Peleffy

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This is a micro release of peleffy that includes support for the new OpenFF flag to manage explicit and implicit hydrogen atoms.

New features
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- `PR 146 <https://github.com/martimunicoy/peleffy/pull/146>`_: Adds support for the new explicit hydrogens flag

Tests added
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- `PR 146 <https://github.com/martimunicoy/peleffy/pull/146>`_: New test to check new explicit hydrogens flag

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This is a micro release of peleffy that includes a migration to openff.toolkit to support future releases.

New features
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- `PR 144 <https://github.com/martimunicoy/peleffy/pull/144>`_: Migrated openforcefield imports to openff.toolkit

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This is a micro release of peleffy that includes minor adjustments for the PELE Platform and other small fixes.

New features
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- `PR 142 <https://github.com/martimunicoy/peleffy/pull/142>`_: Minor adjustments to facilitate platform compatibility.

Bugfixes
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- `PR 143 <https://github.com/martimunicoy/peleffy/pull/143>`_: Minor error when parsing Impact templates.

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This is a minor release of peleffy that includes a new method to read ligand conformations from the BCE server and prepare the input files for PELE. It also contains a new PDBFile class that allows the user to automatically load all the heteromolecules from a PDB file.

New features
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- `PR 135 <https://github.com/martimunicoy/peleffy/pull/135>`_: New class to load conformations from the BCE server (Bioactive Conformational Ensemble) and generate the required input files for PELE.
- `PR 137 <https://github.com/martimunicoy/peleffy/pull/137>`_: New PDB class that allows to handle an input PDB file with multiple heteromolecules.

Tests added
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- `PR 135 <https://github.com/martimunicoy/peleffy/pull/135>`_: Adds tests to validate the new BCEConformations class.
- `PR 137 <https://github.com/martimunicoy/peleffy/pull/137>`_: Adds tests to validate the new PDBFile class.

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This is a micro release of peleffy that includes and new method to load parameters from a JSON file and solves different bugs in the documentation and the OPLS parametrization.

New features
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- `PR 131 <https://github.com/martimunicoy/peleffy/pull/131>`_: New method to load parameters from a JSON file.

Tests added
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- `PR 131 <https://github.com/martimunicoy/peleffy/pull/131>`_: Adds tests to validate the new method to load parameters from a JSON file.

Bugfixes
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- `PR 129 <https://github.com/martimunicoy/peleffy/pull/129>`_: Some format errors in the API documentation are fixed. Links to the PELE documentation are updated.
- `PR 134 <https://github.com/martimunicoy/peleffy/pull/134>`_: Fixes bug when parsing the parameters of the ligand when OPLS is used to parameterize.

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This is a minor release of peleffy that includes new useful tools to handle parameters and their templates more easily. It also supports the newest version of the OpenForceField toolkit, which is 0.8.3.

New features
""""""""""""
- `PR 117 <https://github.com/martimunicoy/peleffy/pull/117>`_: New method to assign external partial charges.
- `PR 118 <https://github.com/martimunicoy/peleffy/pull/118>`_: New method to load parameters from an Impact Template.
- `PR 119 <https://github.com/martimunicoy/peleffy/pull/119>`_: Adds explanatory error message when using an invalid Impact Template in the from_impact_template method.
- `PR 119 <https://github.com/martimunicoy/peleffy/pull/119>`_: Supports Openforcefield-0.8.3 .
- `PR 126 <https://github.com/martimunicoy/peleffy/pull/126>`_: Allows the Solvent class to be compatible with multiple topologies.

Bugfixes
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- `PR 125 <https://github.com/martimunicoy/peleffy/pull/125>`_: A bad index slicing in the molecule.Molecule._pdb_checkup() is now fixed.

Tests added
"""""""""""
- `PR 117 <https://github.com/martimunicoy/peleffy/pull/117>`_: Adds tests to validate the MAE parse for external partial charges.
- `PR 118 <https://github.com/martimunicoy/peleffy/pull/118>`_: Adds tests to validate the new method to load parameters from an Impact Template.
- `PR 119 <https://github.com/martimunicoy/peleffy/pull/119>`_: Adds tests for the new error message when using an invalid Impact Template in the from_impact_template method.
- `PR 126 <https://github.com/martimunicoy/peleffy/pull/126>`_: Adds tests for the new compatibility of the Solvent class with multiple topologies.