IMP.modeller.ModelLoader Class Reference

Read a Modeller model into IMP. More...

Inherits object.

Public Member Functions
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. 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...

Detailed Description

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().

Parameters

modeller_model

The Modeller model object to read.

Note

This class is only available in Python.

Definition at line 708 of file modeller/__init__.py.

Member Function Documentation

def IMP.modeller.ModelLoader.load_angles

(

self

)

See load_bonds() for more details.

Definition at line 796 of file modeller/__init__.py.

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

Parameters

model

The 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 719 of file modeller/__init__.py.

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def IMP.modeller.ModelLoader.load_bonds

(

self

)

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 763 of file modeller/__init__.py.

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def IMP.modeller.ModelLoader.load_dihedrals

(

self

)

See load_bonds() for more details.

Definition at line 802 of file modeller/__init__.py.

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

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 871 of file modeller/__init__.py.

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def IMP.modeller.ModelLoader.load_impropers

(

self

)

See load_bonds() for more details.

Definition at line 808 of file modeller/__init__.py.

def IMP.modeller.ModelLoader.load_static_restraints

(

self

)

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 839 of file modeller/__init__.py.

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

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

Parameters

filename

Name 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 824 of file modeller/__init__.py.

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

• modeller/__init__.py