pdb_numpy.format package
Submodules
pdb_numpy.format.gro module
- pdb_numpy.format.gro.get_gro_string(gro_coor)[source]
Return a coor object as a gro string.
- Parameters:
- selfCoor
Coor object
- Returns:
- str
Coor object as a gro string
- pdb_numpy.format.gro.parse(gro_lines)[source]
Parse the gro lines and return atom information’s as a Coor.
- Parameters:
- gro_lineslist
list of gro lines
- Returns:
- Coor
Coor object
- pdb_numpy.format.gro.write(coor, gro_out, overwrite=False)[source]
Write a gro file.
- Parameters:
- coorCoor
Coor object
- gro_outstr
path of the gro file to write
- overwritebool, optional, default=False
flag to overwrite or not if file has already been created.
- Returns:
- None
Examples
>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb')) >>> prot_coor.write(os.path.join(TEST_OUT, 'tmp.gro')) Succeed to save file tmp.gro
pdb_numpy.format.mmcif module
- pdb_numpy.format.mmcif.fetch(pdb_ID)[source]
Get a mmcif file from the PDB using its ID and return a Coor object.
- Parameters:
- pdb_IDstr
pdb ID
- Returns:
- Coor
Coor object
Examples
>>> prot_coor = Coor() >>> prot_coor.get_PDB_mmcif('3EAM')
- pdb_numpy.format.mmcif.fetch_BioAssembly(pdb_ID, index=1)[source]
Get a Bio Assembly mmcif file from the PDB using its ID and return a Coor object.
- Parameters:
- pdb_IDstr
pdb ID
- indexint
Bio Assembly index
- Returns:
- Coor
Coor object
Examples
>>> prot_coor = Coor() >>> prot_coor.get_PDB('3EAM')
- pdb_numpy.format.mmcif.get_mmcif_string(coor)[source]
Return a coor object as a mmcif string.
- Parameters:
- coorCoor
Coor object to write
- Returns:
- str
Coor object as a pdb string
- pdb_numpy.format.mmcif.parse(mmcif_lines)[source]
Parse the mmcif lines and return atom information as a dictionary
- Parameters:
- mmcif_lineslist
list of pdb lines
- Returns:
- Coor
Coor object
- pdb_numpy.format.mmcif.parse_crystal_pack(data_mmCIF)[source]
Parse crystal packing information from a mmcif file. treat the following mmcif tags: - _cell - _symmetry
- Parameters:
- data_mmCIFdict
mmcif data
- Returns:
- crystal_packstr
crystal packing
- pdb_numpy.format.mmcif.parse_symmetry(data_mmCIF)[source]
Parse information from a mmcif file. treat the following mmcif tags: - _symmetry_equiv_pos_as_xyz
- Parameters:
- data_mmCIFdict
mmcif data
- Returns:
- symmetry_dictdict
symmetry dict
- pdb_numpy.format.mmcif.parse_transformation(data_mmCIF)[source]
Parse information from a mmcif file. treat the following mmcif tags: - _pdbx_struct_assembly_gen - _pdbx_struct_oper_list - _pdbx_struct_assembly
- Parameters:
- data_mmCIFdict
mmcif data
- Returns:
- transformation_dictdict
transformation dict
pdb_numpy.format.pdb module
- pdb_numpy.format.pdb.fetch(pdb_ID)[source]
Get a pdb file from the PDB using its ID and return a Coor object.
- Parameters:
- pdb_IDstr
pdb ID
- Returns:
- Coor
Coor object
Examples
>>> prot_coor = Coor() >>> prot_coor.get_PDB('3EAM')
- pdb_numpy.format.pdb.fetch_BioAssembly(pdb_ID, index=1)[source]
Get a Bio Assembly pdb file from the PDB using its ID and return a Coor object.
- Parameters:
- pdb_IDstr
pdb ID
- indexint
Bio Assembly index
- Returns:
- Coor
Coor object
Examples
>>> prot_coor = Coor() >>> prot_coor.get_PDB('3EAM')
- pdb_numpy.format.pdb.get_pdb_string(pdb_coor)[source]
Return a coor object as a pdb string.
- Parameters:
- pdb_coorCoor
Coor object
- Returns:
- str
Coor object as a pdb string
Examples
>>> prot_coor = Coor() >>> prot_coor.read_file(os.path.join(TEST_PATH, '1y0m.pdb')) Succeed to read file ...1y0m.pdb , 648 atoms found >>> pdb_str = prot_coor.get_structure_string() >>> print(f'Number of caracters: {len(pdb_str)}') Number of caracters: 51264
- pdb_numpy.format.pdb.parse(pdb_lines, pqr_format=False)[source]
Parse the pdb lines and return atom information’s as a dictionary
- Parameters:
- pdb_lineslist
list of pdb lines
- pqr_formatbool, optional
if True, parse pqr format, by default False
- Returns:
- Coor
Coor object
- pdb_numpy.format.pdb.parse_symmetry(text)[source]
Parse the REMARK 290 SMTRY information from a pdb file.
- Parameters:
- textstr
pdb file
- Returns:
- symetry_dictdict
symetry information
- pdb_numpy.format.pdb.parse_transformation(text)[source]
Parse the REMARK 350 BIOMT information from a pdb file.
- Parameters:
- textstr
pdb file
- Returns:
- symetry_dictdict
symetry information
- pdb_numpy.format.pdb.write(coor, pdb_out, overwrite=False)[source]
Write a pdb file.
- Parameters:
- coorCoor
Coor object
- pdb_outstr
path of the pdb file to write
- overwritebool, optional, default=False
flag to overwrite or not if file has already been created.
- Returns:
- None
Examples
>>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb')) >>> prot_coor.write_pdb(os.path.join(TEST_OUT, 'tmp.pdb')) Succeed to save file tmp.pdb
pdb_numpy.format.pqr module
- pdb_numpy.format.pqr.get_pqr_string(coor)[source]
Return a coor object as a pqr string.
- Parameters:
- coorCoor
Coor object
- Returns:
- str
Coor object as a pqr string
Examples
>>> prot_coor = Coor() >>> prot_coor.read_pdb(os.path.join(TEST_PATH, '1y0m.pdb')) Succeed to read file ...1y0m.pdb , 648 atoms found >>> pqr_str = prot_coor.get_pqr_structure_string() >>> print('Number of caracters: {}'.format(len(pqr_str))) Number of caracters: 46728
- pdb_numpy.format.pqr.parse(pqr_lines)[source]
Parse the pqr lines and return atom information’s as a dictionary
- Parameters:
- pqr_lineslist
list of pdb lines
- Returns:
- Coor
Coor object
- pdb_numpy.format.pqr.write(coor, pqr_out, overwrite=False)[source]
Write a pdb file.
- Parameters:
- coorCoor
Coor object
- pqr_outstr
path of the pqr file to write
- overwritebool, optional, default=False
flag to overwrite or not if file has already been created.
- Returns:
- None
Examples
>>> TEST_OUT = str(getfixture('tmpdir')) >>> prot_coor = Coor(os.path.join(TEST_PATH, '1y0m.pdb')) Succeed to read file ...1y0m.pdb , 648 atoms found >>> prot_coor.write_pdb(os.path.join(TEST_OUT, 'tmp.pdb')) Succeed to save file ...tmp.pdb
Module contents
Format library for pdb_numpy module.