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IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
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Read a Modeller model into IMP. More...
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).
Definition at line 377 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... | |
| def IMP.modeller.ModelLoader.__init__ | ( | self, | |
| modeller_model | |||
| ) |
Constructor.
| modeller_model | The Modeller model or alignment structure object to read. |
Definition at line 389 of file modeller/__init__.py.
| 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 478 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.
| model | The IMP::Model object in which the hierarchy will be created. The highest level hierarchy node is a PROTEIN. |
Definition at line 401 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.
Definition at line 445 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 484 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.)
Definition at line 554 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 490 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.
Definition at line 521 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.
| 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. |
Definition at line 506 of file modeller/__init__.py.