8000 Remember bond order where applicable by swails · Pull Request #692 · ParmEd/ParmEd · GitHub
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Remember bond order where applicable #692

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Merged
merged 2 commits into from
Apr 19, 2016
Merged

Remember bond order where applicable #692

merged 2 commits into from
Apr 19, 2016

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swails
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@swails swails commented Apr 19, 2016

This adds a new attribute "order" to the Bond class to remember the bond order. So far, it's only specified in mol2 files, so this only affects saving mol2 files from residue templates or structures that have been created by parsing a mol2 file.

Whenever bond information is present without specifying an order (i.e., every file type except mol2 files), a bond order of 1.0 is assumed.

Still needs documentation. This adds a test, though.

Fixes #691

@swails swails mentioned this pull request Apr 19, 2016
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@swails swails merged commit dff51c4 into ParmEd:master Apr 19, 2016
@swails swails deleted the mol2bo branch April 19, 2016 02:30
@davidlmobley
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Excellent. It'll be nice having that... :)

DM

On Mon, Apr 18, 2016 at 6:45 PM, Jason Swails notifications@github.com
wrote:

This adds a new attribute "order" to the Bond class to remember the bond
order. So far, it's only specified in mol2 files, so this only affects
saving mol2 files from residue templates or structures that have been
created by parsing a mol2 file.

Whenever bond information is present without specifying an order (i.e.,
every file type except mol2 files), a bond order of 1.0 is assumed.

Still needs documentation. This adds a test, though.

Fixes #691 #691

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#692
Commit Summary

  • Add a test to make sure bond order in mol2 file parsing/writing is
    retained.
  • Start storing bond orders where available, defaulting to 1.0 (in
    line with

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#692

David Mobley
Associate Professor
Department of Pharmaceutical Sciences
Department of Chemistry
3134B Natural Sciences I
University of California, Irvine
Irvine, CA 92697
dmobley@uci.edu
work (949) 824-6383
cell (949) 385-2436

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