4.14. XYZ Topology Parser

New in version 0.9.1.

Reads an xyz file and pulls the atom information from it. Because xyz only has atom name information, all information about residues and segments won’t be populated.

4.14.1. Classes

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

Parse a list of atoms from an XYZ file.

New in version 0.9.1.

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]

Read the file and return the structure.

Returns:MDAnalysis internal structure dict.