add-elem-info

Overview

add-elem-info repairs the element-symbol columns (77–78) of ATOM/HETATM records in a PDB file.

Output behavior

  • If -o/--out is omitted and --overwrite is not True, the output is written to <input>_add_elem.pdb (i.e., it replaces a trailing .pdb with _add_elem.pdb).

  • If --overwrite True and -o/--out is omitted, the input file is overwritten in-place. When -o/--out is supplied, --overwrite is ignored.

Usage

pdb2reaction add-elem-info -i INPUT.pdb [-o OUTPUT.pdb] [--overwrite {True\|False}]

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 True

Workflow

  1. Parse the input file with Bio.PDB.PDBParser, mirroring 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.).

  3. Write the structure through PDBIO:

    • default output: <input>_add_elem.pdb (when -o/--out is omitted and --overwrite is not True)

    • -o/--out: write to the specified path; --overwrite is ignored when this is provided

    • --overwrite True (without -o/--out): overwrite the input path in-place

  4. Print a summary reporting how many atoms were assigned/reassigned, plus per-element totals and a truncated list of 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 {True|False}

Overwrite the input file in-place when -o/--out is omitted.

False

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 True is set without -o/--out

  • Console report with totals for processed/assigned atoms, per-element counts, and up to 50 unresolved atoms.

Notes

  • Only columns 77–78 are modified; coordinates, occupancies, B-factors, charges, altlocs, insertion codes, and record ordering stay untouched.

  • ATOM and HETATM records across all models/chains/residues are supported.

  • Deuterium labels map to hydrogen; selenium (SE*) and halogens are recognized automatically.