Issues and History/Change Log¶

Known Issues - To-do List¶

Planned features/fixes (short-term)¶

(Fixed in v1.1.0.hf1) gRINN fails to process GROMACS-generated TPR files in which no chain ID is present. This appears to be the case where only a single protein chain is included. This will be fixed in the next version.
gRINN log file will include parameters used when calling gRINN.
(Fixed in v1.1.0.hf1) gRINN fails to display IEMs and RCs for proteins with less than 100 amino acids. This will be fixed in the next version.
gRINN will let the user export computed shortest paths list.
Exported networks will include better residue labeling instead of simple integers.
NAMD won’t be spawned multiple times, letting the user give as input larger DCD files and avoid insufficient memory errors.
Input file window will be simplified, avoiding the confusion on file types for NAMD/GROMACS data.
Switching will be optional for NAMD-type data, as opposed to the current implementation (off)

Planned features/fixes (longer-term)¶

Support for non-protein residues (organic ligands, lipids, nucleic acids).
Chain ID requirement on input files should be removed. We are working on code to relax this requirement.
View Results UI will allow visualization of Electrostatic and vdW energies separately, in addition to separate network analysis features.
A windows-compatible version is on the way.

Planned features/fixes (unlikely to implement in foreseeable future)¶

Support for AMBER-generated trajectories.

v1.1.0.hf1 (2018/06/21)¶

This hf (hot-fix) version fixes two bugs which rendered gRINN unusable in some cases and an addition to sample input files:

Bug fixes:

A major bug in gRINN which leads to a failure in processing TPR files without chain IDs is corrected. gRINN will assign a default chain ID of “P” to residues which have no chain IDs assigned in input TPR.
IEM annotation is now shown only for smallest proteins (with sizes of at most 20 amino acids).

Additions:

charm27.ff files (used by GROMACS sample trajectory data) are included in the distribution (considering that this force-field may not be included in GROMACS installation of some users).

v1.1.0 (2018/04/06)¶

This version introduces a major internal code rehaul, leaving major features of gRINN unaffected. There are additional new features as well as major/minor bug fixes:

New Features:

A new calculation setting for non-bonded interaction cutoff for NAMD simulation input is introduced. In the previous version, filtering cutoff distance parameter specified both the filtering cutoff distance itself and the non-bonded interaction energy cutoff for NAMD simulation input.
gRINN now supports Charmm simulation input as well.

Major/minor bug fixes:

A bug which caused faulty reading of more than one parameter file for NAMD simulation input is fixed.
A minor bug which caused incorrect protein structure display upon start of View Results interface in Mac OS version is fixed.

v1.0.1 (2017/12/27)¶

Initial release of gRINN.