#include <ReactionBasedAnalogSampler.hh>

Inheritance diagram for protocols::drug_design::ReactionBasedAnalogSampler:

[legend]

Classes
struct	Product

struct	Reagent

Public Member Functions
	ReactionBasedAnalogSampler ()

	~ReactionBasedAnalogSampler () override

void	apply (core::chemical::MutableResidueType &) override
	Modify the passed ResidueType. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datacache) override
	Initialize any data members of this instance from an input tag and a DataMap object. More...

core::chemical::VDVDMapping	get_mapping () const override
	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...

void	reset_spl_ratio ()

void	load_reactions (std::string const &reaction_dir, std::string const &filename)
	load reaction files from a designated path (deprecated) More...

void	load_reactions (std::string const &filename)
	load reactions from a single file 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...

Static Public Member Functions
static std::string	class_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Private Member Functions
void	load_all_reagents ()
	load reagents through corresponding reactions (deprecated) More...

void	load_all_reagents (std::string const &filename)
	load reagents from a single file More...

bool	check_reagent_validity (::RDKit::ROMOL_SPTR reag) const
	check if the reagent contains bad structures that would later fail RDKit More...

utility::vector1< Product >	sample (std::list< std::pair< core::Real, core::Size > > &score_idx_set) const
	Draw samples given a list of fragment similarity to reference input. More...

utility::vector1< Product >	sample_fragment (utility::vector1< std::list< std::pair< core::Real, core::Size > > > &score_idx_set) const
	Draw samples given lists of fragment similarity to first round product reagents. More...

Product	sample_candidate (const utility::vector1< Product > &candidate_set, const ::RDKit::RWMOL_SPTR rdmol)
	Draw a product from the given candidate set. More...

std::shared_ptr<::RDKit::SparseIntVect< unsigned int > >	getMorganFingerprint (::RDKit::ROMol const &mol, bool useFeatures=false) const
	A helper function to easily switch between using ECFP and FCFP. More...

core::chemical::IndexIndexMapping	find_O3A_mapping (::RDKit::ROMOL_SPTR from, ::RDKit::ROMOL_SPTR to) const
	Find a common substructure mapping using RDKit Open3DAlign method. More...

void	geometric_sampling (numeric::random::WeightedSampler &sampler, core::Size N)
	Setup weights for a sampler. Weighted sampling with geometric distribution; common ratio dynamically decided by population size. More...

utility::vector1< Product >	analog_search (const ReactionBasedAnalogSampler::Product &prod) const
	Return analogs of the chosen product, can be itself. More...

void	pair (core::Size r_no, utility::vector1< utility::vector1< core::Size > > const &sets, utility::vector1< Product > &candidates, int &revisits) const
	Find all pair of reagents that can undergo the specific reaction from the current sets. More...

void	pair (core::Size curr_no, core::Size r_no, utility::vector1< core::Size > single_pair, utility::vector1< utility::vector1< core::Size > > &all_pairs, utility::vector1< utility::vector1< core::Size > > const &sets) const
	Helper function for pairing. Use a DFS to generate all pairs. More...

Product	run_reaction (utility::vector1< core::Size > const &reagents) const
	Run the reaction given the list of reagent indices. More...

Static Private Member Functions
static bool	sortbySim (const std::pair< core::Real, core::Size > &a, const std::pair< core::Real, core::Size > &b)
	helper function for comparing score_index paires More...

Private Attributes
std::unordered_set< Product, Product::HashFunction >	visited_

std::string	last_smiles_

std::unordered_map< std::string, ChemicalReactionOP >	rxns_

utility::vector1< Reagent >	reagents_

numeric::random::WeightedSampler	reagent_sampler_

core::Real	geo_spl_ratio_

bool	dynamic_sampling_

utility::vector1< core::Real >	dynamic_spl_ratios_

core::Size	minCandidates_

core::chemical::VDVDMapping	mapping_

Constructor & Destructor Documentation

◆ ReactionBasedAnalogSampler()

protocols::drug_design::ReactionBasedAnalogSampler::ReactionBasedAnalogSampler ( )

◆ ~ReactionBasedAnalogSampler()

protocols::drug_design::ReactionBasedAnalogSampler::~ReactionBasedAnalogSampler ( )

override

Member Function Documentation

◆ analog_search()

utility::vector1< ReactionBasedAnalogSampler::Product > protocols::drug_design::ReactionBasedAnalogSampler::analog_search ( const ReactionBasedAnalogSampler::Product & prod ) const

private

Return analogs of the chosen product, can be itself.

