Bug #2599
do_dssp works incorrectly with unknown residues
Description
The current realization of do_dssp correctly works only with standard amino acids residues.
If in the studied protein unknown residues meet, dssp programm ignores them,
whereas gromacs considers them hydrophilic, and besides, indexation of resudues is broken.
My improuvements also ignores unknown residues, but the result turns out incomplete whereas Gromacs yields incorrect result.
Additionally, the file transfer to dssp programm through pipe eliminating need of repeated creation and removal of files.
Associated revisions
History
#1 Updated by Paul Bauer over 2 years ago
Hello, if you think this is good enough to go into the code, please upload it to gerrit.gromacs.org for code review! :) If you already did this, please link the redmine issue in the code commit.
#2 Updated by Boris Timofeev over 2 years ago
Thank you, Paul. Done.
I recomend to replace also "/dev/null" to NULL_DEVICE elsewhere in code for portability issues
#3 Updated by Gerrit Code Review Bot over 2 years ago
Gerrit received a related patchset '2' for Issue #2599.
Uploader: Paul Bauer (paul.bauer.q@gmail.com)
Change-Id: gromacs~master~I16f09ed33cf86c699a2667d101740ce0fc2c0919
Gerrit URL: https://gerrit.gromacs.org/8252
#4 Updated by Paul Bauer over 2 years ago
- Target version changed from 2016.6 to 2019
As with the other issue, changed to target the next main release.
#5 Updated by Gerrit Code Review Bot about 2 years ago
Gerrit received a related patchset '1' for Issue #2599.
Uploader: Paul Bauer (paul.bauer.q@gmail.com)
Change-Id: gromacs~release-2019~I16f09ed33cf86c699a2667d101740ce0fc2c0919
Gerrit URL: https://gerrit.gromacs.org/8771
#6 Updated by Paul Bauer about 2 years ago
- Status changed from New to Resolved
The issue at hand has been fixed, but we may want to have a separate issue for porting do_dssp to GROMACS natively.
#7 Updated by Paul Bauer about 2 years ago
- Status changed from Resolved to Closed
Updates to do_dssp
As posted by Boris Timofeev on redmine, do_dssp has been
broken before when encountering unknown residues.
This fixes the behaviour.
Refs #2599
Change-Id: I16f09ed33cf86c699a2667d101740ce0fc2c0919