha256:6fac8b097794a90302bdbb17b9b815e732d3c4720583ff1b198499d78470466c"},
-    {file = "Deprecated-1.2.14.tar.gz", hash = "sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3"},
+    {file = "Deprecated-1.2.15-py2.py3-none-any.whl", hash = "sha256:353bc4a8ac4bfc96800ddab349d89c25dec1079f65fd53acdcc1e0b975b21320"},
+    {file = "deprecated-1.2.15.tar.gz", hash = "sha256:683e561a90de76239796e6b6feac66b99030d2dd3fcf61ef996330f14bbb9b0d"},
 ]
 
 [package.dependencies]
 wrapt = ">=1.10,<2"
 
 [package.extras]
-dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "sphinx (<2)", "tox"]
+dev = ["PyTest", "PyTest-Cov", "bump2version (<1)", "jinja2 (>=3.0.3,<3.1.0)", "setuptools", "sphinx (<2)", "tox"]
 
 [[package]]
 name = "dill"
@@ -774,13 +838,13 @@ profile = ["gprof2dot (>=2022.7.29)"]
 
 [[package]]
 name = "distlib"
-version = "0.3.8"
+version = "0.3.9"
 description = "Distribution utilities"
 optional = false
 python-versions = "*"
 files = [
-    {file = "distlib-0.3.8-py2.py3-none-any.whl", hash = "sha256:034db59a0b96f8ca18035f36290806a9a6e6bd9d1ff91e45a7f172eb17e51784"},
-    {file = "distlib-0.3.8.tar.gz", hash = "sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64"},
+    {file = "distlib-0.3.9-py2.py3-none-any.whl", hash = "sha256:47f8c22fd27c27e25a65601af709b38e4f0a45ea4fc2e710f65755fa8caaaf87"},
+    {file = "distlib-0.3.9.tar.gz", hash = "sha256:a60f20dea646b8a33f3e7772f74dc0b2d0772d2837ee1342a00645c81edf9403"},
 ]
 
 [[package]]
@@ -794,6 +858,20 @@ files = [
     {file = "docutils-0.21.2.tar.gz", hash = "sha256:3a6b18732edf182daa3cd12775bbb338cf5691468f91eeeb109deff6ebfa986f"},
 ]
 
+[[package]]
+name = "exceptiongroup"
+version = "1.2.2"
+description = "Backport of PEP 654 (exception groups)"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"},
+    {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"},
+]
+
+[package.extras]
+test = ["pytest (>=6)"]
+
 [[package]]
 name = "filelock"
 version = "3.16.1"
@@ -810,15 +888,26 @@ docs = ["furo (>=2024.8.6)", "sphinx (>=8.0.2)", "sphinx-autodoc-typehints (>=2.
 testing = ["covdefaults (>=2.3)", "coverage (>=7.6.1)", "diff-cover (>=9.2)", "pytest (>=8.3.3)", "pytest-asyncio (>=0.24)", "pytest-cov (>=5)", "pytest-mock (>=3.14)", "pytest-timeout (>=2.3.1)", "virtualenv (>=20.26.4)"]
 typing = ["typing-extensions (>=4.12.2)"]
 
+[[package]]
+name = "flatbuffers"
+version = "24.3.25"
+description = "The FlatBuffers serialization format for Python"
+optional = true
+python-versions = "*"
+files = [
+    {file = "flatbuffers-24.3.25-py2.py3-none-any.whl", hash = "sha256:8dbdec58f935f3765e4f7f3cf635ac3a77f83568138d6a2311f524ec96364812"},
+    {file = "flatbuffers-24.3.25.tar.gz", hash = "sha256:de2ec5b203f21441716617f38443e0a8ebf3d25bf0d9c0bb0ce68fa00ad546a4"},
+]
+
 [[package]]
 name = "fsspec"
-version = "2024.9.0"
+version = "2024.10.0"
 description = "File-system specification"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "fsspec-2024.9.0-py3-none-any.whl", hash = "sha256:a0947d552d8a6efa72cc2c730b12c41d043509156966cca4fb157b0f2a0c574b"},
-    {file = "fsspec-2024.9.0.tar.gz", hash = "sha256:4b0afb90c2f21832df142f292649035d80b421f60a9e1c027802e5a0da2b04e8"},
+    {file = "fsspec-2024.10.0-py3-none-any.whl", hash = "sha256:03b9a6785766a4de40368b88906366755e2819e758b83705c88cd7cb5fe81871"},
+    {file = "fsspec-2024.10.0.tar.gz", hash = "sha256:eda2d8a4116d4f2429db8550f2457da57279247dd930bb12f821b58391359493"},
 ]
 
 [package.extras]
@@ -849,15 +938,29 @@ test-downstream = ["aiobotocore (>=2.5.4,<3.0.0)", "dask-expr", "dask[dataframe,
 test-full = ["adlfs", "aiohttp (!=4.0.0a0,!=4.0.0a1)", "cloudpickle", "dask", "distributed", "dropbox", "dropboxdrivefs", "fastparquet", "fusepy", "gcsfs", "jinja2", "kerchunk", "libarchive-c", "lz4", "notebook", "numpy", "ocifs", "pandas", "panel", "paramiko", "pyarrow", "pyarrow (>=1)", "pyftpdlib", "pygit2", "pytest", "pytest-asyncio (!=0.22.0)", "pytest-benchmark", "pytest-cov", "pytest-mock", "pytest-recording", "pytest-rerunfailures", "python-snappy", "requests", "smbprotocol", "tqdm", "urllib3", "zarr", "zstandard"]
 tqdm = ["tqdm"]
 
+[[package]]
+name = "humanfriendly"
+version = "10.0"
+description = "Human friendly output for text interfaces using Python"
+optional = true
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
+    {file = "humanfriendly-10.0-py2.py3-none-any.whl", hash = "sha256:1697e1a8a8f550fd43c2865cd84542fc175a61dcb779b6fee18cf6b6ccba1477"},
+    {file = "humanfriendly-10.0.tar.gz", hash = "sha256:6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc"},
+]
+
+[package.dependencies]
+pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_version >= \"3.8\""}
+
 [[package]]
 name = "identify"
-version = "2.6.1"
+version = "2.6.3"
 description = "File identification library for Python"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
-    {file = "identify-2.6.1-py2.py3-none-any.whl", hash = "sha256:53863bcac7caf8d2ed85bd20312ea5dcfc22226800f6d6881f232d861db5a8f0"},
-    {file = "identify-2.6.1.tar.gz", hash = "sha256:91478c5fb7c3aac5ff7bf9b4344f803843dc586832d5f110d672b19aa1984c98"},
+    {file = "identify-2.6.3-py2.py3-none-any.whl", hash = "sha256:9edba65473324c2ea9684b1f944fe3191db3345e50b6d04571d10ed164f8d7bd"},
+    {file = "identify-2.6.3.tar.gz", hash = "sha256:62f5dae9b5fef52c84cc188514e9ea4f3f636b1d8799ab5ebc475471f9e47a02"},
 ]
 
 [package.extras]
@@ -924,13 +1027,13 @@ files = [
 
 [[package]]
 name = "invoke"
-version = "1.7.3"
+version = "2.2.0"
 description = "Pythonic task execution"
 optional = false
-python-versions = "*"
+python-versions = ">=3.6"
 files = [
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 ]
 
 [[package]]
@@ -985,22 +1088,22 @@ colors = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "jedi"
-version = "0.19.1"
+version = "0.19.2"
 description = "An autocompletion tool for Python that can be used for text editors."
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [package.dependencies]
-parso = ">=0.8.3,<0.9.0"
+parso = ">=0.8.4,<0.9.0"
 
 [package.extras]
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 qa = ["flake8 (==5.0.4)", "mypy (==0.971)", "types-setuptools (==67.2.0.1)"]
-testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
+testing = ["Django", "attrs", "colorama", "docopt", "pytest (<9.0.0)"]
 
 [[package]]
 name = "jinja2"
@@ -1030,52 +1133,6 @@ files = [
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 ]
 
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-optional = false
-python-versions = ">=3.8"
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-]
-
 [[package]]
 name = "lib-detect-testenv"
 version = "2.0.8"
@@ -1103,71 +1160,72 @@ files = [
 
 [[package]]
 name = "markupsafe"
-version = "2.1.5"
+version = "3.0.2"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.9"
 files = [
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 [[package]]
@@ -1197,13 +1255,13 @@ files = [
 
 [[package]]
 name = "metaflow"
-version = "2.12.24"
+version = "2.12.39"
 description = "Metaflow: More Data Science, Less Engineering"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
@@ -1211,7 +1269,24 @@ boto3 = "*"
 requests = "*"
 
 [package.extras]
-stubs = ["metaflow-stubs (==2.12.24)"]
+stubs = ["metaflow-stubs (==2.12.39)"]
+
+[[package]]
+name = "mpmath"
+version = "1.3.0"
+description = "Python library for arbitrary-precision floating-point arithmetic"
+optional = true
+python-versions = "*"
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+
+[package.extras]
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+docs = ["sphinx"]
+gmpy = ["gmpy2 (>=2.1.0a4)"]
+tests = ["pytest (>=4.6)"]
 
 [[package]]
 name = "multiprocess"
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 [package.extras]
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 [package.extras]
-test = ["enum34", "ipaddress", "mock", "pywin32", "wmi"]
+dev = ["black", "check-manifest", "coverage", "packaging", "pylint", "pyperf", "pypinfo", "pytest-cov", "requests", "rstcheck", "ruff", "sphinx", "sphinx_rtd_theme", "toml-sort", "twine", "virtualenv", "wheel"]
+test = ["pytest", "pytest-xdist", "setuptools"]
 
 [[package]]
 name = "ptyprocess"
@@ -1689,17 +1875,6 @@ files = [
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-optional = false
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 [[package]]
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 version = "0.18.12"
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 test = ["coverage[toml] (>=5.2)", "coveralls (>=2.1.1)", "py-cpuinfo", "pyannotate", "pytest", "pytest-benchmark", "pytest-cov", "pytest-remotedata", "pytest-timeout"]
 test-compat = ["libarchive-c"]
 
+[[package]]
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+
+[package.extras]
+test = ["cffi", "hypothesis", "pandas", "pytest", "pytz"]
+
 [[package]]
 name = "pybcj"
 version = "1.0.2"
@@ -1838,19 +2067,19 @@ files = [
 
 [[package]]
 name = "pydantic"
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+version = "2.10.3"
 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.8"
 files = [
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+typing-extensions = ">=4.12.2"
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
@@ -1858,100 +2087,111 @@ timezone = ["tzdata"]
 
 [[package]]
 name = "pydantic-core"
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 [package.dependencies]
@@ -1973,20 +2213,24 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pylint"
-version = "2.17.7"
+version = "3.3.2"
 description = "python code static checker"
 optional = false
-python-versions = ">=3.7.2"
+python-versions = ">=3.9.0"
 files = [
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 ]
 
 [package.dependencies]
-astroid = ">=2.15.8,<=2.17.0-dev0"
+astroid = ">=3.3.5,<=3.4.0-dev0"
 colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
-dill = {version = ">=0.2", markers = "python_version < \"3.11\""}
-isort = ">=4.2.5,<6"
+dill = [
+    {version = ">=0.2", markers = "python_version < \"3.11\""},
+    {version = ">=0.3.6", markers = "python_version >= \"3.11\" and python_version < \"3.12\""},
+    {version = ">=0.3.7", markers = "python_version >= \"3.12\""},
+]
+isort = ">=4.2.5,<5.13.0 || >5.13.0,<6"
 mccabe = ">=0.6,<0.8"
 platformdirs = ">=2.2.0"
 tomli = {version = ">=1.1.0", markers = "python_version < \"3.11\""}
@@ -2088,62 +2332,59 @@ docs = ["sphinx (>=2.3)", "sphinx-rtd-theme"]
 fuzzer = ["atheris", "hypothesis"]
 test = ["coverage[toml] (>=5.2)", "hypothesis", "pytest (>=6.0)", "pytest-benchmark", "pytest-cov", "pytest-timeout"]
 
+[[package]]
+name = "pyreadline3"
+version = "3.5.4"
+description = "A python implementation of GNU readline."
+optional = true
+python-versions = ">=3.8"
+files = [
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+]
+
+[package.extras]
+dev = ["build", "flake8", "mypy", "pytest", "twine"]
+
 [[package]]
 name = "pytest"
-version = "6.2.5"
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-attrs = ">=19.2.0"
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 iniconfig = "*"
 packaging = "*"
-pluggy = ">=0.12,<2.0"
-py = ">=1.8.2"
-toml = "*"
+pluggy = ">=1.5,<2"
+tomli = {version = ">=1", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xmlschema"]
-
-[[package]]
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-version = "0.3.12"
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-
-[package.dependencies]
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-pytest = ">=3.5.0"
-toml = "*"
+dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
 
 [[package]]
 name = "pytest-cov"
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+version = "6.0.0"
 description = "Pytest plugin for measuring coverage."
 optional = false
-python-versions = ">=3.6"
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 files = [
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 [package.dependencies]
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+coverage = {version = ">=7.5", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
-testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"]
 
 [[package]]
 name = "pytest-datadir"
@@ -2159,21 +2400,6 @@ files = [
 [package.dependencies]
 pytest = ">=5.0"
 
-[[package]]
-name = "pytest-mccabe"
-version = "2.0"
-description = "pytest plugin to run the mccabe code complexity checker."
-optional = false
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-
 [[package]]
 name = "pytest-mock"
 version = "3.14.0"
@@ -2280,100 +2506,94 @@ files = [
 
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 ]
 
 [[package]]
@@ -2446,15 +2666,32 @@ urllib3 = ">=1.21.1,<3"
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
+[[package]]
+name = "requests-mock"
+version = "1.12.1"
+description = "Mock out responses from the requests package"
+optional = false
+python-versions = ">=3.5"
+files = [
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+]
+
+[package.dependencies]
+requests = ">=2.22,<3"
+
+[package.extras]
+fixture = ["fixtures"]
+
 [[package]]
 name = "s3transfer"
-version = "0.10.2"
+version = "0.10.4"
 description = "An Amazon S3 Transfer Manager"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "s3transfer-0.10.2-py3-none-any.whl", hash = "sha256:eca1c20de70a39daee580aef4986996620f365c4e0fda6a86100231d62f1bf69"},
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+    {file = "s3transfer-0.10.4.tar.gz", hash = "sha256:29edc09801743c21eb5ecbc617a152df41d3c287f67b615f73e5f750583666a7"},
 ]
 
 [package.dependencies]
@@ -2507,33 +2744,33 @@ test = ["array-api-strict", "asv", "gmpy2", "hypothesis (>=6.30)", "mpmath", "po
 
 [[package]]
 name = "setuptools"
-version = "75.1.0"
+version = "75.6.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
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-core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.collections", "jaraco.functools", "jaraco.text (>=3.7)", "more-itertools", "more-itertools (>=8.8)", "packaging", "packaging (>=24)", "platformdirs (>=2.6.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)", "ruff (>=0.7.0)"]
+core = ["importlib_metadata (>=6)", "jaraco.collections", "jaraco.functools (>=4)", "jaraco.text (>=3.7)", "more_itertools", "more_itertools (>=8.8)", "packaging", "packaging (>=24.2)", "platformdirs (>=4.2.2)", "tomli (>=2.0.1)", "wheel (>=0.43.0)"]
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-type = ["importlib-metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (==1.11.*)", "pytest-mypy"]
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+type = ["importlib_metadata (>=7.0.2)", "jaraco.develop (>=7.21)", "mypy (>=1.12,<1.14)", "pytest-mypy"]
 
 [[package]]
 name = "six"
-version = "1.16.0"
+version = "1.17.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
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 ]
 
 [[package]]
@@ -2697,6 +2934,23 @@ tqdm = ">=4.33.0"
 groupby = ["ray (>=1.0.0)"]
 notebook = ["ipywidgets (>=7.0.0)"]
 
+[[package]]
+name = "sympy"
+version = "1.13.3"
+description = "Computer algebra system (CAS) in Python"
+optional = true
+python-versions = ">=3.8"
+files = [
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+
+[package.dependencies]
+mpmath = ">=1.1.0,<1.4"
+
+[package.extras]
+dev = ["hypothesis (>=6.70.0)", "pytest (>=7.1.0)"]
+
 [[package]]
 name = "texttable"
 version = "1.7.0"
@@ -2708,26 +2962,45 @@ files = [
     {file = "texttable-1.7.0.tar.gz", hash = "sha256:2d2068fb55115807d3ac77a4ca68fa48803e84ebb0ee2340f858107a36522638"},
 ]
 
-[[package]]
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-description = "Python Library for Tom's Obvious, Minimal Language"
-optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
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-]
-
 [[package]]
 name = "tomli"
-version = "2.0.2"
+version = "2.2.1"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -2754,20 +3027,21 @@ files = [
 
 [[package]]
 name = "tqdm"
-version = "4.66.5"
+version = "4.67.1"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
 colorama = {version = "*", markers = "platform_system == \"Windows\""}
 
 [package.extras]
-dev = ["pytest (>=6)", "pytest-cov", "pytest-timeout", "pytest-xdist"]
+dev = ["nbval", "pytest (>=6)", "pytest-asyncio (>=0.24)", "pytest-cov", "pytest-timeout"]
+discord = ["requests"]
 notebook = ["ipywidgets (>=6)"]
 slack = ["slack-sdk"]
 telegram = ["requests"]
@@ -2787,45 +3061,6 @@ files = [
 docs = ["myst-parser", "pydata-sphinx-theme", "sphinx"]
 test = ["argcomplete (>=3.0.3)", "mypy (>=1.7.0)", "pre-commit", "pytest (>=7.0,<8.2)", "pytest-mock", "pytest-mypy-testing"]
 
-[[package]]
-name = "typed-ast"
-version = "1.4.3"
-description = "a fork of Python 2 and 3 ast modules with type comment support"
-optional = false
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 [[package]]
@@ -3088,13 +3329,13 @@ files = [
 
 [[package]]
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+version = "3.21.0"
 description = "Backport of pathlib-compatible object wrapper for zip files"
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 [package.extras]
@@ -3105,7 +3346,10 @@ enabler = ["pytest-enabler (>=2.2)"]
 test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
 type = ["pytest-mypy"]
 
+[extras]
+models = ["onnxruntime"]
+
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-content-hash = "eeac29b154c59b17959559d2e86dae8378598062ed2eba88f4c8d3accd87d773"
+python-versions = ">=3.9,<3.13"
+content-hash = "46deaea202ff12057a11c95712ec2ef41dc9adda1d3071e667121f9e964a2f58"
diff --git a/pyproject.toml b/pyproject.toml
index d531b78..6114058 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,9 +13,9 @@ packages = [
 ]
 
 [tool.poetry.dependencies]
-python = ">=3.9,<3.11"
-urllib3 = "<2.0"
-pandas = "^1.0.0"
+python = ">=3.9,<3.13"
+urllib3 = "^1.2.26"
+pandas = ">=1.0.0,<3.0.0"
 xxhash = "^2.0.0"
 rdchiral = "^1.1.0"
 PyYAML = "^6.0.1"
@@ -30,21 +30,25 @@ cgrtools = "^4.1.35"
 scipy = "^1.11.4"
 pydantic = "^2.8.2"
 apted = "^1.0.3"
+dask = ">=2024.4.1"
+onnxruntime = {version = "<1.17.0", optional=true}
 
-[tool.poetry.dev-dependencies]
-pytest = "^6.2.2"
-pytest-datadir = "^1.3.1"
-pytest-mock = "^3.7.0"
-pytest-mccabe = "^2.0"
-pytest-black = "^0.3.12"
-pytest-cov = "^3.0.0"
-black = "^22.0.0"
-mypy = "^0.800"
-pre-commit = "^2.10.1"
+[tool.poetry.group.dev.dependencies]
+pytest = "^8.3.3"
+pytest-datadir = "^1.5.0"
+pytest-mock = "^3.14.0"
+pytest-cov = "^6.0.0"
+requests-mock = "^1.12.1"
+black = "^24.10.0"
+mypy = "^1.13.0"
+pre-commit = "^4.0.1"
 ipython = "^7.21.0"
-pylint = "^2.14.1"
-invoke = "^1.7.1"
-Sphinx = "^7.3.7"
+pylint = "^3.3.1"
+invoke = "^2.2.0"
+sphinx = "<8.1.0"
+
+[tool.poetry.extras]
+models = ["onnxruntime"]
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
@@ -57,3 +61,6 @@ max-attributes = 15
 max-public-methods = 25
 min-public-methods = 0
 disable = "W1203, W0707, W1514, W0602, typecheck"
+
+[tool.coverage.run]
+relative_files = true
diff --git a/rxnutils/chem/augmentation.py b/rxnutils/chem/augmentation.py
index 7e9fd83..156bf76 100644
--- a/rxnutils/chem/augmentation.py
+++ b/rxnutils/chem/augmentation.py
@@ -1,6 +1,8 @@
 """ Routines for augmenting chemical reactions
 """
 
+from rxnutils.chem.utils import split_rsmi
+
 _SINGLE_REACTANT_REAGENTS = {"10.1.1": "Br", "10.1.2": "Cl"}
 
 
@@ -12,7 +14,7 @@ def single_reactant_augmentation(smiles: str, classification: str) -> str:
     :param classification: the classification of the reaction or an empty string
     :return: the processed SMILES
     """
-    reactants = smiles.split(">")[0]
+    reactants = split_rsmi(smiles)[0]
     if "." in reactants:
         return smiles
     classification = classification.split(" ")[0]
diff --git a/rxnutils/chem/cgr.py b/rxnutils/chem/cgr.py
index 13eac3a..8b78c2f 100644
--- a/rxnutils/chem/cgr.py
+++ b/rxnutils/chem/cgr.py
@@ -1,5 +1,6 @@
 """ Wrapper class for the CGRTools library
 """
+
 import io
 import warnings
 from typing import List
@@ -28,20 +29,14 @@ def __init__(self, reaction: ChemicalReaction) -> None:
         self._cgr_reactants = []
         self._cgr_products = []
         self._make_cgr_containers()
-        self.reaction_container = ReactionContainer(
-            reactants=self._cgr_reactants, products=self._cgr_products
-        )
+        self.reaction_container = ReactionContainer(reactants=self._cgr_reactants, products=self._cgr_products)
         try:
             self.cgr_container = self.reaction_container.compose()
         except ValueError as err:
             if str(err) == "mapping of graphs is not disjoint":
-                raise ValueError(
-                    "Reaction contains inconsistent atom-mapping, perhaps duplicates"
-                )
+                raise ValueError("Reaction contains inconsistent atom-mapping, perhaps duplicates")
             elif str(err).endswith("} not equal"):
-                raise ValueError(
-                    "Atom with the same atom-mapping in reactant and product is not equal"
-                )
+                raise ValueError("Atom with the same atom-mapping in reactant and product is not equal")
             else:
                 raise ValueError(f"Unknown problem with generating CGR: {err}")
 
@@ -58,10 +53,7 @@ def bonds_broken(self) -> int:
     @property
     def bonds_changed(self) -> int:
         """Returns the number of broken or formed bonds in the reaction"""
-        return sum(
-            bond.p_order is None or bond.order is None
-            for _, _, bond in self.cgr_container.bonds()
-        )
+        return sum(bond.p_order is None or bond.order is None for _, _, bond in self.cgr_container.bonds())
 
     @property
     def bonds_formed(self) -> int:
@@ -71,9 +63,7 @@ def bonds_formed(self) -> int:
     @property
     def total_centers(self) -> int:
         """Returns the number of atom and bond centers in the reaction"""
-        return len(self.cgr_container.center_atoms) + len(
-            self.cgr_container.center_bonds
-        )
+        return len(self.cgr_container.center_atoms) + len(self.cgr_container.center_bonds)
 
     def distance_to(self, other: "CondensedGraphReaction") -> int:
         """
@@ -104,14 +94,11 @@ def _make_renumbered_mols(self):
         # so this adds safe atom-mapping to un-mapped atoms
         renumbered_mols = []
         max_atom_map_numb = max(
-            max(atom_mapping_numbers(smi) or [0])
-            for smi in self.reaction.reactants_list + self.reaction.products_list
+            max(atom_mapping_numbers(smi) or [0]) for smi in self.reaction.reactants_list + self.reaction.products_list
         )
         for mol0 in self.reaction.reactants + self.reaction.products:
             if mol0 is None:
-                raise ValueError(
-                    "Cannot create CGR for this reaction, some molecules are None"
-                )
+                raise ValueError("Cannot create CGR for this reaction, some molecules are None")
             mol = Chem.rdchem.Mol(mol0)
             for atom in mol.GetAtoms():
                 if not atom.GetAtomMapNum():
diff --git a/rxnutils/chem/disconnection_sites/atom_map_tagging.py b/rxnutils/chem/disconnection_sites/atom_map_tagging.py
index e705d26..cdfadcc 100644
--- a/rxnutils/chem/disconnection_sites/atom_map_tagging.py
+++ b/rxnutils/chem/disconnection_sites/atom_map_tagging.py
@@ -7,6 +7,8 @@
 import pandas as pd
 from rdkit import Chem
 
+from rxnutils.chem.utils import split_rsmi
+
 
 def _get_atom_identifier(atom: Chem.rdchem.Atom) -> str:
     """
@@ -21,9 +23,7 @@ def _get_atom_identifier(atom: Chem.rdchem.Atom) -> str:
     return str(atom_id)
 
 
-def _get_bond_environment_identifier(
-    atoms: Sequence[Chem.rdchem.Atom], bond: Chem.rdchem.Bond
-) -> str:
+def _get_bond_environment_identifier(atoms: Sequence[Chem.rdchem.Atom], bond: Chem.rdchem.Bond) -> str:
     """
     Get the environment of a specific bond.
 
