3. Parser for Structure Instance¶

class PDBParser.PDBParser[source]¶

A class to read PDB files either directly from the pdb or a structure instance from Biopython

static fetch_PDB(id, filename, hetatm=False, water=False)[source]¶

static read_PDB_file(id, filename, hetatm=False, water=False)[source]¶

Read PDB file and create Structure instance based upon it.

Argument:

id: id code of pdb file
filename: name of pdb file
hetatm: Boolean representing whether the PDB file contains hetatom.
water: Boolean representing whether to add water to the structure. Default and recommended is False.

class PDBParser.mmCIFParser¶

A class to read mmCIF files either directly from the mmCIF or a structure instance from Biopython

static fetch_mmCIF(id, filename, hetatm=False, water=False)¶

Fetch mmCIF file and create Structure instance based upon it.

Argument:

id: id code of mmCIF file
filename: name of mmCIF file
hetatm: Boolean representing whether the mmCIF file contains hetatom.
water: Boolean representing whether to add water to the structure. Default and recommended is False.

static read_mmCIF_file(id, filename, hetatm=False, water=False)¶

Read mmCIF file and create Structure instance based upon it.

Argument:

id: id code of mmCIF file
filename: name of mmCIF file
hetatm: Boolean representing whether the mmCIF file contains hetatom.
water: Boolean representing whether to add water to the structure. Default and recommended is False.