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FragCatalogEntry.h
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//
// Copyright (C) 2003-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef _RD_FRAGCATALOGENTRY_H_
#define _RD_FRAGCATALOGENTRY_H_
#include "FragCatParams.h"
#include <RDGeneral/utils.h>
#include <Catalogs/CatalogEntry.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Subgraphs/Subgraphs.h>
#include <GraphMol/Subgraphs/SubgraphUtils.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <map>
#include <sstream>
namespace RDKit {
class RDKIT_FRAGCATALOG_EXPORT FragCatalogEntry
: public RDCatalog::CatalogEntry {
public:
FragCatalogEntry() : d_descrip("") {
dp_props = new Dict();
setBitId(-1);
}
FragCatalogEntry(const ROMol *omol, const PATH_TYPE &path,
const MatchVectType &aidToFid);
FragCatalogEntry(const std::string &pickle);
~FragCatalogEntry() override {
delete dp_mol;
dp_mol = nullptr;
if (dp_props) {
delete dp_props;
dp_props = nullptr;
}
}
std::string getDescription() const override { return d_descrip; }
void setDescription(const std::string &val) { d_descrip = val; }
void setDescription(const FragCatParams *params);
// check if this fragment matches the one specified
//
bool match(const FragCatalogEntry *other, double tol) const;
Subgraphs::DiscrimTuple getDiscrims() const;
unsigned int getOrder() const { return dp_mol->getNumBonds(); }
const INT_INT_VECT_MAP &getFuncGroupMap() const { return d_aToFmap; }
// REVIEW: this should be removed?
std::string getSmarts() { return ""; }
// FUnctions on the property dictionary
template <typename T>
void setProp(const char *key, T &val) const {
dp_props->setVal(key, val);
}
template <typename T>
void setProp(const std::string &key, T &val) const {
setProp(key.c_str(), val);
}
void setProp(const char *key, int val) const { dp_props->setVal(key, val); }
void setProp(const std::string &key, int val) const {
setProp(key.c_str(), val);
}
void setProp(const char *key, float val) const { dp_props->setVal(key, val); }
void setProp(const std::string &key, float val) const {
setProp(key.c_str(), val);
}
void setProp(const std::string &key, std::string &val) const {
setProp(key.c_str(), val);
}
template <typename T>
void getProp(const char *key, T &res) const {
dp_props->getVal(key, res);
}
template <typename T>
void getProp(const std::string &key, T &res) const {
getProp(key.c_str(), res);
}
bool hasProp(const char *key) const {
if (!dp_props) {
return false;
}
return dp_props->hasVal(key);
}
bool hasProp(const std::string &key) const { return hasProp(key.c_str()); }
void clearProp(const char *key) const { dp_props->clearVal(key); }
void clearProp(const std::string &key) const { clearProp(key.c_str()); }
void toStream(std::ostream &ss) const override;
std::string Serialize() const override;
void initFromStream(std::istream &ss) override;
void initFromString(const std::string &text) override;
private:
ROMol *dp_mol{nullptr};
Dict *dp_props;
std::string d_descrip;
unsigned int d_order{0};
// a map between the atom ids in mol that connect to
// a functional group and the corresponding functional
// group ID
INT_INT_VECT_MAP d_aToFmap;
};
} // namespace RDKit
#endif
CatalogEntry.h
FragCatParams.h
RDKitBase.h
pulls in the core RDKit functionality
SmilesWrite.h
SubgraphUtils.h
Subgraphs.h
functionality for finding subgraphs and paths in molecules
SubstructMatch.h
RDCatalog::CatalogEntry
Abstract base class to be used to represent an entry in a Catalog.
Definition CatalogEntry.h:20
RDKit::Dict
The Dict class can be used to store objects of arbitrary type keyed by strings.
