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.

class edPDB.selections.ResnameSelect(resnames, complement=False)

Select all atoms that match resnames.

Supply a resname, e.g. ‘SOL’ or ‘PHE’ or a list.

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.

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.

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.

edPDB.selections.residues_by_selection(structure, selection)
General residue selection: supply a Bio.PDB.PDBIO.Select instance.
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

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.

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