#include <ChemistryBase.hh>
Public Member Functions | |
| ChemistryBase (std::string const &name) | |
| std::string | name () const |
| Return the name of this Chemistry object. More... | |
| virtual void | apply (MutableResidueType &)=0 |
| Modify the passed ResidueType. 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... | |
Private Attributes | |
| std::string | name_ |
| ChemistryStatus | last_status_ |
Constructor & Destructor Documentation
◆ ChemistryBase()
|
inline |
Member Function Documentation
◆ apply()
|
pure virtual |
Modify the passed ResidueType.
Implemented in core::chemical::modifications::Reprotonate, protocols::rotamer_gen::RDKitRotamers, protocols::rotamer_gen::FragmentRotamers, protocols::drug_design::ReactionChemistry, protocols::chemistries::Chemistry, protocols::drug_design::SubstructureReplace, protocols::drug_design::SubstituentReplace, protocols::drug_design::ReactionMultiTransform, protocols::drug_design::ReactionGrow, protocols::drug_design::ReactionFragment, protocols::drug_design::ReactionBasedAnalogSampler, protocols::drug_design::RandomFragmentLigand, protocols::chemistries::WrappedBaseChemistry, and protocols::chemistries::PatchChemistry.
◆ get_additional_output()
|
inlinevirtual |
Get additional generated ResidueTypes, if any. This allows for 1-to-many Chemistries.
Reimplemented in protocols::drug_design::ReactionMultiTransform, and protocols::chemistries::WrappedBaseChemistry.
References core::chemical::modifications::FAIL_RETRY, get_last_status(), set_last_status(), and core::chemical::modifications::SUCCESS.
Referenced by protocols::drug_design::DrugPolishMover::apply().
◆ get_last_status()
|
inline |
What was the status of the last call to apply()/get_additional_output()
References last_status_.
Referenced by protocols::drug_design::DrugDesignMover::apply(), protocols::drug_design::DrugPolishMover::apply(), get_additional_output(), and protocols::drug_design::ReactionMultiTransform::get_additional_output().
◆ get_mapping()
|
virtual |
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.
Get the vertex mapping that was used for the last apply() The base class implementation defaults to an identity mapping.
Reimplemented in protocols::drug_design::ReactionChemistry, protocols::drug_design::SubstructureReplace, protocols::drug_design::SubstituentReplace, protocols::drug_design::ReactionMultiTransform, protocols::drug_design::ReactionGrow, protocols::drug_design::ReactionFragment, protocols::drug_design::ReactionBasedAnalogSampler, protocols::drug_design::RandomFragmentLigand, protocols::chemistries::WrappedBaseChemistry, protocols::chemistries::PatchChemistry, and core::chemical::modifications::Reprotonate.
Referenced by protocols::drug_design::DrugDesignMover::apply(), and protocols::drug_design::DrugPolishMover::apply().
◆ has_additional_output()
|
inlinevirtual |
Are there alternate ResidueTypes which are availible from the last time we called apply? (That is, will get_addtional_output() return non-null?)
Reimplemented in protocols::drug_design::ReactionMultiTransform, and protocols::chemistries::WrappedBaseChemistry.
◆ name()
|
inline |
Return the name of this Chemistry object.
References name_.
Referenced by protocols::drug_design::RandomFragmentLigand::apply(), and protocols::drug_design::DrugDesignMover::apply().
◆ set_last_status()
|
inline |
Set the status of the chemistry object.
References last_status_.
Referenced by protocols::chemistries::WrappedBaseChemistry::apply(), protocols::drug_design::RandomFragmentLigand::apply(), protocols::drug_design::ReactionBasedAnalogSampler::apply(), protocols::drug_design::ReactionFragment::apply(), protocols::drug_design::ReactionGrow::apply(), protocols::drug_design::ReactionMultiTransform::apply(), protocols::drug_design::SubstituentReplace::apply(), protocols::drug_design::SubstructureReplace::apply(), core::chemical::modifications::Reprotonate::apply(), get_additional_output(), and protocols::drug_design::ReactionMultiTransform::get_additional_output().
Member Data Documentation
◆ last_status_
|
private |
Referenced by get_last_status(), and set_last_status().
◆ name_
|
private |
Referenced by name().
The documentation for this class was generated from the following files:
- src/core/chemical/modifications/ChemistryBase.hh
- src/core/chemical/modifications/ChemistryBase.cc
