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.
//
#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 FragCatalogEntry : public RDCatalog::CatalogEntry {
public :
FragCatalogEntry() : dp_mol(0),d_descrip(""),d_order(0) {
dp_props = new Dict();
setBitId(-1);
}
FragCatalogEntry(const ROMol *omol, const PATH_TYPE &path, const MatchVectType &aidToFid);
FragCatalogEntry(const std::string &pickle);
~FragCatalogEntry() {
delete dp_mol;
dp_mol=0;
if(dp_props){
delete dp_props;
dp_props=0;
}
}
std::string getDescription() const {return d_descrip;}
void setDescription(std::string val) {d_descrip = val;}
void setDescription(const FragCatParams *params);
// check if this fragment macthes 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;
std::string Serialize() const;
void initFromStream(std::istream &ss);
void initFromString(const std::string &text);
private:
ROMol *dp_mol;
Dict *dp_props;
std::string d_descrip;
unsigned int d_order;
// 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;
};
}
#endif
RDKit::FragCatalogEntry::getDiscrims
Subgraphs::DiscrimTuple getDiscrims() const
RDKit::FragCatalogEntry::setProp
void setProp(const char *key, int val) const
Definition: FragCatalogEntry.h:79
RDKit::FragCatalogEntry::match
bool match(const FragCatalogEntry *other, double tol) const
CatalogEntry.h
RDKit::FragCatalogEntry::clearProp
void clearProp(const std::string &key) const
Definition: FragCatalogEntry.h:120
RDKit::Dict::setVal
void setVal(const std::string &what, T &val)
Sets the value associated with a key.
Definition: Dict.h:170
RDKit::Subgraphs::DiscrimTuple
boost::tuples::tuple< boost::uint32_t, boost::uint32_t, boost::uint32_t > DiscrimTuple
used to return path discriminators (three unsigned ints):
Definition: SubgraphUtils.h:22
RDKit::FragCatalogEntry::initFromString
void initFromString(const std::string &text)
initializes from a string pickle
RDKit::FragCatalogEntry::Serialize
std::string Serialize() const
returns a string with a serialized (pickled) representation
RDKit::FragCatalogEntry::setDescription
void setDescription(std::string val)
Definition: FragCatalogEntry.h:48
RDKit::MatchVectType
std::vector< std::pair< int, int > > MatchVectType
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx) ...
Definition: FragFPGenerator.h:22
RDKit::FragCatalogEntry::toStream
void toStream(std::ostream &ss) const
serializes (pickles) to a stream
RDKit::FragCatalogEntry::getSmarts
std::string getSmarts()
Definition: FragCatalogEntry.h:68
RDKit::FragCatalogEntry::setProp
void setProp(const char *key, float val) const
Definition: FragCatalogEntry.h:87
SmilesWrite.h
SubgraphUtils.h
SubstructMatch.h
utils.h
RDKitBase.h
pulls in the core RDKit functionality
RDKit::FragCatalogEntry::setProp
void setProp(const std::string &key, int val) const
Definition: FragCatalogEntry.h:83
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:105
RDKit::FragCatalogEntry::setProp
void setProp(const std::string &key, std::string &val) const
Definition: FragCatalogEntry.h:95
RDKit::Dict::clearVal
void clearVal(const std::string &what)
Clears the value associated with a particular key, removing the key from the dictionary.
Definition: Dict.h:198
RDKit::FragCatalogEntry::hasProp
bool hasProp(const char *key) const
Definition: FragCatalogEntry.h:108
RDKit::Dict::getVal
void getVal(const std::string &what, T &res) const
Gets the value associated with a particular key.
Definition: Dict.h:86
RDKit::FragCatalogEntry
Definition: FragCatalogEntry.h:26
RDKit::FragCatalogEntry::clearProp
void clearProp(const char *key) const
Definition: FragCatalogEntry.h:116
RDCatalog::CatalogEntry::setBitId
void setBitId(int bid)
sets our bit Id
Definition: CatalogEntry.h:24
RDKit::ROMol::getNumBonds
unsigned int getNumBonds(bool onlyHeavy=1) const
returns our number of Bonds
RDKit::FragCatalogEntry::getFuncGroupMap
const INT_INT_VECT_MAP & getFuncGroupMap() const
Definition: FragCatalogEntry.h:63
RDKit::FragCatalogEntry::getProp
void getProp(const char *key, T &res) const
Definition: FragCatalogEntry.h:100
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::Dict::hasVal
bool hasVal(const char *what) const
Returns whether or not the dictionary contains a particular key.
Definition: Dict.h:50
RDKit::FragCatalogEntry::~FragCatalogEntry
~FragCatalogEntry()
Definition: FragCatalogEntry.h:37
RDCatalog::CatalogEntry
Abstract base class to be used to represent an entry in a Catalog.
Definition: CatalogEntry.h:19
RDKit::FragCatParams
container for user parameters used to create a fragment catalog
Definition: FragCatParams.h:24
RDKit::FragCatalogEntry::getOrder
unsigned int getOrder() const
Definition: FragCatalogEntry.h:59
RDKit::INT_INT_VECT_MAP
std::map< int, INT_VECT > INT_INT_VECT_MAP
Definition: types.h:182
RDKit::FragCatalogEntry::FragCatalogEntry
FragCatalogEntry()
Definition: FragCatalogEntry.h:29
Subgraphs.h
functionality for finding subgraphs and paths in molecules
RDKit::PATH_TYPE
std::vector< int > PATH_TYPE
Definition: Subgraphs.h:37
RDKit::FragCatalogEntry::hasProp
bool hasProp(const std::string &key) const
Definition: FragCatalogEntry.h:112
RDKit::FragCatalogEntry::setProp
void setProp(const std::string &key, T &val) const
Definition: FragCatalogEntry.h:75
RDKit::FragCatalogEntry::setProp
void setProp(const std::string &key, float val) const
Definition: FragCatalogEntry.h:91
FragCatParams.h
RDKit::FragCatalogEntry::getProp
void getProp(const std::string key, T &res) const
Definition: FragCatalogEntry.h:104
RDKit::Dict
The Dict class can be used to store objects of arbitrary type keyed by strings.
Definition: Dict.h:33
RDKit::FragCatalogEntry::setProp
void setProp(const char *key, T &val) const
Definition: FragCatalogEntry.h:71
RDKit::FragCatalogEntry::getDescription
std::string getDescription() const
returns a text description of this entry
Definition: FragCatalogEntry.h:46
RDKit::FragCatalogEntry::initFromStream
void initFromStream(std::istream &ss)
initializes from a stream pickle