Parser for Structure Instance

class StructureParser.PDBParser[source]

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

static calc_SA(pdbfile, rsa=True, outsafile=None)[source]
static fetch_PDB(structure_id, filename, hetatm=False, water=False)[source]

Fetch PDB file and create Structure instance based upon it.

Argument:
structure_id
structure_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.
Return:
Structure Instance
static fetch_PDB_BioPy(structure_id, filename, hetatm=False, water=False)[source]

Fetch PDB file and create Structure instance based upon it.

Argument:
structure_id
structure_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.
Return:
Structure Instance
static read_PDB_file(structure_id, filename, hetatm=False, water=False, chain=None)[source]

Read PDB file and create Structure instance based upon it.

Argument:
structure_id
structure_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.
Return:
Structure Instance
static read_PDB_file_BioPy(structure_id, filename, hetatm=False, water=False, chain=None)[source]

Read PDB file and create Structure instance based upon it.

Argument:
structure_id
structure_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.
Return:
Structure Instance
static write_sasd_to_pdb(dens_map, sasds, pdb)[source]

Outputs sasds to .pdb file

Arguments:

dens_map
Solvent accessible surface on masked array
sasds
dictionary of sasds
pdb
.pdb file sasds were calculated on
static write_sasd_to_txt(sasds, pdb)[source]

Outputs sasds to .txt file

Arguments:

sasds
dictionary of sasds
pdb
.pdb file sasds were calculated on
class StructureParser.mmCIFParser[source]

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

static fetch_mmCIF(structure_id, filename, hetatm=False, water=False)[source]

Fetch mmCIF file and create Structure instance based upon it.

Argument:
structure_id
structure_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.
Return:
Structure Instance
static read_mmCIF_file(structure_id, filename, hetatm=False, water=False)[source]

Read mmCIF file and create Structure instance based upon it.

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