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@martimunicoy
martimunicoy committed Feb 12, 2024
2 parents d952ec0 + c48012c commit b34fae9
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2 changes: 1 addition & 1 deletion .github/workflows/conda.yml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion .github/workflows/master.yml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion .github/workflows/test.yml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion README.md
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@@ -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/) |
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4 changes: 3 additions & 1 deletion devtools/conda/meta.yaml
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Expand Up @@ -10,6 +10,7 @@ source:
build:
script: python -m pip install . --no-deps
number: 0
noarch: python

requirements:
build:
Expand All @@ -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
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6 changes: 4 additions & 2 deletions devtools/envs/standard.yaml
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Expand Up @@ -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

2 changes: 2 additions & 0 deletions docs/index.rst
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Expand Up @@ -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
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28 changes: 28 additions & 0 deletions docs/releasehistory.rst
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Expand Up @@ -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
-------------------------------------------------------------

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40 changes: 20 additions & 20 deletions peleffy/data/tests/alchemical_ligandParams_1.txt
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Expand Up @@ -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,
Expand All @@ -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,
Expand All @@ -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,
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40 changes: 20 additions & 20 deletions peleffy/data/tests/alchemical_ligandParams_2.txt
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Expand Up @@ -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,
Expand All @@ -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,
Expand All @@ -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,
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34 changes: 17 additions & 17 deletions peleffy/data/tests/alchemical_mol2.pdb
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@@ -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
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22 changes: 11 additions & 11 deletions peleffy/data/tests/alchemical_structure.pdb
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Expand Up @@ -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
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3 changes: 2 additions & 1 deletion peleffy/forcefield/selectors.py
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Expand Up @@ -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',
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