Merge branch 'martimunicoy-master'

martimunicoy · Feb 12, 2024 · b34fae9 · b34fae9
2 parents d952ec0 + c48012c
commit b34fae9
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diff --git a/.github/workflows/conda.yml b/.github/workflows/conda.yml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macOS-latest]
-        python-version: [3.7, 3.8]
+        python-version: [3.8, 3.9]
     name: Python ${{ matrix.python-version }} at ${{ matrix.os }}
     steps:
       - uses: actions/checkout@v2

diff --git a/.github/workflows/master.yml b/.github/workflows/master.yml
@@ -17,7 +17,7 @@ jobs:
         uses: s-weigand/setup-conda@v1
         with:
           update-conda: true
-          python-version: 3.7
+          python-version: 3.9
           conda-channels: anaconda, omnia, conda-forge, martimunicoy
 
       - name: Install doc dependencies

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -16,7 +16,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macOS-latest]
-        python-version: [3.7, 3.8]
+        python-version: [3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-| **About** | [![License](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE) [![Python](https://img.shields.io/badge/python-3.7%2C%203.8-blue.svg)](https://martimunicoy.github.io/peleffy) [![Release](https://img.shields.io/github/release/martimunicoy/peleffy.svg?include_prereleases)](https://github.com/martimunicoy/peleffy/releases/) |
+| **About** | [![License](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE) [![Python](https://img.shields.io/badge/python-3.8%2C%203.9-blue.svg)](https://martimunicoy.github.io/peleffy) [![Release](https://img.shields.io/github/release/martimunicoy/peleffy.svg?include_prereleases)](https://github.com/martimunicoy/peleffy/releases/) |
 | :------ | :------- |
 | **Status** | [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/martimunicoy/peleffy.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/martimunicoy/peleffy/context:python) [![Test](https://github.com/martimunicoy/peleffy/workflows/Test/badge.svg)](https://github.com/martimunicoy/peleffy/actions?query=workflow%3ATest) [![codecov](https://codecov.io/gh/martimunicoy/peleffy/branch/master/graph/badge.svg)](https://codecov.io/gh/martimunicoy/peleffy) |
 | **Installation** | [![Conda](https://img.shields.io/conda/v/martimunicoy/peleffy.svg)](https://anaconda.org/martimunicoy/peleffy) [![PyPI](https://img.shields.io/pypi/v/peleffy)](https://pypi.org/project/peleffy/) |

diff --git a/devtools/conda/meta.yaml b/devtools/conda/meta.yaml
@@ -10,6 +10,7 @@ source:
 build:
   script: python -m pip install . --no-deps
   number: 0
+  noarch: python
 
 requirements:
   build:
@@ -25,7 +26,8 @@ requirements:
     - networkx
     - rdkit
     - ambertools
-    - openff-toolkit==0.10.1
+    - openff-toolkit==0.10.7
+    - openff-forcefields==2023.05.1
 
 about:
   home: https://github.com/martimunicoy/peleffy

diff --git a/devtools/envs/standard.yaml b/devtools/envs/standard.yaml
@@ -9,8 +9,10 @@ dependencies:
   - pytest
   - pytest-cov
   - codecov
-  - coverage < 5.0
+  - coverage
   - ipython
   - ambertools
   - rdkit
-  - openff-toolkit==0.10.1
+  - openff-toolkit==0.10.7
+  - openff-forcefields==2023.05.1
+
diff --git a/docs/index.rst b/docs/index.rst
@@ -7,6 +7,8 @@ are:
 
 * The following force field from the `Open Force Field toolkit <https://github.com/openforcefield/openforcefield>`_:
 
+  * openff_unconstrained-2.1.0.offxml
+
   * openff_unconstrained-2.0.0.offxml
 
   * openff_unconstrained-1.3.0.offxml

diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst
@@ -8,6 +8,34 @@ Releases follow the ``major.minor.micro`` scheme recommended by `PEP440 <https:/
 * ``micro`` increments represent bugfix releases or improvements in documentation
 
 
+1.5.0 - OpenFF upgrade and enhancements for alchemistry
+-------------------------------------------------------
+
+This is a minor release of peleffy that supports the latest version of openff-toolkit 0.10. It also
+contains additional enhancements for the alchemistry module.
+
+New features
+""""""""""""
+- `PR #182 <https://github.com/martimunicoy/peleffy/pull/182>`_: support openff-toolkit 0.10.7 and openff-forcefield 2.1.0
+- `PR #182 <https://github.com/martimunicoy/peleffy/pull/182>`_: better alchemical structure alignment
+- `PR #182 <https://github.com/martimunicoy/peleffy/pull/182>`_: more lambda types available (vdw1 and vdw2)
+
+Tests added
+"""""""""""
+- `PR #182 <https://github.com/martimunicoy/peleffy/pull/182>`_: corrections for alchemical and mapper tests
+- `PR #182 <https://github.com/martimunicoy/peleffy/pull/182>`_: new test to check forcefield names
+
+
+1.4.5 - Corrections for alchemistry
+-----------------------------------
+
+This is a micro release of peleffy that contains corrections for alchemistry module.
+
+Bugfixes
+""""""""
+- `PR #180 <https://github.com/martimunicoy/peleffy/pull/180>`_: bug fixes for alchemical topologies
+
+
 1.4.4 - Corrections for alchemistry and new charge calculator
 -------------------------------------------------------------
 

diff --git a/peleffy/data/tests/alchemical_ligandParams_1.txt b/peleffy/data/tests/alchemical_ligandParams_1.txt
@@ -9,24 +9,24 @@
         },
         "HYB": {
             "_C1_": {
-                "radius": 1.625,
-                "scale": 0.755
+                "radius": 1.7,
+                "scale": 0.36
             },
             "_N1_": {
                 "radius": 1.625,
                 "scale": 0.755
             },
             "_C2_": {
-                "radius": 1.625,
-                "scale": 0.755
-            },
-            "_C3_": {
                 "radius": 1.7,
                 "scale": 0.36
             },
+            "_C3_": {
+                "radius": 1.625,
+                "scale": 0.755
+            },
             "_C4_": {
-                "radius": 1.7,
-                "scale": 0.36
+                "radius": 1.625,
+                "scale": 0.755
             },
             "_C5_": {
                 "radius": 1.7,
@@ -41,20 +41,20 @@
                 "scale": 0.425
             },
             "_H1_": {
-                "radius": 1.25,
-                "scale": 0.85
+                "radius": 1.2,
+                "scale": 0.425
             },
             "_H2_": {
-                "radius": 1.25,
-                "scale": 0.85
+                "radius": 1.2,
+                "scale": 0.425
             },
             "_H3_": {
                 "radius": 1.2,
                 "scale": 0.425
             },
             "_H4_": {
-                "radius": 1.25,
-                "scale": 0.85
+                "radius": 1.2,
+                "scale": 0.425
             },
             "_H5_": {
                 "radius": 1.2,
@@ -65,24 +65,24 @@
                 "scale": 0.425
             },
             "_H7_": {
-                "radius": 1.2,
-                "scale": 0.425
+                "radius": 1.25,
+                "scale": 0.85
             },
             "_H8_": {
                 "radius": 1.2,
                 "scale": 0.425
             },
             "_H9_": {
-                "radius": 1.2,
-                "scale": 0.425
+                "radius": 1.25,
+                "scale": 0.85
             },
             "H10_": {
                 "radius": 1.2,
                 "scale": 0.425
             },
             "H11_": {
-                "radius": 1.2,
-                "scale": 0.425
+                "radius": 1.25,
+                "scale": 0.85
             },
             "_C6_": {
                 "radius": 1.7,

diff --git a/peleffy/data/tests/alchemical_ligandParams_2.txt b/peleffy/data/tests/alchemical_ligandParams_2.txt
@@ -9,24 +9,24 @@
         },
         "HYB": {
             "_C1_": {
-                "radius": 1.55,
-                "scale": 0.79
+                "radius": 1.7,
+                "scale": 0.0
             },
             "_N1_": {
                 "radius": 1.7,
                 "scale": 0.72
             },
             "_C2_": {
-                "radius": 1.55,
-                "scale": 0.79
-            },
-            "_C3_": {
                 "radius": 1.7,
                 "scale": 0.0
             },
+            "_C3_": {
+                "radius": 1.55,
+                "scale": 0.79
+            },
             "_C4_": {
-                "radius": 1.7,
-                "scale": 0.0
+                "radius": 1.55,
+                "scale": 0.79
             },
             "_C5_": {
                 "radius": 1.7,
@@ -41,20 +41,20 @@
                 "scale": 0.0
             },
             "_H1_": {
-                "radius": 1.3,
-                "scale": 0.85
+                "radius": 1.2,
+                "scale": 0.0
             },
             "_H2_": {
-                "radius": 1.3,
-                "scale": 0.85
+                "radius": 1.2,
+                "scale": 0.0
             },
             "_H3_": {
                 "radius": 1.2,
                 "scale": 0.0
             },
             "_H4_": {
-                "radius": 1.3,
-                "scale": 0.85
+                "radius": 1.2,
+                "scale": 0.0
             },
             "_H5_": {
                 "radius": 1.2,
@@ -65,24 +65,24 @@
                 "scale": 0.0
             },
             "_H7_": {
-                "radius": 1.2,
-                "scale": 0.0
+                "radius": 1.3,
+                "scale": 0.85
             },
             "_H8_": {
                 "radius": 1.2,
                 "scale": 0.0
             },
             "_H9_": {
-                "radius": 1.2,
-                "scale": 0.0
+                "radius": 1.3,
+                "scale": 0.85
             },
             "H10_": {
                 "radius": 1.2,
                 "scale": 0.0
             },
             "H11_": {
-                "radius": 1.2,
-                "scale": 0.0
+                "radius": 1.3,
+                "scale": 0.85
             },
             "_C6_": {
                 "radius": 1.7,

