IMP::modeller Namespace Reference

---

Detailed Description

This module contains functionality for integrating Modeller with IMP.

Author:

Ben Webb, Daniel Russel

Version:

1.0

Overview:

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

Examples

Examples can be found on the IMP.modeller examples page.

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.

Data Structures
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.
std::string	get_data_path (std::string file_name)
	Return the path to installed data for this module.
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module.
std::string	get_module_name ()
const VersionInfo &	get_module_version_info ()
def	load_restraints_file
def	read_pdb
Variables
dictionary	_unary_func_generators
tuple	modeller = _import_modeller_scripts_optimizers()

---

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.

std::string IMP::modeller::get_data_path

(

std::string

file_name

)

Return the path to installed data for this module.

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

    std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

std::string IMP::modeller::get_example_path

(

std::string

file_name

)

Return the path to installed example data for this module.

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

    IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb", model));

This will ensure that the code works when IMP is installed or used via the tools/imppy.sh script.

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.