4.19. Base topology reader classes — MDAnalysis.topology.base

Derive topology reader classes from the base class in this module. All topology readers raise IOError upon failing to read a topology file and ValueError upon failing to make sense of the read data.

4.19.1. Classes

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

Base class for topology readers

Parameters:
  • filename (str) – name of the topology file
  • universe (Universe, optional) – Supply a Universe to the Parser. This then passes it to the atom instances that are created within parsers.
  • kwargs (optional) – Other keyword arguments that can vary with the specific format. These are stored as self.kwargs
  • topology readers must define a parse method which (All) –
  • a topology dict. (returns) –
Raises:
  • * (exc:IOError upon failing to read a topology file)
  • * (exc:ValueError upon failing to make sense of the read data) –
  • .. versionadded (: 0.9.0)
  • .. versionchanged (: 0.9.2) – Added keyword ‘universe’ to pass to Atom creation.
__delattr__

x.__delattr__(‘name’) <==> del x.name

__format__()

default object formatter

__getattribute__

x.__getattribute__(‘name’) <==> x.name

__hash__
__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__
__setattr__

x.__setattr__(‘name’, value) <==> x.name = value

__sizeof__() → int

size of object in memory, in bytes

__str__
close()

Close the trajectory file.

convert_forces_from_native(force, inplace=True)

Conversion of forces array force from native to base units

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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)

Conversion of force array force from base to native units.

Parameters:
  • force (array_like) – Forces to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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)

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

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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.

Parameters:
  • x (array_like) – Positions to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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.

Parameters:
  • t (array_like) – Time values to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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)

Conversion of velocities array v from native to base units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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)

Conversion of coordinate array v from base to native units

Parameters:
  • v (array_like) – Velocities to transform
  • inplace (bool, optional) – Whether to modify the array inplace, overwriting previous data

Note

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

New in version 0.7.5.