RDKit
Open-source cheminformatics and machine learning.
O3AAlignMolecules.h File Reference
#include <RDGeneral/Invariant.h>
#include <Geometry/Transform3D.h>
#include <Geometry/point.h>
#include <Numerics/Vector.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/Conformer.h>
#include <GraphMol/ForceFieldHelpers/MMFF/AtomTyper.h>
#include <GraphMol/MolAlign/AlignMolecules.h>
#include <vector>
#include <cmath>
#include <boost/shared_ptr.hpp>
#include <boost/multi_array.hpp>
#include <boost/dynamic_bitset.hpp>

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Classes

struct  RDKit::MolAlign::O3AFuncData
 
class  RDKit::MolAlign::O3AConstraint
 
class  RDKit::MolAlign::O3AConstraintVect
 
class  RDKit::MolAlign::MolHistogram
 
class  RDKit::MolAlign::LAP
 
class  RDKit::MolAlign::SDM
 
class  RDKit::MolAlign::O3A
 

Namespaces

 RDKit
 Includes a bunch of functionality for handling Atom and Bond queries.
 
 RDKit::MolAlign
 

Typedefs

typedef struct RDKit::MolAlign::O3AFuncData RDKit::MolAlign::O3AFuncData
 

Enumerations

enum  { RDKit::MolAlign::O3_USE_MMFF_WEIGHTS = (1 << 0), RDKit::MolAlign::O3_ACCURACY_MASK = (1 << 0 | 1 << 1), RDKit::MolAlign::O3_LOCAL_ONLY = (1 << 2) }
 

Functions

bool RDKit::MolAlign::isDoubleZero (const double x)
 
void RDKit::MolAlign::randomTransform (ROMol &mol, const int cid=-1, const int seed=-1)
 
const RDGeom::POINT3D_VECTRDKit::MolAlign::reflect (const Conformer &conf)
 
int RDKit::MolAlign::o3aMMFFCostFunc (const unsigned int prbIdx, const unsigned int refIdx, double hSum, void *data)
 
double RDKit::MolAlign::o3aMMFFWeightFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data)
 
double RDKit::MolAlign::o3aMMFFScoringFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data)
 
int RDKit::MolAlign::o3aCrippenCostFunc (const unsigned int prbIdx, const unsigned int refIdx, double hSum, void *data)
 
double RDKit::MolAlign::o3aCrippenWeightFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data)
 
double RDKit::MolAlign::o3aCrippenScoringFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data)
 
void RDKit::MolAlign::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 RDKit::MolAlign::O3_DUMMY_COST = 100000
 
const int RDKit::MolAlign::O3_LARGE_NEGATIVE_WEIGHT = -1e9
 
const int RDKit::MolAlign::O3_DEFAULT_CONSTRAINT_WEIGHT = 100.0
 
const unsigned int RDKit::MolAlign::O3_MAX_H_BINS = 20
 
const unsigned int RDKit::MolAlign::O3_MAX_SDM_ITERATIONS = 100
 
const unsigned int RDKit::MolAlign::O3_MAX_SDM_THRESHOLD_ITER = 3
 
const double RDKit::MolAlign::O3_RANDOM_TRANS_COEFF = 5.0
 
const double RDKit::MolAlign::O3_THRESHOLD_DIFF_DISTANCE = 0.1
 
const double RDKit::MolAlign::O3_SDM_THRESHOLD_START = 0.7
 
const double RDKit::MolAlign::O3_SDM_THRESHOLD_STEP = 0.3
 
const double RDKit::MolAlign::O3_CHARGE_WEIGHT = 10.0
 
const double RDKit::MolAlign::O3_CRIPPEN_WEIGHT = 10.0
 
const double RDKit::MolAlign::O3_RMSD_THRESHOLD = 1.0e-04
 
const double RDKit::MolAlign::O3_SCORE_THRESHOLD = 0.01
 
const double RDKit::MolAlign::O3_SCORING_FUNCTION_ALPHA = 5.0
 
const double RDKit::MolAlign::O3_SCORING_FUNCTION_BETA = 0.5
 
const double RDKit::MolAlign::O3_CHARGE_COEFF = 5.0
 
const double RDKit::MolAlign::O3_CRIPPEN_COEFF = 1.0
 
const int RDKit::MolAlign::O3_MAX_WEIGHT_COEFF = 5