5.18. PQR topology parser
Read atoms with charges from a PQR file (as written by PDB2PQR). No connectivity is deduced.
Note
The file format is described in MDAnalysis.coordinates.PQR
.
5.18.1. Classes
- class MDAnalysis.topology.PQRParser.PQRParser(filename)[source]
Parse atom information from PQR file filename.
- Creates a MDAnalysis Topology with the following attributes
Atomids
Atomnames
Charges
Radii
RecordTypes (ATOM/HETATM)
Resids
Resnames
Segids
- Guesses the following:
atomtypes (if not present, Gromacs generated PQR files have these)
masses
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).
Changed in version 0.16.1: Now reads insertion codes and splits into new residues around these
Changed in version 0.18.0: Added parsing of Record types Can now read PQR files from Gromacs, these provide atom type as last column but don’t have segids
- 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. In-place operations improve performance because allocating new arrays is avoided.
Added 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. In-place operations improve performance because allocating new arrays is avoided.
Added 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. In-place operations improve performance because allocating new arrays is avoided.
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. In-place operations improve performance because allocating new arrays is avoided.
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.) In-place operations improve performance because allocating new arrays is avoided.
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. In-place operations improve performance because allocating new arrays is avoided.
Added 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. In-place operations improve performance because allocating new arrays is avoided.
Added in version 0.7.5.
- static guess_flavour(line)[source]
Guess which variant of PQR format this line is
- Parameters:
line (str) – entire line of PQR file starting with ATOM/HETATM
- Returns:
flavour (str) – ORIGINAL / GROMACS / NO_CHAINID
.. versionadded:: 0.18.0
- parse(**kwargs)[source]
Parse atom information from PQR file filename.
- Return type:
A MDAnalysis Topology object
- units = {'length': None, 'time': None, 'velocity': None}
dict with units of of time and length (and velocity, force, … for formats that support it)