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Foyer 0.5.0
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@summeraz summeraz released this 20 Aug 21:51
0.5.0
71fd9d6

Features

  • Bond, angles, and dihedral parameters are now assigned based on definition specificity. Specificity is determined by the number “type” attributes (as opposed to “class” attributes) in a bond, angle, or dihedral definition. (#160)
    • This updates the previous behavior which assigned parameters based on the first matching definition regardless of specificity.
  • Foyer now performs sanity checks for parameterization of angles, dihedrals, and impropers in a system. (#155)
    • By default, an error will be raised if parameters are not assigned to all angles and dihedrals in a system, and a warning will be raised if parameters are not assigned to all impropers in a system.
      • The user can toggle these checks to raise warnings or errors as desired.
    • Note that an error for non-parameterized bonds should already be raised by OpenMM.
  • Residue-based atom-typing is now optional, though turned on by default. (#159)
    • This can be toggled through use of the use_residue_map argument to Forcefield.apply
    • See #138 for more details
  • Multiple DOIs can now be assigned to a single atom type definition. (#168)
  • Miscellaneous refactorization and syntax changes
    • Atom-typing has been moved into a separate function: Forcefield.run_atomtyping. (#159)
    • The language in error messages and within the underlying code has been modified to refer to generic atom types as opposed to OPLS-specific types. (#154)

Bug Fixes

  • Fixed bug with atom-typing of polycyclic molecules (#171)
    • Our previous ring identification algorithm did not properly assign ring membership for all atoms within certain polycyclic molecules.
    • A new algorithm for assigning ring membership has been implemented that resolves this issue.
  • Residue-based atom-typing no longer raises an error for systems containing singular atoms. (#151)
    • With the addition of the residue map (#138) to speed up atom-typing of non-unique molecules in the system, systems featuring singular atoms would cause an error to be raised due to a lack of bonded partners.
    • This issue has been resolved, and systems featuring singular atoms can now be properly atom-typed using residue-based atom-typing.
  • Spaces can now be included when defining multiple atom types within an overrides attribute. (#181)
    • Previously multiple atom type names could be listed within a single overrides attribute for an atom type definition in a force field XML file, but these had to be separated by a comma only and no space.
      • e.g. Foyer would process a definition containing overrides="opls_1, opls_2" as only overriding opls_1 due to the space between the two atom type names after the comma.
    • Whitespace is now properly stripped from the overrides strings.
    • A comma separated list of overrides is still expected; however, whitespace between each override will no longer cause unexpected behavior.
  • Travis CI bug fixes (#152)
    • Multiple issues with Travis CI, Ruby, and MacOS when setting up the testing environment with Miniconda.
    • These issues have been resolved.

Documentation

  • DOIs have been added for most OPLS atom types that have SMARTS strings. Future SMARTS additions will require a corresponding DOI tag for merging (#158)
    • Sources, when found, were added to the atom type definitions in the OPLS force field XML through addition of a doi attribute.
    • DOI sources could not be located for the following atom types:
      • Alpha carbons in alkyl pyrroles (opls_678 and opls_679)
      • Carbon atoms in cyclopropanes (opls_711, opls_712, opls_713)
      • Carbon, oxygen, and hydrogen atoms in propylene carbonates (opls_771 – opls_779)
      • Carbon and hydrogen atoms in alkynes (opls_925 – opls_930)
    • References corresponding to these DOIs can be obtained in BibTeX format for systems atom-typed using the OPLS force field by providing a references_file argument to Forcefield.apply.
  • The Foyer web page is now live at http://mosdef-hub.github.io/foyer (#162, #175, #178)
    • This website follows the same readthedocs theme as the mBuild package.
    • We are currently experiencing issues with the stylesheet, so the website is not properly rendered. This issue should be resolved soon.
  • Our documentation now includes a section on supported parameter definitions within a force field XML. (#160)
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