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.
• Some useful functions to help you set up your Molecules:
  • Access the sequence residues with slicing (Molecule[a:b]) or functions like Molecule.get_atomic_residues() and Molecule.get_non_atomic_residues(). These functions all return python sets for easy set arithmetic using & (and), | (or), - (difference)
  • Molecule.add_structure() to add structural information from a PDB file.
  • Molecule.add_representation() to create a representation unit - here you can choose bead resolutions as well as alternate representations like densities or ideal helices.
  • Molecule.create_clone() lets you set up a molecule with identical representations, just a different chain ID. Use Molecule.create_copy() if you want a molecule with the same sequence but that allows custom representations.
• 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...
class	TopologyReader
	Automatically setup Sytem and Degrees of Freedom with a formatted text file. More...