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IMP Reference Guide  develop.c9d213c767,2020/05/28
The Integrative Modeling Platform
IMP.modeller.ModelLoader Class Reference

Read a Modeller model into IMP. More...

Inherits object.

Detailed Description

Read a Modeller model into IMP.

After creating this object, the atoms in the Modeller model can be loaded into IMP using the load_atoms() method, then optionally any Modeller static restraints can be read in with load_static_restraints() or load_static_restraints_file().

This class can also be used to read Modeller alignment structures; however, only load_atoms() will be useful in such a case (since alignment structures don't have restraints or other information).

Note
This class is only available in Python.

Definition at line 720 of file modeller/__init__.py.

Public Member Functions

def __init__
 Constructor. More...
 
def load_angles
 Load the Modeller angle topology into the IMP model. More...
 
def load_atoms
 Construct an IMP::atom::Hierarchy that contains the same atoms as the Modeller model or alignment structure. More...
 
def load_bonds
 Load the Modeller bond topology into the IMP model. More...
 
def load_dihedrals
 Load the Modeller dihedral topology into the IMP model. More...
 
def load_dynamic_restraints
 Convert Modeller dynamic restraints into IMP::Restraint objects. More...
 
def load_impropers
 Load the Modeller improper topology into the IMP model. More...
 
def load_static_restraints
 Convert the current set of Modeller static restraints into equivalent IMP::Restraints. More...
 
def load_static_restraints_file
 Convert a Modeller static restraints file into equivalent IMP::Restraints. More...
 

Constructor & Destructor Documentation

def IMP.modeller.ModelLoader.__init__ (   self,
  modeller_model 
)

Constructor.

Parameters
modeller_modelThe Modeller model or alignment structure object to read.

Definition at line 732 of file modeller/__init__.py.

Member Function Documentation

def IMP.modeller.ModelLoader.load_angles (   self)

Load the Modeller angle topology into the IMP model.

See load_bonds() for more details.

Definition at line 821 of file modeller/__init__.py.

def IMP.modeller.ModelLoader.load_atoms (   self,
  model 
)

Construct an IMP::atom::Hierarchy that contains the same atoms as the Modeller model or alignment structure.

IMP atoms created from a Modeller model will be given charges and CHARMM types, extracted from the model. Alignment structures don't contain this information, so the IMP atoms won't either.

Parameters
modelThe IMP::Model object in which the hierarchy will be created. The highest level hierarchy node is a PROTEIN.
Returns
the newly-created root IMP::atom::Hierarchy.

Definition at line 744 of file modeller/__init__.py.

def IMP.modeller.ModelLoader.load_bonds (   self)

Load the Modeller bond topology into the IMP model.

Each bond is represented in IMP as an IMP::atom::Bond, with no defined length or stiffness. These bonds are primarily useful as input to IMP::atom::StereochemistryPairFilter, to exclude bond interactions from the nonbonded list. Typically the contribution to the scoring function from the bonds is included in the Modeller static restraints (use load_static_restraints() or load_static_restraints_file() to load these). If you want to regenerate the stereochemistry in IMP, do not use these functions (as then stereochemistry scoring terms and exclusions would be double-counted) and instead use the IMP::atom::CHARMMTopology class.

You must call load_atoms() prior to using this function.

See Also
load_angles(), load_dihedrals(), load_impropers()
Returns
A generator listing all of the bonds.

Definition at line 788 of file modeller/__init__.py.

def IMP.modeller.ModelLoader.load_dihedrals (   self)

Load the Modeller dihedral topology into the IMP model.

See load_bonds() for more details.

Definition at line 827 of file modeller/__init__.py.

def IMP.modeller.ModelLoader.load_dynamic_restraints (   self,
  pair_filter = None 
)

Convert Modeller dynamic restraints into IMP::Restraint objects.

For each currently active Modeller dynamic restraint (e.g. soft-sphere, electrostatics) an equivalent IMP::Restraint is created. load_atoms() must have been called first to read in the atoms that the restraints will act upon.

If pair_filter is given, it is an IMP::PairFilter object to exclude pairs from the nonbonded lists used by the dynamic restraints. Otherwise, an IMP::atom::StereochemistryPairFilter object is created to exclude Modeller bonds, angles and dihedrals, as specified by edat.excl_local. (Note that this calls load_bonds(), load_angles() and load_dihedrals(), so will create duplicate lists of bonds if those methods are called manually as well.)

Note
Currently only soft-sphere, electrostatic and Lennard-Jones restraints are loaded.
Returns
A Python generator of the newly-created IMP::Restraint objects.

Definition at line 897 of file modeller/__init__.py.

def IMP.modeller.ModelLoader.load_impropers (   self)

Load the Modeller improper topology into the IMP model.

See load_bonds() for more details.

Definition at line 833 of file modeller/__init__.py.

def IMP.modeller.ModelLoader.load_static_restraints (   self)

Convert the current set of Modeller static restraints into equivalent IMP::Restraints.

load_atoms() must have been called first to read in the atoms that the restraints will act upon.

Returns
A Python generator of the newly-created IMP::Restraint objects.

Definition at line 864 of file modeller/__init__.py.

def IMP.modeller.ModelLoader.load_static_restraints_file (   self,
  filename 
)

Convert a Modeller static restraints file into equivalent IMP::Restraints.

load_atoms() must have been called first to read in the atoms that the restraints will act upon.

Parameters
filenameName of the Modeller restraints file. The restraints in this file are assumed to act upon the model read in by load_atoms(); no checking is done to enforce this.
Returns
A Python generator of the newly-created IMP::Restraint objects.

Definition at line 849 of file modeller/__init__.py.


The documentation for this class was generated from the following file: