Changes conda host channel to mdtools (#34)

* Added RDKit as dependency

* Initial implementation of VolumeOverlap CV

* Changes conda host channel to mdtools

* Revert "Initial implementation of VolumeOverlap CV"

This reverts commit 5726164.

* Revert "Added RDKit as dependency"

This reverts commit 12bbdc9.

* Fixed atomic_function doctest

.github/workflows/Anaconda.yaml

@@ -47,8 +47,8 @@ jobs:
           export CVPACK_VERSION=${{ github.ref_name }}
           conda mambabuild . --no-anaconda-upload -c conda-forge --output-folder $outdir
           echo "::endgroup::"
-          echo "::group::Uploading package to redesign-science conda channel"
+          echo "::group::Uploading package to mdtools conda channel"
           PACKAGE=$(find $outdir -name *.tar.bz2 | head -1)
           export ANACONDA_API_TOKEN=${{ secrets.ANACONDA_TOKEN }}
-          anaconda upload --user redesign-science --force --label main $PACKAGE
+          anaconda upload --user mdtools --force --label main $PACKAGE
           echo "::endgroup::"

README.md

@@ -9,9 +9,9 @@ Collective Variable Package
 [![Documentation Status](https://github.com/RedesignScience/cvpack/workflows/Docs/badge.svg)](https://github.com/RedesignScience/cvpack/actions?query=workflow%3ADocs)
 [![Coverage Report](https://redesignscience.github.io/cvpack/coverage/coverage.svg)](https://redesignscience.github.io/cvpack/coverage)
 
-[![Conda cvpack version](https://img.shields.io/conda/v/redesign-science/cvpack.svg)](https://anaconda.org/redesign-science/cvpack)
-[![Conda cvpack platforms](https://img.shields.io/conda/pn/redesign-science/cvpack.svg)](https://anaconda.org/redesign-science/cvpack)
-[![Conda cvpack downloads](https://img.shields.io/conda/dn/redesign-science/cvpack.svg)](https://anaconda.org/redesign-science/cvpack)
+[![Conda cvpack version](https://img.shields.io/conda/v/mdtools/cvpack.svg)](https://anaconda.org/mdtools/cvpack)
+[![Conda cvpack platforms](https://img.shields.io/conda/pn/mdtools/cvpack.svg)](https://anaconda.org/mdtools/cvpack)
+[![Conda cvpack downloads](https://img.shields.io/conda/dn/mdtools/cvpack.svg)](https://anaconda.org/mdtools/cvpack)
 
 [![License](https://img.shields.io/badge/License-MIT-yellowgreen.svg?style=flat)](https://github.com/RedesignScience/cvpack/blob/main/LICENSE.md)
 [![Twitter](https://badgen.net/badge/follow%20us/@RedesignScience?icon=twitter)](https://twitter.com/RedesignScience)
@@ -54,16 +54,16 @@ The CVs implemented in CVPack are listed in the table below.
 ### Installation and Usage
 
 CVPack is available as a conda package on the
-[redesign-science](https://anaconda.org/redesign-science/cvpack) channel. To install it, simply run:
+[mdtools](https://anaconda.org/mdtools/cvpack) channel. To install it, run:
 
 ```bash
-    conda install -c conda-forge -c redesign-science cvpack
+    conda install -c conda-forge -c mdtools cvpack
 ```
 
-Or, if you prefer to use [mamba](https://mamba.readthedocs.io/en/latest) instead of conda:
+Or:
 
 ```bash
-    mamba install -c conda-forge -c redesign-science cvpack
+    mamba install -c mdtools cvpack
 ```
 
 To use CVPack in your own Python script or Jupyter notebook, simply import it as follows:

cvpack/atomic_function.py

@@ -298,8 +298,8 @@ def fromOpenMMForce(
         Examples
         --------
         >>> import cvpack
+        >>> import numpy as np
         >>> import openmm
-        >>> from collections import deque
         >>> from cvpack import unit
         >>> from openmm import app
         >>> from openmmtools import testsystems
@@ -312,13 +312,15 @@ def fromOpenMMForce(
         >>> mean_x = openmm.CustomExternalForce("x/num_atoms")
         >>> mean_x.addGlobalParameter("num_atoms", num_atoms)
         0
-        >>> deque(map(mean_x.addParticle, range(num_atoms), [[]] * num_atoms), maxlen=0)
-        deque([], maxlen=0)
+        >>> for i in range(num_atoms):
+        ...     _ = mean_x.addParticle(i, [])
         >>> model.system.addForce(mean_x)
         7
         >>> forces = {force.getName(): force for force in model.system.getForces()}
         >>> copies = {
-        ...     name: cvpack.AtomicFunction.fromOpenMMForce(force, unit.kilojoules_per_mole)
+        ...     name: cvpack.AtomicFunction.fromOpenMMForce(
+        ...         force, unit.kilojoules_per_mole
+        ...     )
         ...     for name, force in forces.items()
         ...     if name in [
         ...         "HarmonicBondForce",
@@ -330,18 +332,20 @@ def fromOpenMMForce(
         >>> copies["HelixTorsionContent"] = cvpack.AtomicFunction.fromOpenMMForce(
         ...     helix_content, unit.dimensionless
         ... )
-        >>> [model.system.addForce(force) for force in copies.values()]
-        [8, 9, 10, 11, 12]
+        >>> indices = {}
+        >>> for index, (name, force) in enumerate(copies.items(), start=1):
+        ...     _ = model.system.addForce(force)
+        ...     force.setForceGroup(index)
+        ...     indices[name] = index
         >>> platform = openmm.Platform.getPlatformByName('Reference')
         >>> integrator = openmm.VerletIntegrator(0)
         >>> context = openmm.Context(model.system, integrator, platform)
         >>> context.setPositions(model.positions)
-        >>> for name, force in copies.items():
-        ...    forces[name].setForceGroup(1)
-        ...    state = context.getState(getEnergy=True, groups={1})
-        ...    value = state.getPotentialEnergy().value_in_unit(unit.kilojoules_per_mole)
-        ...    print(f"{name}: original={value:.6f}, copy={force.getValue(context, digits=6)}")
-        ...    forces[name].setForceGroup(0)
+        >>> for name in copies:
+        ...    state = context.getState(getEnergy=True, groups={indices[name]})
+        ...    value = state.getPotentialEnergy() / unit.kilojoules_per_mole
+        ...    copy_value = copies[name].getValue(context, digits=6)
+        ...    print(f"{name}: original={value:.6f}, copy={copy_value}")
         HarmonicBondForce: original=2094.312483, copy=2094.312 kJ/mol
         HarmonicAngleForce: original=3239.795215, copy=3239.795 kJ/mol
         PeriodicTorsionForce: original=4226.051934, copy=4226.052 kJ/mol

docs/getting_started.rst

@@ -18,11 +18,11 @@ Installation
 
 To install CVPack in a conda environment, run the following command::
 
-    conda install -c conda-forge -c redesign-science cvpack
+    conda install -c conda-forge -c mdtools cvpack
 
 Or use mamba instead::
 
-    mamba install -c conda-forge -c redesign-science cvpack
+    mamba install -c mdtools cvpack
 
 Usage
 -----