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 model = IMP.Model(); s = IMP.pmi.topology.System(model). The System will store all the states.
• Then call System.create_state(). You can easily create a multistate system by calling this function multiple 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 an mmCIF or 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	Molecule
	Stores a named protein chain. More...
class	PDBSequences
	Data structure for reading and storing sequence data from PDBs. More...
class	PMIMoleculeHierarchy
	Extends the functionality of IMP.atom.Molecule. 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
	Represent 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 System and Degrees of Freedom with a formatted text file. More...

Functions
def	fasta_pdb_alignments
	This function computes and prints the alignment between the fasta file and the pdb sequence, computes the offsets for each contiguous fragment in the PDB. More...

Function Documentation

def IMP.pmi.topology.fasta_pdb_alignments	(		fasta_sequences,
			pdb_sequences,
			show = False
	)

This function computes and prints the alignment between the fasta file and the pdb sequence, computes the offsets for each contiguous fragment in the PDB.

Parameters

fasta_sequences	IMP.pmi.topology.Sequences object
pdb_sequences	IMP.pmi.topology.PDBSequences object
show	boolean default False, if True prints the alignments. The input objects should be generated using map_name dictionaries such that fasta_id and pdb_chain_id are mapping to the same protein name. It needs BioPython. Returns a dictionary of offsets, organized by peptide range (group): example: offsets={"ProtA":{(1,10):1,(20,30):10}}

Note

This function is only available in Python.

Definition at line 1186 of file pmi/topology/__init__.py.