entity_alg module

Code author: Niklaus Johner <niklaus.johner@a3.epfl.ch>

This module contains basic functions to work with structures (Entities and EntityViews). It notably functions to generate the biounit or crystal packing from a pdb file

FindClosestAtom(v1, v2)

v1 and v2 need to be an Entity, EntityView, ChainView, ResidueView, ChainHandle or ResidueHandle Returns the atom of v2 that is closest to v1 (minimal distance to any atom in v1).

CreateEntityFromVec3List(pos_list, chain_name='A', rname='b', aname_base='C', atom_element='C')

Creates an entity with atoms positioned according to vectors in the pos_list (Vec3List). All atoms are generated in a single chain, with 100 atoms per residue.

AssignFloatPropToEntityResidues(eh, fl, key)

That function will not work if the atom indices are not the same as the order of atoms in the entity

AssignFloatPropToEntity(eh, fl, key, aindex_list=None)

That function will not work if the atom indices are not the same as the order of atoms in the entity

GenerateCrystalPackingFromPDB(pdb_filename, distance_cutoff=20, vec_search_level=4, vec_search_cutoff=None, superpose_sele='aname=CA')

This function loads a pdb and generates the crystal packing around the initial structure, including all structures within distance_cutoff of the initial structure. ref_sele is used to test if a certain structure coming form symmetry operations and translations is already present in the crystal packing being generated.