diff --git a/peleffy/data/tests/alchemical_mol2.pdb b/peleffy/data/tests/alchemical_mol2.pdb
@@ -1,21 +1,21 @@
 COMPND    HYDROLASE (SERINE PROTEINASE)
-HETATM    1  C1  BEN A   1      -0.779   0.348   1.160  1.00 19.86           C  
-HETATM    2  C2  BEN A   1      -0.825  -0.520   2.218  1.00 19.86           C  
-HETATM    3  C3  BEN A   1      -0.996  -0.028   3.518  1.00 19.86           C  
-HETATM    4  C4  BEN A   1      -1.127   1.352   3.741  1.00 19.86           C  
-HETATM    5  C5  BEN A   1      -1.087   2.225   2.651  1.00 19.86           C  
-HETATM    6  C6  BEN A   1      -0.914   1.710   1.369  1.00 19.86           C  
-HETATM    7  C   BEN A   1      -0.600  -0.141  -0.129  1.00 19.86           C  
-HETATM    8  N1  BEN A   1      -0.430  -1.431  -0.359  1.00 19.86           N  
-HETATM    9  N2  BEN A   1      -0.767   0.660  -1.167  1.00 19.86           N  
-HETATM   10  H2  BEN A   1      -0.729  -1.582   2.050  1.00  0.00           H  
-HETATM   11  H3  BEN A   1      -1.027  -0.710   4.355  1.00  0.00           H  
-HETATM   12  H4  BEN A   1      -1.256   1.727   4.746  1.00  0.00           H  
-HETATM   13  H5  BEN A   1      -1.191   3.289   2.807  1.00  0.00           H  
-HETATM   14  H6  BEN A   1      -0.885   2.390   0.531  1.00  0.00           H  
-HETATM   15 H1 1 BEN A   1      -0.302  -1.763  -1.304  1.00  0.00           H  
-HETATM   16 H1 2 BEN A   1      -0.429  -2.085   0.411  1.00  0.00           H  
-HETATM   17  HN2 BEN A   1      -0.637   0.307  -2.104  1.00  0.00           H  
+HETATM    1  C1  BEN A   1       0.918  -1.174   0.729  1.00 19.86           C  
+HETATM    2  C2  BEN A   1       0.521  -1.960   1.777  1.00 19.86           C  
+HETATM    3  C3  BEN A   1       1.179  -3.171   2.031  1.00 19.86           C  
+HETATM    4  C4  BEN A   1       2.249  -3.579   1.219  1.00 19.86           C  
+HETATM    5  C5  BEN A   1       2.648  -2.762   0.158  1.00 19.86           C  
+HETATM    6  C6  BEN A   1       1.975  -1.565  -0.074  1.00 19.86           C  
+HETATM    7  C   BEN A   1       0.257   0.022   0.472  1.00 19.86           C  
+HETATM    8  N1  BEN A   1      -0.779   0.406   1.195  1.00 19.86           N  
+HETATM    9  N2  BEN A   1       0.764   0.882  -0.396  1.00 19.86           N  
+HETATM   10  H2  BEN A   1      -0.298  -1.647   2.407  1.00  0.00           H  
+HETATM   11  H3  BEN A   1       0.864  -3.794   2.854  1.00  0.00           H  
+HETATM   12  H4  BEN A   1       2.752  -4.514   1.417  1.00  0.00           H  
+HETATM   13  H5  BEN A   1       3.472  -3.061  -0.474  1.00  0.00           H  
+HETATM   14  H6  BEN A   1       2.291  -0.938  -0.896  1.00  0.00           H  
+HETATM   15 H1 1 BEN A   1      -1.243   1.279   0.989  1.00  0.00           H  
+HETATM   16 H1 2 BEN A   1      -1.108  -0.175   1.954  1.00  0.00           H  
+HETATM   17  HN2 BEN A   1       0.286   1.751  -0.584  1.00  0.00           H  
 CONECT    1    2    2    6    7
 CONECT    2    3   10
 CONECT    3    4    4   11

