Chemical Data Processing Library C++ API - Version 1.1.1
|
Contains classes and functions related to the generation and processing of pharmacophore and molecule descriptors. More...
Contains classes and functions related to the generation and processing of pharmacophore and molecule descriptors.
CDPL_DESCR_API double CDPL::Descr::calcGeometricalRadius | ( | const Chem::AtomContainer & | cntnr, |
const Chem::Atom3DCoordinatesFunction & | coords_func | ||
) |
CDPL_DESCR_API double CDPL::Descr::calcGeometricalDiameter | ( | const Chem::AtomContainer & | cntnr, |
const Chem::Atom3DCoordinatesFunction & | coords_func | ||
) |
CDPL_DESCR_API double CDPL::Descr::calcGeometricalRadius | ( | const Chem::Entity3DContainer & | cntnr | ) |
CDPL_DESCR_API double CDPL::Descr::calcGeometricalDiameter | ( | const Chem::Entity3DContainer & | cntnr | ) |
CDPL_DESCR_API std::size_t CDPL::Descr::calcTopologicalRadius | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API std::size_t CDPL::Descr::calcTopologicalDiameter | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API double CDPL::Descr::calcRingComplexity | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API double CDPL::Descr::calcMolecularComplexity | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API double CDPL::Descr::calcKierShape1 | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API double CDPL::Descr::calcKierShape2 | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API double CDPL::Descr::calcKierShape3 | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API std::size_t CDPL::Descr::calcWienerIndex | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API double CDPL::Descr::calcRandicIndex | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API std::size_t CDPL::Descr::calcZagrebIndex1 | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API std::size_t CDPL::Descr::calcZagrebIndex2 | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API std::size_t CDPL::Descr::calcTotalWalkCount | ( | const Chem::MolecularGraph & | molgraph | ) |
CDPL_DESCR_API double CDPL::Descr::calcTanimotoSimilarity | ( | const Util::BitSet & | bs1, |
const Util::BitSet & | bs2 | ||
) |
Calculates the Tanimoto Similarity Measure [CITB] for the given bitsets bs1 and bs2.
The Tanimoto Similarity Measure \( S_{ab} \) is calculated by:
\[ S_{ab} = \frac{N_{ab}}{N_a + N_b - N_{ab}} \]
where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are set in the first bitset and \( N_b \) is the number of bits that are set in the second bitset.
If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.
bs1 | The first bitset. |
bs2 | The second bitset. |
CDPL_DESCR_API double CDPL::Descr::calcCosineSimilarity | ( | const Util::BitSet & | bs1, |
const Util::BitSet & | bs2 | ||
) |
Calculates the Cosine Similarity Measure [WCOS] for the given bitsets bs1 and bs2.
The Cosine Similarity Measure \( S_{ab} \) is calculated by:
\[ S_{ab} = \frac{N_{ab}}{\sqrt{N_a * N_b}} \]
where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are set in the first bitset and \( N_b \) is the number of bits that are set in the second bitset.
If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.
bs1 | The first bitset. |
bs2 | The second bitset. |
CDPL_DESCR_API double CDPL::Descr::calcEuclideanSimilarity | ( | const Util::BitSet & | bs1, |
const Util::BitSet & | bs2 | ||
) |
Calculates the Euclidean Similarity Measure [GSIM] for the given bitsets bs1 and bs2.
The Euclidean Similarity Measure \( S_{ab} \) is calculated by:
\[ S_{ab} = \sqrt{\frac{N_{ab} + N_{!ab}}{N_a + N_b + N_{ab} + N_{!ab}}} \]
where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are set only in the first bitset, \( N_b \) is the number of bits that are set only in the second bitset and \( N_{!ab} \) is the number of bits that are not set in both bitsets.
If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.
bs1 | The first bitset. |
bs2 | The second bitset. |
CDPL_DESCR_API double CDPL::Descr::calcManhattanSimilarity | ( | const Util::BitSet & | bs1, |
const Util::BitSet & | bs2 | ||
) |
Calculates the Manhattan Similarity Measure [GSIM] for the given bitsets bs1 and bs2.
The Manhattan Similarity Measure \( S_{ab} \) is calculated by:
\[ S_{ab} = \frac{N_a + N_b}{N_a + N_b + N_{ab} + N_{!ab}} \]
where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are set only in the first bitset, \( N_b \) is the number of bits that are set only in the second bitset and \( N_{!ab} \) is the number of bits that are not set in both bitsets.
If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.
bs1 | The first bitset. |
bs2 | The second bitset. |
CDPL_DESCR_API double CDPL::Descr::calcDiceSimilarity | ( | const Util::BitSet & | bs1, |
const Util::BitSet & | bs2 | ||
) |
Calculates the Dice Similarity Measure [GSIM] for the given bitsets bs1 and bs2.
The Dice Similarity Measure \( S_{ab} \) is calculated by:
\[ S_{ab} = \frac{2 * N_{ab}}{N_a + N_b + 2 * N_{ab}} \]
where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are only set in the first bitset and \( N_b \) is the number of bits that are only set in the second bitset.
If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.
bs1 | The first bitset. |
bs2 | The second bitset. |
CDPL_DESCR_API double CDPL::Descr::calcTverskySimilarity | ( | const Util::BitSet & | bs1, |
const Util::BitSet & | bs2, | ||
double | a, | ||
double | b | ||
) |
Calculates the Tversky Similarity Measure [GSIM] for the given bitsets bs1 and bs2.
The Tversky Similarity Measure \( S_{ab} \) is calculated by:
\[ S_{ab} = \frac{N_{ab}}{a * N_a + b * N_b + N_{ab}} \]
where \( N_{ab} \) is the number of bits that are set in both bitsets, \( N_a \) is the number of bits that are only set in the first bitset and \( N_b \) is the number of bits that are only set in the second bitset. \( a \) and \( b \) are bitset contribution weighting factors.
The Tversky Measure is asymmetric. Setting the parameters \( a = b = 1.0 \) is identical to using the Tanimoto measure.
If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.
bs1 | The first bitset. |
bs2 | The second bitset. |
a | Weights the contribution of the first bitset. |
b | Weights the contribution of the second bitset. |
CDPL_DESCR_API std::size_t CDPL::Descr::calcHammingDistance | ( | const Util::BitSet & | bs1, |
const Util::BitSet & | bs2 | ||
) |
Calculates the Hamming Distance [WHAM, CITB] between the bitsets bs1 and bs2.
The Hamming Distance \( D_{ab} \) is calculated by:
\[ D_{ab} = N_a + N_b \]
where \( N_a \) is the number of bits that are set in the first bitset but not in the second bitset and \( N_b \) is the number of bits that are set in the second bitset but not in the first one.
If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.
bs1 | The first bitset. |
bs2 | The second bitset. |
CDPL_DESCR_API double CDPL::Descr::calcEuclideanDistance | ( | const Util::BitSet & | bs1, |
const Util::BitSet & | bs2 | ||
) |
Calculates the Euclidean Distance [CITB] between the bitsets bs1 and bs2.
The Euclidean Distance \( D_{ab} \) is calculated by:
\[ D_{ab} = \sqrt{N_a + N_b} \]
where \( N_a \) is the number of bits that are set in the first bitset but not in the second bitset and \( N_b \) is the number of bits that are set in the second bitset but not in the first one.
If the specified bitsets bs1 and bs2 are of different size, missing bits at the end of the smaller bitset are assumed to be zero.
bs1 | The first bitset. |
bs2 | The second bitset. |