4.6. PDB topology parser

Use a PDB file to build a minimum internal structure representation.

Note

Only atoms and their names are read; no bond connectivity of (partial) charges are deduced. Masses are guessed and set to 0 if unknown.

See also

MDAnalysis.coordinates.PDB and Bio.PDB

See also

MDAnalysis.topology.PrimitivePDBParser (which can guess conectivity but does not support all subleties of the full PDB format)

4.6.1. Classes

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

Read minimum topology information from a PDB 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.

kwargs

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

close()

Close the trajectory file.

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 PDB file pdbfile.

Only reads the list of atoms.

This functions uses the Bio.PDB.PDBParser as used by MDAnalysis.coordinates.pdb.extensions.get_structure().

Returns:MDAnalysis internal structure dict

See also

The structure dict is defined in MDAnalysis.topology.