`PDBQTFile`#

class biotite.structure.io.pdbqt.PDBQTFile[source]#

Bases: TextFile

This class represents an AutoDock PDBQT file.

This class only provides rudimentary support for reading/writing the pure atom information.

EXPERIMENTAL: Future API changes are probable.

Examples

Write biotin as flexible ligand into a PDBQT file:

>>> import os.path
>>> ligand = residue("BTN")
>>> file = PDBQTFile()
>>> mask = file.set_structure(ligand, rotatable_bonds="all")
>>> # Print removed nonpolar hydrogen atoms
>>> print(ligand[~mask])
HET         0  BTN H101   H         3.745    1.171    0.974
HET         0  BTN H102   H         4.071    1.343   -0.767
HET         0  BTN H91    H         2.802   -0.740   -1.211
HET         0  BTN H92    H         2.476   -0.912    0.530
HET         0  BTN H81    H         1.289    1.265    0.523
HET         0  BTN H82    H         1.616    1.437   -1.218
HET         0  BTN H71    H         0.346   -0.646   -1.662
HET         0  BTN H72    H         0.020   -0.818    0.079
HET         0  BTN H2     H        -0.838    1.576   -1.627
HET         0  BTN H61    H        -3.797    1.837    1.286
HET         0  BTN H62    H        -3.367    2.738   -0.205
HET         0  BTN H5     H        -4.307    0.812   -1.205
HET         0  BTN H4     H        -2.451   -0.038   -2.252
>>> print(file)
ROOT
HETATM    1 C11  BTN     0       5.089  -0.280   0.173  1.00  0.00     0.258 C
HETATM    2 O11  BTN     0       4.956  -1.473   0.030  1.00  0.00    -0.264 OA
ENDROOT
BRANCH   1   3
HETATM    3 O12  BTN     0       6.299   0.233   0.444  1.00  0.00    -0.331 OA
HETATM   17 HO2  BTN     0       7.034  -0.391   0.517  1.00  0.00     0.221 HD
ENDBRANCH   1   3
BRANCH   1   4
HETATM    4 C10  BTN     0       3.896   0.631   0.039  1.00  0.00     0.105 C
BRANCH   4   5
HETATM    5 C9   BTN     0       2.651  -0.200  -0.276  1.00  0.00     0.010 C
BRANCH   5   6
HETATM    6 C8   BTN     0       1.440   0.725  -0.412  1.00  0.00     0.002 C
BRANCH   6   7
HETATM    7 C7   BTN     0       0.196  -0.106  -0.727  1.00  0.00     0.016 C
BRANCH   7   8
HETATM    8 C2   BTN     0      -1.015   0.819  -0.863  1.00  0.00     0.065 C
HETATM    9 S1   BTN     0      -1.419   1.604   0.751  1.00  0.00    -0.154 SA
HETATM   10 C6   BTN     0      -3.205   1.827   0.371  1.00  0.00     0.090 C
HETATM   11 C5   BTN     0      -3.530   0.581  -0.476  1.00  0.00     0.091 C
HETATM   12 N1   BTN     0      -3.970  -0.507   0.412  1.00  0.00    -0.239 NA
HETATM   13 C3   BTN     0      -3.141  -1.549   0.271  1.00  0.00     0.272 C
HETATM   14 O3   BTN     0      -3.271  -2.589   0.888  1.00  0.00    -0.259 OA
HETATM   15 N2   BTN     0      -2.154  -1.343  -0.612  1.00  0.00    -0.239 NA
HETATM   16 C4   BTN     0      -2.289   0.010  -1.175  1.00  0.00     0.093 C
HETATM   18 HN1  BTN     0      -4.738  -0.474   1.004  1.00  0.00     0.132 HD
HETATM   19 HN2  BTN     0      -1.462  -1.982  -0.843  1.00  0.00     0.132 HD
ENDBRANCH   7   8
ENDBRANCH   6   7
ENDBRANCH   5   6
ENDBRANCH   4   5
ENDBRANCH   1   4
TORSDOF 6
>>> file.write(os.path.join(path_to_directory, "1l2y_mod.pdb"))

copy()#

Create a deep copy of this object.

