IMP::modeller Namespace Reference

Interface to the Modeller comparative modeling package. More...

Detailed Description

Interface to the Modeller comparative modeling package.

Functionality includes:

• Loading a Modeller model into IMP
• Calling the Modeller scoring function from IMP
• Calling the IMP scoring function from Modeller
• Converting a set of Modeller static restraints or dynamic restraints into equivalent IMP restraints

Modeller

If you want to use IMP with MODELLER, you should use version 9v7 or later. If you installed the MODELLER Linux RPM or Mac package, it should be detected automatically. Make sure that MODELLER is found in your PYTHONPATH.

Info

Author(s): Ben Webb, Daniel Russel

Maintainer: benmwebb

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.

Publications:

• See main IMP papers list.

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...

Typedefs
typedef IMP::base::Vector < BinormalTerm >	BinormalTermList

Functions
def	add_soft_sphere_radii
	Add radii to the hierarchy using the Modeller radius library, radii.lib. More...
def	load_restraints_file
	Convert a Modeller restraints file into IMP::Restraint objects. More...
def	read_pdb
	Construct an IMP::atom::Hierarchy from a PDB file. More...

Standard module functions
All IMP modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()
std::string	get_module_name ()
std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...

Typedef Documentation

typedef IMP::base::Vector< BinormalTerm > IMP::modeller::BinormalTermList

Pass or store a set of BinormalTerm .

Definition at line 78 of file MultipleBinormalRestraint.h.

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.

Definition at line 693 of file modeller/__init__.py.

std::string IMP::modeller::get_data_path

(

std::string

file_name

)

Return the full path to installed data.

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 setup_environment.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 setup_environment.sh script.

def IMP.modeller.load_restraints_file	(		filename,
			protein
	)

Convert a Modeller restraints file into IMP::Restraint objects.

Deprecated:

Use ModelLoader instead.

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.

Definition at line 635 of file modeller/__init__.py.

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

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

Deprecated:

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

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.

Definition at line 952 of file modeller/__init__.py.