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RDKit
Open-source cheminformatics and machine learning.
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Classes | |
class | LAP |
class | MolAlignException |
class | MolHistogram |
class | O3A |
class | O3AConstraint |
class | O3AConstraintVect |
struct | O3AFuncData |
class | SDM |
Enumerations | |
enum | { O3_USE_MMFF_WEIGHTS = (1 << 0), O3_ACCURACY_MASK = (1 << 0 | 1 << 1), O3_LOCAL_ONLY = (1 << 2) } |
Functions | |
RDKIT_MOLALIGN_EXPORT double | getAlignmentTransform (const ROMol &prbMol, const ROMol &refMol, RDGeom::Transform3D &trans, int prbCid=-1, int refCid=-1, const MatchVectType *atomMap=0, const RDNumeric::DoubleVector *weights=0, bool reflect=false, unsigned int maxIters=50) |
Alignment functions. More... | |
RDKIT_MOLALIGN_EXPORT double | alignMol (ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const MatchVectType *atomMap=0, const RDNumeric::DoubleVector *weights=0, bool reflect=false, unsigned int maxIters=50) |
Optimally (minimum RMSD) align a molecule to another molecule. More... | |
RDKIT_MOLALIGN_EXPORT double | getBestRMS (ROMol &probeMol, ROMol &refMol, int probeId=-1, int refId=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6) |
Returns the optimal RMS for aligning two molecules, taking. More... | |
RDKIT_MOLALIGN_EXPORT void | alignMolConformers (ROMol &mol, const std::vector< unsigned int > *atomIds=0, const std::vector< unsigned int > *confIds=0, const RDNumeric::DoubleVector *weights=0, bool reflect=false, unsigned int maxIters=50, std::vector< double > *RMSlist=0) |
Align the conformations of a molecule using a common set of atoms. If. More... | |
bool | isDoubleZero (const double x) |
RDKIT_MOLALIGN_EXPORT void | randomTransform (ROMol &mol, const int cid=-1, const int seed=-1) |
const RDKIT_MOLALIGN_EXPORT RDGeom::POINT3D_VECT * | reflect (const Conformer &conf) |
RDKIT_MOLALIGN_EXPORT int | o3aMMFFCostFunc (const unsigned int prbIdx, const unsigned int refIdx, double hSum, void *data) |
RDKIT_MOLALIGN_EXPORT double | o3aMMFFWeightFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data) |
RDKIT_MOLALIGN_EXPORT double | o3aMMFFScoringFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data) |
RDKIT_MOLALIGN_EXPORT int | o3aCrippenCostFunc (const unsigned int prbIdx, const unsigned int refIdx, double hSum, void *data) |
RDKIT_MOLALIGN_EXPORT double | o3aCrippenWeightFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data) |
RDKIT_MOLALIGN_EXPORT double | o3aCrippenScoringFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data) |
RDKIT_MOLALIGN_EXPORT void | getO3AForProbeConfs (ROMol &prbMol, const ROMol &refMol, void *prbProp, void *refProp, std::vector< boost::shared_ptr< O3A >> &res, int numThreads=1, O3A::AtomTypeScheme atomTypes=O3A::MMFF94, const int refCid=-1, const bool reflect=false, const unsigned int maxIters=50, unsigned int options=0, const MatchVectType *constraintMap=NULL, const RDNumeric::DoubleVector *constraintWeights=NULL) |
Variables | |
const int | O3_DUMMY_COST = 100000 |
const int | O3_LARGE_NEGATIVE_WEIGHT = -1e9 |
const int | O3_DEFAULT_CONSTRAINT_WEIGHT = 100.0 |
const unsigned int | O3_MAX_H_BINS = 20 |
const unsigned int | O3_MAX_SDM_ITERATIONS = 100 |
const unsigned int | O3_MAX_SDM_THRESHOLD_ITER = 3 |
const double | O3_RANDOM_TRANS_COEFF = 5.0 |
const double | O3_THRESHOLD_DIFF_DISTANCE = 0.1 |
const double | O3_SDM_THRESHOLD_START = 0.7 |
const double | O3_SDM_THRESHOLD_STEP = 0.3 |
const double | O3_CHARGE_WEIGHT = 10.0 |
const double | O3_CRIPPEN_WEIGHT = 10.0 |
const double | O3_RMSD_THRESHOLD = 1.0e-04 |
const double | O3_SCORE_THRESHOLD = 0.01 |
const double | O3_SCORING_FUNCTION_ALPHA = 5.0 |
const double | O3_SCORING_FUNCTION_BETA = 0.5 |
const double | O3_CHARGE_COEFF = 5.0 |
const double | O3_CRIPPEN_COEFF = 1.0 |
const int | O3_MAX_WEIGHT_COEFF = 5 |
anonymous enum |
Enumerator | |
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O3_USE_MMFF_WEIGHTS | |
O3_ACCURACY_MASK | |
O3_LOCAL_ONLY |
Definition at line 127 of file O3AAlignMolecules.h.
RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::alignMol | ( | ROMol & | prbMol, |
const ROMol & | refMol, | ||
int | prbCid = -1 , |
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int | refCid = -1 , |
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const MatchVectType * | atomMap = 0 , |
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const RDNumeric::DoubleVector * | weights = 0 , |
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bool | reflect = false , |
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unsigned int | maxIters = 50 |
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Optimally (minimum RMSD) align a molecule to another molecule.
The 3D transformation required to align the specied conformation in the probe molecule to a specified conformation in the reference molecule is computed so that the root mean squared distance between a specified set of atoms is minimized. This transforms is them applied to the specified conformation in the probe molecule
prbMol | molecule that is to be aligned |
refMol | molecule used as the reference for the alignment |
prbCid | ID of the conformation in the probe to be used for the alignment (defaults to first conformation) |
refCid | ID of the conformation in the ref molecule to which the alignment is computed (defaults to first conformation) |
atomMap | a vector of pairs of atom IDs (probe AtomId, ref AtomId) used to compute the alignments. If this mapping is not specified an attempt is made to generate on by substructure matching |
weights | Optionally specify weights for each of the atom pairs |
reflect | if true reflect the conformation of the probe molecule |
maxIters | maximum number of iteration used in mimizing the RMSD |
Returns RMSD value
RDKIT_MOLALIGN_EXPORT void RDKit::MolAlign::alignMolConformers | ( | ROMol & | mol, |
const std::vector< unsigned int > * | atomIds = 0 , |
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const std::vector< unsigned int > * | confIds = 0 , |
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const RDNumeric::DoubleVector * | weights = 0 , |
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bool | reflect = false , |
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unsigned int | maxIters = 50 , |
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std::vector< double > * | RMSlist = 0 |
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Align the conformations of a molecule using a common set of atoms. If.
mol | The molecule of interest. |
atomIds | vector of atoms to be used to generate the alignment. All atoms will be used is not specified |
confIds | vector of conformations to align - defaults to all |
weights | vector of weights to applied to particular atom pairs defaults to all weights = 1 |
reflect | toggles reflecting (about the origin) the alignment |
maxIters | the maximum number of iterations to attempt |
RMSlist | if nonzero, this will be used to return the RMS values between the reference conformation and the other aligned conformations |
RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::getAlignmentTransform | ( | const ROMol & | prbMol, |
const ROMol & | refMol, | ||
RDGeom::Transform3D & | trans, | ||
int | prbCid = -1 , |
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int | refCid = -1 , |
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const MatchVectType * | atomMap = 0 , |
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const RDNumeric::DoubleVector * | weights = 0 , |
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bool | reflect = false , |
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unsigned int | maxIters = 50 |
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Alignment functions.
Compute the transformation required to align a molecule
The 3D transformation required to align the specied conformation in the probe molecule to a specified conformation in the reference molecule is computed so that the root mean squared distance between a specified set of atoms is minimized
prbMol | molecule that is to be aligned |
refMol | molecule used as the reference for the alignment |
trans | storage for the computed transform |
prbCid | ID of the conformation in the probe to be used for the alignment (defaults to first conformation) |
refCid | ID of the conformation in the ref molecule to which the alignment is computed (defaults to first conformation) |
atomMap | a vector of pairs of atom IDs (probe AtomId, ref AtomId) used to compute the alignments. If this mapping is not specified an attempt is made to generate on by substructure matching |
weights | Optionally specify weights for each of the atom pairs |
reflect | if true reflect the conformation of the probe molecule |
maxIters | maximum number of iteration used in mimizing the RMSD |
Returns RMSD value
RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::getBestRMS | ( | ROMol & | probeMol, |
ROMol & | refMol, | ||
int | probeId = -1 , |
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int | refId = -1 , |
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const std::vector< MatchVectType > & | map = std::vector< MatchVectType >() , |
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int | maxMatches = 1e6 |
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Returns the optimal RMS for aligning two molecules, taking.
This function will attempt to align all permutations of matching atom orders in both molecules, for some molecules it will lead to 'combinatorial explosion' especially if hydrogens are present. Use 'RDKit::MolAlign::alignMol' to align molecules without changing the atom order.
probeMol | the molecule to be aligned to the reference |
refMol | the reference molecule |
probeId | (optional) probe conformation to use |
refId | (optional) reference conformation to use |
map | (optional) a vector of vectors of pairs of atom IDs (probe AtomId, ref AtomId) used to compute the alignments. If not provided, these will be generated using a substructure search. |
maxMatches | (optional) if map is empty, this will be the max number of matches found in a SubstructMatch(). |
Returns Best RMSD value found
RDKIT_MOLALIGN_EXPORT void RDKit::MolAlign::getO3AForProbeConfs | ( | ROMol & | prbMol, |
const ROMol & | refMol, | ||
void * | prbProp, | ||
void * | refProp, | ||
std::vector< boost::shared_ptr< O3A >> & | res, | ||
int | numThreads = 1 , |
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O3A::AtomTypeScheme | atomTypes = O3A::MMFF94 , |
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const int | refCid = -1 , |
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const bool | reflect = false , |
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const unsigned int | maxIters = 50 , |
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unsigned int | options = 0 , |
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const MatchVectType * | constraintMap = NULL , |
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const RDNumeric::DoubleVector * | constraintWeights = NULL |
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inline |
Definition at line 40 of file O3AAlignMolecules.h.
