4.14. MOL2 file format — MDAnalysis.coordinates.MOL2

Classes to read Tripos molecule structure format (MOL2) coordinate and topology files. Used by the DOCK docking code.

4.14.1. Classes

class MDAnalysis.topology.MOL2Parser.MOL2Parser(filename, universe=None, **kwargs)

Read topology from a Tripos MOL2 file.

Changed in version 0.9: Now subclasses TopologyReader

__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.

parse(filename=None)

Parse MOL2 file filename and return the dict structure.

Only reads the list of atoms.

Returns:MDAnalysis internal structure dict

See also

The structure dict is defined in MDAnalysis.topology.PSFParser.PSFParser().