Namespaces
namespace	details

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=nullptr, const RDNumeric::DoubleVector weights=nullptr, bool reflect=false, unsigned int maxIters=50)
	Alignment functions.

RDKIT_MOLALIGN_EXPORT double	alignMol (ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const MatchVectType atomMap=nullptr, const RDNumeric::DoubleVector weights=nullptr, bool reflect=false, unsigned int maxIters=50)
	Optimally (minimum RMSD) align a molecule to another molecule.

RDKIT_MOLALIGN_EXPORT double	getBestAlignmentTransform (const ROMol &prbMol, const ROMol &refMol, RDGeom::Transform3D &bestTrans, MatchVectType &bestMatch, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr, bool reflect=false, unsigned int maxIters=50, int numThreads=1)

RDKIT_MOLALIGN_EXPORT double	getBestRMS (ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr, int numThreads=1)

RDKIT_MOLALIGN_EXPORT std::vector< double >	getAllConformerBestRMS (const ROMol &mol, int numThreads=1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr)

RDKIT_MOLALIGN_EXPORT double	CalcRMS (ROMol &prbMol, const ROMol &refMol, int prbCid=-1, int refCid=-1, const std::vector< MatchVectType > &map=std::vector< MatchVectType >(), int maxMatches=1e6, bool symmetrizeConjugatedTerminalGroups=true, const RDNumeric::DoubleVector *weights=nullptr)

RDKIT_MOLALIGN_EXPORT double	CalcRMS (ROMol &prbMol, const ROMol &refMol, int prbCid, int refCid, const std::vector< MatchVectType > &map, int maxMatches, const RDNumeric::DoubleVector *weights)

RDKIT_MOLALIGN_EXPORT void	alignMolConformers (ROMol &mol, const std::vector< unsigned int > atomIds=nullptr, const std::vector< unsigned int > confIds=nullptr, const RDNumeric::DoubleVector weights=nullptr, bool reflect=false, unsigned int maxIters=50, std::vector< double > RMSlist=nullptr)

bool	isDoubleZero (const double x)

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

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

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

Enumeration Type Documentation

◆ anonymous enum

anonymous enum

Enumerator
O3_USE_MMFF_WEIGHTS
O3_ACCURACY_MASK
O3_LOCAL_ONLY

Definition at line 125 of file O3AAlignMolecules.h.

Function Documentation

◆ alignMol()

RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::alignMol	(	ROMol &	prbMol,
		const ROMol &	refMol,
		int	prbCid = `-1`,
		int	refCid = `-1`,
		const MatchVectType *	atomMap = `nullptr`,
		const RDNumeric::DoubleVector *	weights = `nullptr`,
		bool	reflect = `false`,
		unsigned int	maxIters = `50`
	)

Optimally (minimum RMSD) align a molecule to another molecule.

The 3D transformation required to align the specified 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 transform is then applied to the specified conformation in the probe molecule

Parameters

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 iterations used in minimizing the RMSD

Returns RMSD value

◆ alignMolConformers()

RDKIT_MOLALIGN_EXPORT void RDKit::MolAlign::alignMolConformers	(	ROMol &	mol,
		const std::vector< unsigned int > *	atomIds = `nullptr`,
		const std::vector< unsigned int > *	confIds = `nullptr`,
		const RDNumeric::DoubleVector *	weights = `nullptr`,
		bool	reflect = `false`,
		unsigned int	maxIters = `50`,
		std::vector< double > *	RMSlist = `nullptr`
	)

Align the conformations of a molecule using a common set of atoms. If the molecules contains queries, then the queries must also match exactly.

Parameters

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	(optional) weights for each pair of atoms.
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

◆ CalcRMS() [1/2]

RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::CalcRMS	(	ROMol &	prbMol,
		const ROMol &	refMol,
		int	prbCid,
		int	refCid,
		const std::vector< MatchVectType > &	map,
		int	maxMatches,
		const RDNumeric::DoubleVector *	weights
	)

Returns the RMS between two molecules, taking symmetry into account. In contrast to getBestRMS, the RMS is computed "in place", i.e. probe molecules are not aligned to the reference ahead of the RMS calculation. This is useful, for example, to compute the RMSD between docking poses and the co-crystallized ligand.

