Peleffy

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This minor release introduces improvements to the parameterization API of peleffy. It also integrates the parameterization of OBC radii and scale factors required by the OPLS2005 implementation of PELE. It also improves the initialization of the Molecule class with a PDB checking and fixer and taking RDKit and OpenFF molecular representations as input. It also adds support for the new openff-1.3.0. Besides, it fixes a serious bug in the atom ordering of the Impact template that affected PELE's side chain prediction algorithm.

New features
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- `PR 86 <https://github.com/martimunicoy/peleffy/pull/86>`_: New method to check the input PDB prior building the molecule.
- `PR 88 <https://github.com/martimunicoy/peleffy/pull/88>`_: New method to retrieve atom degrees with RDKit.
- `PR 90 <https://github.com/martimunicoy/peleffy/pull/90>`_: Add support for openff-1.3.0.
- `PR 92 <https://github.com/martimunicoy/peleffy/pull/92>`_: New parameter to skip the stereochemistry assignment (and the checking from the OpenFF toolkit).
- `PR 94 <https://github.com/martimunicoy/peleffy/pull/94>`_: New method for the OPLS OBC parameters.
- `PR 100 <https://github.com/martimunicoy/peleffy/pull/100>`_: New writer for the OPLS OBC parameters.
- `PR 106 <https://github.com/martimunicoy/peleffy/pull/106>`_: New method to initialize a Molecule object directly from an RDKit and OpenFF molecular representations.
- `PR 112 <https://github.com/martimunicoy/peleffy/pull/112>`_: New method to fix an input PDB file with no atomic element identifiers.

Bugfixes
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- `PR 107 <https://github.com/martimunicoy/peleffy/pull/107>`_: A bad ordering of the atoms in the Impact template generated by peleffy is now fixed.
- `PR 115 <https://github.com/martimunicoy/peleffy/pull/115>`_: The rotamer library writer now writes molecule's tag not its name, as expected.

API-breaking changes
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- `PR 94 <https://github.com/martimunicoy/peleffy/pull/94>`_: Methods to write to a file are given a unique standard name, to_file(), to simplify the API.
- `PR 97 <https://github.com/martimunicoy/peleffy/pull/97>`_: The parameterization API changes and a new Topology class is used as a container for all the topological elements.
- `PR 103 <https://github.com/martimunicoy/peleffy/pull/103>`_: The OpenFF output of PELE changes from DataLocal/Templates/OFF/Parsley/HeteroAtoms/ to DataLocal/Templates/OpenFF/Parsley/.

Tests added
"""""""""""
- `PR 88 <https://github.com/martimunicoy/peleffy/pull/88>`_: Adds tests to validate the atom degrees getter.
- `PR 86 <https://github.com/martimunicoy/peleffy/pull/86>`_: Adds tests to validate the PDB check up.
- `PR 90 <https://github.com/martimunicoy/peleffy/pull/90>`_: General validation of supported force fields.
- `PR 92 <https://github.com/martimunicoy/peleffy/pull/92>`_: New test to check the behaviour of the allow_undefined_stereo parameter.
- `PR 94 <https://github.com/martimunicoy/peleffy/pull/94>`_: Adds tests to validate the OPLS OBC parameters generator.
- `PR 97 <https://github.com/martimunicoy/peleffy/pull/97>`_: Includes tests for the new Topology container class.
- `PR 100 <https://github.com/martimunicoy/peleffy/pull/100>`_: Adds tests to validate the solvent template writers.
- `PR 106 <https://github.com/martimunicoy/peleffy/pull/106>`_: Adds tests to check the RDKit and OpenFF molecular initializers.
- `PR 112 <https://github.com/martimunicoy/peleffy/pull/112>`_: Adds one test to check the new PDB fixer method.

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This major release renames the package to peleffy as it now supports both OpenFF and OPLS2005 force fields. Therefore, this release extends the compatibility of peleffy to fully handle OPLS2005 parameters. Some unsupported OpenFF dihedrals now can be handled. Besides, it includes a functionality to generate rotamer libraries with core constraints to allow the user to force an atom to be in the core.