RDKIT_MOLALIGN_EXPORT int RDKit::MolAlign::o3aCrippenCostFunc | ( | const unsigned int | prbIdx, |
const unsigned int | refIdx, | ||
double | hSum, | ||
void * | data | ||
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RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::o3aCrippenScoringFunc | ( | const unsigned int | prbIdx, |
const unsigned int | refIdx, | ||
void * | data | ||
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RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::o3aCrippenWeightFunc | ( | const unsigned int | prbIdx, |
const unsigned int | refIdx, | ||
void * | data | ||
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RDKIT_MOLALIGN_EXPORT int RDKit::MolAlign::o3aMMFFCostFunc | ( | const unsigned int | prbIdx, |
const unsigned int | refIdx, | ||
double | hSum, | ||
void * | data | ||
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RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::o3aMMFFScoringFunc | ( | const unsigned int | prbIdx, |
const unsigned int | refIdx, | ||
void * | data | ||
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RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::o3aMMFFWeightFunc | ( | const unsigned int | prbIdx, |
const unsigned int | refIdx, | ||
void * | data | ||
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RDKIT_MOLALIGN_EXPORT void RDKit::MolAlign::randomTransform | ( | ROMol & | mol, |
const int | cid = -1 , |
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const int | seed = -1 |
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const RDKIT_MOLALIGN_EXPORT RDGeom::POINT3D_VECT* RDKit::MolAlign::reflect | ( | const Conformer & | conf | ) |
const double RDKit::MolAlign::O3_CHARGE_COEFF = 5.0 |
Definition at line 124 of file O3AAlignMolecules.h.
const double RDKit::MolAlign::O3_CHARGE_WEIGHT = 10.0 |
Definition at line 118 of file O3AAlignMolecules.h.
const double RDKit::MolAlign::O3_CRIPPEN_COEFF = 1.0 |
Definition at line 125 of file O3AAlignMolecules.h.
const double RDKit::MolAlign::O3_CRIPPEN_WEIGHT = 10.0 |
Definition at line 119 of file O3AAlignMolecules.h.
const int RDKit::MolAlign::O3_DEFAULT_CONSTRAINT_WEIGHT = 100.0 |
Definition at line 110 of file O3AAlignMolecules.h.
const int RDKit::MolAlign::O3_DUMMY_COST = 100000 |
Definition at line 108 of file O3AAlignMolecules.h.
const int RDKit::MolAlign::O3_LARGE_NEGATIVE_WEIGHT = -1e9 |
Definition at line 109 of file O3AAlignMolecules.h.
const unsigned int RDKit::MolAlign::O3_MAX_H_BINS = 20 |
Definition at line 111 of file O3AAlignMolecules.h.
const unsigned int RDKit::MolAlign::O3_MAX_SDM_ITERATIONS = 100 |
Definition at line 112 of file O3AAlignMolecules.h.
const unsigned int RDKit::MolAlign::O3_MAX_SDM_THRESHOLD_ITER = 3 |
Definition at line 113 of file O3AAlignMolecules.h.
const int RDKit::MolAlign::O3_MAX_WEIGHT_COEFF = 5 |
Definition at line 126 of file O3AAlignMolecules.h.
const double RDKit::MolAlign::O3_RANDOM_TRANS_COEFF = 5.0 |
Definition at line 114 of file O3AAlignMolecules.h.
const double RDKit::MolAlign::O3_RMSD_THRESHOLD = 1.0e-04 |
Definition at line 120 of file O3AAlignMolecules.h.
const double RDKit::MolAlign::O3_SCORE_THRESHOLD = 0.01 |
Definition at line 121 of file O3AAlignMolecules.h.
const double RDKit::MolAlign::O3_SCORING_FUNCTION_ALPHA = 5.0 |
Definition at line 122 of file O3AAlignMolecules.h.
const double RDKit::MolAlign::O3_SCORING_FUNCTION_BETA = 0.5 |
Definition at line 123 of file O3AAlignMolecules.h.
const double RDKit::MolAlign::O3_SDM_THRESHOLD_START = 0.7 |
Definition at line 116 of file O3AAlignMolecules.h.
const double RDKit::MolAlign::O3_SDM_THRESHOLD_STEP = 0.3 |
Definition at line 117 of file O3AAlignMolecules.h.
const double RDKit::MolAlign::O3_THRESHOLD_DIFF_DISTANCE = 0.1 |
Definition at line 115 of file O3AAlignMolecules.h.