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RDKit
Open-source cheminformatics and machine learning.
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A class to store information about a molecule's rings. More...
#include <RingInfo.h>
Public Types | |
typedef std::vector< int > | MemberType |
typedef std::vector< MemberType > | DataType |
typedef std::vector< int > | INT_VECT |
typedef std::vector< INT_VECT > | VECT_INT_VECT |
Public Member Functions | |
RingInfo () | |
RingInfo (const RingInfo &other)=default | |
RingInfo & | operator= (const RingInfo &other)=default |
RingInfo (RingInfo &&other) noexcept=default | |
RingInfo & | operator= (RingInfo &&other) noexcept=default |
bool | isInitialized () const |
checks to see if we've been properly initialized More... | |
void | initialize () |
does initialization More... | |
void | reset () |
blows out all current data and de-initializes More... | |
unsigned int | addRing (const INT_VECT &atomIndices, const INT_VECT &bondIndices) |
adds a ring to our data More... | |
Atom information | |
INT_VECT | atomRingSizes (unsigned int idx) const |
bool | isAtomInRingOfSize (unsigned int idx, unsigned int size) const |
returns whether or not the atom with index idx is in a size - ring. More... | |
unsigned int | numAtomRings (unsigned int idx) const |
returns the number of rings atom idx is involved in More... | |
unsigned int | minAtomRingSize (unsigned int idx) const |
returns the size of the smallest ring atom idx is involved in More... | |
const VECT_INT_VECT & | atomRings () const |
INT_VECT | atomMembers (unsigned int idx) const |
bool | areAtomsInSameRing (unsigned int idx1, unsigned int idx2) const |
bool | areAtomsInSameRingOfSize (unsigned int idx1, unsigned int idx2, unsigned int size) const |
Bond information | |
INT_VECT | bondRingSizes (unsigned int idx) const |
bool | isBondInRingOfSize (unsigned int idx, unsigned int size) const |
returns whether or not the bond with index idx is in a size - ring. More... | |
unsigned int | numBondRings (unsigned int idx) const |
returns the number of rings bond idx is involved in More... | |
unsigned int | minBondRingSize (unsigned int idx) const |
returns the size of the smallest ring bond idx is involved in More... | |
unsigned int | numRings () const |
returns the total number of rings More... | |
const VECT_INT_VECT & | bondRings () const |
INT_VECT | bondMembers (unsigned int idx) const |
bool | areBondsInSameRing (unsigned int idx1, unsigned int idx2) const |
bool | areBondsInSameRingOfSize (unsigned int idx1, unsigned int idx2, unsigned int size) const |
Friends | |
class | MolPickler |
A class to store information about a molecule's rings.
Definition at line 28 of file RingInfo.h.
typedef std::vector<MemberType> RDKit::RingInfo::DataType |
Definition at line 33 of file RingInfo.h.
typedef std::vector<int> RDKit::RingInfo::INT_VECT |
Definition at line 34 of file RingInfo.h.
typedef std::vector<int> RDKit::RingInfo::MemberType |
Definition at line 32 of file RingInfo.h.
typedef std::vector<INT_VECT> RDKit::RingInfo::VECT_INT_VECT |
Definition at line 35 of file RingInfo.h.
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inline |
Definition at line 37 of file RingInfo.h.
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default |
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defaultnoexcept |
unsigned int RDKit::RingInfo::addRing | ( | const INT_VECT & | atomIndices, |
const INT_VECT & | bondIndices | ||
) |
adds a ring to our data
atomIndices | the integer indices of the atoms involved in the ring |
bondIndices | the integer indices of the bonds involved in the ring, this must be the same size as atomIndices . |
Notes:
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inline |
returns whether or not atoms with indices idx1
and idx2
belong to the same ring.
Notes:
Definition at line 118 of file RingInfo.h.
References RDKit::MMFF::areAtomsInSameRingOfSize().
bool RDKit::RingInfo::areAtomsInSameRingOfSize | ( | unsigned int | idx1, |
unsigned int | idx2, | ||
unsigned int | size | ||
) | const |
returns whether or not atoms with indices idx1
and idx2
belong to the same ring of size size
.
