IMP  2.4.0 The Integrative Modeling Platform
IMP::modeller Namespace Reference

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

## Detailed Description

Interface to the Modeller comparative modeling package.

Functionality includes:

# 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:

## 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...

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

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

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

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 )

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 690 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

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:
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 632 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:
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.