@@ -79,17 +79,14 @@ def get_atom_list(reactants_smiles: str, product_smiles: str) -> List[int]:
     ordered_reactant_neighbor_dict = _get_atomic_neighborhoods(reactants_smiles)
     ordered_product_neighbor_dict = _get_atomic_neighborhoods(product_smiles)
 
-    all_indices = set(ordered_product_neighbor_dict.keys()) | set(
-        ordered_reactant_neighbor_dict.keys()
-    )
+    all_indices = set(ordered_product_neighbor_dict.keys()) | set(ordered_reactant_neighbor_dict.keys())
 
     # Checks to see equivlence of atomic enviroments.
     # If environment changed, then add atom to list
     atom_list = [
         atom_map
         for atom_map in all_indices
-        if ordered_reactant_neighbor_dict.get(atom_map, [])
-        != ordered_product_neighbor_dict.get(atom_map, [])
+        if ordered_reactant_neighbor_dict.get(atom_map, []) != ordered_product_neighbor_dict.get(atom_map, [])
     ]
 
     return atom_list
@@ -104,7 +101,7 @@ def atom_map_tag_reactants(mapped_rxn: str) -> str:
     :return: SMILES of the reactants containing tags corresponding to atoms changed in the
         reaction.
     """
-    reactants_smiles, _, product_smiles = mapped_rxn.split(">")
+    reactants_smiles, _, product_smiles = split_rsmi(mapped_rxn)
 
     reactants_mol = Chem.MolFromSmiles(reactants_smiles)
     atom_list = get_atom_list(reactants_smiles, product_smiles)
@@ -128,7 +125,7 @@ def atom_map_tag_products(mapped_rxn: str) -> str:
     :return: SMILES of the product containing tags corresponding to atoms changed in the
         reaction.
     """
-    reactants_smiles, _, product_smiles = mapped_rxn.split(">")
+    reactants_smiles, _, product_smiles = split_rsmi(mapped_rxn)
 
     product_mol = Chem.MolFromSmiles(product_smiles)
     atom_list = get_atom_list(reactants_smiles, product_smiles)
diff --git a/rxnutils/chem/disconnection_sites/tag_converting.py b/rxnutils/chem/disconnection_sites/tag_converting.py
index 154a675..e8e62c4 100644
--- a/rxnutils/chem/disconnection_sites/tag_converting.py
+++ b/rxnutils/chem/disconnection_sites/tag_converting.py
@@ -15,22 +15,21 @@ def smiles_tokens(smiles: str) -> List[str]:
     :param smiles: SMILES to tokenize
     :return: List of tokens identified in SMILES.
     """
-    pattern = r"(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|#|-|\+|\\\\|\\|\/|:|~|@|\?|>|\*|\!|\$|\%[0-9]{2}|[0-9])"
+    pattern = (
+        r"(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|#|-|\+|\\\\|\\|\/|:|~|@|\?|>|\*|\!|\$|\%[0-9]{2}|[0-9])"
+    )
     regex = re.compile(pattern)
     tokens = [token for token in regex.findall(smiles)]
 
     tokenized_smiles = "".join(tokens)
     if smiles != tokenized_smiles:
         raise AssertionError(
-            f"tokenized SMILES not the same as input SMILES: {tokenized_smiles}, "
-            "{smiles}, tokens: {tokens}"
+            f"tokenized SMILES not the same as input SMILES: {tokenized_smiles}, " "{smiles}, tokens: {tokens}"
         )
     return tokens
 
 
-def _next_tagged_token(
-    product_tagged_tokens: List[str], untagged_token: str, tagged_token_idx: int
-) -> Tuple[str, int]:
+def _next_tagged_token(product_tagged_tokens: List[str], untagged_token: str, tagged_token_idx: int) -> Tuple[str, int]:
     """
     Get the next tagged token in the sequence. Includes checks and fixes for
     stereochemistry changes due to removing atom mapping.
@@ -51,19 +50,13 @@ def _next_tagged_token(
             tagged_token_idx += 1
             return product_tagged_tokens[tagged_token_idx], tagged_token_idx
 
-    if (
-        tagged_token != untagged_token
-        and not ":1" in tagged_token
-        and "@" in tagged_token
-    ):
+    if tagged_token != untagged_token and not ":1" in tagged_token and "@" in tagged_token:
         return untagged_token, tagged_token_idx
 
     return tagged_token, tagged_token_idx
 
 
-def tagged_smiles_from_tokens(
-    product_tagged_tokens: List[str], product_untagged_tokens: List[str]
-) -> Tuple[str, str]:
+def tagged_smiles_from_tokens(product_tagged_tokens: List[str], product_untagged_tokens: List[str]) -> Tuple[str, str]:
     """
     Convert the tagged SMILES from atom-mapping to unmapped-token + '!'
 
@@ -81,24 +74,16 @@ def tagged_smiles_from_tokens(
 
     for untagged_token in product_untagged_tokens:
 
-        tagged_token, tagged_token_idx = _next_tagged_token(
-            product_tagged_tokens, untagged_token, tagged_token_idx
-        )
+        tagged_token, tagged_token_idx = _next_tagged_token(product_tagged_tokens, untagged_token, tagged_token_idx)
 
-        if tagged_token != untagged_token and (
-            untagged_token == "/" or untagged_token == "\\"
-        ):
+        if tagged_token != untagged_token and (untagged_token == "/" or untagged_token == "\\"):
             continue
 
         if tagged_token == untagged_token:
             product_converted += untagged_token
         else:
             # Remove brackets around a single letter
-            if (
-                len(untagged_token) == 3
-                and untagged_token.startswith("[")
-                and untagged_token.endswith("]")
-            ):
+            if len(untagged_token) == 3 and untagged_token.startswith("[") and untagged_token.endswith("]"):
                 untagged_token = untagged_token[1]
             product_converted += untagged_token + "!"
 
@@ -109,9 +94,7 @@ def tagged_smiles_from_tokens(
     return product_converted, product_untagged
 
 
-def _canonicalize_tagged_smiles(
-    product_tagged: str, product_untagged: str = None
-) -> Tuple[str, str]:
+def _canonicalize_tagged_smiles(product_tagged: str, product_untagged: str = None) -> Tuple[str, str]:
     """
     Reorder the tagged-product SMILES on canonical form using the canonicalized
     untagged product.
@@ -123,13 +106,7 @@ def _canonicalize_tagged_smiles(
     mol = Chem.MolFromSmiles(product_tagged)
     mol_untagged = Chem.MolFromSmiles(product_untagged)
 
-    _, canonical_atom_order = tuple(
-        zip(
-            *sorted(
-                [(j, i) for i, j in enumerate(Chem.CanonicalRankAtoms(mol_untagged))]
-            )
-        )
-    )
+    _, canonical_atom_order = tuple(zip(*sorted([(j, i) for i, j in enumerate(Chem.CanonicalRankAtoms(mol_untagged))])))
 
     mol = Chem.RenumberAtoms(mol, canonical_atom_order)
     mol_untagged = Chem.RenumberAtoms(mol_untagged, canonical_atom_order)
@@ -158,9 +135,7 @@ def convert_atom_map_tag(product_atom_map_tagged: str) -> str:
     if not Chem.MolFromSmiles(product_untagged):
         return ""
 
-    product_tagged, product_untagged = _canonicalize_tagged_smiles(
-        product_atom_map_tagged, product_untagged
-    )
+    product_tagged, product_untagged = _canonicalize_tagged_smiles(product_atom_map_tagged, product_untagged)
 
     # Update the SMILES string to remove atom-mapping brackets and explicit [H]:s and
     # replace by <atom>!
diff --git a/rxnutils/chem/features/__init__.py b/rxnutils/chem/features/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/rxnutils/chem/features/rxnfp_runner.py b/rxnutils/chem/features/rxnfp_runner.py
new file mode 100644
index 0000000..d2cf4c0
--- /dev/null
+++ b/rxnutils/chem/features/rxnfp_runner.py
@@ -0,0 +1,79 @@
+"""Module containing script to calculate RXNFP for a set of reactions
+"""
+
+import argparse
+from typing import Optional, Sequence
+
+import numpy as np
+import pandas as pd
+
+from rxnutils.data.batch_utils import read_csv_batch
+
+try:
+    from rxnfp.transformer_fingerprints import (  # pylint: disable=all
+        RXNBERTFingerprintGenerator,
+        get_default_model_and_tokenizer,
+    )
+except ImportError:
+    DEPENDENCY_OK = False
+else:
+    DEPENDENCY_OK = True
+
+
+def main(input_args: Optional[Sequence[str]] = None) -> None:
+    """Function for command-line tool"""
+
+    if not DEPENDENCY_OK:
+        raise ImportError("You need to run this tool in an environment where rxnfp is installed")
+
+    parser = argparse.ArgumentParser("Script to calculate RXNFP")
+    parser.add_argument("--input", default="data.csv", help="the file with reactions")
+    parser.add_argument("--output", default="data_rxnfp.npz", help="the output filename")
+    parser.add_argument(
+        "--column",
+        default="reaction_smiles",
+        help="The column with the reaction SMILES",
+    )
+    parser.add_argument(
+        "--batch",
+        type=int,
+        nargs=2,
+        help="Line numbers to start and stop reading rows",
+    )
+    parser.add_argument(
+        "--fp_batch_size",
+        type=int,
+        default=10,
+        help="how many SMILES to calculate at the same time",
+    )
+    args = parser.parse_args(input_args)
+
+    data = read_csv_batch(args.input, sep="\t", index_col=False, batch=args.batch)
+
+    model, tokenizer = get_default_model_and_tokenizer(force_no_cuda=True)
+    rxnfp_generator = RXNBERTFingerprintGenerator(model, tokenizer, force_no_cuda=True)
+
+    fingerprints = []
+    for start in range(0, len(data), args.fp_batch_size):
+        batch = data[args.column].iloc[start : start + args.fp_batch_size].tolist()
+        # Adding zeros for all failed SMILES
+        fail_data = [[0.0] * 256 for _ in range(args.fp_batch_size)]
+        try:
+            fps_batch = rxnfp_generator.convert_batch(batch)
+        except ValueError as err:
+            print(err)
+            print("\n\n".join(batch))
+            fingerprints.extend(fail_data)
+        except RuntimeError as err:
+            print(err)
+            print("\n\n".join(batch))
+            fingerprints.extend(fail_data)
+        else:
+            fingerprints.extend(fps_batch)
+
+    fingerprints = np.asarray(fingerprints)
+    np.savez(args.output, rxnfps=fingerprints)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/rxnutils/chem/features/sc_score.py b/rxnutils/chem/features/sc_score.py
new file mode 100644
index 0000000..d7a7816
--- /dev/null
+++ b/rxnutils/chem/features/sc_score.py
@@ -0,0 +1,63 @@
+""" Module containing the implementation of the SC-score model for synthetic complexity scoring. """
+
+from __future__ import annotations
+
+import numpy as np
+from rdkit.Chem import AllChem
+
+RdMol = AllChem.rdchem.Mol
+
+try:
+    import onnxruntime
+except ImportError:
+    SCORE_SUPPORTED = False
+else:
+    SCORE_SUPPORTED = True
+
+
+class SCScore:
+    """
+    Encapsulation of the SCScore model
+
+    Re-write of the SCScorer from the scscorer package using ONNX
+
+    The predictions of the score is made with a sanitized instance of an RDKit molecule
+
+    .. code-block::
+
+        mol = Chem.MolFromSmiles(CCC)
+        scscorer = SCScorer("path_to_model")
+        score = scscorer(mol)
+
+    :param model_path: the filename of the model weights and biases
+    :param fingerprint_length: the number of bits in the fingerprint
+    :param fingerprint_radius: the radius of the fingerprint
+    """
+
+    def __init__(
+        self,
+        model_path: str,
+        fingerprint_length: int = 1024,
+        fingerprint_radius: int = 2,
+    ) -> None:
+        if not SCORE_SUPPORTED:
+            raise ImportError("Cannot use SCScore model. Install rxnutils with optional dependencies")
+        self._fingerprint_length = fingerprint_length
+        self._fingerprint_radius = fingerprint_radius
+        session_options = onnxruntime.SessionOptions()
+        session_options.intra_op_num_threads = 1
+        self._model = onnxruntime.InferenceSession(model_path, sess_options=session_options)
+
+    def __call__(self, rd_mol: RdMol) -> float:
+        fingerprint = self._make_fingerprint(rd_mol)
+        return self._model.run(None, {"fingerprint": fingerprint})[0][0]
+
+    def _make_fingerprint(self, rd_mol: RdMol) -> np.ndarray:
+        """Returns the molecule's Morgan fingerprint"""
+        fp_vec = AllChem.GetMorganFingerprintAsBitVect(
+            rd_mol,
+            self._fingerprint_radius,
+            nBits=self._fingerprint_length,
+            useChirality=True,
+        )
+        return np.array(fp_vec, dtype=float)
diff --git a/rxnutils/chem/reaction.py b/rxnutils/chem/reaction.py
index 3aea3a5..34ba565 100644
--- a/rxnutils/chem/reaction.py
+++ b/rxnutils/chem/reaction.py
@@ -1,4 +1,5 @@
 """Module containing a class to handle chemical reactions"""
+
 import hashlib
 from typing import Any, Dict, List, Optional, Tuple
 
@@ -10,7 +11,7 @@
 from rxnutils.chem import utils
 from rxnutils.chem.rinchi import rinchi_api
 from rxnutils.chem.template import ReactionTemplate
-from rxnutils.chem.utils import reassign_rsmi_atom_mapping, split_smiles_from_reaction
+from rxnutils.chem.utils import reassign_rsmi_atom_mapping, split_rsmi, split_smiles_from_reaction
 
 
 class ReactionException(Exception):
@@ -40,15 +41,9 @@ def __init__(self, smiles: str, id_: str = None, clean_smiles: bool = True) -> N
         else:
             self._split_reaction()
 
-        self.reactants: List[Chem.rdchem.Mol] = extractor.mols_from_smiles_list(
-            self.reactants_list
-        )
-        self.agents: List[Chem.rdchem.Mol] = extractor.mols_from_smiles_list(
-            self.agents_list
-        )
-        self.products: List[Chem.rdchem.Mol] = extractor.mols_from_smiles_list(
-            self.products_list
-        )
+        self.reactants: List[Chem.rdchem.Mol] = extractor.mols_from_smiles_list(self.reactants_list)
+        self.agents: List[Chem.rdchem.Mol] = extractor.mols_from_smiles_list(self.agents_list)
+        self.products: List[Chem.rdchem.Mol] = extractor.mols_from_smiles_list(self.products_list)
 
         self._pseudo_rinchi: Optional[str] = None
         self._pseudo_rinchi_key: Optional[str] = None
@@ -140,15 +135,9 @@ def generate_coreagent(self):
         extra_reactant_fragment = ""
         for product in self.products:
             # Get unmapped atoms
-            unmapped_ids = [
-                atom.GetIdx()
-                for atom in product.GetAtoms()
-                if not atom.HasProp("molAtomMapNumber")
-            ]
+            unmapped_ids = [atom.GetIdx() for atom in product.GetAtoms() if not atom.HasProp("molAtomMapNumber")]
             if len(unmapped_ids) > extractor.MAXIMUM_NUMBER_UNMAPPED_PRODUCT_ATOMS:
-                raise ReactionException(
-                    f"Template generation failed: too many unmapped atoms ({len(unmapped_ids)})"
-                )
+                raise ReactionException(f"Template generation failed: too many unmapped atoms ({len(unmapped_ids)})")
             # Define new atom symbols for fragment with atom maps, generalizing fully
             atom_symbols = [f"[{atom.GetSymbol()}]" for atom in product.GetAtoms()]
             # And bond symbols...
@@ -169,9 +158,7 @@ def generate_coreagent(self):
         if extra_reactant_fragment:
             extra_reactant_fragment = extra_reactant_fragment[:-1]
         # Consolidate repeated fragments (stoichometry)
-        extra_reactant_fragment = ".".join(
-            sorted(list(set(extra_reactant_fragment.split("."))))
-        )
+        extra_reactant_fragment = ".".join(sorted(list(set(extra_reactant_fragment.split(".")))))
         return extra_reactant_fragment
 
     def generate_reaction_template(
@@ -195,28 +182,20 @@ def generate_reaction_template(
         :returns: the canonical and retrosynthetic templates
         """
         if not self.sanitization_check():
-            raise ReactionException(
-                "Template generation failed: sanitation check failed"
-            )
+            raise ReactionException("Template generation failed: sanitation check failed")
 
         reactants = self.reactants
         products = self.products
 
         for product in products:
-            nunmapped = sum(
-                int(not atom.HasProp("molAtomMapNumber")) for atom in product.GetAtoms()
-            )
+            nunmapped = sum(int(not atom.HasProp("molAtomMapNumber")) for atom in product.GetAtoms())
             if nunmapped > extractor.MAXIMUM_NUMBER_UNMAPPED_PRODUCT_ATOMS:
-                raise ReactionException(
-                    f"Template generation failed: too many unmapped atoms ({nunmapped})"
-                )
+                raise ReactionException(f"Template generation failed: too many unmapped atoms ({nunmapped})")
 
         if self.no_change():
             raise ReactionException("Template generation failed: no change in reaction")
         if None in reactants + products:
-            raise ReactionException(
-                "Template generation failed: None in reactants or products"
-            )
+            raise ReactionException("Template generation failed: None in reactants or products")
 
         extra_atoms = {}
         if expand_ring:
@@ -243,19 +222,13 @@ def generate_reaction_template(
             self._canonical_template = ReactionTemplate(canonical_smarts)
 
             # Retro ReactionTemplate
-            reactants_string = canonical_smarts.split(">>")[0]
-            products_string = canonical_smarts.split(">>")[1]
+            reactants_string, _, products_string = split_rsmi(canonical_smarts)
             retro_smarts = products_string + ">>" + reactants_string
             self._retro_template = ReactionTemplate(retro_smarts, "retro")
 
             # Validate ReactionTemplates
-            if not (
-                self._retro_template.rdkit_validation()
-                and self._canonical_template.rdkit_validation()
-            ):
-                raise ReactionException(
-                    "Template generation failed: RDkit validation of extracted templates failed"
-                )
+            if not (self._retro_template.rdkit_validation() and self._canonical_template.rdkit_validation()):
+                raise ReactionException("Template generation failed: RDkit validation of extracted templates failed")
         except Exception as err:
             raise ReactionException(f"Template generation failed with message: {err}")
 
@@ -285,9 +258,7 @@ def _generate_rdchiral_template(
         :raises ReactionException: Template generation failed: Timed out
         :return: Canonical reaction template
         """
-        changed_atoms, changed_atom_tags, err = extractor.get_changed_atoms(
-            reactants=reactants, products=products
-        )
+        changed_atoms, changed_atom_tags, err = extractor.get_changed_atoms(reactants=reactants, products=products)
 
         if expand_hetero:
             for atom in changed_atoms:
@@ -302,14 +273,16 @@ def _generate_rdchiral_template(
                 changed_atom_tags.append(atom_num)
 
         if err:
-            raise ReactionException(
-                "Template generation failed: could not obtained changed atoms"
-            )
+            raise ReactionException("Template generation failed: could not obtained changed atoms")
         if not changed_atom_tags:
             raise ReactionException("Template generation failed: no atoms changes")
 
         # Get fragments for reactants
-        (reactant_fragments, _, _,) = extractor.get_fragments_for_changed_atoms(
+        (
+            reactant_fragments,
+            _,
+            _,
+        ) = extractor.get_fragments_for_changed_atoms(
             reactants,
             changed_atom_tags,
             radius=radius,
@@ -332,11 +305,11 @@ def _generate_rdchiral_template(
         rxn_string = f"{reactant_fragments}>>{product_fragments}"
         canonical_template = extractor.canonicalize_transform(rxn_string)
         # Change from inter-molecular to intra-molecular
-        canonical_template_split = canonical_template.split(">>")
+        canonical_template_split = split_rsmi(canonical_template)
         canonical_smarts = (
             canonical_template_split[0][1:-1].replace(").(", ".")
             + ">>"
-            + canonical_template_split[1][1:-1].replace(").(", ".")
+            + canonical_template_split[-1][1:-1].replace(").(", ".")
         )
 
         return canonical_smarts
@@ -344,9 +317,7 @@ def _generate_rdchiral_template(
     def has_partial_mapping(self) -> bool:
         """Check product atom mapping."""
         for product in self.products:
-            sum_with = sum(
-                atom.HasProp("molAtomMapNumber") for atom in product.GetAtoms()
-            )
+            sum_with = sum(atom.HasProp("molAtomMapNumber") for atom in product.GetAtoms())
             if sum_with < product.GetNumAtoms():
                 return True
         return False
@@ -383,9 +354,7 @@ def sanitization_check(self) -> bool:
 
         :return: True if all the molecule objects were successfully created, else False
         """
-        return all(
-            mol is not None for mol in self.reactants + self.agents + self.products
-        )
+        return all(mol is not None for mol in self.reactants + self.agents + self.products)
 
     def canonical_template_generate_outcome(self) -> bool:
         """Checks whether the canonical template produces"""
@@ -430,14 +399,10 @@ def retro_template_selectivity(self) -> float:
         for outcome_set in retro_outcomes:
             if not extractor.USE_STEREOCHEMISTRY:
                 outcome_set_inchi = [
-                    Chem.MolToInchi(Chem.MolFromSmiles(outcome.replace("@", "")))
-                    for outcome in outcome_set
+                    Chem.MolToInchi(Chem.MolFromSmiles(outcome.replace("@", ""))) for outcome in outcome_set
                 ]
             else:
-                outcome_set_inchi = [
-                    Chem.MolToInchi(Chem.MolFromSmiles(outcome))
-                    for outcome in outcome_set
-                ]
+                outcome_set_inchi = [Chem.MolToInchi(Chem.MolFromSmiles(outcome)) for outcome in outcome_set]
             precursor_set.append(outcome_set_inchi)
 
         assessment = []
@@ -486,14 +451,12 @@ def _atom_mapping(smiles: str) -> Tuple[int, int]:
             num_atoms_ = 0
             num_mapped_atoms_ = 0
             if mol:
-                num_mapped_atoms_ = sum(
-                    atom.HasProp("molAtomMapNumber") for atom in mol.GetAtoms()
-                )
+                num_mapped_atoms_ = sum(atom.HasProp("molAtomMapNumber") for atom in mol.GetAtoms())
                 num_atoms_ = mol.GetNumAtoms()
 
             return num_atoms_, num_mapped_atoms_
 
-        split_reaction = self.rsmi.split(">")
+        split_reaction = split_rsmi(self.rsmi)
         self.reactants_smiles = extractor.replace_deuterated(split_reaction[0])
         self.agents_smiles = extractor.replace_deuterated(split_reaction[1])
         self.products_smiles = extractor.replace_deuterated(split_reaction[2])
@@ -522,15 +485,11 @@ def _atom_mapping(smiles: str) -> Tuple[int, int]:
 
         # Update reactants with molecules from agents
         if add_reactants:
-            self.reactants_smiles = ".".join(
-                [self.reactants_smiles, self._join_components(add_reactants)]
-            )
+            self.reactants_smiles = ".".join([self.reactants_smiles, self._join_components(add_reactants)])
         # Update agents with molecules from reactants
         if add_agents:
             if self.agents_smiles:
-                self.agents_smiles = ".".join(
-                    [self.agents_smiles, self._join_components(add_agents)]
-                )
+                self.agents_smiles = ".".join([self.agents_smiles, self._join_components(add_agents)])
             else:
                 self.agents_smiles = self._join_components(add_agents)
 
@@ -543,9 +502,7 @@ def _atom_mapping(smiles: str) -> Tuple[int, int]:
         self.products_smiles = self._join_components(neutral_products)
 
         # Reaction SMILES
-        self.rsmi = ">".join(
-            [self.reactants_smiles, self.agents_smiles, self.products_smiles]
-        )
+        self.rsmi = ">".join([self.reactants_smiles, self.agents_smiles, self.products_smiles])
 
         # Clean Reaction SMILES by RDKit
         reaction = AllChem.ReactionFromSmarts(self.rsmi)
@@ -566,11 +523,7 @@ def _product_unique_ring_atoms(self) -> List[int]:
         def find_ring_atom_maps(mol):
             ring_atoms_sets = []
             for ring in mol.GetRingInfo().AtomRings():
-                ring_atoms_sets.append(
-                    tuple(
-                        sorted(mol.GetAtomWithIdx(idx).GetAtomMapNum() for idx in ring)
-                    )
-                )
+                ring_atoms_sets.append(tuple(sorted(mol.GetAtomWithIdx(idx).GetAtomMapNum() for idx in ring)))
             return ring_atoms_sets
 
         reactant_ring_atom_sets = []
@@ -592,13 +545,11 @@ def _split_reaction(self) -> None:
         Stores:
             rsmi (str): Reaction SMILES in the form mapped_reactants>unmapped_reagents>products
         """
-        split_reaction = self.rsmi.split(">")
+        split_reaction = split_rsmi(self.rsmi)
         self.reactants_smiles = extractor.replace_deuterated(split_reaction[0])
         self.agents_smiles = extractor.replace_deuterated(split_reaction[1])
         self.products_smiles = extractor.replace_deuterated(split_reaction[2])
-        self.rsmi = ">".join(
-            [self.reactants_smiles, self.agents_smiles, self.products_smiles]
-        )
+        self.rsmi = ">".join([self.reactants_smiles, self.agents_smiles, self.products_smiles])
         self.clean_rsmi = self.rsmi
 
     def _make_pseudo_rinchi(self) -> str:
@@ -608,16 +559,12 @@ def _make_pseudo_rinchi(self) -> str:
         :rtype: str
         """
         reactant_inchi = (
-            Chem.MolToInchi(
-                Chem.MolFromSmiles(utils.remove_atom_mapping(self.reactants_smiles))
-            )
+            Chem.MolToInchi(Chem.MolFromSmiles(utils.remove_atom_mapping(self.reactants_smiles)))
             if self.reactants_smiles
             else ""
         )
         product_inchi = (
-            Chem.MolToInchi(
-                Chem.MolFromSmiles(utils.remove_atom_mapping(self.products_smiles))
-            )
+            Chem.MolToInchi(Chem.MolFromSmiles(utils.remove_atom_mapping(self.products_smiles)))
             if self.products_smiles
             else ""
         )
@@ -630,11 +577,7 @@ def _make_pseudo_rinchi_key(self) -> str:
         :return: Pseudo Reaction InChI-Key
         :rtype: str
         """
-        reactant_inchi_key = Chem.MolToInchiKey(
-            Chem.MolFromSmiles(utils.remove_atom_mapping(self.reactants_smiles))
-        )
-        product_inchi_key = Chem.MolToInchiKey(
-            Chem.MolFromSmiles(utils.remove_atom_mapping(self.products_smiles))
-        )
+        reactant_inchi_key = Chem.MolToInchiKey(Chem.MolFromSmiles(utils.remove_atom_mapping(self.reactants_smiles)))
+        product_inchi_key = Chem.MolToInchiKey(Chem.MolFromSmiles(utils.remove_atom_mapping(self.products_smiles)))
         concatenated_rinchi_key = "++".join([reactant_inchi_key, product_inchi_key])
         return concatenated_rinchi_key
diff --git a/rxnutils/chem/rinchi/download_rinchi.py b/rxnutils/chem/rinchi/download_rinchi.py
index 6ef9f1a..38599fd 100644
--- a/rxnutils/chem/rinchi/download_rinchi.py
+++ b/rxnutils/chem/rinchi/download_rinchi.py
@@ -1,4 +1,5 @@
 """Module for downloading InChI Trust Reaction InChI."""
+
 import logging
 import os
 import stat
@@ -55,11 +56,7 @@ def main() -> str:
         logging.info("Download completed...")
         logging.info(f"Unziping: {rinchi_fn}")
         with ZipFile(rinchi_fn, "r") as out_fp:
-            bin_path = [
-                x
-                for x in out_fp.namelist()
-                if x.endswith(_exec_folder_ending(os_sep=False) + "/")
-            ]
+            bin_path = [x for x in out_fp.namelist() if x.endswith(_exec_folder_ending(os_sep=False) + "/")]
             logging.debug(bin_path)
             out_fp.extractall(download_loc)
         logging.info("Completed...")
@@ -69,19 +66,13 @@ def main() -> str:
             os.chmod(os.path.join(rinchi_cli_path, "rinchi_cmdline"), stat.S_IEXEC)
     else:
         logging.info(f"RInChI exists at: {rinchi_fn}")
-        bin_path = [
-            r
-            for r, d, f in os.walk(download_loc)
-            if r.endswith(_exec_folder_ending(os_sep=True))
-        ]
+        bin_path = [r for r, d, f in os.walk(download_loc) if r.endswith(_exec_folder_ending(os_sep=True))]
         logging.debug(bin_path)
         rinchi_cli_path = bin_path[0]
         logging.info(f"RInChI CLI: {rinchi_cli_path}")
         if sys.platform == "linux":
             os.chmod(
-                os.path.join(
-                    rinchi_cli_path, f"rinchi_cmdline{PLATFORM2EXTENSION[sys.platform]}"
-                ),
+                os.path.join(rinchi_cli_path, f"rinchi_cmdline{PLATFORM2EXTENSION[sys.platform]}"),
                 stat.S_IEXEC,
             )
 
