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add-elem-info

Repair the element-symbol columns (77–78) of ATOM/HETATM records in a PDB file. Each element is inferred from the fixed-column atom name and residue context; all input lines are preserved, with only the element field replaced where needed. Use it when a PDB file has missing or wrong element columns and downstream subcommands (extract, opt, tsopt, ...) reject it. The all command auto-invokes add-elem-info as a preflight, so manual use is only needed before standalone subcommands.

Examples

# Populate element fields and write to "<input>_add_elem.pdb"
pdb2reaction add-elem-info -i 1abc.pdb

# Write to a specific output file
pdb2reaction add-elem-info -i 1abc.pdb -o 1abc_fixed.pdb

# Overwrite the input file in-place
pdb2reaction add-elem-info -i 1abc.pdb --overwrite

Workflow

  1. Read the raw PDB records and classify atoms with the residue definitions used in extract.py (AMINO_ACIDS, WATER_RES, ION).
  2. For each atom, guess the element by combining the atom name, residue name, and whether the record is HETATM:
  • Monatomic ion residues in the ION dict: use the corresponding element.
  • Proteins/nucleic acids/water: apply special handling for H/D, Se, and first-letter mapping for C/N/O/P/S; carbon side-chain labels default to C.
  • Other ligands: use atom-name prefixes and fall back to element-symbol normalization (recognizing halogens, deuterium → hydrogen, etc.).
  1. Replace only columns 77–78 on ATOM/HETATM records and write all other columns and records unchanged (see Outputs for path precedence).
  2. Print a summary reporting how many atoms were assigned/reassigned, plus per-element totals and a truncated list of unresolved atoms.

Outputs

  • A PDB file with element symbols populated/corrected:
  • <input>_add_elem.pdb by default (when -o/--out is omitted and --overwrite is not True)
  • OUTPUT.pdb if -o/--out is provided (regardless of --overwrite)
  • INPUT.pdb overwritten in-place if --overwrite is set without -o/--out
  • Console report with totals for processed/assigned atoms, per-element counts, and up to 50 unresolved atoms.

CLI options

Option Description Default
-i, --input PATH Input PDB file. Required
-o, --out PATH Output path. When set, --overwrite is ignored. None → <input>_add_elem.pdb
--overwrite/--no-overwrite Overwrite the input file in-place when -o/--out is omitted. False

The full flag list is in the generated command reference.

Notes

  • Every input line is preserved byte-for-byte except columns 77–78 of ATOM/HETATM records selected for repair. HEADER, REMARK, CONECT, ANISOU, and the legacy charge column (79–80) are retained.
  • ATOM and HETATM records across all models/chains/residues are supported.
  • Deuterium labels map to hydrogen; selenium (SE*) and halogens are recognized automatically.
  • Re-running on a PDB that already carries valid element symbols is a no-op (atoms pass through unchanged). See all for how the all preflight invokes add-elem-info automatically only when element columns are missing.

See Also