add-elem-info

Repair the element-symbol columns (77–78) of ATOM/HETATM records in a PDB file. The file is re-parsed with Bio.PDB.PDBParser, each element is inferred from the atom name and residue context, and the structure is re-written via Bio.PDB.PDBIO with the element columns repaired. 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. 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.).

  1. Write the structure through PDBIO to the chosen output path (see Outputs for the default / -o / --overwrite 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

  • The structure is re-serialized via Bio.PDB.PDBIO (not an in-place column edit): ATOM/HETATM coordinates, occupancies, B-factors, altlocs, and insertion codes round-trip, but PDBIO does not preserve non-ATOM records (HEADER/REMARK/CONECT/ANISOU) or the legacy charge column (79–80).

  • 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