@@ -90,9 +81,7 @@ def main() -> str:
 
 def _exec_folder_ending(os_sep: bool) -> str:
     sep = os.sep if os_sep else "/"
-    return sep.join(
-        ["bin", "rinchi_cmdline", f"{PLATFORM2FOLDER[sys.platform]}", "x86_64"]
-    )
+    return sep.join(["bin", "rinchi_cmdline", f"{PLATFORM2FOLDER[sys.platform]}", "x86_64"])
 
 
 if __name__ == "__main__":
diff --git a/rxnutils/chem/rinchi/rinchi_api.py b/rxnutils/chem/rinchi/rinchi_api.py
index d34e17f..b280849 100644
--- a/rxnutils/chem/rinchi/rinchi_api.py
+++ b/rxnutils/chem/rinchi/rinchi_api.py
@@ -1,4 +1,5 @@
 """Module containing an API to the Reaction InChI program"""
+
 import logging
 import os
 import subprocess
@@ -11,9 +12,7 @@
 from rxnutils.chem.rinchi import download_rinchi
 from rxnutils.chem.rinchi.download_rinchi import PLATFORM2FOLDER, RInChIError
 
-RInChIStructure = namedtuple(
-    "RInChI", "rinchi rauxinfo long_rinchikey short_rinchikey web_rinchikey"
-)
+RInChIStructure = namedtuple("RInChI", "rinchi rauxinfo long_rinchikey short_rinchikey web_rinchikey")
 
 
 def generate_rinchi(reaction_smiles: str) -> RInChIStructure:
@@ -91,6 +90,4 @@ def _rinchi_cli(rxn_file: str, options: str = None) -> RInChIStructure:
 
 
 if __name__ == "__main__":
-    import sys
-
     print(generate_rinchi(sys.argv[1]))
diff --git a/rxnutils/chem/template.py b/rxnutils/chem/template.py
index 5b306c8..6652c47 100644
--- a/rxnutils/chem/template.py
+++ b/rxnutils/chem/template.py
@@ -1,5 +1,6 @@
 """Module containing useful representations of templates
 """
+
 import hashlib
 import logging
 import re
@@ -127,9 +128,7 @@ def calc_fp():
             calc_fp()
         return set(bits.keys())
 
-    def fingerprint_vector(
-        self, radius: int = 2, nbits: int = 1024, use_chirality: bool = True
-    ) -> np.ndarray:
+    def fingerprint_vector(self, radius: int = 2, nbits: int = 1024, use_chirality: bool = True) -> np.ndarray:
         """
         Calculate the finger bit vector
 
@@ -297,9 +296,7 @@ def apply(self, mols: str) -> Tuple[Tuple[str, ...], ...]:
         # Get all permutations of molecules
         outcome = []
         num_reactant_templates = self._rd_reaction.GetNumReactantTemplates()
-        logging.debug(
-            f"#Reactants: {len(mols_objs)} Vs. #Reactant Templates: {num_reactant_templates}"
-        )
+        logging.debug(f"#Reactants: {len(mols_objs)} Vs. #Reactant Templates: {num_reactant_templates}")
         reactants_permutations = permutations(mols_objs, num_reactant_templates)
         for idx, reactants in enumerate(reactants_permutations):
             outcome = self._rd_reaction.RunReactants(reactants)
@@ -322,9 +319,7 @@ def create_smiles(mol_list):
 
         return tuple(create_smiles(list_) for list_ in outcome)
 
-    def fingerprint_bits(
-        self, radius: int = 2, use_chirality: bool = True
-    ) -> Dict[int, int]:
+    def fingerprint_bits(self, radius: int = 2, use_chirality: bool = True) -> Dict[int, int]:
         """
         Calculate the difference count of the fingerprint bits set of the reactants and products
 
@@ -341,9 +336,7 @@ def fingerprint_bits(
                 bit_sum[bit] -= 1
         return bit_sum
 
-    def fingerprint_vector(
-        self, radius: int = 2, nbits: int = 1024, use_chirality: bool = True
-    ) -> np.ndarray:
+    def fingerprint_vector(self, radius: int = 2, nbits: int = 1024, use_chirality: bool = True) -> np.ndarray:
         """
         Calculate the difference fingerprint vector
 
@@ -403,15 +396,9 @@ def _cleaned_reaction_copy(self) -> AllChem.ChemicalReaction:
         :rtype: AllChem.ChemicalReaction
         """
         reaction = AllChem.ReactionFromSmarts(self.smarts)
-        mols = [
-            TemplateMolecule(reaction.GetProductTemplate(i))
-            for i in range(reaction.GetNumProductTemplates())
-        ]
+        mols = [TemplateMolecule(reaction.GetProductTemplate(i)) for i in range(reaction.GetNumProductTemplates())]
         mols.extend(
-            [
-                TemplateMolecule(reaction.GetReactantTemplate(i))
-                for i in range(reaction.GetNumReactantTemplates())
-            ]
+            [TemplateMolecule(reaction.GetReactantTemplate(i)) for i in range(reaction.GetNumReactantTemplates())]
         )
 
         for mol in mols:
diff --git a/rxnutils/chem/utils.py b/rxnutils/chem/utils.py
index 93dcd48..4aa183b 100644
--- a/rxnutils/chem/utils.py
+++ b/rxnutils/chem/utils.py
@@ -1,14 +1,62 @@
 """Module containing various chemical utility routines"""
+
 import functools
 import logging
-from typing import List, Tuple
+import re
+from collections import defaultdict
+from typing import List, Optional, Tuple
 
+import numpy as np
 import rdchiral.template_extractor
 from rdkit import Chem
-from rdkit.Chem import AllChem
+from rdkit.Chem import AllChem, Descriptors
 from rdkit.Chem.MolStandardize import rdMolStandardize
 from rdkit.Chem.SaltRemover import SaltRemover
 
+# Pattern for spliting Reaction SMILES should be '>' not prefixed by '-' (i.e. '->')
+rsmi_split_pattern = re.compile(r"(?<!-)>")
+
+
+def get_symmetric_sites(mol: Chem.rdchem.Mol, candidate_atoms: List[int]) -> List[List[int]]:
+    """
+    Get all symmetric sites (atoms) of each atom in the list of atoms defined by their
+    atomic index (not atom-map number). Symmetry is assessed with respect to the molecule.
+    Symmetric atoms will have different atom inds but the same rank index from
+    CanonicalRankAtoms.
+
+    :param mol: RdKit molecule
+    :param candidate_atoms: Indices of the atoms that will be checked for symmetry.
+    :return: A list of all symmetric sites (list of atom-ids) that include the candidate
+        atoms. Returns empty list if no atoms have symmetric sites.
+    """
+    n_atoms = mol.GetNumAtoms()
+    if any(atom_idx >= n_atoms for atom_idx in candidate_atoms):
+        raise ValueError(
+            f"At least one candidate atom-idx is out of bounds in molecule with {n_atoms} atoms: {candidate_atoms}"
+        )
+
+    sites = defaultdict(lambda: [])
+    for atom_idx, rank_idx in enumerate(list(Chem.CanonicalRankAtoms(mol, breakTies=False))):
+        sites[rank_idx].append(atom_idx)
+
+    symmetric_sites = [
+        atoms for atoms in sites.values() if len(atoms) > 1 and any(atom_idx in candidate_atoms for atom_idx in atoms)
+    ]
+    return symmetric_sites
+
+
+def get_mol_weight(smiles: str) -> Optional[float]:
+    """Calculate molecule's exact molecular weight.
+    :param smiles: Molecule's SMILES.
+    :return: Molecule's exact molecular weight.
+    """
+    mol = Chem.MolFromSmiles(smiles)
+    if not mol:
+        return None
+    mol_weight = Descriptors.ExactMolWt(mol)
+
+    return np.round(mol_weight, 6)
+
 
 def get_special_groups(mol) -> List[Tuple[Tuple[int, ...], Tuple[int, ...]]]:
     """
@@ -289,10 +337,8 @@ def get_special_groups(mol) -> List[Tuple[Tuple[int, ...], Tuple[int, ...]]]:
 
     # Build list
     groups = []
-    for (add_if_match, template) in group_templates:
-        matches = mol.GetSubstructMatches(
-            Chem.MolFromSmarts(template), useChirality=True
-        )
+    for add_if_match, template in group_templates:
+        matches = mol.GetSubstructMatches(Chem.MolFromSmarts(template), useChirality=True)
         for match in matches:
             add_if = []
             for pattern_idx, atom_idx in enumerate(match):
@@ -306,9 +352,7 @@ def get_special_groups(mol) -> List[Tuple[Tuple[int, ...], Tuple[int, ...]]]:
 rdchiral.template_extractor.get_special_groups = get_special_groups
 
 
-def has_atom_mapping(
-    smiles: str, is_smarts: bool = False, sanitize: bool = True
-) -> bool:
+def has_atom_mapping(smiles: str, is_smarts: bool = False, sanitize: bool = True) -> bool:
     """
     Returns True if a molecule has atom mapping, else False.
 
@@ -334,9 +378,59 @@ def has_atom_mapping(
     return False
 
 
-def remove_atom_mapping(
-    smiles: str, is_smarts: bool = False, sanitize: bool = True, canonical: bool = True
-) -> str:
+def canonicalize_tautomer(smiles: str) -> str:
+    """
+    Returns the canonical tautomeric form of the input SMILES.
+    """
+    mol = Chem.MolFromSmiles(smiles)
+    if not mol:
+        return smiles
+    tautomer_enumerator = rdMolStandardize.TautomerEnumerator()
+    return Chem.MolToSmiles(tautomer_enumerator.Canonicalize(mol))
+
+
+def enumerate_tautomers(smiles: str) -> List[str]:
+    """
+    Returns (sorted) collection of tautomers for the input SMILES.
+    """
+    mol = Chem.MolFromSmiles(smiles)
+    tautomer_enumerator = rdMolStandardize.TautomerEnumerator()
+    canonical_tautomer = tautomer_enumerator.Canonicalize(mol)
+
+    canonical_tautomer_smiles = Chem.MolToSmiles(canonical_tautomer)
+    tautomers = [canonical_tautomer_smiles]
+
+    mols = tautomer_enumerator.Enumerate(mol)
+    enumerated_smiles = [Chem.MolToSmiles(mol) for mol in mols if mol]
+
+    enumerated_smiles = sorted(smiles for smiles in enumerated_smiles if smiles != canonical_tautomer_smiles)
+
+    tautomers.extend(enumerated_smiles)
+    return tautomers
+
+
+def is_valid_mol(smiles: str) -> bool:
+    """Check if the molecule structure is valid.
+
+    :param smiles: Molecule in SMILES.
+    :return: Return True if molecule structure is valid, return False otherwise.
+    """
+    mol = Chem.MolFromSmiles(smiles)
+    if not mol:
+        return False
+
+    return True
+
+
+def remove_stereochemistry(smiles: str) -> str:
+    """Removing stereo-chemistry information from a SMILES."""
+    mol = Chem.MolFromSmiles(smiles)
+    if mol:
+        return Chem.MolToSmiles(mol, isomericSmiles=False)
+    return smiles
+
+
+def remove_atom_mapping(smiles: str, is_smarts: bool = False, sanitize: bool = True, canonical: bool = True) -> str:
     """
     Returns a molecule without atom mapping
 
@@ -414,11 +508,7 @@ def desalt_molecules(smiles_list: List[str], keep_something: bool = False) -> Li
     """
     remover = SaltRemover()  # use default saltremover
     mols = [Chem.MolFromSmiles(smi) for smi in smiles_list]
-    desalted_mols = [
-        remover.StripMol(mol, dontRemoveEverything=keep_something)
-        for mol in mols
-        if mol
-    ]
+    desalted_mols = [remover.StripMol(mol, dontRemoveEverything=keep_something) for mol in mols if mol]
     if len(mols) > len(desalted_mols):
         logging.warning(
             f"No. of desalted molecules ({len(desalted_mols)}) are less than No. of input molecules ({len(mols)})."
@@ -479,58 +569,58 @@ def reassign_rsmi_atom_mapping(rsmi: str, as_smiles: bool = False) -> str:
 
     # Get Product(s) Atom Maps
     products_atommaps = {
-        atom.GetAtomMapNum()
-        for product in rxn.GetProducts()
-        for atom in product.GetAtoms()
-        if atom.GetAtomMapNum()
+        atom.GetAtomMapNum() for product in rxn.GetProducts() for atom in product.GetAtoms() if atom.GetAtomMapNum()
     }
     logging.debug(f"Product atom maps:{products_atommaps}")
 
     # Reassign Atom Maps for Rectants
     for reactant in rxn.GetReactants():
         reactant_atommaps = {
-            atom.GetIdx(): atom.GetAtomMapNum()
-            for atom in reactant.GetAtoms()
-            if atom.GetAtomMapNum()
+            atom.GetIdx(): atom.GetAtomMapNum() for atom in reactant.GetAtoms() if atom.GetAtomMapNum()
         }
         logging.debug(f"Reactant atom maps:{reactant_atommaps}")
         for atom_idx, atom_map in reactant_atommaps.items():
             # If atom map exists then continue
             if atom_map in products_atommaps:
                 continue
-            logging.debug(
-                f"Atom {atom_idx} map num ({atom_map}) not found in product!!!"
-            )
+            logging.debug(f"Atom {atom_idx} map num ({atom_map}) not found in product!!!")
             atom = reactant.GetAtomWithIdx(atom_idx)
             atom.SetAtomMapNum(0)
         logging.debug(f"Updated reactant: {Chem.MolToSmiles(reactant)}")
     # Reassign Atom Maps for Reagents
     for reagent in rxn.GetAgents():
-        reagent_atommaps = {
-            atom.GetIdx(): atom.GetAtomMapNum()
-            for atom in reagent.GetAtoms()
-            if atom.GetAtomMapNum()
-        }
+        reagent_atommaps = {atom.GetIdx(): atom.GetAtomMapNum() for atom in reagent.GetAtoms() if atom.GetAtomMapNum()}
         logging.debug(f"Reagent atom maps: {reagent_atommaps}")
         for atom_idx, atom_map in reagent_atommaps.items():
             # If atom map exists then continue
             if atom_map in products_atommaps:
                 continue
-            logging.debug(
-                f"Atom {atom_idx} map num ({atom_map}) not found in product!!!"
-            )
+            logging.debug(f"Atom {atom_idx} map num ({atom_map}) not found in product!!!")
             atom = reagent.GetAtomWithIdx(atom_idx)
             atom.SetAtomMapNum(0)
         logging.debug(f"Updated reagent: {Chem.MolToSmiles(reagent)}")
     # Get updated rsmi
-    updated_rsmi = (
-        AllChem.ReactionToSmiles(rxn) if as_smiles else AllChem.ReactionToSmarts(rxn)
-    )
+    updated_rsmi = AllChem.ReactionToSmiles(rxn) if as_smiles else AllChem.ReactionToSmarts(rxn)
     logging.debug(f"Updated rsmi: {updated_rsmi}")
 
     return updated_rsmi
 
 
+def split_rsmi(rsmi: str) -> Tuple[str, str, str]:
+    """
+    Split a reaction SMILES into components SMILES
+
+    :param rsmi: the reaction SMILES
+    :return: the SMILES of the components
+    """
+    reaction_components = rsmi_split_pattern.split(rsmi)
+    num_reaction_components = len(reaction_components)
+    if num_reaction_components != 3:
+        raise ValueError(f"Expected 3 reaction components but got {num_reaction_components} for '{rsmi}'")
+
+    return tuple(reaction_components)
+
+
 def join_smiles_from_reaction(smiles_list: List[str]) -> str:
     """
     Join a part of reaction SMILES, e.g. reactants and products into components.
@@ -583,6 +673,24 @@ def split_smiles_from_reaction(smiles: str) -> List[str]:
     return components
 
 
+def recreate_rsmi(rsmi: str) -> str:
+    """
+    Recreate Reactions SMILES by removing intra-molecular complexes.
+
+    :param rsmi: the original reaction smiles
+    :return: the updated reaction smiles without intra-molecular complexes
+    """
+    reactants, reagents, products = split_rsmi(rsmi)
+    # Split and rejoin the components
+    reactants = ".".join(split_smiles_from_reaction(reactants))
+    reagents = ".".join(split_smiles_from_reaction(reagents))
+    products = ".".join(split_smiles_from_reaction(products))
+
+    new_rsmi = f"{reactants}>{reagents}>{products}"
+
+    return new_rsmi
+
+
 def reaction_centres(rxn: AllChem.ChemicalReaction) -> Tuple[List[int], ...]:
     """
     Return reaction centre atoms, provided that the bonding partners
@@ -608,9 +716,7 @@ def reaction_centres(rxn: AllChem.ChemicalReaction) -> Tuple[List[int], ...]:
             mapnum = ratm.GetAtomMapNum()
             numexplicitH_reactant = ratm.GetNumExplicitHs()
             neighbours = ratm.GetNeighbors()
-            map_neighbours = sorted(
-                [neighbour_atom.GetAtomMapNum() for neighbour_atom in neighbours]
-            )
+            map_neighbours = sorted([neighbour_atom.GetAtomMapNum() for neighbour_atom in neighbours])
             foundit = False
             for product in rxn.GetProducts():
                 for patom in product.GetAtoms():
@@ -618,10 +724,7 @@ def reaction_centres(rxn: AllChem.ChemicalReaction) -> Tuple[List[int], ...]:
                         neighbours_product = patom.GetNeighbors()
                         numexplicitH_product = patom.GetNumExplicitHs()
                         map_neighbours_product = sorted(
-                            [
-                                neighbour_atom.GetAtomMapNum()
-                                for neighbour_atom in neighbours_product
-                            ]
+                            [neighbour_atom.GetAtomMapNum() for neighbour_atom in neighbours_product]
                         )
                         # criterion: check if the map numbers of neighbours are the same in the reactant and the product
                         if map_neighbours == map_neighbours_product:
diff --git a/rxnutils/data/base_pipeline.py b/rxnutils/data/base_pipeline.py
index 63364aa..26aca07 100644
--- a/rxnutils/data/base_pipeline.py
+++ b/rxnutils/data/base_pipeline.py
@@ -1,11 +1,9 @@
 """Module containing base class for data pipelines
 """
-import math
-import os
+
 from pathlib import Path
 from typing import List, Tuple
 
-import pandas as pd
 from metaflow import FlowSpec, Parameter
 
 from rxnutils.data.batch_utils import combine_csv_batches, create_csv_batches
@@ -26,9 +24,7 @@ class DataBaseFlow(FlowSpec):
     def _combine_batches(self, filename: str) -> None:
         combine_csv_batches(filename, self.nbatches)
 
-    def _create_batches(
-        self, input_filename: str, output_filename: str
-    ) -> List[Tuple[int, int, int]]:
+    def _create_batches(self, input_filename: str, output_filename: str) -> List[Tuple[int, int, int]]:
         return create_csv_batches(
             input_filename,
             self.nbatches,
@@ -61,9 +57,7 @@ def _do_cleaning(self):
                     "--data",
                     str(Path(self.folder) / f"{self.data_prefix}_data.csv"),
                     "--output",
-                    str(
-                        Path(self.folder) / f"{self.data_prefix}_data_cleaned.csv.{idx}"
-                    ),
+                    str(Path(self.folder) / f"{self.data_prefix}_data_cleaned.csv.{idx}"),
                     "--batch",
                     str(start),
                     str(end),
@@ -75,6 +69,4 @@ def _do_cleaning(self):
 
     def _join_cleaning(self):
         """Combined cleaned batches of data"""
-        self._combine_batches(
-            Path(self.folder) / f"{self.data_prefix}_data_cleaned.csv"
-        )
+        self._combine_batches(Path(self.folder) / f"{self.data_prefix}_data_cleaned.csv")
diff --git a/rxnutils/data/batch_utils.py b/rxnutils/data/batch_utils.py
index f5622b6..9c10f02 100644
--- a/rxnutils/data/batch_utils.py
+++ b/rxnutils/data/batch_utils.py
@@ -2,6 +2,7 @@
 from pathlib import Path
 from typing import Any, List, Optional, Tuple
 
+import numpy as np
 import pandas as pd
 from scipy import sparse
 
@@ -56,6 +57,27 @@ def _write_csv(data: pd.DataFrame, filename: str) -> None:
     combine_batches(filename, nbatches, _read_csv, _write_csv, _combine_csv)
 
 
+def combine_numpy_array_batches(filename: str, nbatches: int) -> None:
+    """
+    Combine numpy array batches to one master file
+    The batch files are removed from disc
+    :param filename: the filename of the master file
+    :param nbatches: the number of batches
+    """
+
+    def _read_array(filename: str, idx: int) -> Any:
+        filename2 = filename.replace(".npz", f".{idx}.npz")
+        return np.load(filename2)["arr_0"], filename2
+
+    def _write_array(data: np.ndarray, filename: str) -> None:
+        np.savez(filename, data, compressed=True)
+
+    def _combine_array(data: np.ndarray, temp_data: np.ndarray) -> np.ndarray:
+        return np.hstack([data, temp_data])
+
+    return combine_batches(filename, nbatches, _read_array, _write_array, _combine_array)
+
+
 def combine_sparse_matrix_batches(filename: str, nbatches: int) -> None:
     """
     Combine sparse matrix batches to one master file
@@ -98,12 +120,8 @@ def create_csv_batches(
     if output_filename and Path(output_filename).exists():
         return [(-1, None, None)]
 
-    file_size = (
-        nlines(filename) - 1
-    )  # Header should not be counted for batch size calculations
-    nbatches = min(
-        file_size, nbatches
-    )  # Adjust the number of batches to the size of the file
+    file_size = nlines(filename) - 1  # Header should not be counted for batch size calculations
+    nbatches = min(file_size, nbatches)  # Adjust the number of batches to the size of the file
     batch_size, remainder = divmod(file_size, nbatches)
     stop = 1  # 1-indexed to account for header in the .csv file
     batches = []
@@ -114,9 +132,7 @@ def create_csv_batches(
     return batches
 
 
-def read_csv_batch(
-    filename: str, batch: Tuple[int, ...] = None, **kwargs: Any
-) -> pd.DataFrame:
+def read_csv_batch(filename: str, batch: Tuple[int, ...] = None, **kwargs: Any) -> pd.DataFrame:
     """
     Read parts of a CSV file as specified by a batch
 
diff --git a/rxnutils/data/mapping.py b/rxnutils/data/mapping.py
index 9be0d6e..fa3f495 100644
--- a/rxnutils/data/mapping.py
+++ b/rxnutils/data/mapping.py
@@ -1,5 +1,6 @@
 """Module containing script to atom-map USPTO or ORD reactions
 """
+
 import argparse
 from typing import Optional, Sequence
 
@@ -8,26 +9,25 @@
 from rxnutils.data.batch_utils import read_csv_batch
 
 try:
-    from rxnmapper import RXNMapper  # pylint: disable=all
+    from rxnmapper import BatchedMapper  # pylint: disable=all
 except ImportError:
     DEPENDENCY_OK = False
 else:
     DEPENDENCY_OK = True
+    from transformers import logging
+
+    logging.set_verbosity_error()
 
 
 def main(input_args: Optional[Sequence[str]] = None) -> None:
     """Function for command-line tool"""
 
     if not DEPENDENCY_OK:
-        raise ImportError(
-            "You need to run this tool in an environment where rxnmapper is installed"
-        )
+        raise ImportError("You need to run this tool in an environment where rxnmapper is installed")
 
     parser = argparse.ArgumentParser("Script to atom-map USPTO or ORD reactions")
     parser.add_argument("--input", default="data.csv", help="the file with reactions")
-    parser.add_argument(
-        "--output", default="data_mapped.csv", help="the output filename"
-    )
+    parser.add_argument("--output", default="data_mapped.csv", help="the output filename")
     parser.add_argument(
         "--batch",
         type=int,
@@ -49,34 +49,24 @@ def main(input_args: Optional[Sequence[str]] = None) -> None:
 
     data = read_csv_batch(args.input, sep="\t", index_col=False, batch=args.batch)
 
-    rxn_mapper = RXNMapper()
+    rxn_mapper = BatchedMapper(batch_size=args.mapper_batch_size)
     mapped_data = []
+    # Get RXNMapper results in batches with error handling (returning and empty dict for failed reaction)
     for start in range(0, len(data), args.mapper_batch_size):
         batch = data[args.column].iloc[start : start + args.mapper_batch_size].tolist()
-        fail_data = [
-            {
-                "mapped_rxn": None,
-                "confidence": 0.0,
-            }
-            for _ in range(len(batch))
-        ]
-        try:
-            batch_mapped = rxn_mapper.get_attention_guided_atom_maps(
-                batch, canonicalize_rxns=False
-            )
-        except ValueError:
-            print(batch)
-            mapped_data.extend(fail_data)
-        except RuntimeError:
-            print("\n\n".join(batch))
-            mapped_data.extend(fail_data)
-        else:
-            mapped_data.extend(batch_mapped)
+        batch_mapped = list(rxn_mapper.map_reactions_with_info(batch))
+        # Check RXNMapper results and if there is a failure (empty dict) then use the original Reaction SMILES
+        for idx, (original_rsmi, mapped_rsmi) in enumerate(zip(batch, batch_mapped)):
+            # In case of failure return the original Reaction SMILES
+            if not mapped_rsmi:
+                batch_mapped[idx] = {
+                    "mapped_rxn": original_rsmi,
+                    "confidence": 0.0,
+                }
+        mapped_data.extend(batch_mapped)
     mapped_data_df = pd.DataFrame(mapped_data)
 