This function will attempt to match all permutations of matching atom orders in both molecules, for some molecules it will lead to 'combinatorial explosion' especially if hydrogens are present.

Parameters

prbMol	the molecule to be aligned to the reference
refMol	the reference molecule
prbCid	(optional) probe conformation to use
refCid	(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().
weights	(optional) weights for each pair of atoms.

Returns Best RMSD value found

◆ CalcRMS() [2/2]

RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::CalcRMS	(	ROMol &	prbMol,
		const ROMol &	refMol,
		int	prbCid = `-1`,
		int	refCid = `-1`,
		const std::vector< MatchVectType > &	map = `std::vector< MatchVectType >()`,
		int	maxMatches = `1e6`,
		bool	symmetrizeConjugatedTerminalGroups = `true`,
		const RDNumeric::DoubleVector *	weights = `nullptr`
	)

Returns the RMS between two molecules, taking symmetry into account. In contrast to getBestRMS, the RMS is computed "in place", i.e. probe molecules are not aligned to the reference ahead of the RMS calculation. This is useful, for example, to compute the RMSD between docking poses and the co-crystallized ligand.

This function will attempt to match all permutations of matching atom orders in both molecules, for some molecules it will lead to 'combinatorial explosion' especially if hydrogens are present.

Parameters

prbMol	the molecule to be aligned to the reference
refMol	the reference molecule
prbCid	(optional) probe conformation to use
refCid	(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().
symmetrizeConjugatedTerminalGroups	(optional) if set, conjugated terminal functional groups (like nitro or carboxylate) will be considered symmetrically
weights	(optional) weights for each pair of atoms.

Returns Best RMSD value found

◆ getAlignmentTransform()

RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::getAlignmentTransform	(	const ROMol &	prbMol,
		const ROMol &	refMol,
		RDGeom::Transform3D &	trans,
		int	prbCid = `-1`,
		int	refCid = `-1`,
		const MatchVectType *	atomMap = `nullptr`,
		const RDNumeric::DoubleVector *	weights = `nullptr`,
		bool	reflect = `false`,
		unsigned int	maxIters = `50`
	)

Alignment functions.

Compute the transformation required to align a molecule

The 3D transformation required to align the specified 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

Parameters

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 iterations used in minimizing the RMSD

Returns RMSD value

◆ getAllConformerBestRMS()

RDKIT_MOLALIGN_EXPORT std::vector< double > RDKit::MolAlign::getAllConformerBestRMS	(	const ROMol &	mol,
		int	numThreads = `1`,
		const std::vector< MatchVectType > &	map = `std::vector< MatchVectType >()`,
		int	maxMatches = `1e6`,
		bool	symmetrizeConjugatedTerminalGroups = `true`,
		const RDNumeric::DoubleVector *	weights = `nullptr`
	)

Returns the symmetric distance matrix between the conformers of a molecule. getBestRMS() is used to calculate the inter-conformer distances

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.

Parameters

mol	the molecule to be considered
numThreads	(optional) number of threads to use during the calculation
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().
symmetrizeConjugatedTerminalGroups	(optional) if set, conjugated terminal functional groups (like nitro or carboxylate) will be considered symmetrically
weights	(optional) weights for each pair of atoms.

Returns a vector with the RMSD values stored in the order: [(1,0), (2,0), (2,1), (3,0), (3, 2), (3,1), ...]

◆ getBestAlignmentTransform()

RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::getBestAlignmentTransform	(	const ROMol &	prbMol,
		const ROMol &	refMol,
		RDGeom::Transform3D &	bestTrans,
		MatchVectType &	bestMatch,
		int	prbCid = `-1`,
		int	refCid = `-1`,
		const std::vector< MatchVectType > &	map = `std::vector< MatchVectType >()`,
		int	maxMatches = `1e6`,
		bool	symmetrizeConjugatedTerminalGroups = `true`,
		const RDNumeric::DoubleVector *	weights = `nullptr`,
		bool	reflect = `false`,
		unsigned int	maxIters = `50`,
		int	numThreads = `1`
	)

Compute the optimal RMS, transformation and atom map for aligning two molecules, taking symmetry into account. Molecule coordinates are left unaltered.

