4.10. PQR topology parser¶
Read atoms with charges from a PQR file (as written by PDB2PQR). No connectivity is deduced.
See also
The file format is described in MDAnalysis.coordinates.PQR
.
4.10.1. Classes¶
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class
MDAnalysis.topology.PQRParser.
PQRParser
(filename, universe=None, **kwargs)[source]¶ Parse atom information from PQR file filename.
Only reads the list of atoms. Reads the charges and radii from the PQR file and populates the
MDAnalysis.core.AtomGroup.Atom.charge
andMDAnalysis.core.AtomGroup.Atom.radius
attribute.Changed in version 0.9.0: Read chainID from a PQR file and use it as segid (before we always used ‘SYSTEM’ as the new segid).
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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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