-    data = data.assign(
-        **{column: mapped_data_df[column] for column in mapped_data_df.columns}
-    )
+    data = data.assign(**{column: mapped_data_df[column] for column in mapped_data_df.columns})
     data.to_csv(args.output, sep="\t", index=False)
 
 
diff --git a/rxnutils/data/mapping_pipeline.py b/rxnutils/data/mapping_pipeline.py
index 53af1dc..210b26c 100644
--- a/rxnutils/data/mapping_pipeline.py
+++ b/rxnutils/data/mapping_pipeline.py
@@ -2,6 +2,7 @@
 Module containing pipeline for mapping with rxnmapper
 This needs to be run in an environment with rxnmapper installed
 """
+
 from pathlib import Path
 
 from metaflow import Parameter, step
@@ -29,9 +30,7 @@ def start(self):
     def do_mapping(self):
         """Perform atom-mapping of reactions"""
         idx, start, end = self.input
-        output_filename = (
-            Path(self.folder) / f"{self.data_prefix}_data_mapped.csv.{idx}"
-        )
+        output_filename = Path(self.folder) / f"{self.data_prefix}_data_mapped.csv.{idx}"
         if idx > -1 and not output_filename.exists():
             map_data(
                 [
diff --git a/rxnutils/data/ord/import_ord_dataset.py b/rxnutils/data/ord/import_ord_dataset.py
index 9808e53..4086f68 100644
--- a/rxnutils/data/ord/import_ord_dataset.py
+++ b/rxnutils/data/ord/import_ord_dataset.py
@@ -1,6 +1,7 @@
 """
 Module containing script to import ORD dataset to a CSV file
 """
+
 import argparse
 import os
 import re
@@ -24,9 +25,7 @@ def main(input_args: Optional[Sequence[str]] = None) -> None:
     """Function for command-line tool"""
 
     if not DEPENDENCY_OK:
-        raise ImportError(
-            "You need to install the ord-schema package and download the ord-data repository"
-        )
+        raise ImportError("You need to install the ord-schema package and download the ord-data repository")
 
     parser = argparse.ArgumentParser("Script to import ORD datasets")
     parser.add_argument("--filenames", nargs="+", help="the files to import")
@@ -42,14 +41,10 @@ def main(input_args: Optional[Sequence[str]] = None) -> None:
     data = defaultdict(list)
     for filename in tqdm(args.filenames):
         ord_dataset = message_helpers.load_message(filename, dataset_pb2.Dataset)
-        if include_only and not (
-            ord_dataset.dataset_id == include_only or ord_dataset.name == include_only
-        ):
+        if include_only and not (ord_dataset.dataset_id == include_only or ord_dataset.name == include_only):
             continue
         for reaction in tqdm(ord_dataset.reactions, desc=os.path.basename(filename)):
-            smiles = message_helpers.get_reaction_smiles(
-                reaction, generate_if_missing=True
-            )
+            smiles = message_helpers.get_reaction_smiles(reaction, generate_if_missing=True)
             # Trying to remove spurious spaces in reaction SMILES
             smiles = smiles.strip()
             smiles = re.sub(r"\.\s+", ".", smiles)
@@ -63,9 +58,7 @@ def main(input_args: Optional[Sequence[str]] = None) -> None:
             data["Date"].append(reaction.provenance.experiment_start.value)
             data["ReactionSmiles"].append(smiles)
             try:
-                data["Yield"].append(
-                    message_helpers.get_product_yield(reaction.outcomes[0].products[0])
-                )
+                data["Yield"].append(message_helpers.get_product_yield(reaction.outcomes[0].products[0]))
             except IndexError:
                 data["Yield"].append(None)
 
diff --git a/rxnutils/data/ord/preparation_pipeline.py b/rxnutils/data/ord/preparation_pipeline.py
index f76e119..63fc5ae 100644
--- a/rxnutils/data/ord/preparation_pipeline.py
+++ b/rxnutils/data/ord/preparation_pipeline.py
@@ -2,6 +2,7 @@
 Module containing pipeline for extracting, transforming and cleaning Open reaction database data
 This needs to be run in an environment with rxnutils installed
 """
+
 import glob
 import os
 from pathlib import Path
@@ -56,9 +57,7 @@ def join_cleaning(self, _):
     @step
     def end(self):
         """Final step, just print information"""
-        print(
-            f"Processed file is locate here: {Path(self.folder) / 'ord_data_cleaned.csv'}"
-        )
+        print(f"Processed file is locate here: {Path(self.folder) / 'ord_data_cleaned.csv'}")
 
 
 if __name__ == "__main__":
diff --git a/rxnutils/data/uspto/combine.py b/rxnutils/data/uspto/combine.py
index 350f975..abe7899 100644
--- a/rxnutils/data/uspto/combine.py
+++ b/rxnutils/data/uspto/combine.py
@@ -22,15 +22,9 @@
 
 def main(args: Optional[Sequence[str]] = None) -> None:
     """Function for command-line tool"""
-    parser = argparse.ArgumentParser(
-        "Script to combine USPTO SMILES data from Figshare"
-    )
-    parser.add_argument(
-        "--filenames", nargs="+", default=DEFAULT_FILENAMES, help="the files to combine"
-    )
-    parser.add_argument(
-        "--output", default="uspto_data.csv", help="the output filename"
-    )
+    parser = argparse.ArgumentParser("Script to combine USPTO SMILES data from Figshare")
+    parser.add_argument("--filenames", nargs="+", default=DEFAULT_FILENAMES, help="the files to combine")
+    parser.add_argument("--output", default="uspto_data.csv", help="the output filename")
     parser.add_argument("--folder", default=".", help="folder with downloaded files")
     parser.add_argument(
         "--with_yields",
@@ -41,12 +35,7 @@ def main(args: Optional[Sequence[str]] = None) -> None:
     args = parser.parse_args(args)
 
     filenames = [Path(args.folder) / filename for filename in args.filenames]
-    data = pd.concat(
-        [
-            pd.read_csv(filename, sep="\t", dtype={"ParagraphNum": "str"})
-            for filename in filenames
-        ]
-    )
+    data = pd.concat([pd.read_csv(filename, sep="\t", dtype={"ParagraphNum": "str"}) for filename in filenames])
 
     para_num = data["ParagraphNum"].fillna("")
     row_num = data.index.astype(str)
diff --git a/rxnutils/data/uspto/download.py b/rxnutils/data/uspto/download.py
index edf4165..4d37bb5 100644
--- a/rxnutils/data/uspto/download.py
+++ b/rxnutils/data/uspto/download.py
@@ -1,5 +1,6 @@
 """Module containing a script to download USPTO files Figshare
 """
+
 import argparse
 import os
 from pathlib import Path
@@ -25,9 +26,7 @@ def _download_file(url: str, filename: str) -> None:
     with requests.get(url, stream=True) as response:
         response.raise_for_status()
         total_size = int(response.headers.get("content-length", 0))
-        pbar = tqdm.tqdm(
-            total=total_size, desc=os.path.basename(filename), unit="B", unit_scale=True
-        )
+        pbar = tqdm.tqdm(total=total_size, desc=os.path.basename(filename), unit="B", unit_scale=True)
         with open(filename, "wb") as fileobj:
             for chunk in response.iter_content(chunk_size=1024):
                 fileobj.write(chunk)
@@ -37,9 +36,7 @@ def _download_file(url: str, filename: str) -> None:
 
 def main(args: Optional[Sequence[str]] = None) -> None:
     """Function for command-line tool"""
-    parser = argparse.ArgumentParser(
-        "Script to download USPTO SMILES data from Figshare"
-    )
+    parser = argparse.ArgumentParser("Script to download USPTO SMILES data from Figshare")
     parser.add_argument(
         "--overwrite",
         action="store_true",
diff --git a/rxnutils/data/uspto/preparation_pipeline.py b/rxnutils/data/uspto/preparation_pipeline.py
index 348acf0..d8fac79 100644
--- a/rxnutils/data/uspto/preparation_pipeline.py
+++ b/rxnutils/data/uspto/preparation_pipeline.py
@@ -55,9 +55,7 @@ def join_cleaning(self, _):
     @step
     def end(self):
         """Final step, just print information"""
-        print(
-            f"Processed file is locate here: {Path(self.folder) / 'uspto_data_cleaned.csv'}"
-        )
+        print(f"Processed file is locate here: {Path(self.folder) / 'uspto_data_cleaned.csv'}")
 
 
 if __name__ == "__main__":
diff --git a/rxnutils/pipeline/actions/dataframe_mod.py b/rxnutils/pipeline/actions/dataframe_mod.py
index 06c70c4..67584fd 100644
--- a/rxnutils/pipeline/actions/dataframe_mod.py
+++ b/rxnutils/pipeline/actions/dataframe_mod.py
@@ -1,4 +1,5 @@
 """Module containing actions that modify the dataframe in some way"""
+
 from __future__ import annotations
 
 from dataclasses import dataclass
@@ -30,7 +31,7 @@ class DropColumns:
     columns: list[str]
 
     def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
-        return data.drop(self.columns, 1)
+        return data.drop(self.columns, axis=1)
 
     def __str__(self) -> str:
         return f"{self.pretty_name} (drop columns in specified list, keeps the rest)"
@@ -99,7 +100,7 @@ def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
         for name in self.columns:
             drop_columns.remove(name)
 
-        return data.drop(drop_columns, 1)
+        return data.drop(drop_columns, axis=1)
 
     def __str__(self) -> str:
         return f"{self.pretty_name} (keeps columns in specified list, drops the rest)"
@@ -186,7 +187,7 @@ def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
             value_vars=self.in_columns,
             var_name=var_column_name,
             value_name=self.out_column,
-        ).drop(var_column_name, 1)
+        ).drop(var_column_name, axis=1)
 
     def __str__(self) -> str:
         return f"{self.pretty_name} (stacks two columns into a single column)"
diff --git a/rxnutils/pipeline/actions/reaction_mod.py b/rxnutils/pipeline/actions/reaction_mod.py
index 8d16211..53fc73c 100644
--- a/rxnutils/pipeline/actions/reaction_mod.py
+++ b/rxnutils/pipeline/actions/reaction_mod.py
@@ -3,10 +3,11 @@
 from __future__ import annotations
 
 import os
+import re
 import subprocess
 import sys
 import tempfile
-from dataclasses import dataclass
+from dataclasses import dataclass, field
 from pathlib import Path
 from typing import ClassVar, List, Tuple
 
@@ -19,8 +20,12 @@
 from rxnutils.chem.utils import (
     atom_mapping_numbers,
     desalt_molecules,
+    join_smiles_from_reaction,
     neutralize_molecules,
+    recreate_rsmi,
     remove_atom_mapping,
+    split_rsmi,
+    split_smiles_from_reaction,
 )
 from rxnutils.pipeline.base import ReactionActionMixIn, action, global_apply
 
@@ -28,12 +33,9 @@
 if CONTRIB_INSTALLED:
     # RDKit contrib is not default part of PYTHONPATH
     sys.path.append(RDConfig.RDContribDir)
-    sys.path.append(
-        f"{RDConfig.RDContribDir}/RxnRoleAssignment"
-    )  # to make Nadines code import "utils"
+    sys.path.append(f"{RDConfig.RDContribDir}/RxnRoleAssignment")  # to make Nadines code import "utils"
     # fmt: off
-    from RxnRoleAssignment.identifyReactants import \
-        reassignReactionRoles  # pylint: disable=all # noqa
+    from RxnRoleAssignment.identifyReactants import reassignReactionRoles  # pylint: disable=all # noqa
 
     # fmt: on
 
@@ -57,16 +59,10 @@ def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
 
     def _apply_row(self, row: pd.Series) -> pd.Series:
         reactants_list, reagents_list, products_list = self.split_lists(row)
-        reactants_list = desalt_molecules(
-            reactants_list, keep_something=self.keep_something
-        )
+        reactants_list = desalt_molecules(reactants_list, keep_something=self.keep_something)
         if reagents_list:
-            reagents_list = desalt_molecules(
-                reagents_list, keep_something=self.keep_something
-            )
-        products_list = desalt_molecules(
-            products_list, keep_something=self.keep_something
-        )
+            reagents_list = desalt_molecules(reagents_list, keep_something=self.keep_something)
+        products_list = desalt_molecules(products_list, keep_something=self.keep_something)
         return self.join_lists(reactants_list, reagents_list, products_list)
 
     def __str__(self) -> str:
@@ -90,11 +86,13 @@ def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
         data[self.in_column].to_csv(infile, index=False, header=False)
         subprocess.call(["namerxn"] + self.options.split() + [infile, outfile])
         if not os.path.exists(outfile) or os.path.getsize(outfile) == 0:
-            raise FileNotFoundError(
-                "Could not produce namerxn output. Make sure 'namerxn' program is in path"
-            )
+            raise FileNotFoundError("Could not produce namerxn output. Make sure 'namerxn' program is in path")
+        # Set the data types to 'str' classification id must be a string
         namerxn_data = pd.read_csv(
-            outfile, sep=" ", names=[self.nm_rxn_column, self.nmc_column]
+            outfile,
+            sep=" ",
+            names=[self.nm_rxn_column, self.nmc_column],
+            dtype=str,
         )
         return data.assign(**{col: namerxn_data[col] for col in namerxn_data.columns})
 
@@ -146,16 +144,12 @@ def __str__(self) -> str:
     def _row_action(self, row: pd.Series) -> str:
         reactants_list_old, reagents_list, products_list = self.split_lists(row)
 
-        product_indices = {
-            idx for smi in products_list for idx in atom_mapping_numbers(smi)
-        }
+        product_indices = {idx for smi in products_list for idx in atom_mapping_numbers(smi)}
 
         reactants_list = []
         for reactant in reactants_list_old:
             reactant_indices = atom_mapping_numbers(reactant)
-            if not reactant_indices or not any(
-                idx in product_indices for idx in reactant_indices
-            ):
+            if not reactant_indices or not any(idx in product_indices for idx in reactant_indices):
                 reagents_list.append(reactant)
             else:
                 reactants_list.append(reactant)
@@ -179,7 +173,7 @@ def __str__(self) -> str:
         return f"{self.pretty_name} (putting all reagents to reactants)"
 
     def _row_action(self, row: pd.Series) -> str:
-        reactants, reagents, products = row[self.in_column].split(">")
+        reactants, reagents, products = split_rsmi(row[self.in_column])
         if reagents:
             reactants = ".".join([reactants, reagents])
         return reactants + ">>" + products
@@ -203,15 +197,9 @@ def __str__(self) -> str:
 
     def _row_action(self, row: pd.Series) -> str:
         reactants_list, reagents_list, products_list = self.split_lists(row)
-        reactants_list = [
-            remove_atom_mapping(smi, sanitize=False) for smi in reactants_list
-        ]
-        reagents_list = [
-            remove_atom_mapping(smi, sanitize=False) for smi in reagents_list
-        ]
-        products_list = [
-            remove_atom_mapping(smi, sanitize=False) for smi in products_list
-        ]
+        reactants_list = [remove_atom_mapping(smi, sanitize=False) for smi in reactants_list]
+        reagents_list = [remove_atom_mapping(smi, sanitize=False) for smi in reagents_list]
+        products_list = [remove_atom_mapping(smi, sanitize=False) for smi in products_list]
 
         return self.join_lists(reactants_list, reagents_list, products_list)
 
@@ -269,18 +257,16 @@ class IsotopeInfo:
     in_column: str
     isotope_column: str = "Isotope"
     out_column: str = "RxnSmilesWithoutIsotopes"
-    match_regex: str = (
-        r"\[(?P<mass>[0-9]+)(?P<symbol>[A-Za-z][a-z]*)(?P<spec>[^\]]+)*\]"
-    )
+    match_regex: str = r"\[(?P<mass>[0-9]+)(?P<symbol>[A-Za-z][a-z]*)(?P<spec>[^\]]+)*\]"
     sub_regex: str = r"[\g<symbol>\g<spec>]"
 
     def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
         isotop_info = data[self.in_column].str.extract(self.match_regex)
-        isotop_col = isotop_info.mass + isotop_info.symbol
-        rsmi_col = data[self.in_column].str.replace(self.match_regex, self.sub_regex)
-        return data.assign(
-            **{self.isotope_column: isotop_col, self.out_column: rsmi_col}
+        isotop_col = isotop_info["mass"] + isotop_info["symbol"]
+        rsmi_col = data[self.in_column].str.replace(
+            self.match_regex, self.sub_regex, regex=True
         )
+        return data.assign(**{self.isotope_column: isotop_col, self.out_column: rsmi_col})
 
     def __str__(self) -> str:
         return f"{self.pretty_name} (extract and remove isotope information from reactions)"
@@ -314,9 +300,7 @@ def reassign_atom_mapping(smiles: str) -> str:
 
         reactants_list, reagents_list, products_list = self.split_lists(row)
 
-        product_indices = {
-            idx for smi in products_list for idx in atom_mapping_numbers(smi)
-        }
+        product_indices = {idx for smi in products_list for idx in atom_mapping_numbers(smi)}
 
         reactants_list = [reassign_atom_mapping(smi) for smi in reactants_list]
         reagents_list = [reassign_atom_mapping(smi) for smi in reagents_list]
@@ -352,9 +336,7 @@ def _row_action(self, row: pd.Series) -> str:
 
         new_products = []
         for product, product_smi in zip(products_mols, products_list):
-            matches = [
-                self._is_equal(product, r) for r in reactants_mols + reagents_mols
-            ]
+            matches = [self._is_equal(product, r) for r in reactants_mols + reagents_mols]
             if not any(matches):
                 new_products.append(product_smi)
 
@@ -420,9 +402,7 @@ def process_smiles(smiles_list: List[str]) -> Tuple[List[str], List[str]]:
         return pd.Series({"rxn_smi": rxn_smi, "bad_smiles": bad_smiles})
 
     def __str__(self) -> str:
-        return (
-            f"{self.pretty_name} (removing molecules that is not sanitizable by RDKit)"
-        )
+        return f"{self.pretty_name} (removing molecules that is not sanitizable by RDKit)"
 
 
 @action
@@ -436,15 +416,11 @@ class RDKitRxnRoles:
 
     def __post_init__(self):
         if not CONTRIB_INSTALLED:
-            raise ImportError(
-                "This action cannot be used because the RDKit Contrib folder is not installed"
-            )
+            raise ImportError("This action cannot be used because the RDKit Contrib folder is not installed")
 
     def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
 
-        smiles_col = global_apply(
-            data, lambda row: reassignReactionRoles(row[self.in_column]), axis=1
-        )
+        smiles_col = global_apply(data, lambda row: reassignReactionRoles(row[self.in_column]), axis=1)
         return data.assign(**{self.out_column: smiles_col})
 
     def __str__(self) -> str:
@@ -464,9 +440,7 @@ class RxnMapper:
     pretty_name: ClassVar[str] = "rxnmapper"
     in_column: str
     out_column: str = "RxnmapperRxnSmiles"
-    rxnmapper_command: str = "conda run -p ${RXNMAPPER_ENV_PATH} python " + str(
-        _MAP_SCRIPT
-    )
+    rxnmapper_command: str = "conda run -p ${RXNMAPPER_ENV_PATH} python " + str(_MAP_SCRIPT)
 
     def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
         new_column = self._do_action(data[self.in_column])
@@ -475,7 +449,9 @@ def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
     def _do_action(self, column: pd.Series) -> pd.Series:
         input_handle, input_path = tempfile.mkstemp(suffix=".csv")
         output_handle, output_path = tempfile.mkstemp(suffix=".csv")
-        column.to_csv(input_path, sep="\t", index=False)
+        # Recreate Reaction SMILES by removing intra-molecular complexes
+        tmp_column = column.apply(recreate_rsmi)
+        tmp_column.to_csv(input_path, sep="\t", index=False)
 
         cmd = self.rxnmapper_command
         if "CONDA_PATH" in os.environ:
@@ -529,18 +505,14 @@ def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
                     self.out_columns[2]: new_columns.products,
                 }
             )
-        raise ValueError(
-            f"Don't know what to return with {len(self.out_columns)} output columns"
-        )
+        raise ValueError(f"Don't know what to return with {len(self.out_columns)} output columns")
 
     def __str__(self) -> str:
         return f"{self.pretty_name} (rxn => reactants, [reagents], products)"
 
     def _apply_row(self, row: pd.Series) -> pd.Series:
         reactants, reagents, products = self.split_smiles(row)
-        return pd.Series(
-            {"reactants": reactants, "reagents": reagents, "products": products}
-        )
+        return pd.Series({"reactants": reactants, "reagents": reagents, "products": products})
 
 
 @action
diff --git a/rxnutils/pipeline/actions/reaction_props.py b/rxnutils/pipeline/actions/reaction_props.py
index 67f3400..b1ab5cb 100644
--- a/rxnutils/pipeline/actions/reaction_props.py
+++ b/rxnutils/pipeline/actions/reaction_props.py
@@ -1,8 +1,8 @@
 """Module containing actions on reactions that doesn't modify the reactions only compute properties of them"""
+
 from __future__ import annotations
 
 import json
-import os
 from collections import defaultdict
 from dataclasses import dataclass
 from typing import ClassVar, List, Optional, Set, Tuple
@@ -19,8 +19,8 @@
 from rxnutils.chem.utils import (
     atom_mapping_numbers,
     has_atom_mapping,
-    join_smiles_from_reaction,
     reaction_centres,
+    split_rsmi,
     split_smiles_from_reaction,
 )
 from rxnutils.pipeline.base import ReactionActionMixIn, action, global_apply
@@ -51,9 +51,7 @@ def _apply_row(self, row: pd.Series) -> pd.Series:
         def _process_smiles(smiles_list: List[str]) -> Tuple[int, int]:
             if not smiles_list:
                 return 0, 0
-            smiles_list_mapped = [
-                smi for smi in smiles_list if has_atom_mapping(smi, sanitize=False)
-            ]
+            smiles_list_mapped = [smi for smi in smiles_list if has_atom_mapping(smi, sanitize=False)]
             return len(smiles_list), len(smiles_list_mapped)
 
         reactants_list, reagents_list, products_list = self.split_lists(row)
@@ -89,9 +87,7 @@ def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
         return data.assign(**{self.out_column: hash_col})
 
     def __str__(self) -> str:
-        return (
-            f"{self.pretty_name} (calculate the occurence of elements in the reactants)"
-        )
+        return f"{self.pretty_name} (calculate the occurence of elements in the reactants)"
 
     def _row_action(self, row: pd.Series) -> str:
         def count_elements(smiles, counts):
@@ -102,7 +98,7 @@ def count_elements(smiles, counts):
                 counts[atom.GetAtomicNum()] += 1
 
         counts = defaultdict(int)
-        reactants, _, _ = row[self.in_column].split(">")
+        reactants, _, _ = split_rsmi(row[self.in_column])
         for smiles in split_smiles_from_reaction(reactants):
             count_elements(smiles, counts)
 
@@ -147,7 +143,7 @@ def __str__(self) -> str:
         return f"{self.pretty_name} (detect if there is an unmapped radical in the reaction SMILES)"
 
     def _row_action(self, row: pd.Series) -> str:
-        reactants, _, product = row["rsmi_processed"].split(">")
+        reactants, _, product = split_rsmi(row["rsmi_processed"])
 
         react_mol = Chem.MolFromSmiles(reactants)
         if Descriptors.NumRadicalElectrons(react_mol) == 0:
@@ -202,7 +198,7 @@ def _row_action(self, row: pd.Series) -> str:
         if not unsanitize_atom_map_num:
             return False
 
-        _, _, product = row[self.rsmi_column].split(">")
+        _, _, product = split_rsmi(row[self.rsmi_column])
         prod_atom_map_num = set(atom_mapping_numbers(product))
         return bool(prod_atom_map_num.intersection(unsanitize_atom_map_num))
 
@@ -213,9 +209,7 @@ def _process_bad_column(smiles_list: str) -> Set[int]:
             mol = Chem.MolFromSmiles(smiles, sanitize=False)
             if not mol:
                 continue
-            unsanitize_atom_map_num |= {
-                atom.GetAtomMapNum() for atom in mol.GetAtoms() if atom.GetAtomMapNum()
-            }
+            unsanitize_atom_map_num |= {atom.GetAtomMapNum() for atom in mol.GetAtoms() if atom.GetAtomMapNum()}
         return unsanitize_atom_map_num
 
 
@@ -287,7 +281,7 @@ def __str__(self) -> str:
         return f"{self.pretty_name} (count number of number of unmapped and widow product atoms)"
 
     def _row_action(self, row: pd.Series) -> str:
-        reactants, _, products = row[self.in_column].split(">")
+        reactants, _, products = split_rsmi(row[self.in_column])
         prod_mol = Chem.MolFromSmiles(products)
         nprod_atoms = prod_mol.GetNumAtoms() if prod_mol else 0
 
@@ -322,7 +316,7 @@ def __str__(self) -> str:
         return f"{self.pretty_name} (number of heavy atoms in product)"
 
     def _row_action(self, row: pd.Series) -> str:
-        _, _, products = row[self.in_column].split(">")
+        _, _, products = split_rsmi(row[self.in_column])
         products_mol = Chem.MolFromSmiles(products)
 
         if products_mol:
@@ -352,20 +346,14 @@ def __str__(self) -> str:
 
     def _row_action(self, row: pd.Series) -> str:
         def components_to_inchi(smiles):
-            mols = [
-                Chem.MolFromSmiles(smi) for smi in split_smiles_from_reaction(smiles)
-            ]
+            mols = [Chem.MolFromSmiles(smi) for smi in split_smiles_from_reaction(smiles)]
             return ".".join(sorted([Chem.MolToInchiKey(mol) for mol in mols if mol]))
 
         if self.no_reagents:
-            reactants, _, products = row[self.in_column].split(">")
-            return ">>".join(
-                [components_to_inchi(smi) for smi in [reactants, products]]
-            )
+            reactants, _, products = split_rsmi(row[self.in_column])
+            return ">>".join([components_to_inchi(smi) for smi in [reactants, products]])
 
-        return ">".join(
-            components_to_inchi(smi) for smi in row[self.in_column].split(">")
-        )
+        return ">".join(components_to_inchi(smi) for smi in split_rsmi(row[self.in_column]))
 
 
 @action
@@ -386,9 +374,7 @@ def __str__(self) -> str:
 
     def _row_action(self, row: pd.Series) -> str:
         def components_to_inchi(smiles):
-            mols = [
-                Chem.MolFromSmiles(smi) for smi in split_smiles_from_reaction(smiles)
-            ]
+            mols = [Chem.MolFromSmiles(smi) for smi in split_smiles_from_reaction(smiles)]
             return ".".join(sorted([Chem.MolToInchiKey(mol) for mol in mols if mol]))
 
         return components_to_inchi(row[self.in_column])
@@ -411,7 +397,7 @@ def __str__(self) -> str:
         return f"{self.pretty_name} (product atom count minus reactants atom count)"
 
     def _row_action(self, row: pd.Series) -> str:
-        reactants, _, products = row[self.in_column].split(">")
+        reactants, _, products = split_rsmi(row[self.in_column])
 
         reactants_mol = Chem.MolFromSmiles(reactants)
         if reactants_mol:
@@ -445,7 +431,7 @@ def __str__(self) -> str:
         return f"{self.pretty_name} (number of heavy atoms in reactant)"
 
     def _row_action(self, row: pd.Series) -> str:
-        reactants, _, _ = row[self.in_column].split(">")
+        reactants, _, _ = split_rsmi(row[self.in_column])
         reactants_mol = Chem.MolFromSmiles(reactants)
 
         if reactants_mol:
@@ -476,7 +462,7 @@ def __str__(self) -> str:
         return f"{self.pretty_name} (maximum number of rings)"
 
     def _row_action(self, row: pd.Series) -> str:
-        reactants, _, products = row[self.in_column].split(">")
+        reactants, _, products = split_rsmi(row[self.in_column])
 
         reactants_mols = [Chem.MolFromSmiles(smi) for smi in reactants.split(".")]
         nrings_reactants = [CalcNumRings(mol) for mol in reactants_mols if mol]
@@ -511,7 +497,7 @@ def __str__(self) -> str:
         return f"{self.pretty_name} (ring change based on number of rings)"
 
     def _row_action(self, row: pd.Series) -> str:
-        reactants, _, products = row[self.in_column].split(">")
+        reactants, _, products = split_rsmi(row[self.in_column])
         prod_mol = Chem.MolFromSmiles(products)
 
         if not prod_mol:
@@ -540,7 +526,7 @@ def __str__(self) -> str:
         return f"{self.pretty_name} (ring change based on ring bond made)"
 
     def _row_action(self, row: pd.Series) -> str:
-        reactants, _, products = row[self.in_column].split(">")
+        reactants, _, products = split_rsmi(row[self.in_column])
 
         prod_mol = Chem.MolFromSmiles(products)
         if not prod_mol:
@@ -575,11 +561,7 @@ def _row_action(self, row: pd.Series) -> str:
 
