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Bug #2599

do_dssp works incorrectly with unknown residues

Added by Boris Timofeev 11 months ago. Updated 7 months ago.

Status:
Closed
Priority:
Normal
Assignee:
David van der Spoel
Category:
analysis tools
Target version:
2019
Affected version - extra info:
Affected version:
2016.6
Difficulty:
simple
Close

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.

gmx_do_dssp.cpp (23.9 KB) gmx_do_dssp.cpp Boris Timofeev, 08/07/2018 05:17 PM

Associated revisions

Revision 61051bf0 (diff)
Added by boristim 7 months ago

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

History

#1 Updated by Paul Bauer 10 months 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 10 months 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 10 months ago

Gerrit received a related patchset '2' for Issue #2599.
Uploader: Paul Bauer ()
Change-Id: gromacs~master~I16f09ed33cf86c699a2667d101740ce0fc2c0919
Gerrit URL: https://gerrit.gromacs.org/8252

#4 Updated by Paul Bauer 10 months 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 7 months ago

Gerrit received a related patchset '1' for Issue #2599.
Uploader: Paul Bauer ()
Change-Id: gromacs~release-2019~I16f09ed33cf86c699a2667d101740ce0fc2c0919
Gerrit URL: https://gerrit.gromacs.org/8771

#6 Updated by Paul Bauer 7 months 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 7 months ago

  • Status changed from Resolved to Closed

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