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Add command to fix duplicate atom names #1202

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Merged
drroe merged 20 commits into from
Oct 22, 2026
Merged

Add command to fix duplicate atom names #1202

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cd8e10e
Start command for fixing duplicate atom names in residues
Oct 21, 2026
2af8e76
Add code to dissect atom names into tokens
Oct 22, 2026
c344f68
Put the dissect name routine into AtomName
Oct 22, 2026
2f0344e
Start the naive increment routine
Oct 22, 2026
945ef68
Do integer increment
Oct 22, 2026
8318bed
Save/write molecule type and charge type from/to mol2 files
Oct 22, 2026
e422a16
Create placeholder routine so that modxna mol2s do not have their sub…
Oct 22, 2026
34135b0
Really no need for the placeholder
Oct 22, 2026
f7b65fc
Print mask selection. Add help text and warning
Oct 22, 2026
ca6993c
Hide debug info. Improve output. Add fixed (nonduplicated) atom name …
Oct 22, 2026
136f26a
Add fix atom names test
Oct 22, 2026
5de81ca
Fix help
Oct 22, 2026
bdbe9cc
Enable test
Oct 22, 2026
a26fde8
CPPTRAJ now preserves the charge type for mol2 files
Oct 22, 2026
f7a63a0
When incrementing, if a name does not have a digit component add one
Oct 22, 2026
bba756d
Merge branch 'master' into fix.duplicate.anames
Oct 22, 2026
e5e9a93
Version 7.12.7. Revision bump for new fixatomnames command.
Oct 22, 2026
ef8f534
Update manual lyx
Oct 22, 2026
c642b1a
Update manual
Oct 22, 2026
76a8ac2
V7.13.0. Actually needs to be a minor version bump instead of a revis…
Oct 22, 2026
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Binary file modified doc/CpptrajManual.pdf
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2 changes: 1 addition & 1 deletion doc/DocumentChecksums.txt
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
f6f8cb1a79951d80a9d2656fd9c30f55 CpptrajDevelopmentGuide.lyx
676d7874e4942cf94f91fee003cf3c28 cpptraj.lyx
fb6089fe17cca73c0a3b8914a5590a22 cpptraj.lyx
5d9b5b5ed47a3ded57b6464df99b3585 CpptrajManual.lyx
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