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().
| modeller_model | The Modeller model object to read. |
Public Member Functions | |
| def | load_angles |
| Load the Modeller angle topology into the IMP model. | |
| def | load_atoms |
| Construct an IMP::atom::Hierarchy that contains the same atoms as the Modeller model. | |
| def | load_bonds |
| Load the Modeller bond topology into the IMP model. | |
| def | load_dihedrals |
| Load the Modeller dihedral topology into the IMP model. | |
| def | load_dynamic_restraints |
| Convert the current set of Modeller dynamic restraints (e.g. | |
| def | load_impropers |
| Load the Modeller improper topology into the IMP model. | |
| def | load_static_restraints |
| Convert the current set of Modeller static restraints into equivalent IMP::Restraints. | |
| def | load_static_restraints_file |
| Convert a Modeller static restraints file into equivalent IMP::Restraints. | |
| def IMP::modeller::ModelLoader::load_angles | ( | self | ) |
Load the Modeller angle topology into the IMP model.
See load_bonds() for more details.
| def IMP::modeller::ModelLoader::load_atoms | ( | self, | ||
| model | ||||
| ) |
Construct an IMP::atom::Hierarchy that contains the same atoms as the Modeller model.
| model | The IMP::Model object in which the hierarchy will be created. The highest level hierarchy node is a PROTEIN. |
| 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.
| def IMP::modeller::ModelLoader::load_dihedrals | ( | self | ) |
Load the Modeller dihedral topology into the IMP model.
See load_bonds() for more details.
| def IMP::modeller::ModelLoader::load_dynamic_restraints | ( | self, | ||
pair_filter = None | ||||
| ) |
Convert the current set of Modeller dynamic restraints (e.g.
soft-sphere, electrostatics) into equivalent IMP::Restraints. 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.)
| def IMP::modeller::ModelLoader::load_impropers | ( | self | ) |
Load the Modeller improper topology into the IMP model.
See load_bonds() for more details.
| 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.
| 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. |