References protocols::drug_design::ReactionBasedAnalogSampler::Reagent::fp_, protocols::drug_design::ReactionBasedAnalogSampler::Product::frags_, reagents_, sample_fragment(), and protocols::hybridization::score.

◆ apply()

void protocols::drug_design::ReactionBasedAnalogSampler::apply ( core::chemical::MutableResidueType & )

overridevirtual

Modify the passed ResidueType.

if you have a Pose, call the one which takes the Pose context

Implements protocols::chemistries::Chemistry.

References core::chemical::ResidueTypeBase::add_string_property(), core::chemical::MutableResidueType::atom_name(), core::chemical::MutableResidueType::bonded_heavyatoms(), core::chemical::AtomRefMapping< FromRef, ToRef >::clear(), core::chemical::combine(), dynamic_sampling_, dynamic_spl_ratios_, core::chemical::AtomRefMapping< FromRef, ToRef >::empty(), core::chemical::modifications::FAIL_DO_NOT_RETRY, find_O3A_mapping(), core::chemical::rdkit::RDMolToRestype::generate_restype(), geo_spl_ratio_, geometric_sampling(), core::chemical::AtomRefMapping< FromRef, ToRef >::identity(), core::chemical::rdkit::RDMolToRestype::index_to_vd(), core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_entry(), core::chemical::INVALID_VD, core::chemical::rdkit::label_with_index(), last_smiles_, mapping_, protocols::mean_field::min(), core::chemical::rdkit::RestypeToRDMol::Mol(), core::chemical::MutableResidueType::nbr_vertex(), core::pack::dunbrack::product(), core::chemical::ResidueTypeBase::properties(), reagent_sampler_, reagents_, reset_spl_ratio(), rxns_, sample(), sample_candidate(), protocols::hybridization::score, core::chemical::modifications::ChemistryBase::set_last_status(), core::chemical::rdkit::RDMolToRestype::set_nbr(), core::chemical::ResidueProperties::string_properties(), core::chemical::modifications::SUCCESS, core::id::to_string(), protocols::drug_design::TR(), core::chemical::rdkit::RestypeToRDMol::vd_to_index(), and visited_.

◆ check_reagent_validity()

bool protocols::drug_design::ReactionBasedAnalogSampler::check_reagent_validity ( ::RDKit::ROMOL_SPTR reag ) const

private

check if the reagent contains bad structures that would later fail RDKit

Referenced by load_all_reagents().

◆ class_name()

std::string protocols::drug_design::ReactionBasedAnalogSampler::class_name ( )

static

Referenced by protocols::drug_design::ReactionBasedAnalogSamplerCreator::keyname(), and provide_xml_schema().

◆ find_O3A_mapping()

core::chemical::IndexIndexMapping protocols::drug_design::ReactionBasedAnalogSampler::find_O3A_mapping	(	::RDKit::ROMOL_SPTR	from,
		::RDKit::ROMOL_SPTR	to
	)		const

private

Find a common substructure mapping using RDKit Open3DAlign method.

References core::chemical::rdkit::convert_match_vect_to_index_index_map(), core::chemical::AtomRefMapping< FromRef, ToRef >::reverse(), protocols::hybridization::score, and protocols::drug_design::TR().

Referenced by apply().

◆ geometric_sampling()

void protocols::drug_design::ReactionBasedAnalogSampler::geometric_sampling	(	numeric::random::WeightedSampler &	sampler,
		core::Size	N
	)

private

Setup weights for a sampler. Weighted sampling with geometric distribution; common ratio dynamically decided by population size.

References geo_spl_ratio_, protocols::mean_field::max(), core::chemical::element::N, and core::chemical::rings::q.

Referenced by apply(), load_all_reagents(), and sample_candidate().

◆ get_mapping()

core::chemical::VDVDMapping protocols::drug_design::ReactionBasedAnalogSampler::get_mapping ( ) const

overridevirtual

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.

References mapping_.

◆ getMorganFingerprint()

std::shared_ptr<::RDKit::SparseIntVect< unsigned int > > protocols::drug_design::ReactionBasedAnalogSampler::getMorganFingerprint	(	::RDKit::ROMol const &	mol,
		bool	useFeatures = `false`
	)		const

private

A helper function to easily switch between using ECFP and FCFP.

◆ load_all_reagents() [1/2]

void protocols::drug_design::ReactionBasedAnalogSampler::load_all_reagents ( )

private

load reagents through corresponding reactions (deprecated)

References protocols::drug_design::ReactionBasedAnalogSampler::Reagent::fp_, geometric_sampling(), protocols::drug_design::ReactionBasedAnalogSampler::Reagent::no_, protocols::drug_design::ReactionBasedAnalogSampler::Reagent::rdmol_, reagent_sampler_, reagents_, protocols::drug_design::ReactionBasedAnalogSampler::Reagent::rxn_, rxns_, and protocols::drug_design::TR().

