v0.7.4: Bugfixes and feature extension

Featured in this release:

• A critical bugfix to the amberparser, related to fixed-width parsing of parm.dat files.
• Critical fixes to the travis build pipeline
• An extension of the forcefield_generators to make normalizing molecules optional.

Service release

This is a bugfix maintenance release featuring the following changes:

• Add option to use alternate leaprc to run_tleap
• Allow option to skip checking force parameters of impropers.
• Add additional debug info to system checker for harmonic angles

0.7.2

Updates to system comparison tools.

v0.7.1

Updates to forcefield generators.

v0.7.0

This release adds:

• New module forcefield_generators.py with OpenMM ForceField residue template generator functions to parametrize small molecules with GAFF/AM1-BCC.
• New module schrodinger.py with wrapper functions for several Schrodinger's command line tools.
• Various fixes.
• Support for Python 3.5. Python 3.3 is no longer supported.

v0.6.9

Adding a variety of new functionality and refinements, including:

• build_mixture_prmtop now by default assumes water is intended to be TIP3P, though flexible GAFF water can still be obtained by providing an optional argument, as can other three-point water models
• Removing some AMBER and GROMACS limitations on filenames
• Updating openeye.get_charges to apply the charges to the provided conformer rather than obliterating it
• Bugfixes
• Fixes for Windows

v0.6.8

This version is compatible with ParmEd 2.0, which is utilized by utils. Additionally, in this release a substantial number of functions in gromacs are significantly simplified using ParmEd. A new amber_to_gromacs functionality is also provided in utils, using ParmEd for conversion. This functionality is also tested via energy evaluations (using OpenMM). Older AMBER to GROMACS conversion using convert_via_acpype in utils is now deprecated.

It is worth noting that some ParmEd functionality requires OpenMM 6.3, which is not yet released, though it can be conda installed using conda install openmm-dev

v0.6.7

Add first-draft support for conversions to GROMACS topologies/coordinates, solvation in GROMACS, merging of GROMACS topology files in the gromacs module. Tests for GROMACS. Additionally, moves AMBER-related functionality from utils to amber, with skeletons left in utils for backwards compatibility.

v0.6.6

Fixes to allow handling of construction of binary (and higher order) mixtures with tleap; implementing of acpype conversion to GROMACS format; adding tool for assigning checkmol functional group descriptors to compounds. Some fixes to documentation strings and test descriptors.

v0.6.5

Name has been changed from gaff2xml to openmoltools.