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RDKit
Open-source cheminformatics and machine learning.
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Substtructure Search a library of molecules. More...
#include <SubstructLibrary.h>
Public Member Functions | |
SubstructLibrary () | |
SubstructLibrary (boost::shared_ptr< MolHolderBase > molecules) | |
SubstructLibrary (boost::shared_ptr< MolHolderBase > molecules, boost::shared_ptr< FPHolderBase > fingerprints) | |
MolHolderBase & | getMolHolder () |
Get the underlying molecule holder implementation. More... | |
const MolHolderBase & | getMolecules () const |
FPHolderBase & | getFingerprints () |
Get the underlying fingerprint implementation. More... | |
const FPHolderBase & | getFingerprints () const |
unsigned int | addMol (const ROMol &mol) |
Add a molecule to the library. More... | |
std::vector< unsigned int > | getMatches (const ROMol &query, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1, int maxResults=-1) |
Get the matching indices for the query. More... | |
std::vector< unsigned int > | getMatches (const ROMol &query, unsigned int startIdx, unsigned int endIdx, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1, int maxResults=-1) |
Get the matching indices for the query between the given indices. More... | |
unsigned int | countMatches (const ROMol &query, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1) |
Return the number of matches for the query. More... | |
unsigned int | countMatches (const ROMol &query, unsigned int startIdx, unsigned int endIdx, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1) |
Return the number of matches for the query between the given indices. More... | |
bool | hasMatch (const ROMol &query, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1) |
Returns true if any match exists for the query. More... | |
bool | hasMatch (const ROMol &query, unsigned int startIdx, unsigned int endIdx, bool recursionPossible=true, bool useChirality=true, bool useQueryQueryMatches=false, int numThreads=-1) |
Returns true if any match exists for the query between the specified indices. More... | |
boost::shared_ptr< ROMol > | getMol (unsigned int idx) const |
Returns the molecule at the given index. More... | |
boost::shared_ptr< ROMol > | operator[] (unsigned int idx) |
Returns the molecule at the given index. More... | |
unsigned int | size () const |
return the number of molecules in the library More... | |
Substtructure Search a library of molecules.
This class allows for multithreaded substructure searches os large datasets.
The implementations can use fingerprints to speed up searches and have molecules cached as binary forms to reduce memory usage.
Definition at line 279 of file SubstructLibrary.h.
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Definition at line 286 of file SubstructLibrary.h.
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Definition at line 292 of file SubstructLibrary.h.
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Definition at line 295 of file SubstructLibrary.h.
unsigned int RDKit::SubstructLibrary::addMol | ( | const ROMol & | mol | ) |
Add a molecule to the library.
mol | Molecule to add |
returns index for the molecule in the library
unsigned int RDKit::SubstructLibrary::countMatches | ( | const ROMol & | query, |
bool | recursionPossible = true , |
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bool | useChirality = true , |
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bool | useQueryQueryMatches = false , |
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int | numThreads = -1 |
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Return the number of matches for the query.
query | Query to match against molecules |
recursionPossible | flags whether or not recursive matches are allowed [ default true ] |
useChirality | use atomic CIP codes as part of the comparison [ default true ] |
useQueryQueryMatches | if set, the contents of atom and bond queries [ default false ] will be used as part of the matching |
numThreads | If -1 use all available processors [default -1] |
unsigned int RDKit::SubstructLibrary::countMatches | ( | const ROMol & | query, |
unsigned int | startIdx, | ||
unsigned int | endIdx, | ||
bool | recursionPossible = true , |
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bool | useChirality = true , |
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bool | useQueryQueryMatches = false , |
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int | numThreads = -1 |
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Return the number of matches for the query between the given indices.
query | Query to match against molecules |
startIdx | Start index of the search |
endIdx | Ending idx (non-inclusive) of the search. |
recursionPossible | flags whether or not recursive matches are allowed [ default true ] |
useChirality | use atomic CIP codes as part of the comparison [ default true ] |
useQueryQueryMatches | if set, the contents of atom and bond queries [ default false ] will be used as part of the matching |
numThreads | If -1 use all available processors [default -1] |
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Get the underlying fingerprint implementation.
