structure_formats.rst

Supported Structure File Formats

The following file formats are supported by :func:`LoadEntity`:

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 :func:`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 :func:`LoadMMCIF` function. Most notably, this gives you access to the :class:`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

mmcif

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 (V2000; read-only V3000 experimental support), aka MDL Molfile. The SDF format does not support residues, chains or atom names natively. The SDF importer supports loading gzipped files, which are auto-detected by the .gz file extension.

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