New features
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- `PR 56 <https://github.com/martimunicoy/peleffy/pull/56>`_: Dynamic output path handler.
- `PR 62 <https://github.com/martimunicoy/peleffy/pull/62>`_: New functionality to generate rotamer libraries forcing an atom to be in the core.
- `PR 63 <https://github.com/martimunicoy/peleffy/pull/63>`_: Enhancements to the core constraints to allow the selection of multiple core atoms.
- `PR 66 <https://github.com/martimunicoy/peleffy/pull/66>`_: Full compatibility with OpenFF dihedrals.
- `PR 69 <https://github.com/martimunicoy/peleffy/pull/69>`_: Full compatibility with OPLS2005 force field.
- `PR 85 <https://github.com/martimunicoy/peleffy/pull/85>`_: Package is renamed to peleffy.

Bugfixes
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- `PR 74 <https://github.com/martimunicoy/peleffy/pull/74>`_: Corrects wrong assignment of PDB atom names when using the OPLS2005 force field.
- `PR 79 <https://github.com/martimunicoy/peleffy/pull/79>`_: Corrects error with missing modules in the Conda installation.
- `PR 82 <https://github.com/martimunicoy/peleffy/pull/82>`_: Corrects a bug that caused some important propers obtained with OPLS2005 to be missing.
- `PR 84 <https://github.com/martimunicoy/peleffy/pull/84>`_: Corrects a bug that caused unparameterized Molecules to be undetected.

Tests added
"""""""""""
- `PR 56 <https://github.com/martimunicoy/peleffy/pull/56>`_: Adds tests to validate the new output path handler.
- `PR 62 <https://github.com/martimunicoy/peleffy/pull/62>`_: Adds tests to validate the new rotamer library with core constraints.
- `PR 63 <https://github.com/martimunicoy/peleffy/pull/63>`_: More tests are added to validate the new rotamer library with core constraints.
- `PR 66 <https://github.com/martimunicoy/peleffy/pull/66>`_: Adds tests to validate the handling of non standard dihedrals.
- `PR 69 <https://github.com/martimunicoy/peleffy/pull/69>`_: Adds tests to validate the integration of OPLS2005 force field.
- `PR 70 <https://github.com/martimunicoy/peleffy/pull/70>`_: Adds tests to validate main CLI.
- `PR 84 <https://github.com/martimunicoy/peleffy/pull/840>`_: Adds tests to validate the Impact class.

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This is a micro release that includes general bug fixes and stability improvements. It is still a preliminary version of the Open Force Field to PELE package which is under development.

New features
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- `PR 52 <https://github.com/martimunicoy/peleffy/pull/52>`_: Molecule connectivity can be assigned from an RDKit molecular template when loading it from a PDB file without connectivity.
- `PR 55 <https://github.com/martimunicoy/peleffy/pull/55>`_: Standard output prints follow the logging hierarchy and can be modified by the user.
- `PR 59 <https://github.com/martimunicoy/peleffy/pull/59>`_: Set alternative conformers to the peleffy's molecule representation.

Bugfixes
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- `PR 48 <https://github.com/martimunicoy/peleffy/pull/48>`_: Fixes CLI's default output paths.
- `PR 58 <https://github.com/martimunicoy/peleffy/pull/58>`_: Fixes unconsistencies between PDB residue name and molecule tag.

Tests added
"""""""""""
- `PR 48 <https://github.com/martimunicoy/peleffy/pull/48>`_: Adds tests to validate the assignment of the default output paths.
- `PR 52 <https://github.com/martimunicoy/peleffy/pull/52>`_: Adds tests to validate the initialization using a connectivity template.
- `PR 55 <https://github.com/martimunicoy/peleffy/pull/55>`_: Adds tests for the new Logger class.
- `PR 58 <https://github.com/martimunicoy/peleffy/pull/58>`_: Adds tests to validate consistency between PDB residue name and molecule tag.
- `PR 59 <https://github.com/martimunicoy/peleffy/pull/59>`_: Adds tests for the new conformer setter.

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This is a minor release that includes a refactoring of the classes and methods that involve the rotamer library builder. Besides, now it is possible to combine parameters from OPLS2005 and OFF. This release also contains a new method to define a molecule through a SMILES tag. It is still a preliminary version of the Open Force Field to PELE package which is under development.