Definition Dict.h:36
RDKit::FragCatParams
container for user parameters used to create a fragment catalog
Definition FragCatParams.h:24
RDKit::FragCatalogEntry
Definition FragCatalogEntry.h:28
RDKit::FragCatalogEntry::setDescription
void setDescription(const FragCatParams *params)
RDKit::FragCatalogEntry::getFuncGroupMap
const INT_INT_VECT_MAP & getFuncGroupMap() const
Definition FragCatalogEntry.h:63
RDKit::FragCatalogEntry::~FragCatalogEntry
~FragCatalogEntry() override
Definition FragCatalogEntry.h:39
RDKit::FragCatalogEntry::match
bool match(const FragCatalogEntry *other, double tol) const
RDKit::FragCatalogEntry::getProp
void getProp(const std::string &key, T &res) const
Definition FragCatalogEntry.h:100
RDKit::FragCatalogEntry::FragCatalogEntry
FragCatalogEntry()
Definition FragCatalogEntry.h:30
RDKit::FragCatalogEntry::initFromStream
void initFromStream(std::istream &ss) override
initializes from a stream pickle
RDKit::FragCatalogEntry::setProp
void setProp(const std::string &key, std::string &val) const
Definition FragCatalogEntry.h:91
RDKit::FragCatalogEntry::setDescription
void setDescription(const std::string &val)
Definition FragCatalogEntry.h:50
RDKit::FragCatalogEntry::getDiscrims
Subgraphs::DiscrimTuple getDiscrims() const
RDKit::FragCatalogEntry::hasProp
bool hasProp(const char *key) const
Definition FragCatalogEntry.h:104
RDKit::FragCatalogEntry::FragCatalogEntry
FragCatalogEntry(const ROMol *omol, const PATH_TYPE &path, const MatchVectType &aidToFid)
RDKit::FragCatalogEntry::setProp
void setProp(const char *key, float val) const
Definition FragCatalogEntry.h:85
RDKit::FragCatalogEntry::getSmarts
std::string getSmarts()
Definition FragCatalogEntry.h:66
RDKit::FragCatalogEntry::FragCatalogEntry
FragCatalogEntry(const std::string &pickle)
RDKit::FragCatalogEntry::setProp
void setProp(const char *key, int val) const
Definition FragCatalogEntry.h:79
RDKit::FragCatalogEntry::setProp
void setProp(const std::string &key, float val) const
Definition FragCatalogEntry.h:87
RDKit::FragCatalogEntry::Serialize
std::string Serialize() const override
returns a string with a serialized (pickled) representation
RDKit::FragCatalogEntry::getOrder
unsigned int getOrder() const
Definition FragCatalogEntry.h:61
RDKit::FragCatalogEntry::setProp
void setProp(const std::string &key, T &val) const
Definition FragCatalogEntry.h:75
RDKit::FragCatalogEntry::getProp
void getProp(const char *key, T &res) const
Definition FragCatalogEntry.h:96
RDKit::FragCatalogEntry::setProp
void setProp(const std::string &key, int val) const
Definition FragCatalogEntry.h:81
RDKit::FragCatalogEntry::setProp
void setProp(const char *key, T &val) const
Definition FragCatalogEntry.h:70
RDKit::FragCatalogEntry::clearProp
void clearProp(const std::string &key) const
Definition FragCatalogEntry.h:114
RDKit::FragCatalogEntry::clearProp
void clearProp(const char *key) const
Definition FragCatalogEntry.h:112
RDKit::FragCatalogEntry::initFromString
void initFromString(const std::string &text) override
initializes from a string pickle
RDKit::FragCatalogEntry::getDescription
std::string getDescription() const override
returns a text description of this entry
Definition FragCatalogEntry.h:48
RDKit::FragCatalogEntry::toStream
void toStream(std::ostream &ss) const override
serializes (pickles) to a stream
RDKit::FragCatalogEntry::hasProp
bool hasProp(const std::string &key) const
Definition FragCatalogEntry.h:110
RDKit::ROMol
Definition ROMol.h:199
export.h
RDKIT_FRAGCATALOG_EXPORT
#define RDKIT_FRAGCATALOG_EXPORT
Definition export.h:201
RDKit::Subgraphs::DiscrimTuple
std::tuple< std::uint32_t, std::uint32_t, std::uint32_t > DiscrimTuple
used to return path discriminators (three unsigned ints):
Definition SubgraphUtils.h:26
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::MatchVectType
std::vector< std::pair< int, int > > MatchVectType
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx)
Definition FragFPGenerator.h:24
RDKit::INT_INT_VECT_MAP
std::map< int, INT_VECT > INT_INT_VECT_MAP
Definition types.h:327
RDKit::PATH_TYPE
std::vector< int > PATH_TYPE
Definition Subgraphs.h:42
utils.h