5.15. PDB Topology Parser
This topology parser uses a standard PDB file to build a minimum internal structure representation (list of atoms).
The topology reader reads a PDB file line by line and ignores atom
numbers but only reads residue numbers up to 9,999 correctly. If you
have systems containing at least 10,000 residues then you need to use
a different file format (e.g. the “extended” PDB, XPDB format, see
ExtendedPDBParser) that can handle residue
numbers up to 99,999.
Note
The parser processes atoms and their names. Masses are guessed and set to 0 if unknown. Partial charges are not set. Elements are parsed if they are valid. If partially missing or incorrect, empty records are assigned.
See also
5.15.1. Classes
- class MDAnalysis.topology.PDBParser.PDBParser(filename)[source]
Parser that obtains a list of atoms from a standard PDB file.
- Creates the following Attributes:
names
chainids
tempfactors
occupancies
record_types (ATOM/HETATM)
resids
resnames
segids
elements
bonds
- Guesses the following Attributes:
masses
See also
New in version 0.8.
Changed in version 0.18.0: Added parsing of Record types
Changed in version 1.0.0: Added parsing of valid Elements
Changed in version 2.0.0: Bonds attribute is not added if no bonds are present in PDB file. If elements are invalid or partially missing, empty elements records are now assigned (Issue #2422). Aliased
bfactorstopologyattribute totempfactors.bfactorsis deprecated and will be removed in 3.0 (Issue #1901)- 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.
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. In-place operations improve performance because allocating new arrays is avoided.
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. In-place operations improve performance because allocating new arrays is avoided.
Changed in version 0.7.5: Keyword inplace can be set to
Falseso 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
Falseso 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
Falseso 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
Falseso 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.
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. In-place operations improve performance because allocating new arrays is avoided.
New in version 0.7.5.
- parse(**kwargs)[source]
Parse atom information from PDB file
- Return type
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)