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Add command to fix duplicate atom names - #1202

Merged

drroe merged 20 commits into

Amber-MD:masterfrom

drroe:fix.duplicate.anames

Oct 22, 2026

Merged

Add command to fix duplicate atom names#1202
drroe merged 20 commits into
Amber-MD:masterfrom
drroe:fix.duplicate.anames

Commits on Oct 21, 2026
- Start command for fixing duplicate atom names in residues
  Daniel R. Roe
  committed
  cd8e10e
Commits on Oct 22, 2026
- Add code to dissect atom names into tokens
  Daniel R. Roe
  committed
  2af8e76
- Put the dissect name routine into AtomName
  Daniel R. Roe
  committed
  c344f68
- Start the naive increment routine
  Daniel R. Roe
  committed
  2f0344e
- Do integer increment
  Daniel R. Roe
  committed
  945ef68
- Save/write molecule type and charge type from/to mol2 files
  Daniel R. Roe
  committed
  8318bed
- Create placeholder routine so that modxna mol2s do not have their substructure section altered
  Daniel R. Roe
  committed
  e422a16
- Really no need for the placeholder
  Daniel R. Roe
  committed
  34135b0
- Print mask selection. Add help text and warning
  Daniel R. Roe
  committed
  f7b65fc
- Hide debug info. Improve output. Add fixed (nonduplicated) atom name to set of names to check
  Daniel R. Roe
  committed
  ca6993c
- Add fix atom names test
  Daniel R. Roe
  committed
  136f26a
- Fix help
  Daniel R. Roe
  committed
  5de81ca
- Enable test
  Daniel R. Roe
  committed
  bdbe9cc
- CPPTRAJ now preserves the charge type for mol2 files
  Daniel R. Roe
  committed
  a26fde8
- When incrementing, if a name does not have a digit component add one
  Daniel R. Roe
  committed
  f7a63a0
- Merge branch 'master' into fix.duplicate.anames
  Daniel R. Roe
  committed
  bba756d
- Version 7.12.7. Revision bump for new fixatomnames command.
  Daniel R. Roe
  committed
  e5e9a93
- Update manual lyx
  Daniel R. Roe
  committed
  ef8f534
- Update manual
  Daniel R. Roe
  committed
  c642b1a
- V7.13.0. Actually needs to be a minor version bump instead of a revision bump since the mol2 files produced by cpptraj might be different now (since the charge and molecule type fields are preserve…
  Daniel R. Roe
  committed
  76a8ac2

Commits

Commits on Oct 21, 2026

Commits on Oct 22, 2026