biotite.structure.io.pdbx.get_component¶

biotite.structure.io.pdbx.get_component(pdbx_file, data_block=None, use_ideal_coord=True, res_name=None)[source]¶

Create an AtomArray for a chemical component from the chem_comp_atom and, if available, the chem_comp_bond category in a PDBxFile.

Parameters

pdbx_fileCIFFile or CIFBlock or BinaryCIFFile or BinaryCIFBlock: The file object.
data_blockstr, optional: The name of the data block. Default is the first (and most times only) data block of the file. If the data block object is passed directly to pdbx_file, this parameter is ignored.
use_ideal_coordbool, optional: If true, the ideal coordinates are read from the file (pdbx_model_Cartn_<dim>_ideal fields), typically originating from computations. If set to false, alternative coordinates are read (model_Cartn_<dim>_ fields).
res_namestr: In rare cases the categories may contain rows for multiple components. In this case, the component with the given residue name is read. By default, all rows would be read in this case.

Returns

arrayAtomArray: The parsed chemical component.

Examples

>>> import os.path
>>> file = CIFFile.read(
...     os.path.join(path_to_structures, "molecules", "TYR.cif")
... )
>>> comp = get_component(file)
>>> print(comp)
HET         0  TYR N      N         1.320    0.952    1.428
HET         0  TYR CA     C        -0.018    0.429    1.734
HET         0  TYR C      C        -0.103    0.094    3.201
HET         0  TYR O      O         0.886   -0.254    3.799
HET         0  TYR CB     C        -0.274   -0.831    0.907
HET         0  TYR CG     C        -0.189   -0.496   -0.559
HET         0  TYR CD1    C         1.022   -0.589   -1.219
HET         0  TYR CD2    C        -1.324   -0.102   -1.244
HET         0  TYR CE1    C         1.103   -0.282   -2.563
HET         0  TYR CE2    C        -1.247    0.210   -2.587
HET         0  TYR CZ     C        -0.032    0.118   -3.252
HET         0  TYR OH     O         0.044    0.420   -4.574
HET         0  TYR OXT    O        -1.279    0.184    3.842
HET         0  TYR H      H         1.977    0.225    1.669
HET         0  TYR H2     H         1.365    1.063    0.426
HET         0  TYR HA     H        -0.767    1.183    1.489
HET         0  TYR HB2    H         0.473   -1.585    1.152
HET         0  TYR HB3    H        -1.268   -1.219    1.134
HET         0  TYR HD1    H         1.905   -0.902   -0.683
HET         0  TYR HD2    H        -2.269   -0.031   -0.727
HET         0  TYR HE1    H         2.049   -0.354   -3.078
HET         0  TYR HE2    H        -2.132    0.523   -3.121
HET         0  TYR HH     H        -0.123   -0.399   -5.059
HET         0  TYR HXT    H        -1.333   -0.030    4.784