Module selections
source code
:mod:`edPDB.selections` --- Selections
Extensions to Bio.PDB, some useful selections.
Partly published on
http://biopython.org/wiki/Reading_large_PDB_files
License: like Biopython
Selection classes
Provide an instance to PDBIO to select a subset of a structure or
use it with :func:`residues_by_selection` to obtain a list of
residues.
.. autoclass:: ResnameSelect .. autoclass:: ResidueSelect ..
autoclass:: NotResidueSelect .. autoclass:: ProteinSelect ..
autoclass:: NotProteinSelect
Selection functions
Functions always act on a structure and return a list of
residues.
.. autofunction:: residues_by_resname .. autofunction::
residues_by_selection .. autofunction:: find_water
Utility functions
.. autofunction:: canonical .. autodata::
PROTEIN_RESNAMES
|
|
|
|
|
|
|
|
residues_by_selection(structure,
selection)
General residue selection: supply a Bio.PDB.PDBIO.Select instance. |
source code
|
|
|
|
find_water(structure,
ligand,
radius=3.0,
water='SOL')
Find all water (SOL) molecules within radius of ligand. |
source code
|
|
|
|
PROTEIN_RESNAMES = {'ALA': 'A', 'ALAD': 'AA', 'ARG': 'R', 'ASN...
List of residue names that determine what is recognized as a protein
with :class:`ProteinSelect`.
|
|
Return canonical representation of resname.
space stripped and upper case
|
|
Return a list of residue instances that match *resnames*.
*resnames* can be a single string or a list of strings.
|
find_water(structure,
ligand,
radius=3.0,
water='SOL')
| source code
|
Find all water (SOL) molecules within radius of ligand.
:Arguments:
*structure*
Bio.PDB structure of system with water
*ligand* : list
Bio.PDB list of atoms of the ligand (Bio.PDB.Atom.Atom
instances)
*radius* : float
Find waters for which the ligand-atom - OW distance is <
radius [3.0]
*water* : string
resname of a water molecule [SOL]
:Returns: list of residue instances
|
PROTEIN_RESNAMES
List of residue names that determine what is recognized as a protein
with :class:`ProteinSelect`. Can be extended with non-standard
residues.
- Value:
{'ALA': 'A',
'ALAD': 'AA',
'ARG': 'R',
'ASN': 'N',
'ASP': 'D',
'CHO': '?',
'CYS': 'C',
'EAM': '?',
...
|
|