4.8. Extended PDB topology parser

New in version 0.8.

This topology parser uses a PDB file to build a minimum internal structure representation (list of atoms). The only difference from PrimitivePDBParser is that this parser reads a non-standard PDB-like format in which residue numbers can be five digits instead of four.

The topology reader reads a PDB file line by line and ignores atom numbers but reads residue numbers up to 99,999 correctly. If you have systems containing at least 100,000 residues then you need to use a different file format that can handle such residue numbers.

Note

The parser processes atoms and their names. Masses are guessed and set to 0 if unknown. Partial charges are not set.

See also

4.8.1. Classes

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

Parser that obtains a list of atoms from an non-standard “extended” PDB file.

Extended PDB files (MDAnalysis format specifier XPDB) may contain residue sequence numbers up to 99,999 by utilizing the insertion character field of the PDB standard.

See also

MDAnalysis.coordinates.PDB.ExtendedPDBReader

New in version 0.8.

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.

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()

Parse atom information from PDB file filename.

Returns:MDAnalysis internal structure dict

See also

The structure dict is defined in MDAnalysis.topology and the file is read with MDAnalysis.coordinates.PDB.PrimitivePDBReader.