#include <ReactionChemistry.hh>
Public Member Functions | |
| ReactionChemistry (std::string const &type) | |
| void | apply (core::chemical::MutableResidueType &) override=0 |
| Modify the passed ResidueType. More... | |
| virtual void | reaction_file (std::string filename, bool append=false) |
| The file which contains the reactions which to use. More... | |
| virtual void | add_reaction (::RDKit::ChemicalReactionOP rxn, core::Real weight) |
| Add a reaction to the list of reactions known by this Chemistry. More... | |
| void | prefilter_reactions (utility::vector1< ::RDKit::ROMolOP > const &reactants, bool exclude_first=true) |
| Filter reaction list for those compatible with the given reactants. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datacache) override=0 |
| Initialize any data members of this instance from an input tag and a DataMap object. More... | |
| core::chemical::VDVDMapping | get_mapping () const override=0 |
| 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... | |
 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... | |
| 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... | |
Protected Member Functions | |
| void | filter_reactions (::RDKit::ROMol const &rdmol, utility::vector1< ::RDKit::ChemicalReactionOP > &rxns, numeric::random::WeightedSampler &rxn_sampler) const |
| Filter the reactions to just the ones which can be applied to rdmol If the reactions are multi-component, is assumed that the rdmol (derived from input residue passed to apply()) will be passed as the first reactant to the reaction. More... | |
| bool | cleanup_product (::RDKit::RWMol &prod) const |
| attempt to clean up the product of an RDKit reaction Modifies the RWMol in place - if modification unsuccessful, it will return true. More... | |
| utility::vector1< std::pair< ::RDKit::ChemicalReactionOP, core::Real > > const & | get_reactions () const |
Private Member Functions | |
| ReactionChemistry () | |
Private Attributes | |
| utility::vector1< std::pair< ::RDKit::ChemicalReactionOP, core::Real > > | reactions_ |
| The chemical reactions to use. More... | |
Constructor & Destructor Documentation
◆ ReactionChemistry() [1/2]
|
private |
◆ ReactionChemistry() [2/2]
| protocols::drug_design::ReactionChemistry::ReactionChemistry | ( | std::string const & | type | ) |
Member Function Documentation
◆ add_reaction()
|
virtual |
Add a reaction to the list of reactions known by this Chemistry.
Default reaction addition - just add as is;.
Reimplemented in protocols::drug_design::ReactionMultiTransform, protocols::drug_design::ReactionGrow, and protocols::drug_design::ReactionFragment.
References reactions_, and protocols::drug_design::TR().
Referenced by protocols::drug_design::ReactionFragment::add_reaction(), protocols::drug_design::ReactionGrow::add_reaction(), protocols::drug_design::ReactionMultiTransform::add_reaction(), and reaction_file().
◆ apply()
|
overridepure virtual |
Modify the passed ResidueType.
if you have a Pose, call the one which takes the Pose context
Implements protocols::chemistries::Chemistry.
Implemented in protocols::drug_design::ReactionMultiTransform, protocols::drug_design::ReactionGrow, and protocols::drug_design::ReactionFragment.
◆ cleanup_product()
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protected |
attempt to clean up the product of an RDKit reaction Modifies the RWMol in place - if modification unsuccessful, it will return true.
References core::chemical::rdkit::get_forcefield(), and protocols::drug_design::TR().
Referenced by protocols::drug_design::ReactionFragment::apply(), protocols::drug_design::ReactionGrow::apply(), and protocols::drug_design::ReactionMultiTransform::apply().
◆ filter_reactions()
|
protected |
Filter the reactions to just the ones which can be applied to rdmol If the reactions are multi-component, is assumed that the rdmol (derived from input residue passed to apply()) will be passed as the first reactant to the reaction.
References reactions_.
Referenced by protocols::drug_design::ReactionFragment::apply(), protocols::drug_design::ReactionGrow::apply(), and protocols::drug_design::ReactionMultiTransform::apply().
◆ get_mapping()
|
overridepure 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 from core::chemical::modifications::ChemistryBase.
Implemented in protocols::drug_design::ReactionMultiTransform, protocols::drug_design::ReactionGrow, and protocols::drug_design::ReactionFragment.
◆ get_reactions()
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protected |
References reactions_.
Referenced by protocols::drug_design::ReactionGrow::prefilter_fragments().
◆ parse_my_tag()
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overridepure virtual |
Initialize any data members of this instance from an input tag and a DataMap object.
Implements protocols::chemistries::Chemistry.
Implemented in protocols::drug_design::ReactionMultiTransform, protocols::drug_design::ReactionGrow, and protocols::drug_design::ReactionFragment.
◆ prefilter_reactions()
| void protocols::drug_design::ReactionChemistry::prefilter_reactions | ( | utility::vector1< ::RDKit::ROMolOP > const & | reactants, |
| bool | exclude_first = true |
||
| ) |
Filter reaction list for those compatible with the given reactants.
Discarded reactions will be discarded permanently. Only call with the finalized fragment list.
References reactions_, core::id::swap(), and protocols::drug_design::TR().
Referenced by protocols::drug_design::ReactionGrow::prefilter_reactions().
◆ reaction_file()
|
virtual |
The file which contains the reactions which to use.
References add_reaction(), protocols::abinitio::filename(), reactions_, and protocols::drug_design::TR().
Referenced by protocols::drug_design::ReactionFragment::parse_my_tag(), protocols::drug_design::ReactionGrow::parse_my_tag(), and protocols::drug_design::ReactionMultiTransform::parse_my_tag().
Member Data Documentation
◆ reactions_
|
private |
The chemical reactions to use.
Referenced by add_reaction(), filter_reactions(), get_reactions(), prefilter_reactions(), and reaction_file().
The documentation for this class was generated from the following files:
- src/protocols/drug_design/ReactionChemistry.hh
- src/protocols/drug_design/ReactionChemistry.cc