Returns:

copy: A copy of this object.

get_remarks(model=None)#

Get the content of REMARKS lines.

Parameters:

modelint, optional: If this parameter is given, the function will return a string from the remarks corresponding to the given model number (starting at 1). Negative values are used to index models starting from the last model insted of the first model. If this parameter is omitted, a list of strings containing all models will be returned, even if the structure contains only one model.

Returns:

linesstr or list of str: The content of REMARKS lines, without the leading 'REMARKS'.

get_structure(model=None)#

Get an AtomArray or AtomArrayStack from the PDBQT file.

Parameters:

modelint, optional: If this parameter is given, the function will return an AtomArray from the atoms corresponding to the given model number (starting at 1). Negative values are used to index models starting from the last model insted of the first model. If this parameter is omitted, an AtomArrayStack containing all models will be returned, even if the structure contains only one model.

Returns:

arrayAtomArray or AtomArrayStack: The return type depends on the model parameter.

classmethod read(file, *args, **kwargs)#

Parse a file (or file-like object).

Parameters:

filefile-like object or str: The file to be read. Alternatively a file path can be supplied.

Returns:

fileFile: An instance from the respective File subclass representing the parsed file.

static read_iter(file)#

Create an iterator over each line of the given text file.

Parameters:

filefile-like object or str: The file to be read. Alternatively a file path can be supplied.

Yields:

linestr: The current line in the file.

set_structure(atoms, charges=None, atom_types=None, rotatable_bonds=None, root=None, include_torsdof=True)#

Write an AtomArray into the PDBQT file.

Parameters:

atomsAtomArray, shape=(n,)

The atoms to be written into this file. Must have an associated BondList.

chargesndarray, shape=(n,), dtype=float, optional

Partial charges for each atom in atoms. By default, the charges are calculated using the PEOE method (partial_charges()).

atom_typesndarray, shape=(n,), dtype=”U1”, optional

Custom AutoDock atom types for each atom in atoms.

rotatable_bondsNone or ‘rigid’ or ‘all’ or BondList, optional

This parameter describes, how rotatable bonds are handled, with respect to ROOT, BRANCH and ENDBRANCH lines.

None - The molecule is handled as rigid receptor: No ROOT, BRANCH and ENDBRANCH lines will be written.

'rigid' - The molecule is handled as rigid ligand: Only a ROOT line will be written.

'all' - The molecule is handled as flexible ligand: A ROOT line will be written and all rotatable bonds are included using BRANCH and ENDBRANCH lines.

BondList - The molecule is handled as flexible ligand: A ROOT line will be written and all bonds in the given BondList are considered flexible via BRANCH and ENDBRANCH lines.

rootint, optional

Specifies the index of the atom following the ROOT line. Setting the root atom is useful for specifying the anchor in flexible side chains. This parameter has no effect, if rotatable_bonds is None. By default, the first atom is also the root atom.

include_torsdofbool, optional

By default, a TORSDOF (torsional degrees of freedom) record is written at the end of the file. By setting this parameter to false, the record is omitted.

Returns:

maskndarray, shape=(n,), dtype=bool: A boolean mask, that is False for each atom of the input atoms, that was removed due to being a nonpolar hydrogen.

write(file)#

Write the contents of this object into a file (or file-like object).

Parameters:

filefile-like object or str: The file to be written to. Alternatively a file path can be supplied.

static write_iter(file, lines)#

Iterate over the given lines of text and write each line into the specified file.

In contrast to write(), each line of text is not stored in an intermediate TextFile, but is directly written to the file. Hence, this static method may save a large amount of memory if a large file should be written, especially if the lines are provided as generator.

Parameters:

filefile-like object or str: The file to be written to. Alternatively a file path can be supplied.
linesgenerator or array-like of str: The lines of text to be written. Must not include line break characters.

PDBQTFile#

`PDBQTFile`#