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::getAlignmentTransform' to align molecules without changing the atom order.

Parameters

prbMol	the molecule to be aligned to the reference
refMol	the reference molecule
bestTrans	storage for the best computed transform
bestMatch	storage for the MatchVectType corresponding to the best match found.
prbCid	(optional) probe conformation to use
refCid	(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().
symmetrizeConjugatedTerminalGroups	(optional) if set, conjugated terminal functional groups (like nitro or carboxylate) will be considered symmetrically
weights	(optional) weights for each pair of atoms.
reflect	if true reflect the conformation of the probe molecule
maxIters	maximum number of iterations used in minimizing the RMSD
numThreads	(optional) number of threads to use during the calculation

Returns Best RMSD value found

◆ getBestRMS()

RDKIT_MOLALIGN_EXPORT double RDKit::MolAlign::getBestRMS	(	ROMol &	prbMol,
		const ROMol &	refMol,
		int	prbCid = `-1`,
		int	refCid = `-1`,
		const std::vector< MatchVectType > &	map = `std::vector< MatchVectType >()`,
		int	maxMatches = `1e6`,
		bool	symmetrizeConjugatedTerminalGroups = `true`,
		const RDNumeric::DoubleVector *	weights = `nullptr`,
		int	numThreads = `1`
	)

Returns the optimal RMS for aligning two molecules, taking symmetry into account. As a side-effect, the probe molecule is left in the aligned state.

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.

Parameters

prbMol	the molecule to be aligned to the reference
refMol	the reference molecule
trans	storage for the computed transform
prbCid	(optional) probe conformation to use
refCid	(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().
symmetrizeConjugatedTerminalGroups	(optional) if set, conjugated terminal functional groups (like nitro or carboxylate) will be considered symmetrically
weights	(optional) weights for each pair of atoms.
numThreads	(optional) number of threads to use during the calculation

Returns Best RMSD value found

◆ getO3AForProbeConfs()

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`
	)

◆ isDoubleZero()

bool RDKit::MolAlign::isDoubleZero ( const double x )

inline

Definition at line 39 of file O3AAlignMolecules.h.

◆ o3aCrippenCostFunc()

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

◆ o3aCrippenScoringFunc()

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

◆ o3aCrippenWeightFunc()

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

◆ o3aMMFFCostFunc()

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

◆ o3aMMFFScoringFunc()

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

◆ o3aMMFFWeightFunc()

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

◆ randomTransform()

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

◆ reflect()

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

Variable Documentation

◆ O3_CHARGE_COEFF

const double RDKit::MolAlign::O3_CHARGE_COEFF = 5.0

Definition at line 122 of file O3AAlignMolecules.h.

◆ O3_CHARGE_WEIGHT

const double RDKit::MolAlign::O3_CHARGE_WEIGHT = 10.0

Definition at line 116 of file O3AAlignMolecules.h.

◆ O3_CRIPPEN_COEFF

const double RDKit::MolAlign::O3_CRIPPEN_COEFF = 1.0

Definition at line 123 of file O3AAlignMolecules.h.

◆ O3_CRIPPEN_WEIGHT

const double RDKit::MolAlign::O3_CRIPPEN_WEIGHT = 10.0

Definition at line 117 of file O3AAlignMolecules.h.

◆ O3_DEFAULT_CONSTRAINT_WEIGHT

const int RDKit::MolAlign::O3_DEFAULT_CONSTRAINT_WEIGHT = 100.0

Definition at line 108 of file O3AAlignMolecules.h.

◆ O3_DUMMY_COST

const int RDKit::MolAlign::O3_DUMMY_COST = 100000

Definition at line 106 of file O3AAlignMolecules.h.

◆ O3_LARGE_NEGATIVE_WEIGHT

const int RDKit::MolAlign::O3_LARGE_NEGATIVE_WEIGHT = -1e9

Definition at line 107 of file O3AAlignMolecules.h.

◆ O3_MAX_H_BINS

const unsigned int RDKit::MolAlign::O3_MAX_H_BINS = 20

Definition at line 109 of file O3AAlignMolecules.h.