Notes:
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inline |
returns whether or not bonds with indices idx1
and idx2
belong to the same ring.
Notes:
Definition at line 195 of file RingInfo.h.
bool RDKit::RingInfo::areBondsInSameRingOfSize | ( | unsigned int | idx1, |
unsigned int | idx2, | ||
unsigned int | size | ||
) | const |
returns whether or not bonds with indices idx1
and idx2
belong to the same ring of size size
.
Notes:
INT_VECT RDKit::RingInfo::atomMembers | ( | unsigned int | idx | ) | const |
returns our atom-members
vector for atom idx (i.e., a vector of ints reporting the ring indices that atom idx is member of), or an empty vector if the atom is not in any ring.
Notes:
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inline |
returns our atom-rings
vectors, i.e. a vector of int vectors reporting the atom indices which are part of each ring
Notes:
Definition at line 100 of file RingInfo.h.
INT_VECT RDKit::RingInfo::atomRingSizes | ( | unsigned int | idx | ) | const |
returns a vector with sizes of the rings that atom with index idx
is in.
Notes:
INT_VECT RDKit::RingInfo::bondMembers | ( | unsigned int | idx | ) | const |
returns our bond-members
vector for bond idx (i.e., a vector of ints reporting the ring indices that bond idx is member of), or an empty vector if the bond is not in any ring.
Notes:
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inline |
returns our bond-rings
vectors, i.e. a vector of int vectors reporting the bond indices which are part of each ring
Notes:
Definition at line 177 of file RingInfo.h.
Referenced by RDKit::FMCS::RingMatchTableSet::addTargetBondRingsIndeces(), RDKit::FMCS::RingMatchTableSet::computeRingMatchTable(), and RDKit::FMCS::RingMatchTableSet::init().
INT_VECT RDKit::RingInfo::bondRingSizes | ( | unsigned int | idx | ) | const |
returns a vector with sizes of the rings that bond with index idx
is in.
Notes:
void RDKit::RingInfo::initialize | ( | ) |
does initialization
bool RDKit::RingInfo::isAtomInRingOfSize | ( | unsigned int | idx, |
unsigned int | size | ||
) | const |
returns whether or not the atom with index idx
is in a size
- ring.
Notes:
Referenced by RDKit::queryAtomIsInRingOfSize().
bool RDKit::RingInfo::isBondInRingOfSize | ( | unsigned int | idx, |
unsigned int | size | ||
) | const |
returns whether or not the bond with index idx
is in a size
- ring.
Notes:
Referenced by RDKit::queryBondIsInRingOfSize().
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inline |
checks to see if we've been properly initialized
Definition at line 43 of file RingInfo.h.
unsigned int RDKit::RingInfo::minAtomRingSize | ( | unsigned int | idx | ) | const |
returns the size of the smallest ring atom idx
is involved in
Notes:
Referenced by RDKit::queryAtomMinRingSize().
unsigned int RDKit::RingInfo::minBondRingSize | ( | unsigned int | idx | ) | const |
returns the size of the smallest ring bond idx
is involved in
Notes:
Referenced by RDKit::queryBondMinRingSize().
unsigned int RDKit::RingInfo::numAtomRings | ( | unsigned int | idx | ) | const |
returns the number of rings atom idx
is involved in
Notes:
Referenced by RDKit::queryAtomRingMembership(), RDKit::queryIsAtomInNRings(), and RDKit::queryIsAtomInRing().
unsigned int RDKit::RingInfo::numBondRings | ( | unsigned int | idx | ) | const |
returns the number of rings bond idx
is involved in
Notes:
Referenced by RDKit::queryAtomHasRingBond(), RDKit::queryAtomRingBondCount(), RDKit::queryIsBondInNRings(), and RDKit::queryIsBondInRing().
unsigned int RDKit::RingInfo::numRings | ( | ) | const |
returns the total number of rings
Notes:
void RDKit::RingInfo::reset | ( | ) |
blows out all current data and de-initializes
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friend |
Definition at line 29 of file RingInfo.h.