#include <RDKitRotamers.hh>
Public Member Functions | |
| RDKitRotamers () | |
| void | parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override |
| Initialize any data members of this instance from an input tag and a DataMap object. More... | |
| void | apply (core::chemical::MutableResidueType &restype) override |
| Modify the passed ResidueType. More... | |
 Public Member Functions inherited from protocols::chemistries::Chemistry | |
| Chemistry (std::string const &name) | |
| virtual void | apply (core::chemical::MutableResidueType &restype, core::pose::Pose const &) |
| Modify the passed ResidueType, context sensitive. More... | |
| Public Member Functions inherited from core::chemical::modifications::ChemistryBase | |
| ChemistryBase (std::string const &name) | |
| std::string | name () const |
| Return the name of this Chemistry object. More... | |
| virtual bool | has_additional_output () const |
| Are there alternate ResidueTypes which are availible from the last time we called apply? (That is, will get_addtional_output() return non-null?) More... | |
| virtual core::chemical::MutableResidueTypeOP | get_additional_output () |
| Get additional generated ResidueTypes, if any. This allows for 1-to-many Chemistries. More... | |
| virtual VDVDMapping | get_mapping () const |
| Get the vertex mapping that was used for the last apply() or get_additional_output() This is a mapping FROM the vds in the BEFORE MutableResidueType TO the vds in the AFTER MutableResidueType. The base class implementation defaults to an identity mapping. More... | |
| ChemistryStatus | get_last_status () const |
| What was the status of the last call to apply()/get_additional_output() More... | |
| void | set_last_status (ChemistryStatus setting) |
| Set the status of the chemistry object. More... | |
Static Public Member Functions | |
| static std::string | class_name () |
| static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
| static utility::vector1< std::map< std::string, core::Vector > > | generate_conformers (core::chemical::MutableResidueType const &rsdtype, core::Size nconf, bool minimize=false) |
Constructor & Destructor Documentation
◆ RDKitRotamers()
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inline |
Member Function Documentation
◆ apply()
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overridevirtual |
Modify the passed ResidueType.
if you have a Pose, call the one which takes the Pose context
Implements protocols::chemistries::Chemistry.
References generate_conformers(), core::chemical::ResidueTypeBase::name(), core::chemical::MutableResidueType::nchi(), core::chemical::ResidueTypeBase::rotamer_library_specification(), and protocols::rotamer_gen::TR().
◆ class_name()
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static |
Referenced by protocols::rotamer_gen::RDKitRotamersCreator::keyname(), and provide_xml_schema().
◆ generate_conformers()
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static |
References core::chemical::MutableResidueType::all_atoms(), core::chemical::MutableResidueType::atom_name(), core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_entry(), protocols::antibody::design::minimize, core::chemical::rdkit::RestypeToRDMol::Mol(), core::chemical::ResidueTypeBase::name(), protocols::rotamer_gen::TR(), and core::chemical::rdkit::RestypeToRDMol::vd_to_index().
Referenced by apply().
◆ parse_my_tag()
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overridevirtual |
Initialize any data members of this instance from an input tag and a DataMap object.
Implements protocols::chemistries::Chemistry.
◆ provide_xml_schema()
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static |
References class_name(), and protocols::chemistries::xsd_type_definition_w_attributes().
Referenced by protocols::rotamer_gen::RDKitRotamersCreator::provide_xml_schema().
The documentation for this class was generated from the following files:
- src/protocols/rotamer_gen/RDKitRotamers.hh
- src/protocols/rotamer_gen/RDKitRotamers.cc