     @staticmethod
     def _mapping_to_index(mol):
-        return {
-            atom.GetAtomMapNum(): atom.GetIdx()
-            for atom in mol.GetAtoms()
-            if atom.GetAtomMapNum()
-        }
+        return {atom.GetAtomMapNum(): atom.GetIdx() for atom in mol.GetAtoms() if atom.GetAtomMapNum()}
 
 
 @action
@@ -599,7 +581,7 @@ def __str__(self) -> str:
         return f"{self.pretty_name} (largest ring made)"
 
     def _row_action(self, row: pd.Series) -> str:
-        reactants, _, products = row[self.in_column].split(">")
+        reactants, _, products = split_rsmi(row[self.in_column])
 
         prod_mol = Chem.MolFromSmiles(products)
         if not prod_mol:
@@ -698,15 +680,13 @@ def __call__(self, data: pd.DataFrame) -> pd.DataFrame:
         return data.assign(**{self.out_column: smiles_col})
 
     def __str__(self) -> str:
-        return (
-            f"{self.pretty_name} (Reactants with no stereo, turn into stereo compounds)"
-        )
+        return f"{self.pretty_name} (Reactants with no stereo, turn into stereo compounds)"
 
     def _has_stereo(self, smiles: str) -> bool:
         return "@" in smiles
 
     def _row_action(self, row: pd.Series) -> bool:
-        reactants, _, products = row[self.in_column].split(">")
+        reactants, _, products = split_rsmi(row[self.in_column])
 
         return self._has_stereo(products) and not self._has_stereo(reactants)
 
@@ -761,9 +741,7 @@ def _row_action(self, row: pd.Series) -> str:
             product_chirality = product_chiral_flags.get(atom_map, None)
             if product_chirality != reactant_chirality:
                 output[atom_map] = (reactant_chirality, product_chirality)
-        return pd.Series(
-            {self.out_column: True, self.stereo_changes_column: json.dumps(output)}
-        )
+        return pd.Series({self.out_column: True, self.stereo_changes_column: json.dumps(output)})
 
 
 @action
@@ -788,7 +766,7 @@ def __str__(self) -> str:
 
     def _row_action(self, row: pd.Series) -> bool:
         smiles = row[self.in_column]
-        return "@" in smiles.split(">")[1]
+        return "@" in split_rsmi(smiles)[1]
 
 
 @action
@@ -889,8 +867,7 @@ def _row_action(self, row: pd.Series) -> str:
             if any(
                 not str(info.type).startswith("Bond")
                 and info.centeredOn in centers
-                and str(reactant.GetAtomWithIdx(info.centeredOn).GetChiralTag())
-                == "CHI_UNSPECIFIED"
+                and str(reactant.GetAtomWithIdx(info.centeredOn).GetChiralTag()) == "CHI_UNSPECIFIED"
                 for info in stereo_info
             ):
                 return True
@@ -904,8 +881,7 @@ def _row_action(self, row: pd.Series) -> str:
         if any(
             not str(info.type).startswith("Bond")
             and product0.GetAtomWithIdx(info.centeredOn).GetAtomMapNum() in atom_maps
-            and str(product.GetAtomWithIdx(info.centeredOn).GetChiralTag())
-            == "CHI_UNSPECIFIED"
+            and str(product.GetAtomWithIdx(info.centeredOn).GetChiralTag()) == "CHI_UNSPECIFIED"
             for info in stereo_info
         ):
             return True
diff --git a/rxnutils/pipeline/actions/templates.py b/rxnutils/pipeline/actions/templates.py
index c0f4cc5..72f22a1 100644
--- a/rxnutils/pipeline/actions/templates.py
+++ b/rxnutils/pipeline/actions/templates.py
@@ -1,4 +1,5 @@
 """Module containing template validation actions"""
+
 from __future__ import annotations
 
 from dataclasses import dataclass
@@ -9,7 +10,7 @@
 from rdkit.Chem import AllChem
 
 from rxnutils.chem.template import ReactionTemplate
-from rxnutils.chem.utils import split_smiles_from_reaction
+from rxnutils.chem.utils import split_rsmi, split_smiles_from_reaction
 from rxnutils.pipeline.base import action, global_apply
 
 rd_logger = RDLogger.logger()
@@ -51,9 +52,7 @@ def _apply_row(self, row: pd.Series) -> pd.Series:
         )
 
     def __str__(self) -> str:
-        return (
-            f"{self.pretty_name} (counting reactants, reagents, products in template)"
-        )
+        return f"{self.pretty_name} (counting reactants, reagents, products in template)"
 
 
 @action
@@ -83,15 +82,11 @@ def _apply_row(self, row: pd.Series) -> pd.Series:
         if not isinstance(row[self.template_column], str):
             return no_oututcome_response
 
-        reactants, _, products = row[self.smiles_column].split(">")
+        reactants, _, products = split_rsmi(row[self.smiles_column])
         # Flattening the list of SMILES, i.e. intramolecular -> intermolecular,
         # because all produced templates will be intermolecular
         expected_reactants = self._smiles_to_inchiset(
-            [
-                smi
-                for reactant in split_smiles_from_reaction(reactants)
-                for smi in reactant.split(".")
-            ]
+            [smi for reactant in split_smiles_from_reaction(reactants) for smi in reactant.split(".")]
         )
         template = ReactionTemplate(row[self.template_column], direction="retro")
 
diff --git a/rxnutils/pipeline/base.py b/rxnutils/pipeline/base.py
index 57d5316..6ef675e 100644
--- a/rxnutils/pipeline/base.py
+++ b/rxnutils/pipeline/base.py
@@ -1,4 +1,5 @@
 """Module containing routines for the validation framework"""
+
 from __future__ import annotations
 
 from collections import defaultdict
@@ -9,7 +10,7 @@
 import swifter  # noqa #pylint: disable=unused-import
 from tqdm import tqdm
 
-from rxnutils.chem.utils import join_smiles_from_reaction, split_smiles_from_reaction
+from rxnutils.chem.utils import join_smiles_from_reaction, split_rsmi, split_smiles_from_reaction
 
 ActionType = Callable[[pd.DataFrame], pd.DataFrame]
 
@@ -147,4 +148,4 @@ def split_smiles(self, row: pd.Series) -> Tuple[str, str, str]:
         :param row: the row with the SMILES
         :return: the SMILES of the components
         """
-        return row[self.in_column].split(">")
+        return split_rsmi(row[self.in_column])
diff --git a/rxnutils/pipeline/runner.py b/rxnutils/pipeline/runner.py
index 2e48949..8b41673 100644
--- a/rxnutils/pipeline/runner.py
+++ b/rxnutils/pipeline/runner.py
@@ -1,4 +1,5 @@
 """Module containg routines and interface to run pipelines"""
+
 import argparse
 from typing import Any, Dict, Optional, Sequence
 
@@ -36,9 +37,7 @@ def run_pipeline(
     :param save_intermediates: if True will save intermediate results
     :return: the dataset after completing the pipeline
     """
-    actions = [
-        create_action(name, **(options or {})) for name, options in pipeline.items()
-    ]
+    actions = [create_action(name, **(options or {})) for name, options in pipeline.items()]
 
     for idx, action in enumerate(actions):
         print(f"Running {action}", flush=True)
@@ -52,12 +51,8 @@ def main(args: Optional[Sequence[str]] = None) -> None:
     """Function for command line argument"""
     parser = argparse.ArgumentParser("Runner of validation pipeline")
     parser.add_argument("--pipeline", help="the yaml file with a pipeline")
-    parser.add_argument(
-        "--data", help="the data to be processed. Should be a tab-separated CSV-file"
-    )
-    parser.add_argument(
-        "--output", help="the processed data. Will be a tab-separated CSV-file"
-    )
+    parser.add_argument("--data", help="the data to be processed. Should be a tab-separated CSV-file")
+    parser.add_argument("--output", help="the processed data. Will be a tab-separated CSV-file")
     parser.add_argument("--max-workers", type=int, help="the maximum number of works")
     parser.add_argument(
         "--batch",
diff --git a/rxnutils/routes/base.py b/rxnutils/routes/base.py
index 35ffd87..1931b80 100644
--- a/rxnutils/routes/base.py
+++ b/rxnutils/routes/base.py
@@ -5,6 +5,7 @@
 """
 
 import warnings
+from collections import defaultdict
 from copy import deepcopy
 from operator import itemgetter
 from typing import Any, Callable, Dict, List, Set, Tuple, Union
@@ -14,11 +15,7 @@
 from rdkit import Chem
 
 from rxnutils.chem.augmentation import single_reactant_augmentation
-from rxnutils.chem.utils import (
-    atom_mapping_numbers,
-    join_smiles_from_reaction,
-    split_smiles_from_reaction,
-)
+from rxnutils.chem.utils import atom_mapping_numbers, join_smiles_from_reaction, split_rsmi, split_smiles_from_reaction
 from rxnutils.pipeline.actions.reaction_mod import NameRxn, RxnMapper
 from rxnutils.routes.image import RouteImageFactory
 from rxnutils.routes.utils.validation import validate_dict
@@ -62,11 +59,9 @@ def mapped_root_smiles(self) -> str:
 
         first_reaction = self.reaction_tree["children"][0]
         if "mapped_reaction_smiles" not in first_reaction.get("metadata", {}):
-            raise ValueError(
-                "It appears that the route has no atom-mapping information"
-            )
+            raise ValueError("It appears that the route has no atom-mapping information")
 
-        return first_reaction["metadata"]["mapped_reaction_smiles"].split(">")[-1]
+        return split_rsmi(first_reaction["metadata"]["mapped_reaction_smiles"])[-1]
 
     @property
     def nsteps(self) -> int:
@@ -81,12 +76,10 @@ def atom_mapped_reaction_smiles(self) -> List[str]:
         _collect_atom_mapped_smiles(self.reaction_tree, smiles)
         return smiles
 
-    def assign_atom_mapping(
-        self, overwrite: bool = False, only_rxnmapper: bool = False
-    ) -> None:
+    def assign_atom_mapping(self, overwrite: bool = False, only_rxnmapper: bool = False) -> None:
         """
         Assign atom-mapping to each reaction in the route and
-        ensure that it is consistent from root compound and throughout
+        ensure that is is consistent from root compound and throughout
         the route.
 
         It will use NameRxn to assign classification and possiblty atom-mapping,
@@ -100,9 +93,7 @@ def assign_atom_mapping(
         max_atomnum = max(atom_mapping_numbers(self.mapped_root_smiles))
         _inherit_atom_mapping(self.reaction_tree, max_atomnum + 100)
 
-    def chains(
-        self, complexity_func: Callable[[str], float]
-    ) -> List[List[Dict[str, Any]]]:
+    def chains(self, complexity_func: Callable[[str], float]) -> List[List[Dict[str, Any]]]:
         """
         Returns linear sequences or chains extracted from the route.
 
@@ -150,9 +141,7 @@ def chains(
                     mol["chain"] = "sub1"
         return chains
 
-    def image(
-        self, show_atom_mapping: bool = False, factory_kwargs: Dict[str, Any] = None
-    ) -> PilImage:
+    def image(self, show_atom_mapping: bool = False, factory_kwargs: Dict[str, Any] = None) -> PilImage:
         """
         Depict the route.
 
@@ -167,6 +156,28 @@ def image(
             dict_ = self.reaction_tree
         return RouteImageFactory(dict_, **factory_kwargs).image
 
+    def intermediate_counts(self) -> Dict[str, int]:
+        """
+        Extract the counts of all intermediates
+
+        return: the counts
+        """
+        intermediates = defaultdict(int)
+        children = self.reaction_tree.get("children", [])
+        if children:
+            _collect_intermediates(children[0], intermediates)
+        return intermediates
+
+    def intermediates(
+        self,
+    ) -> Set[str]:
+        """
+        Extract a set with the SMILES of all the intermediates nodes
+
+        :return: a set of SMILES strings
+        """
+        return set(self.intermediate_counts().keys())
+
     def is_solved(self) -> bool:
         """
         Find if this route is solved, i.e. if all starting material
@@ -181,6 +192,16 @@ def is_solved(self) -> bool:
             return False
         return True
 
+    def leaf_counts(self) -> Dict[str, int]:
+        """
+        Extract the counts of all leaf nodes, i.e. starting material
+
+        return: the counts
+        """
+        leaves = defaultdict(int)
+        _collect_leaves(self.reaction_tree, leaves)
+        return leaves
+
     def leaves(
         self,
     ) -> Set[str]:
@@ -190,9 +211,7 @@ def leaves(
 
         :return: a set of SMILES strings
         """
-        leaves = set()
-        _collect_leaves(self.reaction_tree, leaves)
-        return leaves
+        return set(self.leaf_counts().keys())
 
     def reaction_data(self) -> List[Dict[str, Any]]:
         """
@@ -249,9 +268,7 @@ def remap(self, other: Union["SynthesisRoute", str, Dict[int, int]]) -> None:
         if isinstance(other, SynthesisRoute):
             if len(self.reaction_smiles()) == 0 or len(other.reaction_smiles()) == 0:
                 return
-            mapping_dict = _find_remapping(
-                other.mapped_root_smiles, self.mapped_root_smiles
-            )
+            mapping_dict = _find_remapping(other.mapped_root_smiles, self.mapped_root_smiles)
         elif isinstance(other, str):
             if len(self.reaction_smiles()) == 0:
                 return
@@ -262,9 +279,7 @@ def remap(self, other: Union["SynthesisRoute", str, Dict[int, int]]) -> None:
             raise ValueError(f"Cannot perform re-mapping using a {type(other)}")
         _remap_reactions(self.reaction_tree, mapping_dict)
 
-    def _assign_mapping(
-        self, overwrite: bool = False, only_rxnmapper: bool = False
-    ) -> None:
+    def _assign_mapping(self, overwrite: bool = False, only_rxnmapper: bool = False) -> None:
         if not overwrite:
             try:
                 self.atom_mapped_reaction_smiles()
@@ -283,9 +298,7 @@ def _assign_mapping(
             # Raised by nextmove_action if namerxn not in path
             except FileNotFoundError:
                 df = df.assign(NMC=["0.0"] * len(df), mapped_smiles=[""] * len(df))
-                warnings.warn(
-                    "namerxn does not appear to be in $PATH. Run failed and proceeding with rxnmapper only"
-                )
+                warnings.warn("namerxn does not appear to be in $PATH. Run failed and proceeding with rxnmapper only")
         else:
             df = df.assign(NMC=["0.0"] * len(df), mapped_smiles=[""] * len(df))
         df = rxnmapper_action(df)
@@ -293,7 +306,7 @@ def _assign_mapping(
             df["mapped_smiles"] = df["RxnmapperRxnSmiles"]
         else:
             sel = df["NMC"] == "0.0"
-            df["mapped_smiles"].mask(sel, df["RxnmapperRxnSmiles"], inplace=True)
+            df.loc[sel, "mapped_smiles"] = df.loc[sel, "RxnmapperRxnSmiles"]
         datamap = df.set_index("smiles").to_dict("index")
         _copy_mapping_from_datamap(self.reaction_tree, datamap)
 
@@ -322,12 +335,9 @@ def _apply_remapping(
     :param keep_original: determines the behavior of atoms not in `remapping`
     :return: the remapped reaction SMILES
     """
-    reactants_smiles, reagent_smiles, product_smiles = reaction_smiles.split(">")
+    reactants_smiles, reagent_smiles, product_smiles = split_rsmi(reaction_smiles)
     product_mol = Chem.MolFromSmiles(product_smiles)
-    reactant_mols = [
-        Chem.MolFromSmiles(smiles)
-        for smiles in split_smiles_from_reaction(reactants_smiles)
-    ]
+    reactant_mols = [Chem.MolFromSmiles(smiles) for smiles in split_smiles_from_reaction(reactants_smiles)]
     atoms_to_renumber = list(product_mol.GetAtoms())
     for mol in reactant_mols:
         atoms_to_renumber.extend(mol.GetAtoms())
@@ -430,9 +440,7 @@ def smiles2inchikey(smiles: str, ignore_stereo: bool = False) -> str:
 # Recursive functions acting on reaction trees
 
 
-def _assign_atom_mapped_smiles(
-    tree_dict: Dict[str, Any], reactants_smiles: List[str] = None
-) -> None:
+def _assign_atom_mapped_smiles(tree_dict: Dict[str, Any], reactants_smiles: List[str] = None) -> None:
     """
     Used to copy the atom-mapped SMILES from the reaction metadata
     to the SMILES property of each molecule node. This is used to
@@ -458,15 +466,13 @@ def _assign_atom_mapped_smiles(
     else:
         reaction_dict = tree_dict["children"][0]
         reaction_smiles = reaction_dict["metadata"]["mapped_reaction_smiles"]
-        tree_dict["smiles"] = reaction_smiles.split(">")[-1]
-        reactants_smiles = split_smiles_from_reaction(reaction_smiles.split(">")[0])
+        reactants, _, tree_dict["smiles"] = split_rsmi(reaction_smiles)
+        reactants_smiles = split_smiles_from_reaction(reactants)
         for grandchild in reaction_dict["children"]:
             _assign_atom_mapped_smiles(grandchild, reactants_smiles)
 
 
-def _assign_forward_step(
-    tree_dict: Dict[str, Any], max_depth: int, depth: int = 1
-) -> None:
+def _assign_forward_step(tree_dict: Dict[str, Any], max_depth: int, depth: int = 1) -> None:
     """
     Assign the forward_step property of each reaction node.
     The forward step is defined as "maximum depth - node depth + 1"
@@ -520,19 +526,32 @@ def _collect_atom_mapped_smiles(tree_dict: Dict[str, Any], smiles: List[str]) ->
         _collect_atom_mapped_smiles(grandchild, smiles)
 
 
-def _collect_leaves(tree_dict: Dict[str, Any], leaves: Set[str]) -> None:
+def _collect_intermediates(tree_dict: Dict[str, Any], intermediates: Dict[str, int]) -> None:
+    """
+    Traverse the tree and collect SMILES of molecule nodes that has children
+
+    :param tree_dict: the current molecule node
+    :param intermediates: the list of collected leaves and their counts
+    """
+    if tree_dict["type"] == "mol" and tree_dict.get("children"):
+        intermediates[tree_dict["smiles"]] += 1
+    for child in tree_dict.get("children", []):
+        _collect_intermediates(child, intermediates)
+
+
+def _collect_leaves(tree_dict: Dict[str, Any], leaves: Dict[str, int]) -> None:
     """
     Traverse the tree and collect SMILES of molecule nodes that has no children
 
     :param tree_dict: the current molecule node
-    :param leaves: the list of collected leaves
+    :param leaves: the list of collected leaves and their counts
     """
     children = tree_dict.get("children", [])
     if children:
         for child in children:
             _collect_leaves(child, leaves)
     else:
-        leaves.add(tree_dict["smiles"])
+        leaves[tree_dict["smiles"]] += 1
 
 
 def _collect_ngrams(
@@ -554,9 +573,7 @@ def _collect_ngrams(
     """
     accumulation = accumulation or []
     if tree_dict["type"] == "mol":
-        raise ValueError(
-            "Found _collect_ngrams at molecule node. This should not happen."
-        )
+        raise ValueError("Found _collect_ngrams at molecule node. This should not happen.")
 
     data = tree_dict.get("metadata", {}).get(metadata_key)
     accumulation.append(data)
@@ -567,14 +584,10 @@ def _collect_ngrams(
 
     for mol_child in tree_dict["children"]:
         for rxn_grandchild in mol_child.get("children", []):
-            _collect_ngrams(
-                rxn_grandchild, nitems, metadata_key, result, list(accumulation)
-            )
+            _collect_ngrams(rxn_grandchild, nitems, metadata_key, result, list(accumulation))
 
 
-def _collect_reaction_data(
-    tree_dict: Dict[str, Any], data: List[Dict[str, Any]]
-) -> None:
+def _collect_reaction_data(tree_dict: Dict[str, Any], data: List[Dict[str, Any]]) -> None:
     """
     Save the reaction metadata to a list and augment it
     with the un-mapped reaction SMILES and reaction depth
@@ -586,9 +599,7 @@ def _collect_reaction_data(
     if children is None:
         return
     grandchildren = children[0]["children"]
-    reactants = join_smiles_from_reaction(
-        [grandchild["smiles"] for grandchild in grandchildren]
-    )
+    reactants = join_smiles_from_reaction([grandchild["smiles"] for grandchild in grandchildren])
     metadata = deepcopy(children[0]["metadata"])
     metadata["reaction_smiles"] = f"{reactants}>>{tree_dict['smiles']}"
     data.append(metadata)
@@ -607,17 +618,13 @@ def _collect_reaction_smiles(tree_dict: Dict[str, Any], smiles: List[str]) -> No
     if children is None:
         return
     grandchildren = children[0]["children"]
-    reactants = join_smiles_from_reaction(
-        [grandchild["smiles"] for grandchild in grandchildren]
-    )
+    reactants = join_smiles_from_reaction([grandchild["smiles"] for grandchild in grandchildren])
     smiles.append(f"{reactants}>>{tree_dict['smiles']}")
     for grandchild in grandchildren:
         _collect_reaction_smiles(grandchild, smiles)
 
 
-def _copy_mapping_from_datamap(
-    tree_dict: Dict[str, Any], datamap: Dict[str, Dict[str, str]]
-) -> None:
+def _copy_mapping_from_datamap(tree_dict: Dict[str, Any], datamap: Dict[str, Dict[str, str]]) -> None:
     """
     Store the generated atom-mapping and classification to the reaction
     metadata.
@@ -631,9 +638,7 @@ def _copy_mapping_from_datamap(
     if children is None:
         return
     grandchildren = children[0]["children"]
-    reactants = join_smiles_from_reaction(
-        [grandchild["smiles"] for grandchild in grandchildren]
-    )
+    reactants = join_smiles_from_reaction([grandchild["smiles"] for grandchild in grandchildren])
     rxnsmi = f"{reactants}>>{tree_dict['smiles']}"
     metadata = children[0].get("metadata", {})
     metadata["classification"] = datamap[rxnsmi]["NMC"]
@@ -684,9 +689,7 @@ def _extract_chain_molecules(
         mol_dict["reaction_id"] = metadata.get("id", metadata.get("ID"))
         mol_dict["hash"] = hash((mol_dict["smiles"], mol_dict["step"]))
         for grandchild in children[0]["children"]:
-            _extract_chain_molecules(
-                grandchild, chain_molecules, step - 1, mol_dict["hash"]
-            )
+            _extract_chain_molecules(grandchild, chain_molecules, step - 1, mol_dict["hash"])
     chain_molecules.append(mol_dict)
 
 
@@ -704,9 +707,7 @@ def _find_leaves_not_in_stock(tree_dict: Dict[str, Any]) -> None:
             _find_leaves_not_in_stock(child)
 
 
-def _inherit_atom_mapping(
-    tree_dict: Dict[str, Any], new_atomnum: int, parent_smiles: str = ""
-) -> None:
+def _inherit_atom_mapping(tree_dict: Dict[str, Any], new_atomnum: int, parent_smiles: str = "") -> None:
     """
     Replace atom-mapping in the route so that it keeps the atom-mapping
     from the root node, i.e. the target molecule
@@ -732,7 +733,7 @@ def _inherit_atom_mapping(
     if parent_smiles == "":
         mapped_rsmi = mapped_rsmi0
     else:
-        _, _, product0 = mapped_rsmi0.split(">")
+        _, _, product0 = split_rsmi(mapped_rsmi0)
         remapping = _find_remapping(parent_smiles, product0)
         product_mol = Chem.MolFromSmiles(product0)
         for atom in product_mol.GetAtoms():
@@ -746,11 +747,13 @@ def _inherit_atom_mapping(
     # Recursing to reactants
     inchi2mapped = {
         smiles2inchikey(smiles, ignore_stereo=True): smiles
-        for smiles in split_smiles_from_reaction(mapped_rsmi.split(">>")[0])
+        for smiles in split_smiles_from_reaction(split_rsmi(mapped_rsmi)[0])
     }
     for grandchild in reaction_dict["children"]:
-        inchi = smiles2inchikey(grandchild["smiles"], ignore_stereo=True)
-        _inherit_atom_mapping(grandchild, new_atomnum, inchi2mapped[inchi])
+        # When a molecule is a complex use each part to inherit atom mapping
+        for smiles in split_smiles_from_reaction(grandchild["smiles"]):
+            inchi = smiles2inchikey(smiles, ignore_stereo=True)
+            _inherit_atom_mapping(grandchild, new_atomnum, inchi2mapped[inchi])
 
 
 def _remap_reactions(tree_dict: Dict[str, Any], remapping: Dict[int, int]) -> None:
@@ -764,8 +767,6 @@ def _remap_reactions(tree_dict: Dict[str, Any], remapping: Dict[int, int]) -> No
     if children is None:
         return
     reaction_smiles = children[0]["metadata"]["mapped_reaction_smiles"]
-    children[0]["metadata"]["mapped_reaction_smiles"] = _apply_remapping(
-        reaction_smiles, remapping, keep_original=True
-    )
+    children[0]["metadata"]["mapped_reaction_smiles"] = _apply_remapping(reaction_smiles, remapping, keep_original=True)
     for grandchild in children[0]["children"]:
         _remap_reactions(grandchild, remapping)
diff --git a/rxnutils/routes/comparison.py b/rxnutils/routes/comparison.py
index 4e0bd70..2d3307c 100644
--- a/rxnutils/routes/comparison.py
+++ b/rxnutils/routes/comparison.py
@@ -1,12 +1,13 @@
 """ Contains routines for computing route similarities
 """
+
 import functools
 from typing import Any, Callable, Dict, List, Sequence, Set, Tuple
 
 import numpy as np
 
 from rxnutils.chem.reaction import ChemicalReaction
-from rxnutils.chem.utils import atom_mapping_numbers
+from rxnutils.chem.utils import atom_mapping_numbers, split_rsmi
 from rxnutils.routes.base import SynthesisRoute
 from rxnutils.routes.ted.distances_calculator import ted_distances_calculator
 
@@ -159,11 +160,9 @@ def _extract_atom_mapping_numbers(route: SynthesisRoute) -> List[List[int]]:
     root_atom_numbers = sorted(atom_mapping_numbers(route.mapped_root_smiles))
     mapping_list = [root_atom_numbers]
     for reaction_smiles in route.atom_mapped_reaction_smiles():
-        reactants_smiles = reaction_smiles.split(">")[0]
+        reactants_smiles = split_rsmi(reaction_smiles)[0]
         for smi in reactants_smiles.split("."):
-            atom_numbers = sorted(
-                [num for num in atom_mapping_numbers(smi) if num in root_atom_numbers]
-            )
+            atom_numbers = sorted([num for num in atom_mapping_numbers(smi) if num in root_atom_numbers])
             mapping_list.append(atom_numbers)
     return mapping_list
 
@@ -209,9 +208,7 @@ def _extract_molecule_bond_tuple(molecules: List) -> Set[int]:
     return bonds
 
