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update xml_writer for improper dihedral (for example, EMIM+ using GAFF) #477

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@XiaoboLinlin XiaoboLinlin commented Nov 18, 2021

PR Summary:

xml_writer.py produce error for improper dihedral in GAFF force field for EMIM+, and this pull request will solve it.
Specially, I was trying to produce XML file from the parmed structure imported from the GAFF server, but it produced error for EMIM+.The issue is that we need to use like dihedral.type[0].per to get the values in .per for dihedral (improper). For normal dihedral function, we don't need the "[0]".

PR Checklist


  • Includes appropriate unit test(s)
  • Appropriate docstring(s) are added/updated
  • Code is (approximately) PEP8 compliant
  • Issue(s) raised/addressed?
    xml_writer.py produce error for improper dihedral in GAFF force field, and this pull request will solve it.

@XiaoboLinlin XiaoboLinlin changed the title update xml_writer for improper dihedral update xml_writer for improper dihedral (for example, EMIM+ using GAFF) Nov 18, 2021
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lgtm-com bot commented Nov 18, 2021

This pull request introduces 1 alert when merging 107f137 into 5fed7d3 - view on LGTM.com

new alerts:

  • 1 for Except block handles 'BaseException'

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codecov bot commented Nov 18, 2021

Codecov Report

Merging #477 (5fed7d3) into master (5fed7d3) will not change coverage.
The diff coverage is n/a.

❗ Current head 5fed7d3 differs from pull request most recent head 107f137. Consider uploading reports for the commit 107f137 to get more accurate results

@@           Coverage Diff           @@
##           master     #477   +/-   ##
=======================================
  Coverage   73.77%   73.77%           
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  Files          17       17           
  Lines        1861     1861           
=======================================
  Hits         1373     1373           
  Misses        488      488           

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