IMP::modeller Namespace Reference

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Detailed Description

This module contains functionality for integrating Modeller with IMP.

This module supports integration of Modeller with IMP. See the Modeller page for more information about Modeller.

Examples:

• modeller examples
• All examples using IMP.modeller

Author(s): Ben Webb, Daniel Russel

Version: SVN.r12662

License: LGPL. This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. Modeller itself is free for academic users. See the Modeller page for more information about licensing Modeller.

Publications:

• Andrej Sali, Tom Blundell, “Comparative protein modelling by satisfaction of spatial restraints”, Journal of Molecular Biology, 1993.

Classes
class	BinormalTerm
	A single binormal term in a MultipleBinormalRestraint. More...
class	IMPRestraints
	A Modeller restraint which evaluates all defined IMP restraints. More...
class	ModellerRestraints
	An IMP restraint using all defined Modeller restraints. More...
class	ModelLoader
	Read a Modeller model into IMP. More...
class	MultipleBinormalRestraint
	Modeller-style multiple binormal (phi/psi) restraint. More...
Functions
def	add_soft_sphere_radii
	Add radii to the hierarchy using the Modeller radius library, radii.lib.
def	load_restraints_file
def	read_pdb
Variables
tuple	modeller = _import_modeller_scripts_optimizers()

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Function Documentation

def IMP::modeller::add_soft_sphere_radii	(		hierarchy,
			submodel,
			scale = 1.0,
			filename = None
	)

Add radii to the hierarchy using the Modeller radius library, radii.lib.

Each radius is scaled by the given scale (Modeller usually scales radii by a factor of 0.82). submodel specifies the topology submodel, which is the column in radii.lib to use.

def IMP::modeller::load_restraints_file	(		filename,
			protein
	)

Deprecated:

Use ModelLoader instead.

Convert a Modeller restraints file into equivalent IMP::Restraints.

Parameters:

filename	Name of the Modeller restraints file.
protein	An IMP::atom::Hierarchy containing the protein atoms (e.g. as returned by read_pdb). The Modeller restraints file is assumed to act on the same PDB described by protein.

Returns:

A Python list of the newly-created IMP::Restraint objects.

def IMP::modeller::read_pdb	(		name,
			model,
			special_patches = None
	)

Deprecated:

Use IMP::atom::read_pdb() instead to read a PDB file, or ModelLoader to read a Modeller model.

Construct an IMP::atom::Hierarchy from a PDB file.

Parameters:

name	The name of the PDB file to read.
model	The IMP::Model object in which the hierarchy will be created. The highest level hierarchy node is a PROTEIN.
special_patches	If given, a function that applies patches (e.g. nucleic acid termini) to the Modeller model.

Returns:

the newly-created root IMP::atom::Hierarchy.