Peleffy

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This is a micro release of peleffy that contains corrections for alchemistry module. A new charge calculator
called Mulliken is also available.

New features
""""""""""""
- `PR 174 <https://github.com/martimunicoy/peleffy/pull/174>`_: minor fix in the logger to prevent conflicts with external loggers
- `PR 176 <https://github.com/martimunicoy/peleffy/pull/176>`_: new charge calculator called Mulliken
- `PR 177 <https://github.com/martimunicoy/peleffy/pull/177>`_: new method to save alchemical mapping as a PNG file

Bugfixes
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- `PR 177 <https://github.com/martimunicoy/peleffy/pull/177>`_: bug fixes for alchemical solvent templates and affected tests

Tests added
"""""""""""
- `PR 176 <https://github.com/martimunicoy/peleffy/pull/176>`_: new tests to validate the new charge calculator

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This is a micro release of peleffy that contains minor improvements for the CLI interface and the usage of the ffld_server.

New features
""""""""""""
- `PR 171 <https://github.com/martimunicoy/peleffy/pull/171>`_: improvements for the CLI interface. Also, ffld_server will not raise an exception but any warning or error found will be raised by peleffy's logger

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This is a micro release of peleffy that fixes several bugs related with latest versions of RDKit and Schrodinger. Affected modules are rotamer libraries, the runner and parser of the ffld server, and the alchemistry package. It also adds some minor improvements to log handlers.

New features
""""""""""""
- `PR 166 <https://github.com/martimunicoy/peleffy/pull/166>`_: New options for log handlers.

Bugfixes
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- `PR 167 <https://github.com/martimunicoy/peleffy/pull/167>`_: Bug fixes for rotamer libraries and affected tests
- `PR 168 <https://github.com/martimunicoy/peleffy/pull/168>`_: Compatibility changes for the ffld server shipped with latest Schrodinger version
- `PR 169 <https://github.com/martimunicoy/peleffy/pull/169>`_: Support new RDKit versions.

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This is a micro release of peleffy that fixes a bug that affected heteromolecules extraction.

Bugfixes
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- `PR 163 <https://github.com/martimunicoy/peleffy/pull/163>`_: Fix problem when extracting heteromolecules from a specific chain

Tests added
"""""""""""
- `PR 163 <https://github.com/martimunicoy/peleffy/pull/163>`_: Adds a test to validate heteromolecule extraction

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This is a minor release of peleffy that adds a new module to generate alchemical templates. It also adds support for AMBER's implementation in PELE.

New features
""""""""""""
- `PR 154 <https://github.com/martimunicoy/peleffy/pull/154>`_: Introduces Alchemizer module to generate hybrid topologies
- `PR 155 <https://github.com/martimunicoy/peleffy/pull/155>`_: Adds support for PELE's AMBER with a new Impact template
- `PR 162 <https://github.com/martimunicoy/peleffy/pull/162>`_: Upgrade to openff-toolkit 0.10.1

Bugfixes
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- `PR 158 <https://github.com/martimunicoy/peleffy/pull/158>`_: Fix minor bug when using the --chain flag and introduces checks for the input PDB in the peleffy.main module
- `PR 159 <https://github.com/martimunicoy/peleffy/pull/159>`_: Fix issues with long atom numbers and heteromolecules extraction

Tests added
"""""""""""
- `PR 154 <https://github.com/martimunicoy/peleffy/pull/154>`_: Adds a collection of tests for Alchemizer module
- `PR 155 <https://github.com/martimunicoy/peleffy/pull/155>`_: Extends the tests for utils module and introduces new tests for the new AMBER-compatible Impact template
- `PR 158 <https://github.com/martimunicoy/peleffy/pull/158>`_: Extends the tests for the new checks in the peleffy.main module

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This is a micro release of peleffy that adds support for the new openff-2.0.0. It also solves minor bugs in the OPLS2005 parametrization.

New features
""""""""""""
- `PR 151 <https://github.com/martimunicoy/peleffy/pull/151>`_: Add support for openff-2.0.0.

Bugfixes
""""""""
- `PR 149 <https://github.com/martimunicoy/peleffy/pull/149>`_: Minor error when parsing ffld output file.
- `PR 153 <https://github.com/martimunicoy/peleffy/pull/153>`_: Fix parameters inconsistencies.