4.4. CRD topology parser¶
Read a list of atoms from a CHARMM CARD coordinate file (CRD) to build a basic topology.
Atom types, charges and masses are guessed.
4.4.1. Classes¶
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class
MDAnalysis.topology.CRDParser.
CRDParser
(filename, universe=None, **kwargs)[source]¶ Parse a CHARMM CARD coordinate file for topology information.
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__delattr__
¶ x.__delattr__(‘name’) <==> del x.name
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__format__
()¶ default object formatter
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__getattribute__
¶ x.__getattribute__(‘name’) <==> x.name
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__hash__
¶
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__reduce__
()¶ helper for pickle
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__reduce_ex__
()¶ helper for pickle
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__repr__
¶
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__setattr__
¶ x.__setattr__(‘name’, value) <==> x.name = value
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__sizeof__
() → int¶ size of object in memory, in bytes
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__str__
¶
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close
()¶ Close the trajectory file.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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