◆ O3_MAX_SDM_ITERATIONS

const unsigned int RDKit::MolAlign::O3_MAX_SDM_ITERATIONS = 100

Definition at line 110 of file O3AAlignMolecules.h.

◆ O3_MAX_SDM_THRESHOLD_ITER

const unsigned int RDKit::MolAlign::O3_MAX_SDM_THRESHOLD_ITER = 3

Definition at line 111 of file O3AAlignMolecules.h.

◆ O3_MAX_WEIGHT_COEFF

const int RDKit::MolAlign::O3_MAX_WEIGHT_COEFF = 5

Definition at line 124 of file O3AAlignMolecules.h.

◆ O3_RANDOM_TRANS_COEFF

const double RDKit::MolAlign::O3_RANDOM_TRANS_COEFF = 5.0

Definition at line 112 of file O3AAlignMolecules.h.

◆ O3_RMSD_THRESHOLD

const double RDKit::MolAlign::O3_RMSD_THRESHOLD = 1.0e-04

Definition at line 118 of file O3AAlignMolecules.h.

◆ O3_SCORE_THRESHOLD

const double RDKit::MolAlign::O3_SCORE_THRESHOLD = 0.01

Definition at line 119 of file O3AAlignMolecules.h.

◆ O3_SCORING_FUNCTION_ALPHA

const double RDKit::MolAlign::O3_SCORING_FUNCTION_ALPHA = 5.0

Definition at line 120 of file O3AAlignMolecules.h.

◆ O3_SCORING_FUNCTION_BETA

const double RDKit::MolAlign::O3_SCORING_FUNCTION_BETA = 0.5

Definition at line 121 of file O3AAlignMolecules.h.

◆ O3_SDM_THRESHOLD_START

const double RDKit::MolAlign::O3_SDM_THRESHOLD_START = 0.7

Definition at line 114 of file O3AAlignMolecules.h.

◆ O3_SDM_THRESHOLD_STEP

const double RDKit::MolAlign::O3_SDM_THRESHOLD_STEP = 0.3

Definition at line 115 of file O3AAlignMolecules.h.

◆ O3_THRESHOLD_DIFF_DISTANCE

const double RDKit::MolAlign::O3_THRESHOLD_DIFF_DISTANCE = 0.1

Definition at line 113 of file O3AAlignMolecules.h.

Namespaces

Classes

Enumerations

Functions

Variables

Enumeration Type Documentation

◆ anonymous enum

Function Documentation

◆ alignMol()

◆ alignMolConformers()

◆ CalcRMS() [1/2]

◆ CalcRMS() [2/2]

◆ getAlignmentTransform()

◆ getAllConformerBestRMS()

◆ getBestAlignmentTransform()

◆ getBestRMS()

◆ getO3AForProbeConfs()

◆ isDoubleZero()

◆ o3aCrippenCostFunc()

◆ o3aCrippenScoringFunc()

◆ o3aCrippenWeightFunc()

◆ o3aMMFFCostFunc()

◆ o3aMMFFScoringFunc()

◆ o3aMMFFWeightFunc()

◆ randomTransform()

◆ reflect()

Variable Documentation

◆ O3_CHARGE_COEFF

◆ O3_CHARGE_WEIGHT

◆ O3_CRIPPEN_COEFF

◆ O3_CRIPPEN_WEIGHT

◆ O3_DEFAULT_CONSTRAINT_WEIGHT

◆ O3_DUMMY_COST

◆ O3_LARGE_NEGATIVE_WEIGHT

◆ O3_MAX_H_BINS

◆ O3_MAX_SDM_ITERATIONS

◆ O3_MAX_SDM_THRESHOLD_ITER

◆ O3_MAX_WEIGHT_COEFF

◆ O3_RANDOM_TRANS_COEFF

◆ O3_RMSD_THRESHOLD

◆ O3_SCORE_THRESHOLD

◆ O3_SCORING_FUNCTION_ALPHA

◆ O3_SCORING_FUNCTION_BETA

◆ O3_SDM_THRESHOLD_START

◆ O3_SDM_THRESHOLD_STEP

◆ O3_THRESHOLD_DIFF_DISTANCE