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 parsedFalse
: 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 withMDAnalysis.coordinates.PDBQT.PDBQTReader
.