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offpele v0.3.0 - Rotamers, OPLS2005, SMILES and stability improvements
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@martimunicoy martimunicoy released this 03 Sep 22:19
· 611 commits to master since this release
v0.3.0
3a94344

v0.3.0 - Rotamers, OPLS2005, SMILES and stability improvements

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: 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: Adds the possibility to combine nonbonding and solvent parameters from OPLS2005 with bonding parameters from OFF.
  • PR #36: Minor changes to improve the quality of the code.
  • PR #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: Improves the documentation, adding a section specific for CLI-usage and API examples.
  • PR #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

  • PR #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: Minor fixes in ToolkitWrapper classes.
  • PR #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: Prevents molecule to be untagged when loading it from a SMILES tag.

Tests added

  • PR #31: Adds tests to validate some functions of the new SchrodingerToolkitWrapper.
  • PR #34: Adds tests to further validate the assignment of parameters from the Open Force Field Toolkit.
  • PR #38: Adds tests to validate the new OPLS charge calculator.
  • PR #46: Adds tests to validate the name and tag assignment to Molecule class.
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