 
-def _bond_formed_overlap_score(
-    bonds1: List[Tuple[int]], bonds2: List[Tuple[int]]
-) -> float:
+def _bond_formed_overlap_score(bonds1: List[Tuple[int]], bonds2: List[Tuple[int]]) -> float:
     """
     Computes a similarity score of two routes by comparing the overlap
     of bonds formed in the synthesis routes.
diff --git a/rxnutils/routes/deepset/__init__.py b/rxnutils/routes/deepset/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/rxnutils/routes/deepset/featurizers.py b/rxnutils/routes/deepset/featurizers.py
new file mode 100644
index 0000000..45a05d4
--- /dev/null
+++ b/rxnutils/routes/deepset/featurizers.py
@@ -0,0 +1,118 @@
+""" Module with featurizers for molecules and reactions
+"""
+
+from operator import itemgetter
+from typing import Any, Callable, Dict, List, Tuple
+
+import numpy as np
+from rdkit.Chem import AllChem, DataStructs
+
+from rxnutils.chem.reaction import ChemicalReaction
+
+
+def collect_reaction_features(
+    reaction_data: List[Dict[str, Any]],
+    target_fingerprint: np.ndarray,
+    reaction_class_ranks: Dict[str, int],
+    featurizer: Callable[[Dict[str, Any]], np.ndarray],
+    prefactor: float = 1.1,
+    default_rank: int = 5,
+    default_cls: str = "0.0",
+) -> Tuple[float, np.ndarray]:
+    """
+    Collect all reaction features and compute the prior reaction feasibility score
+
+    :params reaction_data: the reactions of the route
+    :params target_fingerprint: the precomputed fingerprint of the target
+    :params reaction_class_ranks: the ranks of the reaction classes
+    :params featurizer: the featurizer to use for reactions
+    :params prefactor: the factor for the feasibility score
+    :params default_rank: the rank of reactions not parameterized
+    :params default_cls: the class of reactions not parameterized
+    :returns: the prior feasibility score
+    :returns: the reaction features
+    """
+    weights = [prefactor**idx for idx in range(1, len(reaction_data) + 1)]
+    weights_sum = sum(weights)
+
+    classes = []
+    ranks = []
+    fingerprints = []
+    rank_score = 0.0
+    # This result in reactions being traversed breadth-first instead of depth-first
+    reaction_data_sorted = sorted(reaction_data, key=itemgetter("tree_depth"))
+    for weight, reaction_data in zip(weights, reaction_data_sorted):
+        norm_weight = weight / weights_sum
+        cls = reaction_data.get("classification", default_cls)
+        if " " in cls:
+            cls = cls.split(" ")[0]
+        if cls in reaction_class_ranks:
+            rank = reaction_class_ranks[cls]
+        else:
+            rank = default_rank
+            cls = default_cls
+        rank_score += norm_weight * rank
+
+        class_vector = [int(item) for item in cls.split(".")]
+        class_vector += [0] * (3 - len(class_vector))
+        classes.append(class_vector)
+        ranks.append(rank)
+        fingerprints.append(featurizer(reaction_data))
+
+    features = []
+    for class_, rank, fingerprint in zip(classes, ranks, fingerprints):
+        vector = np.asarray(class_ + [rank])
+        vector = np.concatenate([vector, target_fingerprint, fingerprint])
+        features.append(vector)
+    return rank_score, np.asarray(features)
+
+
+def default_reaction_featurizer(reaction_data: Dict[str, Any], radius: int = 2, numbits: int = 64) -> np.ndarray:
+    """
+    Given an item of reaction data, returned by the `reaction_data` method
+    of `SynthesisRoute` this features the reaction using a difference ECFP
+
+    Currently it featurizes the reaction in the retro-sense
+
+    :params reaction_data: the reaction as a dictionary
+    :params radius: the radius of the fingerprint
+    :params numbits: the number of bits
+    :returns: the fingerprint
+    """
+    rsmi = ">>".join(reaction_data["reaction_smiles"].split(">>")[::-1])
+    rxn = ChemicalReaction(rsmi, clean_smiles=False)
+    return reaction_difference_fingerprint(rxn, radius, numbits)
+
+
+def ecfp_fingerprint(mol: AllChem.rdchem.Mol, radius: int = 2, numbits: int = 64) -> np.ndarray:
+    """
+    Computes a ECFP with a given radius and length
+
+    :params mol: the RDKit molecule
+    :params radius: the radius of the fingerprint
+    :params numbits: the number of bits
+    :returns: the fingerprint
+    """
+    array = np.zeros((0,), dtype=np.int8)
+    fingerprint = AllChem.GetMorganFingerprintAsBitVect(mol, radius, nBits=numbits)
+    DataStructs.ConvertToNumpyArray(fingerprint, array)
+    return array
+
+
+def reaction_difference_fingerprint(reaction: ChemicalReaction, radius: int = 2, numbits: int = 64) -> np.ndarray:
+    """
+    Computes the difference fingerprint of given reaction
+
+    :params reaction: the reaction to featurize
+    :params radius: the radius of the fingerprint
+    :params numbits: the number of bits
+    :returns: the fingerprint
+    """
+    fp = np.zeros(numbits)
+    for product in reaction.products:
+        if product is not None:
+            fp += ecfp_fingerprint(product, radius, numbits)
+    for reactant in reaction.reactants:
+        if reactant is not None:
+            fp -= ecfp_fingerprint(reactant, radius, numbits)
+    return fp
diff --git a/rxnutils/routes/deepset/scoring.py b/rxnutils/routes/deepset/scoring.py
new file mode 100644
index 0000000..aaa5abf
--- /dev/null
+++ b/rxnutils/routes/deepset/scoring.py
@@ -0,0 +1,104 @@
+""" 
+Module containing routines for Deepset route scoring
+
+This is an implementation of the code used in the following publication,
+original implementation by Guo Yujia
+
+Yujia G, Kabeshov M, Le THD, Genheden S, Bergonzini G, Engkvist O, et al. 
+A Deep Learning with Expert Augmentation Approach for Route Scoring in Organic Synthesis. ChemRxiv. 2024; 
+doi:10.26434/chemrxiv-2024-tp7rh 
+"""
+
+from typing import Dict
+
+import numpy as np
+from rdkit import Chem
+
+from rxnutils.chem.features.sc_score import SCScore
+from rxnutils.routes.base import SynthesisRoute
+from rxnutils.routes.deepset.featurizers import collect_reaction_features, default_reaction_featurizer, ecfp_fingerprint
+
+try:
+    import onnxruntime
+except ImportError:
+    SCORE_SUPPORTED = False
+else:
+    SCORE_SUPPORTED = True
+
+
+class DeepsetModelClient:
+    """
+    Interface for an in-memory instance of a Deepset model for route scoring
+
+    :params model_path: the path to an ONNX model file
+    """
+
+    def __init__(self, model_path: str):
+        if not SCORE_SUPPORTED:
+            raise ImportError("Cannot score routes with Deepset model. Install rxnutils with optional dependencies")
+
+        session_options = onnxruntime.SessionOptions()
+        session_options.intra_op_num_threads = 1
+        self._deepnet = onnxruntime.InferenceSession(model_path, sess_options=session_options)
+
+    def __call__(self, reaction_features: np.ndarray, route_features: np.ndarray) -> float:
+        """
+        Computes the route score using reaction and route features
+
+        :param reaction_features: the packed reaction features
+        :param route_features: the route features
+        """
+        input_ = {
+            "reaction_features": reaction_features.astype(np.float32),
+            "route_features": route_features.astype(np.float32),
+        }
+        return float(self._deepnet.run(None, input_)[0])
+
+
+def deepset_route_score(
+    route: SynthesisRoute,
+    model_client: DeepsetModelClient,
+    scscorer: SCScore,
+    reaction_class_ranks: Dict[str, int],
+) -> float:
+    """
+    Scores a synthesis route using a Deepset model
+
+    Currently, it uses defaults for featurizers as
+    described in the original publication.
+
+    :params route: the route to score
+    :params model_client: the interface to the model
+    :params scscorer: the interface to the SCScore
+    :params reaction_class_ranks: the lookup from reaction class to rank
+    :returns: the computed score
+    """
+    # To avoid circular imports
+    from rxnutils.routes.scoring import badowski_route_score
+
+    target_mol = Chem.MolFromSmiles(route.reaction_tree["smiles"])
+    target_fp = ecfp_fingerprint(target_mol)
+
+    rank_score, reaction_features = collect_reaction_features(
+        route.reaction_data(),
+        target_fp,
+        reaction_class_ranks,
+        default_reaction_featurizer,
+    )
+    cost_score = badowski_route_score(route)
+    volume_score = sum(route.leaf_counts().values())
+    complexity_score = _complexity_score(route, scscorer)
+    route_features = np.asarray([cost_score, volume_score, complexity_score, rank_score])
+    return model_client(reaction_features, route_features)
+
+
+def _complexity_score(route: SynthesisRoute, scscorer: SCScore) -> float:
+    """Sums up the SCScore of all the intermediates in the route"""
+    score = 0
+    for smiles, count in route.intermediate_counts().items():
+        mol = Chem.MolFromSmiles(smiles)
+        if not mol:
+            continue
+        scscore = scscorer(mol)
+        score += count * scscore
+    return score
diff --git a/rxnutils/routes/image.py b/rxnutils/routes/image.py
index 53eb048..ea7f899 100644
--- a/rxnutils/routes/image.py
+++ b/rxnutils/routes/image.py
@@ -1,5 +1,6 @@
 """ This module contains a collection of routines to produce pretty images
 """
+
 from __future__ import annotations
 
 import io
@@ -18,9 +19,7 @@
     from PIL.Image import Image as PilImage
 
 
-def molecule_to_image(
-    mol: Chem.rdchem.Mol, frame_color: PilColor, size: int = 300
-) -> PilImage:
+def molecule_to_image(mol: Chem.rdchem.Mol, frame_color: PilColor, size: int = 300) -> PilImage:
     """
     Create a pretty image of a molecule,
     with a colored frame around it
@@ -53,9 +52,7 @@ def molecules_to_images(
     :return: the produced images
     """
     draw_kwargs = draw_kwargs or {}
-    all_mols = Draw.MolsToGridImage(
-        mols, molsPerRow=len(mols), subImgSize=(size, size), **draw_kwargs
-    )
+    all_mols = Draw.MolsToGridImage(mols, molsPerRow=len(mols), subImgSize=(size, size), **draw_kwargs)
     if not hasattr(all_mols, "crop"):  # Is not a PIL image
         fileobj = io.BytesIO(all_mols.data)
         all_mols = Image.open(fileobj)
@@ -109,9 +106,7 @@ def crop_image(img: PilImage, margin: int = 20) -> PilImage:
     return out
 
 
-def draw_rounded_rectangle(
-    img: PilImage, color: PilColor, arc_size: int = 20
-) -> PilImage:
+def draw_rounded_rectangle(img: PilImage, color: PilColor, arc_size: int = 20) -> PilImage:
     """
     Draw a rounded rectangle around an image
 
@@ -186,8 +181,7 @@ def __init__(
 
         pos0 = (
             self._mol_tree["eff_width"] - self._mol_tree["image"].width + self.margin,
-            int(self._mol_tree["eff_height"] * 0.5)
-            - int(self._mol_tree["image"].height * 0.5),
+            int(self._mol_tree["eff_height"] * 0.5) - int(self._mol_tree["image"].height * 0.5),
         )
         self._add_pos(self._mol_tree, pos0)
 
@@ -205,13 +199,9 @@ def _add_effective_size(self, tree_dict: Dict[str, Any]) -> None:
         for child in children:
             self._add_effective_size(child)
         if children:
-            tree_dict["eff_height"] = sum(
-                child["eff_height"] for child in children
-            ) + self.margin * (len(children) - 1)
+            tree_dict["eff_height"] = sum(child["eff_height"] for child in children) + self.margin * (len(children) - 1)
             tree_dict["eff_width"] = (
-                max(child["eff_width"] for child in children)
-                + tree_dict["image"].size[0]
-                + self.margin
+                max(child["eff_width"] for child in children) + tree_dict["image"].size[0] + self.margin
             )
         else:
             tree_dict["eff_height"] = tree_dict["image"].size[1]
@@ -224,15 +214,9 @@ def _add_pos(self, tree_dict: Dict[str, Any], pos: Tuple[int, int]) -> None:
         if not children:
             return
 
-        mid_y = pos[1] + int(
-            tree_dict["image"].height * 0.5
-        )  # Mid-point of image along y
-        children_height = sum(
-            child["eff_height"] for child in children
-        ) + self.margin * (len(children) - 1)
-        childen_leftmost = min(
-            pos[0] - self.margin - child["image"].width for child in children
-        )
+        mid_y = pos[1] + int(tree_dict["image"].height * 0.5)  # Mid-point of image along y
+        children_height = sum(child["eff_height"] for child in children) + self.margin * (len(children) - 1)
+        childen_leftmost = min(pos[0] - self.margin - child["image"].width for child in children)
         child_y = mid_y - int(children_height * 0.5)  # Top-most edge of children
         child_ys = []
         # Now compute first guess of y-pos for children
@@ -248,9 +232,7 @@ def _add_pos(self, tree_dict: Dict[str, Any], pos: Tuple[int, int]) -> None:
             if not child.get("children") and idx == 0 and len(children) > 1:
                 child_y = child_ys[idx + 1] - self.margin - child["image"].height
             elif not child.get("children") and idx > 0:
-                child_y = (
-                    child_ys[idx - 1] + self.margin + children[idx - 1]["image"].height
-                )
+                child_y = child_ys[idx - 1] + self.margin + children[idx - 1]["image"].height
             self._add_pos(child, (child_x, child_y))
 
     def _extract_mol_tree(self, tree_dict: Dict[str, Any]) -> Dict[str, Any]:
@@ -269,9 +251,7 @@ def _extract_mol_tree(self, tree_dict: Dict[str, Any]) -> Dict[str, Any]:
     def _extract_molecules(self, tree_dict: Dict[str, Any]) -> None:
         if tree_dict["type"] == "mol":
             self._stock_lookup[tree_dict["smiles"]] = tree_dict.get("in_stock", False)
-            self._mol_lookup[tree_dict["smiles"]] = Chem.MolFromSmiles(
-                tree_dict["smiles"]
-            )
+            self._mol_lookup[tree_dict["smiles"]] = Chem.MolFromSmiles(tree_dict["smiles"])
         for child in tree_dict.get("children", []):
             self._extract_molecules(child)
 
@@ -300,6 +280,4 @@ def _make_image(self, tree_dict: Dict[str, Any]) -> None:
                 ),
                 fill="black",
             )
-        self._draw.ellipse(
-            (mid_x - 8, mid_y - 8, mid_x + 8, mid_y + 8), fill="black", outline="black"
-        )
+        self._draw.ellipse((mid_x - 8, mid_y - 8, mid_x + 8, mid_y + 8), fill="black", outline="black")
diff --git a/rxnutils/routes/readers.py b/rxnutils/routes/readers.py
index 308adfb..ac7c9bd 100644
--- a/rxnutils/routes/readers.py
+++ b/rxnutils/routes/readers.py
@@ -7,7 +7,7 @@
 from rdkit import Chem
 from rdkit.Chem import AllChem
 
-from rxnutils.chem.utils import join_smiles_from_reaction, split_smiles_from_reaction
+from rxnutils.chem.utils import join_smiles_from_reaction, split_rsmi, split_smiles_from_reaction
 from rxnutils.routes.base import SynthesisRoute, smiles2inchikey
 
 
@@ -52,14 +52,23 @@ def read_aizynthcli_dataframe(data: pd.DataFrame) -> pd.Series:
     """
 
     def read_row(row: pd.Series) -> List[SynthesisRoute]:
-        trees = [copy.deepcopy(tree) for tree in row.trees]
-        for tree in trees:
-            _transform_retrosynthesis_atom_mapping(tree)
-        return [SynthesisRoute(tree) for tree in trees]
+        return [read_aizynthfinder_dict(tree) for tree in row.trees]
 
     return data.apply(read_row, axis=1)
 
 
+def read_aizynthfinder_dict(tree: Dict[str, Any]) -> SynthesisRoute:
+    """
+    Read a single aizynthfinder dictionary
+
+    :param tree: the aizynthfinder structure
+    :return: the created routes
+    """
+    dict_ = copy.deepcopy(tree)
+    _transform_retrosynthesis_atom_mapping(dict_)
+    return SynthesisRoute(dict_)
+
+
 def read_reactions_dataframe(
     data: pd.DataFrame,
     smiles_column: str,
@@ -97,12 +106,11 @@ def reaction_dataframe2routes(subdata):
         return route
 
     metadata_columns = metadata_columns or []
-    return data.groupby(group_by).apply(reaction_dataframe2routes)
+    grouped = data.groupby(group_by)[data.columns.to_list()]
+    return grouped.apply(reaction_dataframe2routes)
 
 
-def reactions2route(
-    reactions: Sequence[str], metadata: Sequence[Dict[str, Any]] = None
-) -> SynthesisRoute:
+def reactions2route(reactions: Sequence[str], metadata: Sequence[Dict[str, Any]] = None) -> SynthesisRoute:
     """
     Convert a list of reactions into a retrosynthesis tree
 
@@ -122,11 +130,7 @@ def make_dict(product_smiles):
         reaction = product2reaction.get(product_inchi)
         if reaction is not None:
             metadata = dict(reaction["metadata"])
-            metadata["reaction_smiles"] = (
-                join_smiles_from_reaction(reaction["reactants"])
-                + ">>"
-                + reaction["product"]
-            )
+            metadata["reaction_smiles"] = join_smiles_from_reaction(reaction["reactants"]) + ">>" + reaction["product"]
             dict_["children"] = [
                 {
                     "type": "reaction",
@@ -141,7 +145,7 @@ def make_dict(product_smiles):
     product2reaction = {}
     inchi_map = {}
     for reaction, meta in zip(reactions, metadata):
-        reactants_smiles, _, product_smiles = reaction.split(">")
+        reactants_smiles, _, product_smiles = split_rsmi(reaction)
         product_smiles = Chem.CanonSmiles(product_smiles)
         partial_product_inchi = smiles2inchikey(product_smiles, ignore_stereo=True)
         inchi_map[partial_product_inchi] = product_smiles
@@ -150,9 +154,7 @@ def make_dict(product_smiles):
             reactants = [Chem.CanonSmiles(smi) for smi in reactants]
         except:
             raise ValueError(f"Cannot canonicalize SMILES: {reactants_smiles}")
-        all_reactants = all_reactants.union(
-            [smiles2inchikey(smi, ignore_stereo=True) for smi in reactants]
-        )
+        all_reactants = all_reactants.union([smiles2inchikey(smi, ignore_stereo=True) for smi in reactants])
         product2reaction[partial_product_inchi] = {
             "smiles": reaction,
             "product": product_smiles,
@@ -162,9 +164,7 @@ def make_dict(product_smiles):
 
     only_products = set(product2reaction.keys()) - all_reactants
     if len(only_products) != 1:
-        raise ValueError(
-            f"Could not identify one and only one target product: {only_products}"
-        )
+        raise ValueError(f"Could not identify one and only one target product: {only_products}")
 
     target_inchi = list(only_products)[0]
     return SynthesisRoute(make_dict(inchi_map[target_inchi]))
@@ -174,9 +174,7 @@ def read_rdf_file(filename: str) -> SynthesisRoute:
     def finish_reaction():
         if not rxnblock:
             return
-        rxn = AllChem.ReactionFromRxnBlock(
-            "\n".join(rxnblock), sanitize=False, strictParsing=False
-        )
+        rxn = AllChem.ReactionFromRxnBlock("\n".join(rxnblock), sanitize=False, strictParsing=False)
         reactions.append(AllChem.ReactionToSmiles(rxn))
 
     with open(filename, "r") as fileobj:
@@ -218,11 +216,9 @@ def _transform_retrosynthesis_atom_mapping(tree_dict: Dict[str, Any]) -> None:
     reaction_dict = tree_dict["children"][0]
     mapped_rsmi = reaction_dict["metadata"]["mapped_reaction_smiles"]
 
-    product, _, reactants = mapped_rsmi.split(">")
+    product, _, reactants = split_rsmi(mapped_rsmi)
     product_mol = Chem.MolFromSmiles(product)
-    product_maps = {
-        atom.GetAtomMapNum() for atom in product_mol.GetAtoms() if atom.GetAtomMapNum()
-    }
+    product_maps = {atom.GetAtomMapNum() for atom in product_mol.GetAtoms() if atom.GetAtomMapNum()}
     reactant_mols = []
     for smiles in reactants.split("."):
         mol = Chem.MolFromSmiles(smiles)
diff --git a/rxnutils/routes/retro_bleu/__init__.py b/rxnutils/routes/retro_bleu/__init__.py
index 5946c1d..866f5a8 100644
--- a/rxnutils/routes/retro_bleu/__init__.py
+++ b/rxnutils/routes/retro_bleu/__init__.py
@@ -1,4 +1,2 @@
-from rxnutils.routes.retro_bleu.scoring import (
-    ngram_overlap_score,  # noqa
-    retro_bleu_score,
-)
+from rxnutils.routes.retro_bleu.scoring import ngram_overlap_score  # noqa
+from rxnutils.routes.retro_bleu.scoring import retro_bleu_score
diff --git a/rxnutils/routes/retro_bleu/ngram_collection.py b/rxnutils/routes/retro_bleu/ngram_collection.py
index bb0d3a1..6ed7345 100644
--- a/rxnutils/routes/retro_bleu/ngram_collection.py
+++ b/rxnutils/routes/retro_bleu/ngram_collection.py
@@ -46,9 +46,7 @@ def from_file(cls, filename: str) -> "NgramCollection":
         return NgramCollection(dict_["nitems"], dict_["metadata_key"], ngrams)
 
     @classmethod
-    def from_tree_collection(
-        cls, filename: str, nitems: int, metadata_key: str
-    ) -> "NgramCollection":
+    def from_tree_collection(cls, filename: str, nitems: int, metadata_key: str) -> "NgramCollection":
         """
         Make a n-gram collection by extracting them from a collection of
         synthesis routes.
@@ -85,24 +83,16 @@ def save_to_file(self, filename: str) -> None:
 if __name__ == "__main__":
     import argparse
 
-    parser = argparse.ArgumentParser(
-        "Tool for making n-gram collections from a set of synthesis routes"
-    )
-    parser.add_argument(
-        "--filename", nargs="+", help="the path to the synthesis routes"
-    )
+    parser = argparse.ArgumentParser("Tool for making n-gram collections from a set of synthesis routes")
+    parser.add_argument("--filename", nargs="+", help="the path to the synthesis routes")
     parser.add_argument("--output", help="the path to the n-gram collection")
     parser.add_argument("--nitems", type=int, help="the length of the gram")
-    parser.add_argument(
-        "--metadata", help="the reaction metadata to extract for making the n-grams"
-    )
+    parser.add_argument("--metadata", help="the reaction metadata to extract for making the n-grams")
     args = parser.parse_args()
 
     collection = None
     for filename in args.filename:
-        temp = NgramCollection.from_tree_collection(
-            filename, args.nitems, args.metadata
-        )
+        temp = NgramCollection.from_tree_collection(filename, args.nitems, args.metadata)
         if collection is None:
             collection = temp
         else:
diff --git a/rxnutils/routes/retro_bleu/scoring.py b/rxnutils/routes/retro_bleu/scoring.py
index 72f6921..8bce824 100644
--- a/rxnutils/routes/retro_bleu/scoring.py
+++ b/rxnutils/routes/retro_bleu/scoring.py
@@ -25,9 +25,7 @@ def ngram_overlap_score(
     return len(route_ngrams.intersection(ref.ngrams)) / len(route_ngrams)
 
 
-def retro_bleu_score(
-    route: SynthesisRoute, ref: NgramCollection, ideal_steps: int = 3
-) -> float:
+def retro_bleu_score(route: SynthesisRoute, ref: NgramCollection, ideal_steps: int = 3) -> float:
     """
     Calculate the Retro-BLEU score according to the paper:
 
diff --git a/rxnutils/routes/scoring.py b/rxnutils/routes/scoring.py
index 1c16bb4..897068f 100644
--- a/rxnutils/routes/scoring.py
+++ b/rxnutils/routes/scoring.py
@@ -6,10 +6,10 @@
 import numpy as np
 
 from rxnutils.routes.base import SynthesisRoute
-from rxnutils.routes.retro_bleu.scoring import (
-    ngram_overlap_score,  # noqa
-    retro_bleu_score,
-)
+from rxnutils.routes.deepset.scoring import DeepsetModelClient  # noqa
+from rxnutils.routes.deepset.scoring import deepset_route_score
+from rxnutils.routes.retro_bleu.scoring import ngram_overlap_score  # noqa
+from rxnutils.routes.retro_bleu.scoring import retro_bleu_score
 
 
 def route_sorter(
@@ -78,9 +78,75 @@ def traverse(tree_dict):
         if not reactions:
             return mol_cost[tree_dict.get("in_stock", True)]
 
-        child_sum = sum(
-            1 / average_yield * traverse(child) for child in reactions[0]["children"]
-        )
+        child_sum = sum(1 / average_yield * traverse(child) for child in reactions[0]["children"])
         return reaction_cost + child_sum
 
     return traverse(route.reaction_tree)
+
+
+def reaction_class_rank_score(
+    route: SynthesisRoute,
+    reaction_class_ranks: Dict[str, int],
+    preferred_classes: List[str],
+    non_preferred_factor: float = 0.25,
+) -> float:
+    """
+    Calculates a score of a route based on the reaction class rank score, i.e.
+    how likely a particular reaction class is to succeed.
+
+    Each step in the route is scored based on the following factors:
+        * The reaction class rank
+        * The step in the synthesis sequence
+        * The preference of the reaction class
+
+    The score is min-max normalized relative to the maximum depth of the three
+    and the max/min of the class ranks.
+
+    :param route: the route to score
+    :param reaction_class_ranks: the rank score of NextMove classes
+    :param preferred_classes: the preferred reaction classes
+    :param non_preferred_factor: steps with non-preferred classes are multiplied by this
+    :return: the computed score
+    """
+
+    def _score_reaction_tree(tree_dict):
+        cls = tree_dict["metadata"]["classification"]
+        if " " in cls:
+            cls = cls.split(" ")[0]
+        if _nextmove_superclass(cls) in preferred_superclasses:
+            pref_factor = 1.0
+        else:
+            pref_factor = non_preferred_factor
+        step_weight = tree_dict["metadata"]["forward_step"]
+        score = pref_factor * step_weight * reaction_class_ranks.get(cls, min_rank)
+
+        child_scores = []
+        for child in tree_dict["children"]:
+            grandchildren = child.get("children", [])
+            if grandchildren:
+                child_score = _score_reaction_tree(grandchildren[0])
+                child_scores.append(child_score)
+        if child_scores:
+            score += min(child_scores)
+
+        return score
+
+    min_rank = min(reaction_class_ranks.values())
+    max_step_weight = sum(range(1, route.max_depth + 1))
+    min_score = max_step_weight * min_rank * non_preferred_factor
+    max_score = max_step_weight * max(reaction_class_ranks.values())
+
+    preferred_superclasses = [_nextmove_superclass(cls) for cls in preferred_classes]
+    first_reaction = route.reaction_tree["children"][0]
+    score = _score_reaction_tree(first_reaction)
+    return (score - min_score) / (max_score - min_score)
+
+
+def _nextmove_superclass(cls: str) -> str:
+    """Extracting the NextMove superclass"""
+    cls = str(cls).strip()
+    if cls == "nan":
+        return cls
+    if cls.count(".") == 1:
+        return cls
+    return ".".join(cls.split(".")[:2])
diff --git a/rxnutils/routes/ted/distances_calculator.py b/rxnutils/routes/ted/distances_calculator.py
index 338a699..01a2ad6 100644
--- a/rxnutils/routes/ted/distances_calculator.py
+++ b/rxnutils/routes/ted/distances_calculator.py
@@ -1,4 +1,5 @@
 """ Module contain method to compute distance matrix using TED """
+
 import time
 from typing import Sequence
 
diff --git a/rxnutils/routes/ted/reactiontree.py b/rxnutils/routes/ted/reactiontree.py
index 91ab3aa..9d5d56e 100644
--- a/rxnutils/routes/ted/reactiontree.py
+++ b/rxnutils/routes/ted/reactiontree.py
@@ -3,6 +3,7 @@
 Since APTED is based on ordered trees and the reaction trees are unordered, plenty of
 heuristics are implemented to deal with this.
 """
+
 from __future__ import annotations
 
 import itertools
@@ -15,11 +16,7 @@
 from apted import APTED as Apted
 
 from rxnutils.routes.base import SynthesisRoute
-from rxnutils.routes.ted.utils import (
-    AptedConfig,
-    StandardFingerprintFactory,
-    TreeContent,
-)
+from rxnutils.routes.ted.utils import AptedConfig, StandardFingerprintFactory, TreeContent
 