Referenced by parse_my_tag().

◆ load_all_reagents() [2/2]

void protocols::drug_design::ReactionBasedAnalogSampler::load_all_reagents ( std::string const & filename )

private

load reagents from a single file

References check_reagent_validity(), protocols::abinitio::filename(), protocols::drug_design::ReactionBasedAnalogSampler::Reagent::fp_, geometric_sampling(), protocols::drug_design::ReactionBasedAnalogSampler::Reagent::no_, protocols::drug_design::ReactionBasedAnalogSampler::Reagent::rdmol_, reagent_sampler_, reagents_, protocols::drug_design::ReactionBasedAnalogSampler::Reagent::rxn_, and protocols::drug_design::TR().

◆ load_reactions() [1/2]

void protocols::drug_design::ReactionBasedAnalogSampler::load_reactions ( std::string const & filename )

load reactions from a single file

References protocols::abinitio::filename(), rxns_, and protocols::drug_design::TR().

◆ load_reactions() [2/2]

void protocols::drug_design::ReactionBasedAnalogSampler::load_reactions	(	std::string const &	reaction_dir,
		std::string const &	filename
	)

load reaction files from a designated path (deprecated)

References protocols::abinitio::filename(), rxns_, and protocols::drug_design::TR().

Referenced by parse_my_tag().

◆ pair() [1/2]

void protocols::drug_design::ReactionBasedAnalogSampler::pair	(	core::Size	curr_no,
		core::Size	r_no,
		utility::vector1< core::Size >	single_pair,
		utility::vector1< utility::vector1< core::Size > > &	all_pairs,
		utility::vector1< utility::vector1< core::Size > > const &	sets
	)		const

private

Helper function for pairing. Use a DFS to generate all pairs.

References pair().

◆ pair() [2/2]

void protocols::drug_design::ReactionBasedAnalogSampler::pair	(	core::Size	r_no,
		utility::vector1< utility::vector1< core::Size > > const &	sets,
		utility::vector1< Product > &	candidates,
		int &	revisits
	)		const

private

Find all pair of reagents that can undergo the specific reaction from the current sets.

References protocols::drug_design::ReactionBasedAnalogSampler::Product::rdmol_, run_reaction(), and visited_.

Referenced by pair(), sample(), and sample_fragment().

◆ parse_my_tag()

void protocols::drug_design::ReactionBasedAnalogSampler::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datacache
	)

overridevirtual

Initialize any data members of this instance from an input tag and a DataMap object.

Implements protocols::chemistries::Chemistry.

References dynamic_sampling_, dynamic_spl_ratios_, geo_spl_ratio_, last_smiles_, load_all_reagents(), load_reactions(), minCandidates_, and protocols::drug_design::TR().

◆ provide_xml_schema()

void protocols::drug_design::ReactionBasedAnalogSampler::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and protocols::chemistries::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::drug_design::ReactionBasedAnalogSamplerCreator::provide_xml_schema().

◆ reset_spl_ratio()

void protocols::drug_design::ReactionBasedAnalogSampler::reset_spl_ratio ( )

inline

References dynamic_spl_ratios_, and geo_spl_ratio_.

Referenced by apply().

◆ run_reaction()

ReactionBasedAnalogSampler::Product protocols::drug_design::ReactionBasedAnalogSampler::run_reaction ( utility::vector1< core::Size > const & reagents ) const

private

Run the reaction given the list of reagent indices.

References protocols::drug_design::ReactionBasedAnalogSampler::Product::fp_, protocols::drug_design::ReactionBasedAnalogSampler::Product::frags_, core::chemical::rdkit::neutralize_rdmol(), protocols::drug_design::ReactionBasedAnalogSampler::Product::rdmol_, reagents_, rxns_, protocols::drug_design::ReactionBasedAnalogSampler::Product::smiles_, and protocols::drug_design::TR().

Referenced by pair().

◆ sample()

utility::vector1< ReactionBasedAnalogSampler::Product > protocols::drug_design::ReactionBasedAnalogSampler::sample ( std::list< std::pair< core::Real, core::Size > > & score_idx_set ) const

private

Draw samples given a list of fragment similarity to reference input.

References core::sequence::end, minCandidates_, pair(), reagent_sampler_, reagents_, rxns_, and protocols::drug_design::TR().

Referenced by apply(), and sample_fragment().

