IMP
2.2.0
The Integrative Modeling Platform
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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... | |
Pass or store a set of BinormalTerm .
Definition at line 78 of file MultipleBinormalRestraint.h.
def IMP.modeller.add_soft_sphere_radii | ( | hierarchy, | |
submodel, | |||
scale = 1.0 , |
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filename = None |
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) |
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
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
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 | |||
) |
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. |
Definition at line 635 of file modeller/__init__.py.
def IMP.modeller.read_pdb | ( | name, | |
model, | |||
special_patches = None |
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) |
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. |
Definition at line 952 of file modeller/__init__.py.