diff --git a/peleffy/data/tests/alchemical_structure.pdb b/peleffy/data/tests/alchemical_structure.pdb
@@ -17,17 +17,17 @@ HETATM   16  H8  HYB L   1      -1.108  -0.781   1.667  1.00  0.00           H
 HETATM   17  H9  HYB L   1      -0.323   0.825   1.846  1.00  0.00           H  
 HETATM   18 H10  HYB L   1       1.237   0.709  -1.316  1.00  0.00           H  
 HETATM   19 H11  HYB L   1       0.622   1.801  -0.063  1.00  0.00           H  
-HETATM   20  C6  HYB L   1      -0.779   0.348   1.160  1.00  0.00           C  
-HETATM   21  C7  HYB L   1      -0.825  -0.520   2.218  1.00  0.00           C  
-HETATM   22  C8  HYB L   1      -0.996  -0.028   3.518  1.00  0.00           C  
-HETATM   23  C9  HYB L   1      -1.127   1.352   3.741  1.00  0.00           C  
-HETATM   24 C10  HYB L   1      -1.087   2.225   2.651  1.00  0.00           C  
-HETATM   25 C11  HYB L   1      -0.914   1.710   1.369  1.00  0.00           C  
-HETATM   26 H12  HYB L   1      -0.729  -1.582   2.050  1.00  0.00           H  
-HETATM   27 H13  HYB L   1      -1.027  -0.710   4.355  1.00  0.00           H  
-HETATM   28 H14  HYB L   1      -1.256   1.727   4.746  1.00  0.00           H  
-HETATM   29 H15  HYB L   1      -1.191   3.289   2.807  1.00  0.00           H  
-HETATM   30 H16  HYB L   1      -0.885   2.390   0.531  1.00  0.00           H  
+HETATM   20  C6  HYB L   1       0.918  -1.174   0.729  1.00  0.00           C  
+HETATM   21  C7  HYB L   1       0.521  -1.960   1.777  1.00  0.00           C  
+HETATM   22  C8  HYB L   1       1.179  -3.171   2.031  1.00  0.00           C  
+HETATM   23  C9  HYB L   1       2.249  -3.579   1.219  1.00  0.00           C  
+HETATM   24 C10  HYB L   1       2.648  -2.762   0.158  1.00  0.00           C  
+HETATM   25 C11  HYB L   1       1.975  -1.565  -0.074  1.00  0.00           C  
+HETATM   26 H12  HYB L   1      -0.298  -1.647   2.407  1.00  0.00           H  
+HETATM   27 H13  HYB L   1       0.864  -3.794   2.854  1.00  0.00           H  
+HETATM   28 H14  HYB L   1       2.752  -4.514   1.417  1.00  0.00           H  
+HETATM   29 H15  HYB L   1       3.472  -3.061  -0.474  1.00  0.00           H  
+HETATM   30 H16  HYB L   1       2.291  -0.938  -0.896  1.00  0.00           H  
 CONECT    1    2    9   10   11
 CONECT    2    3    4    5   20
 CONECT    3   12   13   14

diff --git a/peleffy/forcefield/selectors.py b/peleffy/forcefield/selectors.py
@@ -12,7 +12,8 @@ class ForceFieldSelector(object):
     It defines a force field selector.
     """
     _FF_TYPES = {'OPLS2005': ('OPLS2005', ),
-                 'OpenFF': ('openff_unconstrained-2.0.0.offxml',
+                 'OpenFF': ('openff_unconstrained-2.1.0.offxml',
+                            'openff_unconstrained-2.0.0.offxml',
                             'openff_unconstrained-1.3.0.offxml',
                             'openff_unconstrained-1.2.1.offxml',
                             'openff_unconstrained-1.2.0.offxml',