◆ sample_candidate()

ReactionBasedAnalogSampler::Product protocols::drug_design::ReactionBasedAnalogSampler::sample_candidate	(	const utility::vector1< Product > &	candidate_set,
		const ::RDKit::RWMOL_SPTR	rdmol
	)

private

Draw a product from the given candidate set.

References geometric_sampling(), protocols::drug_design::ReactionBasedAnalogSampler::Product::smiles_, sortbySim(), and protocols::drug_design::TR().

Referenced by apply().

◆ sample_fragment()

utility::vector1< ReactionBasedAnalogSampler::Product > protocols::drug_design::ReactionBasedAnalogSampler::sample_fragment ( utility::vector1< std::list< std::pair< core::Real, core::Size > > > & score_idx_set ) const

private

Draw samples given lists of fragment similarity to first round product reagents.

References core::sequence::end, minCandidates_, pair(), reagent_sampler_, reagents_, rxns_, sample(), and protocols::drug_design::TR().

Referenced by analog_search().

◆ sortbySim()

bool protocols::drug_design::ReactionBasedAnalogSampler::sortbySim	(	const std::pair< core::Real, core::Size > &	a,
		const std::pair< core::Real, core::Size > &	b
	)

staticprivate

helper function for comparing score_index paires

References core::pose::motif::a(), and protocols::match::upstream::b.

Referenced by sample_candidate().

Member Data Documentation

◆ dynamic_sampling_

bool protocols::drug_design::ReactionBasedAnalogSampler::dynamic_sampling_

private

Referenced by apply(), and parse_my_tag().

◆ dynamic_spl_ratios_

utility::vector1< core::Real > protocols::drug_design::ReactionBasedAnalogSampler::dynamic_spl_ratios_

private

Referenced by apply(), parse_my_tag(), and reset_spl_ratio().

◆ geo_spl_ratio_

core::Real protocols::drug_design::ReactionBasedAnalogSampler::geo_spl_ratio_

private

Referenced by apply(), geometric_sampling(), parse_my_tag(), and reset_spl_ratio().

◆ last_smiles_

std::string protocols::drug_design::ReactionBasedAnalogSampler::last_smiles_

private

Referenced by apply(), and parse_my_tag().

◆ mapping_

core::chemical::VDVDMapping protocols::drug_design::ReactionBasedAnalogSampler::mapping_

private

Referenced by apply(), and get_mapping().

◆ minCandidates_

core::Size protocols::drug_design::ReactionBasedAnalogSampler::minCandidates_

private

Referenced by parse_my_tag(), sample(), and sample_fragment().

◆ reagent_sampler_

numeric::random::WeightedSampler protocols::drug_design::ReactionBasedAnalogSampler::reagent_sampler_

private

Referenced by apply(), load_all_reagents(), sample(), and sample_fragment().

◆ reagents_

utility::vector1< Reagent > protocols::drug_design::ReactionBasedAnalogSampler::reagents_

private

Referenced by analog_search(), apply(), load_all_reagents(), run_reaction(), sample(), and sample_fragment().

◆ rxns_

std::unordered_map< std::string, ChemicalReactionOP > protocols::drug_design::ReactionBasedAnalogSampler::rxns_

private

Referenced by apply(), load_all_reagents(), load_reactions(), run_reaction(), sample(), and sample_fragment().

◆ visited_

std::unordered_set< Product, Product::HashFunction > protocols::drug_design::ReactionBasedAnalogSampler::visited_

private

Referenced by apply(), and pair().

The documentation for this class was generated from the following files:

src/protocols/drug_design/ReactionBasedAnalogSampler.hh
src/protocols/drug_design/ReactionBasedAnalogSampler.cc

Classes

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ ReactionBasedAnalogSampler()

◆ ~ReactionBasedAnalogSampler()

Member Function Documentation

◆ analog_search()

◆ apply()

◆ check_reagent_validity()

◆ class_name()

◆ find_O3A_mapping()

◆ geometric_sampling()

◆ get_mapping()

◆ getMorganFingerprint()

◆ load_all_reagents() [1/2]

◆ load_all_reagents() [2/2]

◆ load_reactions() [1/2]

◆ load_reactions() [2/2]

◆ pair() [1/2]

◆ pair() [2/2]

◆ parse_my_tag()

◆ provide_xml_schema()

◆ reset_spl_ratio()

◆ run_reaction()

◆ sample()

◆ sample_candidate()

◆ sample_fragment()

◆ sortbySim()

Member Data Documentation

◆ dynamic_sampling_

◆ dynamic_spl_ratios_

◆ geo_spl_ratio_

◆ last_smiles_

◆ mapping_

◆ minCandidates_

◆ reagent_sampler_

◆ reagents_

◆ rxns_

◆ visited_