#include <RDGeneral/export.h>
#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>

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
namespace	RDKit
	Std stuff.

namespace	RDKit::MolAlign

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)

RDKIT_MOLALIGN_EXPORT void	RDKit::MolAlign::randomTransform (ROMol &mol, const int cid=-1, const int seed=-1)

RDKIT_MOLALIGN_EXPORT const RDGeom::POINT3D_VECT *	RDKit::MolAlign::reflect (const Conformer &conf)

RDKIT_MOLALIGN_EXPORT int	RDKit::MolAlign::o3aMMFFCostFunc (const unsigned int prbIdx, const unsigned int refIdx, double hSum, void *data)

RDKIT_MOLALIGN_EXPORT double	RDKit::MolAlign::o3aMMFFWeightFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data)

RDKIT_MOLALIGN_EXPORT double	RDKit::MolAlign::o3aMMFFScoringFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data)

RDKIT_MOLALIGN_EXPORT int	RDKit::MolAlign::o3aCrippenCostFunc (const unsigned int prbIdx, const unsigned int refIdx, double hSum, void *data)

RDKIT_MOLALIGN_EXPORT double	RDKit::MolAlign::o3aCrippenWeightFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data)

RDKIT_MOLALIGN_EXPORT double	RDKit::MolAlign::o3aCrippenScoringFunc (const unsigned int prbIdx, const unsigned int refIdx, void *data)

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, 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=nullptr, const RDNumeric::DoubleVector constraintWeights=nullptr)

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

Classes

Namespaces

Enumerations

Functions

Variables