IMP Reference Guide  2.6.0 The Integrative Modeling Platform
IMP.pmi.topology Namespace Reference

Set of python classes to create a multi-state, multi-resolution IMP hierarchy. More...

## Detailed Description

Set of python classes to create a multi-state, multi-resolution IMP hierarchy.

• Start by creating a System with mdl = IMP.Model(); s = IMP.pmi.topology.System(mdl). The System will store all the states.
• Then call System.create_state(). You can easily create a multistate system by calling this function multiples times.
• For each State, call State.create_molecule() to add a Molecule (a uniquely named polymer). This function returns the Molecule object which can be passed to various PMI functions.
• Once data has been added and representations chosen, call System.build() to create a canonical IMP hierarchy.
• Following hierarchy construction, setup rigid bodies, flexible beads, etc in IMP::pmi::dof.
• Check your representation with a nice printout: IMP::atom::show_with_representation() See a comprehensive example for using these classes.

Alternatively one can construct the entire topology and degrees of freedom via formatted text file with TopologyReader and IMP::pmi::macros::BuildSystem(). This is used in the PMI tutorial. Note that this only allows a limited set of the full options available to PMI users (rigid bodies only, fixed resolutions).

## Classes

class  ComponentTopology
Stores the components required to build a standard IMP hierarchy using IMP.pmi.BuildModel() More...

class  Molecule
Stores a named protein chain. More...

class  Sequences
A dictionary-like wrapper for reading and storing sequence data. More...

class  State
Stores a list of Molecules all with the same State index. More...

class  System
This class initializes the root node of the global IMP.atom.Hierarchy. More...

class  TempResidue
Temporarily stores residue information, even without structure available. More...