Supported Structure File Formats¶

CRD - CARD format file used by CHARMM¶

This trajectory file format is used by the CHARMM program suite (Molecular Modelling).

Recognized File Extensions

.crd

PDB - Brookhaven PDB File¶

Fine grained control over PDB file import is available via the LoadPDB() function. The PDB importer supports loading gzipped PDB files, which are auto- detected by the .gz file extension.

Recognized File Extensions

.ent, .pdb, .ent.gz, .pdb.gz

Format Name

pdb

mmCIF - macromolecular Crystallographic Information File¶

Fine grained control over mmCIFile import is available via the LoadMMCIF() function. Most notably, this gives you access to the MMCifInfo class. The mmCIF importer supports loading gzipped files, which are auto-detected by the .gz file extension.

Recognized File Extensions

.cif, .cif.gz

Format Name

cif

PQR¶

A variant of the PDB format that contains data related to atom charges and radii.

Recognized File Extensions

.pqr

Format Name

pqr

SDF - Structured Data File¶

Chemical table (Ctab) file format, aka SDF, aka MDL Molfile, originally named after Molecular Design Limited, Inc. Follows the “BIOVIA Databases 2020” format specification (V2000; read-only V3000 experimental support). The SDF importer supports loading gzipped files, which are auto-detected by the .gz file extension.

The SDF format does not support residues, chains or atom names natively. The reader assigns 1-based atom indices as atom names. SDF files containing several molecules are loaded into distinct chains, named after the molecule name in the MOLfile header with a numerical prefix. Residues are named after the name in the MOLfile header as well.

Chains are written as separate molecules. If a chain contains more than one residue, they will be merged into a single molecule.

Recognized File Extensions

.sdf, .sdf.gz, .mol, .mol.gz