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RDKit
Open-source cheminformatics and machine learning.
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#include <RGroupDecompData.h>
Classes | |
class | UsedLabels |
Public Member Functions | |
RGroupDecompData (const RWMol &inputCore, RGroupDecompositionParameters inputParams) | |
RGroupDecompData (const std::vector< ROMOL_SPTR > &inputCores, RGroupDecompositionParameters inputParams) | |
void | prepareCores () |
void | setRlabel (Atom *atom, int rlabel) |
void | prune () |
std::vector< RGroupMatch > | GetCurrentBestPermutation () const |
void | relabelCore (RWMol &core, std::map< int, int > &mappings, UsedLabels &used_labels, const std::set< int > &indexLabels, std::map< int, std::vector< int >> extraAtomRLabels) |
void | relabelRGroup (RGroupData &rgroup, const std::map< int, int > &mappings) |
void | relabel () |
size_t | compute_num_added_rgroups (const std::vector< size_t > &tied_permutation, std::vector< int > &heavy_counts) |
bool | process (bool pruneMatches, bool finalize=false) |
Public Attributes | |
std::map< int, RCore > | cores |
std::map< std::string, int > | newCores |
int | newCoreLabel = EMPTY_CORE_LABEL |
RGroupDecompositionParameters | params |
std::vector< std::vector< RGroupMatch > > | matches |
std::set< int > | labels |
std::vector< size_t > | permutation |
std::map< int, std::vector< int > > | userLabels |
std::vector< int > | processedRlabels |
std::map< int, int > | finalRlabelMapping |
Definition at line 22 of file RGroupDecompData.h.
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Definition at line 38 of file RGroupDecompData.h.
References cores, and prepareCores().
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Definition at line 45 of file RGroupDecompData.h.
References cores, and prepareCores().
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Definition at line 379 of file RGroupDecompData.h.
References labels, and matches.
Referenced by process().
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Definition at line 95 of file RGroupDecompData.h.
References CHECK_INVARIANT, cores, RDKit::getRlabels(), labels, matches, params, permutation, and RDKit::RGroupDecompositionParameters::removeAllHydrogenRGroups.
Referenced by relabel().
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Definition at line 55 of file RGroupDecompData.h.
References CHECK_INVARIANT, cores, RDKit::RGroupDecompositionParameters::onlyMatchAtRGroups, params, and RDKit::RGroupDecompositionParameters::prepareCore().
Referenced by RGroupDecompData().
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Definition at line 405 of file RGroupDecompData.h.
References RDKit::checkForTimeout(), compute_num_added_rgroups(), labels, matches, RDKit::CartesianProduct::maxPermutations, RDKit::CartesianProduct::next(), params, permutation, RDKit::CartesianProduct::permutation, prune(), relabel(), RDKit::score(), RDKit::RGroupDecompositionParameters::timeout, and RDKit::CartesianProduct::value().
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Definition at line 84 of file RGroupDecompData.h.
References matches, and permutation.
Referenced by process().
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Definition at line 322 of file RGroupDecompData.h.
References cores, finalRlabelMapping, GetCurrentBestPermutation(), relabelCore(), relabelRGroup(), and userLabels.
Referenced by process().
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Definition at line 172 of file RGroupDecompData.h.
References RDKit::RGroupDecompData::UsedLabels::add(), RDKit::RWMol::addAtom(), RDKit::RWMol::addBond(), CHECK_INVARIANT, RDKit::Atom::getAtomicNum(), RDKit::getRlabels(), RDKit::RGroupDecompData::UsedLabels::next(), setRlabel(), RDKit::Bond::SINGLE, and RDKit::ROMol::updatePropertyCache().
Referenced by relabel().
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Definition at line 267 of file RGroupDecompData.h.
References RDKit::RWMol::addAtom(), RDKit::RWMol::addBond(), RDKit::ROMol::beginAtoms(), CHECK_INVARIANT, RDKit::RGroupData::combinedMol, RDKit::done, RDKit::ROMol::endAtoms(), RDKit::Atom::getAtomicNum(), RDKit::RDProps::getProp(), RDKit::RDProps::hasProp(), RDKit::RGroupData::labelled, params, PRECONDITION, RDKit::MolOps::removeHs(), RDKit::RGroupDecompositionParameters::removeHydrogensPostMatch, RDKit::Atom::setIsotope(), RDKit::RDProps::setProp(), setRlabel(), RDKit::SIDECHAIN_RLABELS, RDKit::Bond::SINGLE, and RDKit::ROMol::updatePropertyCache().
Referenced by relabel().
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Definition at line 67 of file RGroupDecompData.h.
References RDKit::AtomMap, RDKit::common_properties::dummyLabel, RDKit::Isotope, RDKit::MDLRGroup, params, PRECONDITION, RDKit::RGroupDecompositionParameters::rgroupLabelling, RDKit::Atom::setAtomMapNum(), RDKit::setAtomRLabel(), RDKit::Atom::setIsotope(), RDKit::RDProps::setProp(), and RDKit::CIPLabeler::to_string().
Referenced by relabelCore(), and relabelRGroup().
std::map<int, RCore> RDKit::RGroupDecompData::cores |
Definition at line 24 of file RGroupDecompData.h.
Referenced by GetCurrentBestPermutation(), prepareCores(), relabel(), and RGroupDecompData().
std::map<int, int> RDKit::RGroupDecompData::finalRlabelMapping |
Definition at line 36 of file RGroupDecompData.h.
Referenced by relabel().
std::set<int> RDKit::RGroupDecompData::labels |
Definition at line 30 of file RGroupDecompData.h.
Referenced by compute_num_added_rgroups(), GetCurrentBestPermutation(), and process().
std::vector<std::vector<RGroupMatch> > RDKit::RGroupDecompData::matches |
Definition at line 29 of file RGroupDecompData.h.
Referenced by compute_num_added_rgroups(), GetCurrentBestPermutation(), process(), and prune().
int RDKit::RGroupDecompData::newCoreLabel = EMPTY_CORE_LABEL |
Definition at line 26 of file RGroupDecompData.h.
std::map<std::string, int> RDKit::RGroupDecompData::newCores |
Definition at line 25 of file RGroupDecompData.h.
RGroupDecompositionParameters RDKit::RGroupDecompData::params |
Definition at line 27 of file RGroupDecompData.h.
Referenced by GetCurrentBestPermutation(), prepareCores(), process(), relabelRGroup(), and setRlabel().
std::vector<size_t> RDKit::RGroupDecompData::permutation |
Definition at line 31 of file RGroupDecompData.h.
Referenced by GetCurrentBestPermutation(), process(), and prune().
std::vector<int> RDKit::RGroupDecompData::processedRlabels |
Definition at line 34 of file RGroupDecompData.h.
std::map<int, std::vector<int> > RDKit::RGroupDecompData::userLabels |
Definition at line 32 of file RGroupDecompData.h.
Referenced by relabel().