New features
""""""""""""
- `PR 28 <https://github.com/martimunicoy/peleffy/pull/28>`_: Adds a new method to define a `Molecule` object through a SMILES tag. This molecule can be written as a PDB file later for PELE.
- `PR 31 <https://github.com/martimunicoy/peleffy/pull/31>`_: Adds the possibility to combine nonbonding and solvent parameters from OPLS2005 with bonding parameters from OFF.
- `PR 36 <https://github.com/martimunicoy/peleffy/pull/36>`_: Minor changes to improve the quality of the code.
- `PR 38 <https://github.com/martimunicoy/peleffy/pull/38>`_: Adds a new partial charge calculator that uses OPLS2005 to assign partial charges. Includes new flags in the CLI from main.py to combine bonding and nonbonding parameters and partial charges from OPLS2005.
- `PR 42 <https://github.com/martimunicoy/peleffy/pull/42>`_: Improves the documentation, adding a section specific for CLI-usage and API examples.
- `PR 46 <https://github.com/martimunicoy/peleffy/pull/46>`_: Adds a tag to Molecule class. Besides, the handling of Molecule names is improved. Both attributes can be set when initiating the molecule.

Bugfixes
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- `PR 22 <https://github.com/martimunicoy/peleffy/pull/22>`_: Fixes many bugs. For example, the default output name of the solvent parameters template is changed to `ligandParams.txt`, which is the name that PELE expects.
- `PR 32 <https://github.com/martimunicoy/peleffy/pull/32>`_: Minor fixes in ToolkitWrapper classes.
- `PR 34 <https://github.com/martimunicoy/peleffy/pull/34>`_: Improves the translation of dihedrals coming from the Open Force Fielf Toolkit and corrects the lack of exclusions in PELE 1-4 list that result from Impact's dihedral definitions.
- `PR 46 <https://github.com/martimunicoy/peleffy/pull/46>`_: Prevents molecule to be untagged when loading it from a SMILES tag.

Tests added
"""""""""""
- `PR 31 <https://github.com/martimunicoy/peleffy/pull/31>`_: Adds tests to validate some functions of the new SchrodingerToolkitWrapper.
- `PR 34 <https://github.com/martimunicoy/peleffy/pull/34>`_: Adds tests to further validate the assignment of parameters from the Open Force Field Toolkit.
- `PR 38 <https://github.com/martimunicoy/peleffy/pull/38>`_: Adds tests to validate the new OPLS charge calculator.
- `PR 46 <https://github.com/martimunicoy/peleffy/pull/46>`_: Adds tests to validate the name and tag assignment to Molecule class.

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This is a micro release that includes new features and parameters to configurate the behaviour of the program.
It is designed to be employed to run the first benchmarks of the implementation in PELE.
It also includes many stability improvements and an extended test coverage.

New features
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- `PR 15 <https://github.com/martimunicoy/peleffy/pull/15>`_: Adds a new method (Antechamber's gasteiger) to calculate partial charges.
- `PR 19 <https://github.com/martimunicoy/peleffy/pull/19>`_: Adds a new option to ignore terminal rotatable bonds of each rotamer's branch.
- `PR 17 <https://github.com/martimunicoy/peleffy/pull/17>`_: Adds and updates the documentation. However, it is still not completed.

Bugfixes
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- `PR 18 <https://github.com/martimunicoy/peleffy/pull/18>`_: Fixes some problems with proper and improper constructors.

Tests added
"""""""""""
- `PR 15 <https://github.com/martimunicoy/peleffy/pull/15>`_: Adds tests ensuring that the run_peleffy call from main and the partial charge calculators work as expected.
- `PR 19 <https://github.com/martimunicoy/peleffy/pull/19>`_: Adds tests to validate the construction of the `RotamerLibrary` class and the filtering of terminal rotatable bonds.

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This is a preliminary version of the Open Force Field to PELE package.

New features
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A first implementation of the package that allows to:

- Build a rotamer library for a small molecule using RDKit's API
- Build a template with the Molecular Mechanics' parameters for a small molecule using the Open Force Field Toolkit
- Assign the OBC implicit solvent parameters to a small molecule using the Open Force Field Toolkit