Throws a value error if no fingerprints have been set
Definition at line 315 of file SubstructLibrary.h.
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Definition at line 321 of file SubstructLibrary.h.
References RDKit::MolHolderBase::addMol().
std::vector<unsigned int> RDKit::SubstructLibrary::getMatches | ( | const ROMol & | query, |
bool | recursionPossible = true , |
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bool | useChirality = true , |
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bool | useQueryQueryMatches = false , |
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int | numThreads = -1 , |
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int | maxResults = -1 |
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Get the matching indices for the query.
query | Query to match against molecules |
recursionPossible | flags whether or not recursive matches are allowed [ default true ] |
useChirality | use atomic CIP codes as part of the comparison [ default true ] |
useQueryQueryMatches | if set, the contents of atom and bond queries [ default false ] will be used as part of the matching |
numThreads | If -1 use all available processors [default -1] |
maxResults | Maximum results to return, -1 means return all [default -1] |
std::vector<unsigned int> RDKit::SubstructLibrary::getMatches | ( | const ROMol & | query, |
unsigned int | startIdx, | ||
unsigned int | endIdx, | ||
bool | recursionPossible = true , |
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bool | useChirality = true , |
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bool | useQueryQueryMatches = false , |
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int | numThreads = -1 , |
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int | maxResults = -1 |
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) |
Get the matching indices for the query between the given indices.
query | Query to match against molecules |
startIdx | Start index of the search |
endIdx | Ending idx (non-inclusive) of the search. |
recursionPossible | flags whether or not recursive matches are allowed [ default true ] |
useChirality | use atomic CIP codes as part of the comparison [ default true ] |
useQueryQueryMatches | if set, the contents of atom and bond queries [ default false ] will be used as part of the matching |
numThreads | If -1 use all available processors [default -1] |
maxResults | Maximum results to return, -1 means return all [default -1] |
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Returns the molecule at the given index.
idx | Index of the molecule in the library |
Definition at line 441 of file SubstructLibrary.h.
References RDKit::MolHolderBase::getMol(), and PRECONDITION.
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Definition at line 308 of file SubstructLibrary.h.
References PRECONDITION.
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Get the underlying molecule holder implementation.
Definition at line 303 of file SubstructLibrary.h.
References PRECONDITION.
bool RDKit::SubstructLibrary::hasMatch | ( | const ROMol & | query, |
bool | recursionPossible = true , |
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bool | useChirality = true , |
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bool | useQueryQueryMatches = false , |
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int | numThreads = -1 |
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Returns true if any match exists for the query.
query | Query to match against molecules |
recursionPossible | flags whether or not recursive matches are allowed [ default true ] |
useChirality | use atomic CIP codes as part of the comparison [ default true ] |
useQueryQueryMatches | if set, the contents of atom and bond queries [ default false ] will be used as part of the matching |
numThreads | If -1 use all available processors [default -1] |
bool RDKit::SubstructLibrary::hasMatch | ( | const ROMol & | query, |
unsigned int | startIdx, | ||
unsigned int | endIdx, | ||
bool | recursionPossible = true , |
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bool | useChirality = true , |
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bool | useQueryQueryMatches = false , |
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int | numThreads = -1 |
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Returns true if any match exists for the query between the specified indices.
query | Query to match against molecules |
startIdx | Start index of the search |
endIdx | Ending idx (inclusive) of the search. |
recursionPossible | flags whether or not recursive matches are allowed [ default true ] |
useChirality | use atomic CIP codes as part of the comparison [ default true ] |
useQueryQueryMatches | if set, the contents of atom and bond queries [ default false ] will be used as part of the matching |
numThreads | If -1 use all available processors [default -1] |
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Returns the molecule at the given index.
idx | Index of the molecule in the library |
Definition at line 451 of file SubstructLibrary.h.
References RDKit::MolHolderBase::getMol(), and PRECONDITION.
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return the number of molecules in the library
Definition at line 458 of file SubstructLibrary.h.
References PRECONDITION.