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. If the all preflight finds any blank element field, it re-infers every recognizable ATOM/HETATM record. Run this utility explicitly for wrong nonblank symbols or before a standalone command that receives missing fields.

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.

  • When the all preflight is triggered, recognizable nonblank fields are re-inferred as part of the same pass. See all for the automatic repair boundary.

See Also