IMP::modeller Namespace Reference

See IMP.modeller for more information.

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...
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...
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 methods
All IMP modules have a set of standard methods to help get information about the module and about files associated with the module.
std::string	get_module_version ()
std::string	get_module_name ()

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
	)

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

)

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

)

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
	)

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
	)

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.