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 residues_by_selection() to obtain a list of residues.
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class edPDB.selections.ResnameSelect(resnames, complement=False)
Select all atoms that match resnames.
Supply a resname, e.g. ‘SOL’ or ‘PHE’ or a list.
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class edPDB.selections.ResidueSelect(residues, complement=False)
Select all atoms that are in the residues list.
Supply a list of Bio.PDB residues for the search.
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class edPDB.selections.NotResidueSelect(residues, complement=False)
Select all atoms that are not in the residues list.
(Same as ResidueSelect(residues, complement=True).)
Supply a list of Bio.PDB residues for the search.
-
class edPDB.selections.ProteinSelect(complement=False)
- Select all amino acid residues.
Selection functions
Functions always act on a structure and return a list of residues.
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edPDB.selections.residues_by_resname(structure, resnames)
Return a list of residue instances that match resnames.
resnames can be a single string or a list of strings.
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edPDB.selections.residues_by_selection(structure, selection)
- General residue selection: supply a Bio.PDB.PDBIO.Select instance.
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edPDB.selections.find_water(structure, ligand, radius=3.0, water='SOL')
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
|
Utility functions
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edPDB.selections.canonical(resname)
Return canonical representation of resname.
space stripped and upper case
-
edPDB.selections.PROTEIN_RESNAMES
- List of residue names that determine what is recognized as a
protein with ProteinSelect. Can be extended with non-standard residues.