4.9. PDBQT topology parser

Use a PDBQT file to build a minimum internal structure representation (list of atoms), including AutoDock atom types (stored as Atom.type) and partial charges (Atom.charge).

  • Reads a PDBQT file line by line and does not require sequential atom numbering.
  • Multi-model PDBQT files are not supported.

Note

Only reads atoms and their names; connectivity is not deduced. Masses are guessed and set to 0 if unknown.

See also

MDAnalysis.coordinates.PDBQT

4.9.1. Classes

class MDAnalysis.topology.PDBQTParser.PDBQTParser(filename, universe=None, guess_bonds_mode=False, **kwargs)[source]

Read topology from a PDBQT file.

Standard arguments for a TopologyReader:

Arguments:
filename

name of the topology file

Keywords:
universe

Supply a Universe to the Parser. This then passes it to the atom instances that are created within parsers.

guess_bonds_mode
  • True: attempt to derive bonds from a distance search if no connectivity information is available or parsed
  • False: only load a list of atoms (and possibly identify residues and segments)
  • default: False
kwargs

Other keyword arguments that can vary with the specific format. These are stored as self.kwargs

close()

Close the trajectory file.

close_trajectory()

Specific implementation of trajectory closing.

convert_forces_from_native(force, inplace=True)

In-place conversion of forces array force from native units to base units.

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_forces_to_native(force, inplace=True)

In-place conversion of force array force from base units to native units.

By default, the input force is modified in place and also returned.

New in version 0.7.7.

convert_pos_from_native(x, inplace=True)

In-place conversion of coordinate array x from native units to base units.

By default, the input x is modified in place and also returned.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_pos_to_native(x, inplace=True)

Conversion of coordinate array x from base units to native units.

By default, the input x is modified in place and also returned.

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_from_native(t, inplace=True)

Convert time t from native units to base units.

By default, the input t is modified in place and also returned (although note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_time_to_native(t, inplace=True)

Convert time t from base units to native units.

By default, the input t is modified in place and also returned. (Also note that scalar values t are passed by value in Python and hence an in-place modification has no effect on the caller.)

Changed in version 0.7.5: Keyword inplace can be set to False so that a modified copy is returned unless no conversion takes place, in which case the reference to the unmodified x is returned.

convert_velocities_from_native(v, inplace=True)

In-place conversion of velocities array v from native units to base units.

By default, the input v is modified in place and also returned.

New in version 0.7.5.

convert_velocities_to_native(v, inplace=True)

In-place conversion of coordinate array v from base units to native units.

By default, the input v is modified in place and also returned.

New in version 0.7.5.

parse()[source]

Parse atom information from PDBQT file filename.

Returns:MDAnalysis internal structure dict

See also

The structure dict is defined in MDAnalysis.topology.PSFParser.PSFParser() and the file is read with MDAnalysis.coordinates.PDBQT.PDBQTReader.