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Release version 1.5.0 #182

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merged 10 commits into from
Feb 12, 2024
Merged

Release version 1.5.0 #182

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74ce952
Improve alchemical mapping
martimunicoy Jan 13, 2024
692ebfd
Add missing import
martimunicoy Jan 13, 2024
36367de
Implement vdw1 and vdw2 lambdas
martimunicoy Feb 12, 2024
cd575e0
Fix mapper tests
martimunicoy Feb 12, 2024
366b767
Upgrade to openff 0.10.7
martimunicoy Feb 12, 2024
97fab63
Remove openff_unconstrained-2.1.1.offxml from available FF list
martimunicoy Feb 12, 2024
b04991a
Downgrade openff-forcefields to 2023.05.1
martimunicoy Feb 12, 2024
29ab7fe
Update README.md
martimunicoy Feb 12, 2024
c464422
Update release version
martimunicoy Feb 12, 2024
2beed37
Merge branch 'devel' of github.com:martimunicoy/peleffy into devel
martimunicoy Feb 12, 2024
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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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3 changes: 2 additions & 1 deletion devtools/conda/meta.yaml
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Expand Up @@ -26,7 +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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18 changes: 18 additions & 0 deletions docs/releasehistory.rst
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Expand Up @@ -8,6 +8,24 @@ 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
-----------------------------------

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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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