IMP.pmi.topology Namespace Reference

Set up of system representation from topology files. More...

Detailed Description

Set up of system representation from topology files.

• Class for storing topology elements of PMI components
• Functions for reading these elementsfrom a formatted PMI topology file
• Functions for converting an existing IMP hierarchy into PMI topology
• TopologyWriter for writing PMI topology files

Namespaces
	system_tools
	Tools to help build structures.

Classes
class	ComponentTopology
	Topology class stores the components required to build a standard IMP hierarchy using IMP.pmi.autobuild_model() More...
class	Molecule
	This class is constructed from within the State class. More...
class	Sequences
	A dictionary-like wrapper for reading and storing sequence data. More...
class	State
	This private class is constructed from within the System class. More...
class	System
	This class initializes the root node of the global IMP.atom.Hierarchy. More...
class	SystemBase
	The base class for System, State and Molecule classes. More...
class	TopologyReader
	Read a pipe-delimited PMI topology file. More...

Functions
def	get_particles_within_zone
	Utility to retrieve particles from a hierarchy within a zone around a set of ps. More...

Function Documentation

def IMP.pmi.topology.get_particles_within_zone	(		hier,
			target_ps,
			sel_zone,
			entire_residues,
			exclude_backbone
	)

Utility to retrieve particles from a hierarchy within a zone around a set of ps.

Parameters

hier	The hierarchy in which to look for neighbors
target_ps	The particles for zoning
sel_zone	The maximum distance
entire_residues	If True, will grab entire residues
exclude_backbone	If True, will only return sidechain particles

Note

This function is only available in Python.

Definition at line 32 of file pmi/topology/__init__.py.