IMP  2.0.0
The Integrative Modeling Platform
IMP::modeller Namespace Reference

See IMP.modeller Overview 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
 
def read_pdb
 

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

Pass or store a set of BinormalTerm .

Definition at line 77 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 53 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 tools/imppy.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 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
filenameName of the Modeller restraints file.
proteinAn 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 46 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.

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

Parameters
nameThe name of the PDB file to read.
modelThe IMP::Model object in which the hierarchy will be created. The highest level hierarchy node is a PROTEIN.
special_patchesIf 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 155 of file modeller/__init__.py.

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