 StrDict = Dict[str, Any]
 _FloatIterator = Iterable[float]
@@ -37,9 +34,7 @@ class ReactionTreeWrapper:
     :param dist_func: the distance function to use when renaming nodes
     """
 
-    _index_permutations = {
-        n: list(itertools.permutations(range(n), n)) for n in range(1, 8)
-    }
+    _index_permutations = {n: list(itertools.permutations(range(n), n)) for n in range(1, 8)}
 
     def __init__(
         self,
@@ -51,9 +46,7 @@ def __init__(
     ) -> None:
         single_node_tree = not bool(route.reaction_smiles())
         if single_node_tree and content == TreeContent.REACTIONS:
-            raise ValueError(
-                "Cannot create wrapping with content = reactions for a tree without reactions"
-            )
+            raise ValueError("Cannot create wrapping with content = reactions for a tree without reactions")
 
         self._logger = getLogger()
         # Will convert string input automatically
@@ -69,9 +62,7 @@ def __init__(
         if self._content == TreeContent.MOLECULES:
             self._base_tree = self._remove_children_nodes(self._base_tree)
         elif not single_node_tree and self._content == TreeContent.REACTIONS:
-            self._base_tree = self._remove_children_nodes(
-                self._base_tree["children"][0]
-            )
+            self._base_tree = self._remove_children_nodes(self._base_tree["children"][0])
 
         self._trees = []
         self._tree_count, self._node_index_list = self._inspect_tree()
@@ -103,9 +94,7 @@ def trees(self) -> List[StrDict]:
         """Return a list of all created ordered trees"""
         return self._trees
 
-    def distance_iter(
-        self, other: "ReactionTreeWrapper", exhaustive_limit: int = 20
-    ) -> _FloatIterator:
+    def distance_iter(self, other: "ReactionTreeWrapper", exhaustive_limit: int = 20) -> _FloatIterator:
         """
         Iterate over all distances computed between this and another tree
 
@@ -133,9 +122,7 @@ def distance_iter(
         else:
             yield from self._distance_iter_random(other, exhaustive_limit)
 
-    def distance_to(
-        self, other: "ReactionTreeWrapper", exhaustive_limit: int = 20
-    ) -> float:
+    def distance_to(self, other: "ReactionTreeWrapper", exhaustive_limit: int = 20) -> float:
         """
         Calculate the minimum distance from this route to another route
 
@@ -147,9 +134,7 @@ def distance_to(
         """
         min_dist = 1e6
         min_iter = -1
-        for iteration, distance in enumerate(
-            self.distance_iter(other, exhaustive_limit)
-        ):
+        for iteration, distance in enumerate(self.distance_iter(other, exhaustive_limit)):
             if distance < min_dist:
                 min_iter = iteration
                 min_dist = distance
@@ -187,9 +172,7 @@ def _create_all_trees(self) -> None:
         self._trees = []
         # Iterate over all possible combinations of child order
         for order_list in itertools.product(*self._node_index_list):
-            self._trees.append(
-                self._create_tree_recursively(self._base_tree, list(order_list))
-            )
+            self._trees.append(self._create_tree_recursively(self._base_tree, list(order_list)))
 
     def _create_tree_recursively(
         self,
@@ -201,41 +184,27 @@ def _create_tree_recursively(
         if children:
             child_order = order_list.pop(0)
             assert len(child_order) == len(children)
-            new_children = [
-                self._create_tree_recursively(child, order_list) for child in children
-            ]
+            new_children = [self._create_tree_recursively(child, order_list) for child in children]
             new_tree["children"] = [new_children[idx] for idx in child_order]
         return new_tree
 
     def _distance_iter_exhaustive(self, other: "ReactionTreeWrapper") -> _FloatIterator:
-        self._logger.debug(
-            f"APTED: Exhaustive search. {len(self.trees)} {len(other.trees)}"
-        )
+        self._logger.debug(f"APTED: Exhaustive search. {len(self.trees)} {len(other.trees)}")
         config = AptedConfig(randomize=False, dist_func=self._dist_func)
         for tree1, tree2 in itertools.product(self.trees, other.trees):
             yield Apted(tree1, tree2, config).compute_edit_distance()
 
-    def _distance_iter_random(
-        self, other: "ReactionTreeWrapper", ntimes: int
-    ) -> _FloatIterator:
-        self._logger.debug(
-            f"APTED: Heuristic search. {len(self.trees)} {len(other.trees)}"
-        )
+    def _distance_iter_random(self, other: "ReactionTreeWrapper", ntimes: int) -> _FloatIterator:
+        self._logger.debug(f"APTED: Heuristic search. {len(self.trees)} {len(other.trees)}")
         config = AptedConfig(randomize=False, dist_func=self._dist_func)
         yield Apted(self.first_tree, other.first_tree, config).compute_edit_distance()
 
         config = AptedConfig(randomize=True, dist_func=self._dist_func)
         for _ in range(ntimes):
-            yield Apted(
-                self.first_tree, other.first_tree, config
-            ).compute_edit_distance()
-
-    def _distance_iter_semi_exhaustive(
-        self, other: "ReactionTreeWrapper"
-    ) -> _FloatIterator:
-        self._logger.debug(
-            f"APTED: Semi-exhaustive search. {len(self.trees)} {len(other.trees)}"
-        )
+            yield Apted(self.first_tree, other.first_tree, config).compute_edit_distance()
+
+    def _distance_iter_semi_exhaustive(self, other: "ReactionTreeWrapper") -> _FloatIterator:
+        self._logger.debug(f"APTED: Semi-exhaustive search. {len(self.trees)} {len(other.trees)}")
         if len(self.trees) < len(other.trees):
             first_wrapper = self
             second_wrapper = other
@@ -245,9 +214,7 @@ def _distance_iter_semi_exhaustive(
 
         config = AptedConfig(randomize=False, dist_func=self._dist_func)
         for tree1 in first_wrapper.trees:
-            yield Apted(
-                tree1, second_wrapper.first_tree, config
-            ).compute_edit_distance()
+            yield Apted(tree1, second_wrapper.first_tree, config).compute_edit_distance()
 
     def _inspect_tree(self) -> Tuple[int, List[List[int]]]:
         """
@@ -293,9 +260,6 @@ def _remove_children_nodes(tree: StrDict) -> StrDict:
             new_tree["children"] = []
             for child in tree["children"]:
                 new_tree["children"].extend(
-                    [
-                        ReactionTreeWrapper._remove_children_nodes(grandchild)
-                        for grandchild in child.get("children", [])
-                    ]
+                    [ReactionTreeWrapper._remove_children_nodes(grandchild) for grandchild in child.get("children", [])]
                 )
         return new_tree
diff --git a/rxnutils/routes/ted/utils.py b/rxnutils/routes/ted/utils.py
index 81c3fc6..f0972b5 100644
--- a/rxnutils/routes/ted/utils.py
+++ b/rxnutils/routes/ted/utils.py
@@ -1,4 +1,5 @@
 """ Module containing utilities for TED calculations """
+
 from __future__ import annotations
 
 import random
@@ -77,9 +78,7 @@ def __init__(self, radius: int = 2, nbits: int = 2048) -> None:
     def __call__(self, tree: StrDict, parent: StrDict = None) -> None:
         if tree["type"] == "reaction":
             if parent is None:
-                raise ValueError(
-                    "Must specify parent when making Morgan fingerprints for reaction nodes"
-                )
+                raise ValueError("Must specify parent when making Morgan fingerprints for reaction nodes")
             self._add_rxn_fingerprint(tree, parent)
         else:
             self._add_mol_fingerprints(tree)
diff --git a/rxnutils/routes/utils/validation.py b/rxnutils/routes/utils/validation.py
index 9f2905b..119db77 100644
--- a/rxnutils/routes/utils/validation.py
+++ b/rxnutils/routes/utils/validation.py
@@ -1,4 +1,5 @@
 """ Module containing routes to validate AiZynthFinder-like input dictionaries """
+
 from __future__ import annotations
 
 from typing import Any, Dict, List, Optional
diff --git a/tasks.py b/tasks.py
index cbe7dc7..dac4b34 100644
--- a/tasks.py
+++ b/tasks.py
@@ -10,9 +10,9 @@ def build_docs(context):
 @task
 def run_tests(context):
     cmd = (
-        "pytest --black --mccabe "
+        "pytest "
         "--cov rxnutils --cov-branch --cov-report html:coverage --cov-report xml "
-        "-vv tests/"
+        "tests/"
     )
     context.run(cmd)
 
@@ -20,4 +20,4 @@ def run_tests(context):
 @task
 def run_linting(context):
     print("Running pylint...")
-    context.run("pylint rxnutils")
\ No newline at end of file
+    context.run("pylint rxnutils")
diff --git a/tests/data/scscore_dummy_model.onnx b/tests/data/scscore_dummy_model.onnx
new file mode 100644
index 0000000..85a6867
Binary files /dev/null and b/tests/data/scscore_dummy_model.onnx differ
diff --git a/tests/test_batch_utils.py b/tests/test_batch_utils.py
index ab77775..de5c2e0 100644
--- a/tests/test_batch_utils.py
+++ b/tests/test_batch_utils.py
@@ -1,11 +1,13 @@
 import os
 
+import numpy as np
 import pandas as pd
 import pytest
 from scipy import sparse
 
 from rxnutils.data.batch_utils import (
     combine_csv_batches,
+    combine_numpy_array_batches,
     combine_sparse_matrix_batches,
     create_csv_batches,
     nlines,
@@ -142,3 +144,30 @@ def test_combine_sparse_matrix_batches(tmpdir):
         0,
     ]
     assert sparse.load_npz(filename).toarray().flatten().tolist() == expected
+
+
+def test_combine_numpy_array_batches(tmpdir):
+    filename1 = str(tmpdir / "temp.0.npz")
+    np.savez(filename1, np.array([0, 0, 0, 1]), compressed=True)
+    filename2 = str(tmpdir / "temp.1.npz")
+    np.savez(filename2, np.array([1, 1, 1, 0]), compressed=True)
+    filename = str(tmpdir / "temp.npz")
+
+    assert os.path.exists(filename1)
+    assert os.path.exists(filename2)
+
+    combine_numpy_array_batches(filename, 2)
+
+    assert not os.path.exists(filename1)
+    assert not os.path.exists(filename2)
+    expected = [
+        0,
+        0,
+        0,
+        1,
+        1,
+        1,
+        1,
+        0,
+    ]
+    assert np.load(filename)["arr_0"].tolist() == expected
diff --git a/tests/test_cgr.py b/tests/test_cgr.py
index ba91297..c355c2f 100644
--- a/tests/test_cgr.py
+++ b/tests/test_cgr.py
@@ -1,7 +1,7 @@
 import pytest
 
-from rxnutils.chem.reaction import ChemicalReaction
 from rxnutils.chem.cgr import CondensedGraphReaction
+from rxnutils.chem.reaction import ChemicalReaction
 
 
 @pytest.fixture
diff --git a/tests/test_chem_utils.py b/tests/test_chem_utils.py
index 22e9e41..11efa27 100644
--- a/tests/test_chem_utils.py
+++ b/tests/test_chem_utils.py
@@ -2,19 +2,84 @@
 from rdkit import Chem
 from rdkit.Chem import AllChem
 
+from rxnutils.chem.augmentation import single_reactant_augmentation
 from rxnutils.chem.utils import (
+    atom_mapping_numbers,
+    canonicalize_tautomer,
+    get_mol_weight,
+    get_special_groups,
+    get_symmetric_sites,
     has_atom_mapping,
+    is_valid_mol,
+    neutralize_molecules,
+    reaction_centres,
+    reassign_rsmi_atom_mapping,
+    recreate_rsmi,
     remove_atom_mapping,
     remove_atom_mapping_template,
-    neutralize_molecules,
+    remove_stereochemistry,
     same_molecule,
-    atom_mapping_numbers,
+    split_rsmi,
     split_smiles_from_reaction,
-    reassign_rsmi_atom_mapping,
-    get_special_groups,
-    reaction_centres,
 )
-from rxnutils.chem.augmentation import single_reactant_augmentation
+
+
+def test_canonicalize_tautomer():
+    input_smiles = ["c1nc2cncnc2[nH]1", "c1ncc2[nH]cnc2n1", "c1cc[nH]cn1"]
+    expected_outputs = ["c1ncc2[nH]cnc2n1", "c1ncc2[nH]cnc2n1", "c1cc[nH]cn1"]
+
+    for smiles, expected in zip(input_smiles, expected_outputs):
+        assert canonicalize_tautomer(smiles) == expected
+
+
+def test_remove_stereochemistry() -> None:
+    input_smiles = ["C[C@@H]CCO[C@H]", "CC(=O)C", "C[C@H]CCO[C@@H]", "C[C@H]CCOC"]
+
+    expected_output = [
+        "[CH]OCC[CH]C",
+        "CC(C)=O",
+        "[CH]OCC[CH]C",
+        "C[CH]CCOC",
+    ]
+    for smiles, expected in zip(input_smiles, expected_output):
+        output = remove_stereochemistry(smiles)
+        assert output == expected
+
+    smiles_invalid = "not-a-smiles"
+    assert smiles_invalid == remove_stereochemistry(smiles_invalid)
+
+
+def test_is_valid_mol():
+    assert is_valid_mol("CCO")
+    assert not is_valid_mol("C!O")
+
+
+def test_get_mol_weight():
+    smiles = "CCCCCC(=O)CCCC"
+    smiles_invalid = "not-a-smiles"
+    assert round(get_mol_weight(smiles), 2) == 156.15
+    assert get_mol_weight(smiles_invalid) is None
+
+
+@pytest.mark.parametrize(
+    ("smiles", "atoms_inds", "expected"),
+    [
+        ("Oc1cccc(O)c1", [0], [[0, 6]]),
+        ("Oc1cccc(O)c1", [2], [[2, 4]]),
+        ("Oc1cccc(O)c1", [0, 2], [[0, 6], [2, 4]]),
+        ("Oc1cccc(O)c1", [0, 2, 6], [[0, 6], [2, 4]]),
+        ("Oc1cccc(O)c1", [3], []),
+    ],
+)
+def test_get_symmetric_sites(smiles, atoms_inds, expected):
+    mol = Chem.MolFromSmiles(smiles)
+    assert get_symmetric_sites(mol, atoms_inds) == expected
+
+
+def test_get_symmetric_sites_error():
+    mol = Chem.MolFromSmiles("Oc1cccc(O)c1")
+    with pytest.raises(ValueError, match="At least one candidate atom-idx is out of bounds"):
+        get_symmetric_sites(mol, [13])
 
 
 @pytest.mark.parametrize(
@@ -175,3 +240,68 @@ def test_reaction_centers(smiles, expected):
 )
 def test_single_reactant_agumentation(smiles, classification, expected):
     assert single_reactant_augmentation(smiles, classification) == expected
+
+
+@pytest.mark.parametrize(
+    ("rsmi", "expected_components"),
+    [
+        (
+            "A.B>>C",
+            ("A.B", "", "C"),
+        ),
+        (
+            "A>B>C",
+            ("A", "B", "C"),
+        ),
+        (
+            "A->B>>C",
+            ("A->B", "", "C"),
+        ),
+        (
+            "A>B->C>D",
+            ("A", "B->C", "D"),
+        ),
+    ],
+)
+def test_split_rsmi(rsmi, expected_components):
+    reaction_components = split_rsmi(rsmi)
+    assert reaction_components == expected_components
+
+
+def test_split_rsmi_error():
+    with pytest.raises(ValueError, match="Expected 3 reaction components but got 4 for 'A>B>C>D'"):
+        _ = split_rsmi("A>B>C>D")
+
+    with pytest.raises(ValueError, match="Expected 3 reaction components but got 2 for 'A>B'"):
+        _ = split_rsmi("A>B")
+
+
+@pytest.mark.parametrize(
+    ("rsmi", "expected_rsmi"),
+    [
+        (
+            "A.B>>C",
+            "A.B>>C",
+        ),
+        (
+            "(A.B).C>>D",
+            "A.B.C>>D",
+        ),
+        (
+            "(A->B.C).D>E.F>G",
+            "A->B.C.D>E.F>G",
+        ),
+        (
+            "A.(B.C).D>(E.F)>G",
+            "A.B.C.D>E.F>G",
+        ),
+        (
+            "(A.B).C>(E.F)>(D.G)",
+            "A.B.C>E.F>D.G",
+        ),
+    ],
+)
+def test_recreate_rsmi(rsmi, expected_rsmi):
+    new_rsmi = recreate_rsmi(rsmi)
+
+    assert new_rsmi == expected_rsmi
diff --git a/tests/test_df_mod_actions.py b/tests/test_df_mod_actions.py
index 1abacd2..06dfd1f 100644
--- a/tests/test_df_mod_actions.py
+++ b/tests/test_df_mod_actions.py
@@ -62,9 +62,7 @@ def test_stack_columns():
 
 def test_stack_multi_columns():
     action = StackMultiColumns(stack_columns=["A", "B"], target_columns=["C", "D"])
-    df = pd.DataFrame(
-        {"A": [1, 1, 1], "B": ["A", "B", "C"], "C": [3, 4, 3], "D": ["X", "Y", "Z"]}
-    )
+    df = pd.DataFrame({"A": [1, 1, 1], "B": ["A", "B", "C"], "C": [3, 4, 3], "D": ["X", "Y", "Z"]})
 
     df2 = action(df)
 
diff --git a/tests/test_product_tagging.py b/tests/test_product_tagging.py
index 14c2339..e3a02c9 100644
--- a/tests/test_product_tagging.py
+++ b/tests/test_product_tagging.py
@@ -1,13 +1,11 @@
 import pytest
+
 from rxnutils.chem.disconnection_sites.atom_map_tagging import (
     atom_map_tag_products,
     atom_map_tag_reactants,
     get_atom_list,
 )
-from rxnutils.chem.disconnection_sites.tag_converting import (
-    convert_atom_map_tag,
-    tagged_smiles_from_tokens,
-)
+from rxnutils.chem.disconnection_sites.tag_converting import convert_atom_map_tag, tagged_smiles_from_tokens
 
 
 @pytest.mark.parametrize(
diff --git a/tests/test_reaction.py b/tests/test_reaction.py
index 55278d3..85e619e 100644
--- a/tests/test_reaction.py
+++ b/tests/test_reaction.py
@@ -2,8 +2,7 @@
 
 import pytest
 
-from rxnutils.chem.reaction import ChemicalReaction
-from rxnutils.chem.reaction import ReactionException
+from rxnutils.chem.reaction import ChemicalReaction, ReactionException
 
 
 @pytest.fixture
@@ -156,17 +155,10 @@ def test_template_creation(make_template_dataframe):
         rxn.generate_reaction_template()
 
         if record["retrotemplate"] != rxn.retro_template.smarts:
-            failures.append(
-                (record["rsmi"], rxn.retro_template.smarts, record["retrotemplate"])
-            )
+            failures.append((record["rsmi"], rxn.retro_template.smarts, record["retrotemplate"]))
 
     if failures:
-        print(
-            "\n"
-            + "\n\n".join(
-                f"{failed[0]}\t{failed[1]}\t{failed[2]}" for failed in failures
-            )
-        )
+        print("\n" + "\n\n".join(f"{failed[0]}\t{failed[1]}\t{failed[2]}" for failed in failures))
     assert len(failures) == 0
 
 
@@ -241,9 +233,7 @@ def test_timedout_template_creation():
     )
     rxn = ChemicalReaction(rsmi)
     # Capture ReactionException
-    with pytest.raises(
-        ReactionException, match="Template generation failed with message: Timed out"
-    ):
+    with pytest.raises(ReactionException, match="Template generation failed with message: Timed out"):
         rxn.generate_reaction_template()
 
 
@@ -254,18 +244,14 @@ def test_ringbreaker_template_creation():
     )
     rxn = ChemicalReaction(rsmi, clean_smiles=False)
 
-    _, retro_template = rxn.generate_reaction_template(
-        radius=0, expand_ring=True, expand_hetero=True
-    )
+    _, retro_template = rxn.generate_reaction_template(radius=0, expand_ring=True, expand_hetero=True)
     expected = (
         "[Cl;H0;D1;+0:3]-[c;H0;D3;+0:2]1:[cH;D2;+0:1]:[c;H0;D3;+0:4]:[nH;D2;+0:5]:[n;H0;D2;+0:6]:1>>"
         "[CH;D1;+0:1]#[C;H0;D2;+0:2]-[Cl;H0;D1;+0:3].[CH;D2;+0:4]=[N+;H0;D2:5]=[N-;H0;D1:6]"
     )
     assert retro_template.smarts == expected
 
-    _, retro_template = rxn.generate_reaction_template(
-        radius=0, expand_ring=True, expand_hetero=False
-    )
+    _, retro_template = rxn.generate_reaction_template(radius=0, expand_ring=True, expand_hetero=False)
     expected = (
         "[c;H0;D3;+0:1]1:[cH;D2;+0:2]:[c;H0;D3;+0:3]:[nH;D2;+0:4]:[n;H0;D2;+0:5]:1"
         ">>[C;H0;D2;+0:1]#[CH;D1;+0:2].[CH;D2;+0:3]=[N+;H0;D2:4]=[N-;H0;D1:5]"
diff --git a/tests/test_reaction_mods_actions.py b/tests/test_reaction_mods_actions.py
index 5a6c91d..5bb1f49 100644
--- a/tests/test_reaction_mods_actions.py
+++ b/tests/test_reaction_mods_actions.py
@@ -1,23 +1,26 @@
 import pandas as pd
 import pytest
 
-from rxnutils.pipeline.actions.reaction_props import CountComponents
+from rxnutils.chem.disconnection_sites.tag_converting import smiles_tokens
+from rxnutils.chem.utils import split_rsmi
 from rxnutils.pipeline.actions.reaction_mod import (
+    CONTRIB_INSTALLED,
+    AtomMapTagDisconnectionSite,
+    ConvertAtomMapDisconnectionTag,
+    DesaltMolecules,
+    IsotopeInfo,
+    NameRxn,
+    RDKitRxnRoles,
     ReactantsToReagents,
     ReagentsToReactants,
     RemoveAtomMapping,
     RemoveExtraAtomMapping,
+    RemoveUnchangedProducts,
     RemoveUnsanitizable,
-    RDKitRxnRoles,
+    RxnMapper,
     SplitReaction,
-    RemoveUnchangedProducts,
-    IsotopeInfo,
-    AtomMapTagDisconnectionSite,
-    ConvertAtomMapDisconnectionTag,
-    DesaltMolecules,
-    CONTRIB_INSTALLED,
 )
-from rxnutils.chem.disconnection_sites.tag_converting import smiles_tokens
+from rxnutils.pipeline.actions.reaction_props import CountComponents
 from rxnutils.pipeline.base import global_apply
 
 global_apply.max_workers = 1
@@ -148,9 +151,7 @@ def test_remove_unsanitizable(make_reaction_dataframe):
     assert df2["BadMolecules"].to_list() == ["C(C(CC)(O[Mg+2])C)CN(C)(C)(C)", ""]
 
 
-@pytest.mark.xfail(
-    not CONTRIB_INSTALLED, reason="RDKit Contrib folder is not installed"
-)
+@pytest.mark.xfail(not CONTRIB_INSTALLED, reason="RDKit Contrib folder is not installed")
 def test_rdit_rxn_roles(make_reaction_dataframe):
     action1 = RDKitRxnRoles(in_column="rsmi")
     action2 = CountComponents(in_column="rsmi")
@@ -174,9 +175,7 @@ def test_rdit_rxn_roles(make_reaction_dataframe):
 
 
 def test_split_reaction(make_reaction_dataframe):
-    action = SplitReaction(
-        in_column="rsmi", out_columns=["Reactants", "Reagents", "Products"]
-    )
+    action = SplitReaction(in_column="rsmi", out_columns=["Reactants", "Reagents", "Products"])
     df = make_reaction_dataframe
 
     df2 = action(df)
@@ -230,9 +229,7 @@ def test_disconnection_tagging(shared_datadir):
     df_atom_map_tag = action_atom_map_tag(df)
     df_tag = action_convert_tag(df_atom_map_tag)
 
-    df_ground_truth = pd.Series(
-        ["Cl!c!1ccccc1", "CO!c!1ccccc1"], name="products_tagged"
-    )
+    df_ground_truth = pd.Series(["Cl!c!1ccccc1", "CO!c!1ccccc1"], name="products_tagged")
 
     assert df_ground_truth.equals(df_tag["products_tagged"])
 
@@ -253,7 +250,7 @@ def test_smiles_tokenization_unknown_token_error(shared_datadir):
 def test_converting_no_atom_map_tag(shared_datadir):
 
     df = pd.read_csv(shared_datadir / "mapped_tests_reactions.csv", sep="\t")
-    df["products"] = [rxn.split(">")[-1] for rxn in df.smiles]
+    df["products"] = [split_rsmi(rxn)[-1] for rxn in df.smiles]
 
     action_convert_tag = ConvertAtomMapDisconnectionTag(in_column="products")
 
@@ -288,3 +285,82 @@ def test_desalting():
         "CCO>>CCC(=O)O",
         "CCO.O>>CCC(=O)O",
     ]
+
+
+def test_namerxn_fail(make_reaction_dataframe):
+    df = make_reaction_dataframe
+    action1 = RemoveAtomMapping(in_column="rsmi", out_column="rsmi_nomap")
+    action2 = NameRxn(in_column="rsmi_nomap")
+
+    df1 = action1(df)
+    with pytest.raises(FileNotFoundError, match="No such file or directory: 'namerxn'"):
+        df1 = action2(df1)
+
+
+def test_namerxn(make_reaction_dataframe, mocker):
+    df = make_reaction_dataframe
+    action1 = RemoveAtomMapping(in_column="rsmi", out_column="rsmi_nomap")
+    action2 = NameRxn(in_column="rsmi_nomap")
+
+    # Mock namerxn call
+    # Use the mocker fixture to mock subprocess.call
+    mock_suprocess_call = mocker.patch("rxnutils.pipeline.actions.reaction_mod.subprocess.call")
+    # Set up the mock to return a specific response
+    mock_result = mocker.MagicMock()
+    mock_suprocess_call.return_value = mock_result
+
+    df1 = action1(df)
+    with pytest.raises(FileNotFoundError, match="Could not produce namerxn output."):
+        df1 = action2(df1)
+
+    mock_suprocess_call.assert_called_once()
+
+    # Mock os.path action
+    mock_os_path_exists = mocker.patch("rxnutils.pipeline.actions.reaction_mod.os.path.exists")
+    mock_os_path_getsize = mocker.patch("rxnutils.pipeline.actions.reaction_mod.os.path.getsize")
+    # Set up the mock to return a specific response
+    mock_os_path_exists.return_value = True
+    mock_os_path_getsize.return_value = 1
+
+    # Mock pd.read_csv
+    mock_pd_read_csv = mocker.patch("rxnutils.pipeline.actions.reaction_mod.pd.read_csv")
+    # Set up the mock to return a specific response
+    mock_result = pd.DataFrame(data={"NextMoveRxnSmiles": list(df["rsmi"]), "NMC": ["1.1", "1.2"]})
+    mock_pd_read_csv.return_value = mock_result
+
+    df1 = action2(df1)
+
+    mock_os_path_exists.assert_called_once()
+    mock_os_path_getsize.assert_called_once()
+
+    assert list(df1.columns) == ["rsmi", "rsmi_nomap", "NextMoveRxnSmiles", "NMC"]
+    assert df1.shape == (2, 4)
+    assert df1["NMC"].to_list() == ["1.1", "1.2"]
+    assert df1["NextMoveRxnSmiles"].to_list() == df1["rsmi"].to_list()
+
+
+def test_rxnmapper(make_reaction_dataframe, mocker):
+    df = make_reaction_dataframe
+    action1 = RemoveAtomMapping(in_column="rsmi", out_column="rsmi_nomap")
+    action2 = RxnMapper(in_column="rsmi_nomap")
+
+    df1 = action1(df)
+
+    # Mock rnxmapper call
+    # Use the mocker fixture to mock subprocess.call
+    mock_suprocess = mocker.patch("rxnutils.pipeline.actions.reaction_mod.subprocess.check_output")
+    # Set up the mock to return a specific response
+    mock_result = mocker.MagicMock()
+    mock_suprocess.return_value = mock_result
+
+    # Mock pd.read_csv
+    mock_pd_read_csv = mocker.patch("rxnutils.pipeline.actions.reaction_mod.pd.read_csv")
+    # Set up the mock to return a specific response
+    mock_result = pd.DataFrame(data={"mapped_rxn": list(df["rsmi"]), "confidence": [1.0, 1.0]})
+    mock_pd_read_csv.return_value = mock_result
+
+    df1 = action2(df1)
+
+    assert list(df1.columns) == ["rsmi", "rsmi_nomap", "RxnmapperRxnSmiles"]
+    assert df1.shape == (2, 3)
+    assert df1["RxnmapperRxnSmiles"].to_list() == df1["rsmi"].to_list()
diff --git a/tests/test_reaction_props_actions.py b/tests/test_reaction_props_actions.py
index 2a60579..77f8308 100644
--- a/tests/test_reaction_props_actions.py
+++ b/tests/test_reaction_props_actions.py
@@ -2,32 +2,33 @@
 
 import pandas as pd
 
+from rxnutils.chem.utils import split_rsmi
+from rxnutils.pipeline.actions.reaction_mod import RemoveUnsanitizable
 from rxnutils.pipeline.actions.reaction_props import (
+    CgrCreated,
+    CgrNumberOfDynamicBonds,
     CountComponents,
     CountElements,
     HasUnsanitizableReactants,
+    MaxRingNumber,
     ProductAtomMappingStats,
     ProductSize,
     PseudoReactionHash,
     ReactantProductAtomBalance,
     ReactantSize,
-    SmilesLength,
-    SmilesSanitizable,
     RingBondMade,
     RingMadeSize,
     RingNumberChange,
-    StereoMesoProduct,
-    StereoCentreChanges,
+    SmilesLength,
+    SmilesSanitizable,
+    StereoCenterInReactantPotential,
     StereoCenterIsCreated,
     StereoCenterIsRemoved,
-    StereoHasChiralReagent,
-    StereoCenterInReactantPotential,
     StereoCenterOutsideReaction,
-    CgrCreated,
-    CgrNumberOfDynamicBonds,
-    MaxRingNumber,
+    StereoCentreChanges,
+    StereoHasChiralReagent,
+    StereoMesoProduct,
 )
-from rxnutils.pipeline.actions.reaction_mod import RemoveUnsanitizable
 from rxnutils.pipeline.base import global_apply
 
 global_apply.max_workers = 1
@@ -88,8 +89,7 @@ def test_pseudo_hash(make_reaction_dataframe):
     assert ">>" not in df2["PseudoHash"].iloc[0]
     assert df2["PseudoHash"].iloc[0].count(".") == 2
     assert (
-        df2["PseudoHash"].iloc[0]
-        == "GWIBCCZNAYLLCD-UHFFFAOYSA-N.QAOWNCQODCNURD-UHFFFAOYSA-N>"
+        df2["PseudoHash"].iloc[0] == "GWIBCCZNAYLLCD-UHFFFAOYSA-N.QAOWNCQODCNURD-UHFFFAOYSA-N>"
         "OFOBLEOULBTSOW-UHFFFAOYSA-L.UHOVQNZJYSORNB-UHFFFAOYSA-N>KOJXGMJOTRYLBD-UHFFFAOYSA-N"
     )
 
@@ -124,7 +124,7 @@ def test_smiles_length(make_reaction_dataframe):
 def test_smiles_sanitizable(make_reaction_dataframe):
     action = SmilesSanitizable(in_column="new_column")
     df = make_reaction_dataframe
-    df["new_column"] = df["rsmi"].apply(lambda row: row.split(">")[0])
+    df["new_column"] = df["rsmi"].apply(lambda row: split_rsmi(row)[0])
 
     df2 = action(df)
 
@@ -133,9 +133,7 @@ def test_smiles_sanitizable(make_reaction_dataframe):
 
 def test_unsanitizable_reactants(make_reaction_dataframe):
     action1 = RemoveUnsanitizable(in_column="rsmi")
-    action2 = HasUnsanitizableReactants(
-        rsmi_column="rsmi", bad_columns=["BadMolecules"]
-    )
+    action2 = HasUnsanitizableReactants(rsmi_column="rsmi", bad_columns=["BadMolecules"])
     df = make_reaction_dataframe
 
     df2 = action1(df)
diff --git a/tests/test_rinchi.py b/tests/test_rinchi.py
index dc30607..01fb4e0 100644
--- a/tests/test_rinchi.py
+++ b/tests/test_rinchi.py
@@ -4,10 +4,8 @@
 import pytest
 from requests.exceptions import HTTPError
 
-from rxnutils.chem.rinchi.download_rinchi import (
-    main as download_rinchi,
-    PLATFORM2FOLDER,
-)
+from rxnutils.chem.rinchi.download_rinchi import PLATFORM2FOLDER
+from rxnutils.chem.rinchi.download_rinchi import main as download_rinchi
 from rxnutils.chem.rinchi.rinchi_api import generate_rinchi
 
 
@@ -45,11 +43,5 @@ def test_generate_rinchi(rinchi_download):
 
     resp = generate_rinchi(rsmi)
 
-    assert (
-        resp.long_rinchikey
-        == "Long-RInChIKey=SA-BUHFF-MSQCQINLJMEVNJ-UHFFFAOYSA-N--VEXZGXHMUGYJMC-UHFFFAOYSA-N"
-    )
-    assert (
-        resp.short_rinchikey
-        == "Short-RInChIKey=SA-BUHFF-MSQCQINLJM-VEXZGXHMUG-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ"
-    )
+    assert resp.long_rinchikey == "Long-RInChIKey=SA-BUHFF-MSQCQINLJMEVNJ-UHFFFAOYSA-N--VEXZGXHMUGYJMC-UHFFFAOYSA-N"
+    assert resp.short_rinchikey == "Short-RInChIKey=SA-BUHFF-MSQCQINLJM-VEXZGXHMUG-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ"
diff --git a/tests/test_routes_base.py b/tests/test_routes_base.py
index a9b02d2..76a3f5e 100644
--- a/tests/test_routes_base.py
+++ b/tests/test_routes_base.py
@@ -1,9 +1,10 @@
 import copy
 
-import pytest
 import pandas as pd
+import pytest
 from rdkit import Chem
 
+from rxnutils.chem.utils import split_rsmi
 from rxnutils.routes.base import SynthesisRoute
 
 
@@ -61,9 +62,7 @@ def test_atom_mapping_no_namerxn(synthesis_route, setup_mapper_no_namerxn, recwa
     )
 
 
-def test_atom_mapping_no_namerxn_choose_rxnmapper(
-    synthesis_route, setup_mapper_no_namerxn, recwarn
-):
+def test_atom_mapping_no_namerxn_choose_rxnmapper(synthesis_route, setup_mapper_no_namerxn, recwarn):
     synthesis_route.assign_atom_mapping(only_rxnmapper=True)
 
     assert len(recwarn) == 0
@@ -86,10 +85,7 @@ def test_root_smiles(synthesis_route, setup_mapper):
         synthesis_route.mapped_root_smiles
 
     synthesis_route.assign_atom_mapping()
-    assert (
-        synthesis_route.mapped_root_smiles
-        == "[CH3:1][O:2][c:3]1[cH:4][cH:5][cH:6][cH:7][cH:8]1"
-    )
+    assert synthesis_route.mapped_root_smiles == "[CH3:1][O:2][c:3]1[cH:4][cH:5][cH:6][cH:7][cH:8]1"
 
 
 def test_reaction_data(synthesis_route, setup_mapper):
@@ -121,13 +117,13 @@ def test_remap_ref_smiles(synthesis_route, setup_mapper):
     route1 = synthesis_route
     route1.assign_atom_mapping()
     old_reaction_smiles = route1.atom_mapped_reaction_smiles()
-    reactants, products = old_reaction_smiles[0].split(">>")
+    reactants, _, products = split_rsmi(old_reaction_smiles[0])
     rsmi_old = Chem.MolToSmiles(Chem.MolFromSmiles(reactants))
     psmi_old = Chem.MolToSmiles(Chem.MolFromSmiles(products))
 
     route1.remap(products)
 
-    reactants, products = route1.atom_mapped_reaction_smiles()[0].split(">>")
+    reactants, _, products = split_rsmi(route1.atom_mapped_reaction_smiles()[0])
     rsmi = Chem.MolToSmiles(Chem.MolFromSmiles(reactants))
     psmi = Chem.MolToSmiles(Chem.MolFromSmiles(products))
     assert rsmi == rsmi_old
@@ -135,7 +131,7 @@ def test_remap_ref_smiles(synthesis_route, setup_mapper):
 
     route1.remap("[CH3:10][O:2][c:3]1[cH:4][cH:5][cH:6][cH:7][cH:8]1")
 
-    reactants, products = route1.atom_mapped_reaction_smiles()[0].split(">>")
+    reactants, _, products = split_rsmi(route1.atom_mapped_reaction_smiles()[0])
     rsmi = Chem.MolToSmiles(Chem.MolFromSmiles(reactants))
     psmi = Chem.MolToSmiles(Chem.MolFromSmiles(products))
     assert rsmi != rsmi_old
@@ -146,13 +142,13 @@ def test_remap_ref_dict(synthesis_route, setup_mapper):
     route1 = synthesis_route
     route1.assign_atom_mapping()
     old_reaction_smiles = route1.atom_mapped_reaction_smiles()
-    reactants, products = old_reaction_smiles[0].split(">>")
+    reactants, _, products = split_rsmi(old_reaction_smiles[0])
     rsmi_old = Chem.MolToSmiles(Chem.MolFromSmiles(reactants))
     psmi_old = Chem.MolToSmiles(Chem.MolFromSmiles(products))
 
     route1.remap({1: 10, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8})
 
-    reactants, products = route1.atom_mapped_reaction_smiles()[0].split(">>")
+    reactants, _, products = split_rsmi(route1.atom_mapped_reaction_smiles()[0])
     rsmi = Chem.MolToSmiles(Chem.MolFromSmiles(reactants))
     psmi = Chem.MolToSmiles(Chem.MolFromSmiles(products))
     assert rsmi != rsmi_old
@@ -213,6 +209,24 @@ def test_route_leaves(synthesis_route):
     assert leaves == {"c1ccccc1", "Cl", "CO"}
 
 
+def test_route_leaves_count(synthesis_route):
+    counts = synthesis_route.leaf_counts()
+
+    assert counts == {"c1ccccc1": 1, "Cl": 1, "CO": 1}
+
+
+def test_route_intermediates(synthesis_route):
+    intermediates = synthesis_route.intermediates()
+
+    assert intermediates == {"Clc1ccccc1"}
+
+
+def test_route_intermediates_count(synthesis_route):
+    counts = synthesis_route.intermediate_counts()
+
+    assert counts == {"Clc1ccccc1": 1}
+
+
 def test_route_is_solved(synthesis_route, setup_stock):
     assert synthesis_route.is_solved()
 
diff --git a/tests/test_routes_comparison.py b/tests/test_routes_comparison.py
index 7c9097e..193d982 100644
--- a/tests/test_routes_comparison.py
+++ b/tests/test_routes_comparison.py
@@ -5,10 +5,10 @@
 
 from rxnutils.routes.base import SynthesisRoute
 from rxnutils.routes.comparison import (
-    simple_route_similarity,
-    simple_bond_forming_similarity,
     atom_matching_bonanza_similarity,
     route_distances_calculator,
+    simple_bond_forming_similarity,
+    simple_route_similarity,
 )
 
 
diff --git a/tests/test_routes_readers.py b/tests/test_routes_readers.py
index 8d1755d..b1154fc 100644
--- a/tests/test_routes_readers.py
+++ b/tests/test_routes_readers.py
@@ -2,18 +2,17 @@
 
 import pandas as pd
 
-from rxnutils.routes.readers import reactions2route
 from rxnutils.routes.readers import (
-    read_reactions_dataframe,
+    reactions2route,
     read_aizynthcli_dataframe,
+    read_aizynthfinder_dict,
     read_rdf_file,
+    read_reactions_dataframe,
 )
 
 
 def test_create_route_from_reaction(synthesis_route):
-    route = reactions2route(
-        ["Cl.C1=CC=CC=C1>>ClC1=CC=CC=C1", "CO.ClC1=CC=CC=C1>>COC1=CC=CC=C1"]
-    )
+    route = reactions2route(["Cl.C1=CC=CC=C1>>ClC1=CC=CC=C1", "CO.ClC1=CC=CC=C1>>COC1=CC=CC=C1"])
 
     assert route.reaction_tree == synthesis_route.reaction_tree
 
@@ -54,6 +53,16 @@ def test_create_route_from_dataframe():
     assert list(data[1].keys()) == expected_keys
 
 
+def test_create_route_from_aizynth_dict(shared_datadir):
+    with open(shared_datadir / "branched_route.json", "r") as fileobj:
+        tree_dict = json.load(fileobj)
+
+    route = read_aizynthfinder_dict(tree_dict)
+
+    assert len(route.reaction_smiles()) == 4
+    assert route.reaction_smiles()[-1] == "NC1CCCCC1.C1=CCC=C1>>NC1CCCC(C2C=CC=C2)C1"
+
+
 def test_create_route_from_aizynth_cli(shared_datadir):
     with open(shared_datadir / "branched_route.json", "r") as fileobj:
         tree_dict = json.load(fileobj)
@@ -65,10 +74,7 @@ def test_create_route_from_aizynth_cli(shared_datadir):
     assert len(routes) == 1
     assert len(routes[0]) == 1
     assert len(routes[0][0].reaction_smiles()) == 4
-    assert (
-        routes[0][0].reaction_smiles()[-1]
-        == "NC1CCCCC1.C1=CCC=C1>>NC1CCCC(C2C=CC=C2)C1"
-    )
+    assert routes[0][0].reaction_smiles()[-1] == "NC1CCCCC1.C1=CCC=C1>>NC1CCCC(C2C=CC=C2)C1"
 
 
 def test_create_route_from_rdf(shared_datadir):
diff --git a/tests/test_routes_scoring.py b/tests/test_routes_scoring.py
index 511e71a..f135b4a 100644
--- a/tests/test_routes_scoring.py
+++ b/tests/test_routes_scoring.py
@@ -5,15 +5,21 @@
 import pandas as pd
 import pytest
 import requests
+from rdkit import Chem
 
+from rxnutils.chem.features.sc_score import SCORE_SUPPORTED, SCScore
+from rxnutils.routes.deepset.featurizers import collect_reaction_features, default_reaction_featurizer, ecfp_fingerprint
+from rxnutils.routes.retro_bleu.ngram_collection import NgramCollection
 from rxnutils.routes.scoring import (
-    route_sorter,
-    route_ranks,
+    DeepsetModelClient,
     badowski_route_score,
-    retro_bleu_score,
+    deepset_route_score,
     ngram_overlap_score,
+    reaction_class_rank_score,
+    retro_bleu_score,
+    route_ranks,
+    route_sorter,
 )
-from rxnutils.routes.retro_bleu.ngram_collection import NgramCollection
 
 
 def test_route_sorter(synthesis_route, setup_stock):
@@ -48,6 +54,14 @@ def test_badowski_score(synthesis_route, setup_stock):
     assert badowski_route_score(synthesis_route) == pytest.approx(6.625, abs=1e-4)
 
 
+def test_class_rank_score(synthesis_route, setup_mapper):
+    synthesis_route.assign_atom_mapping()
+
+    score = reaction_class_rank_score(synthesis_route, {"10.1.2": 15, "1.7.11": 2}, ["10.1.2"])
+
+    assert pytest.approx(score, abs=0.01) == 0.33
+
+
 def test_read_and_write_ngram_collection(tmpdir):
     collection = NgramCollection(2, "dummy", {("a", "b"), ("a", "c")})
 
@@ -97,3 +111,60 @@ def test_retro_bleu_score_short_nsteps(augmentable_sythesis_route):
     score = retro_bleu_score(augmentable_sythesis_route, ref, 1)
 
     assert pytest.approx(score, abs=1e-4) == 3.0443
+
+
+def test_ecfp_featurizer():
+    mol = Chem.MolFromSmiles("O")
+
+    fp = ecfp_fingerprint(mol, 2, 10)
+
+    assert len(fp) == 10
+    assert sum(fp) == 1
+
+
+def test_reaction_featurizer():
+    reaction_data = {"reaction_smiles": "C.O>>CO"}
+
+    fp = default_reaction_featurizer(reaction_data, 2, 10)
+
+    assert len(fp) == 10
+    assert sum(fp) == 0.0
+
+
+def test_collect_reaction_features():
+    reaction_data = {
+        "reaction_smiles": "C.O>>CO",
+        "classification": "5.1.1",
+        "tree_depth": 1,
+    }
+    class_ranks = {"5.1.1": 3}
+    target_fp = ecfp_fingerprint(Chem.MolFromSmiles("CO"), 2, 10)
+
+    score, features = collect_reaction_features([reaction_data], target_fp, class_ranks, default_reaction_featurizer)
+
+    assert score == 3.0
+    assert features.shape == (1, 78)
+    assert features[0, :3].tolist() == [5, 1, 1]
+    assert features[0, 3] == 3.0
+    assert features[0, 4:14].tolist() == target_fp.tolist()
+
+
+@pytest.mark.xfail(condition=not SCORE_SUPPORTED, reason="onnx support not installed")
+def test_deepsetscorer(mocker, shared_datadir, augmentable_sythesis_route):
+    filename = str(shared_datadir / "scscore_dummy_model.onnx")
+    scscorer = SCScore(filename, 5)
+    mocked_model = mocker.patch("rxnutils.routes.deepset.scoring.onnxruntime.InferenceSession")
+    mocked_model.return_value.run.return_value = [5.0]
+    model = DeepsetModelClient("dummy")
+    class_ranks = {"5.1.1": 3}
+
+    score = deepset_route_score(augmentable_sythesis_route, model, scscorer, class_ranks)
+
+    model._deepnet.run.assert_called_once()
+    assert score == 5.0
+    mocked_model.return_value.run.assert_called_once()
+
+    call_args = mocked_model.return_value.run.call_args
+    assert isinstance(call_args[0][1], dict)
+    assert call_args[0][1]["reaction_features"].shape == (3, 132)
+    assert len(call_args[0][1]["route_features"]) == 4
diff --git a/tests/test_scscore.py b/tests/test_scscore.py
new file mode 100644
index 0000000..1329c89
--- /dev/null
+++ b/tests/test_scscore.py
@@ -0,0 +1,13 @@
+import pytest
+from rdkit import Chem
+
+from rxnutils.chem.features.sc_score import SCORE_SUPPORTED, SCScore
+
+
+@pytest.mark.xfail(condition=not SCORE_SUPPORTED, reason="onnx support not installed")
+def test_scscore(shared_datadir):
+    filename = str(shared_datadir / "scscore_dummy_model.onnx")
+    scorer = SCScore(filename, 5)
+    mol = Chem.MolFromSmiles("C")
+
+    assert pytest.approx(scorer(mol), abs=1e-3) == 4.523
diff --git a/tests/test_ted.py b/tests/test_ted.py
index 207b2a4..a014391 100644
--- a/tests/test_ted.py
+++ b/tests/test_ted.py
@@ -3,13 +3,9 @@
 import pytest
 
 from rxnutils.routes.base import SynthesisRoute
-from rxnutils.routes.ted.utils import (
-    AptedConfig,
-    TreeContent,
-    StandardFingerprintFactory,
-)
-from rxnutils.routes.ted.reactiontree import ReactionTreeWrapper
 from rxnutils.routes.ted.distances_calculator import ted_distances_calculator
+from rxnutils.routes.ted.reactiontree import ReactionTreeWrapper
+from rxnutils.routes.ted.utils import AptedConfig, StandardFingerprintFactory, TreeContent
 
 
 def collect_smiles(tree, query_type, smiles_list):
@@ -143,9 +139,7 @@ def test_create_one_tree_of_reactions(load_reaction_tree):
     tree = load_reaction_tree("example_routes.json", 0)
     route = SynthesisRoute(tree)
 
-    wrapper = ReactionTreeWrapper(
-        route, content=TreeContent.REACTIONS, exhaustive_limit=1
-    )
+    wrapper = ReactionTreeWrapper(route, content=TreeContent.REACTIONS, exhaustive_limit=1)
 
     assert wrapper.info["tree count"] == 1
     assert len(wrapper.trees) == 1
@@ -314,10 +308,7 @@ def test_route_distances_longer_routes(load_reaction_tree):
 
 
 def test_distance_matrix(load_reaction_tree):
-    routes = [
-        SynthesisRoute(load_reaction_tree("example_routes.json", idx))
-        for idx in range(3)
-    ]
+    routes = [SynthesisRoute(load_reaction_tree("example_routes.json", idx)) for idx in range(3)]
 
     dist_mat = ted_distances_calculator(routes, content="molecules")
 
@@ -328,10 +319,7 @@ def test_distance_matrix(load_reaction_tree):
 
 
 def test_distance_matrix_timeout(load_reaction_tree):
-    routes = [
-        SynthesisRoute(load_reaction_tree("example_routes.json", idx))
-        for idx in range(3)
-    ]
+    routes = [SynthesisRoute(load_reaction_tree("example_routes.json", idx)) for idx in range(3)]
 
     with pytest.raises(ValueError):
         ted_distances_calculator(routes, content="molecules", timeout=0)
@@ -339,9 +327,7 @@ def test_distance_matrix_timeout(load_reaction_tree):
 
 def test_fingerprint_calculations():
     example_route = SynthesisRoute(example_tree)
-    wrapper = ReactionTreeWrapper(
-        example_route, content="both", fp_factory=StandardFingerprintFactory(nbits=128)
-    )
+    wrapper = ReactionTreeWrapper(example_route, content="both", fp_factory=StandardFingerprintFactory(nbits=128))
 
     fp = wrapper.first_tree["sort_key"]
     mol1 = "1000010000000000000010001000100101000101100000010000010000100001"
diff --git a/tests/test_template.py b/tests/test_template.py
index 12c37e1..577c2b4 100644
--- a/tests/test_template.py
+++ b/tests/test_template.py
@@ -1,6 +1,5 @@
 import pytest
-from rdkit import Chem
-from rdkit import RDLogger
+from rdkit import Chem, RDLogger
 
 from rxnutils.chem.template import TemplateMolecule
 
@@ -142,9 +141,7 @@ def test_hash_from_smarts(create_mol):
 
 
 def test_template_with_aromaticity():
-    rd_mol = Chem.MolFromSmarts(
-        "C-C-O-[C;H0;D3;+0:1](=[O;D1;H0:2])-[c:3](:[#7;a:4]):[#8;a:5]:[#7;a:6]"
-    )
+    rd_mol = Chem.MolFromSmarts("C-C-O-[C;H0;D3;+0:1](=[O;D1;H0:2])-[c:3](:[#7;a:4]):[#8;a:5]:[#7;a:6]")
     tmpl_mol = TemplateMolecule(rd_mol)
 
     assert tmpl_mol.fingerprint_bits() != {}
@@ -169,6 +166,4 @@ def test_template_equality_chiral():
     mol2 = TemplateMolecule(smarts="C-S(=O)(=O)-O-[C@H;D3;+0:1](-[C:2])-[C:3]")
 
     assert mol1.fingerprint_bits() != mol2.fingerprint_bits()
-    assert mol1.fingerprint_bits(use_chirality=False) == mol2.fingerprint_bits(
-        use_chirality=False
-    )
+    assert mol1.fingerprint_bits(use_chirality=False) == mol2.fingerprint_bits(use_chirality=False)
diff --git a/tests/test_template_actions.py b/tests/test_template_actions.py
index aa572df..e707dad 100644
--- a/tests/test_template_actions.py
+++ b/tests/test_template_actions.py
@@ -1,10 +1,7 @@
 import pandas as pd
 import pytest
 
-from rxnutils.pipeline.actions.templates import (
-    CountTemplateComponents,
-    RetroTemplateReproduction,
-)
+from rxnutils.pipeline.actions.templates import CountTemplateComponents, RetroTemplateReproduction
 from rxnutils.pipeline.base import global_apply
 
 global_apply.max_workers = 1
@@ -26,9 +23,7 @@ def test_count_components(make_template_dataframe):
 
 
 def test_template_reproduction(make_template_dataframe):
-    action = RetroTemplateReproduction(
-        template_column="retrotemplate", smiles_column="rsmi"
-    )
+    action = RetroTemplateReproduction(template_column="retrotemplate", smiles_column="rsmi")
     df = make_template_dataframe
 
     df2 = action(df)
diff --git a/tests/test_uspto.py b/tests/test_uspto.py
index 623783f..3a52e8d 100644
--- a/tests/test_uspto.py
+++ b/tests/test_uspto.py
@@ -5,9 +5,7 @@
 
 
 def test_combine_uspto(shared_datadir):
-    combine_uspto(
-        ["--filenames", "uspto_example_reactions.rsmi", "--folder", str(shared_datadir)]
-    )
+    combine_uspto(["--filenames", "uspto_example_reactions.rsmi", "--folder", str(shared_datadir)])
 
     data = pd.read_csv(shared_datadir / "uspto_data.csv", sep="\t")