RDDepictor.h File Reference

#include <RDGeneral/export.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <RDGeneral/types.h>
#include <Geometry/point.h>
#include <boost/smart_ptr.hpp>

Go to the source code of this file.

Classes
class	RDDepict::DepictException
struct	RDDepict::Compute2DCoordParameters
struct	RDDepict::ConstrainedDepictionParams

Namespaces
namespace	RDKit
	Std stuff.
namespace	RDDepict

Functions
void RDKIT_DEPICTOR_EXPORT	RDDepict::setRingSystemTemplates (const std::string templatePath)
	Set the path to the file containing the ring system templates.
void RDKIT_DEPICTOR_EXPORT	RDDepict::addRingSystemTemplates (const std::string templatePath)
	Add ring system templates to be used in 2D coordinater generation. If there are duplicates, the most recently added template will be used.
void RDKIT_DEPICTOR_EXPORT	RDDepict::loadDefaultRingSystemTemplates ()
	Load default ring system templates to be used in 2D coordinate generation.
RDKIT_DEPICTOR_EXPORT unsigned int	RDDepict::compute2DCoords (RDKit::ROMol &mol, const Compute2DCoordParameters &params)
	Generate 2D coordinates (a depiction) for a molecule.
RDKIT_DEPICTOR_EXPORT unsigned int	RDDepict::compute2DCoords (RDKit::ROMol &mol, const RDGeom::INT_POINT2D_MAP *coordMap=nullptr, bool canonOrient=false, bool clearConfs=true, unsigned int nFlipsPerSample=0, unsigned int nSamples=0, int sampleSeed=0, bool permuteDeg4Nodes=false, bool forceRDKit=false, bool useRingTemplates=false)
	Generate 2D coordinates (a depiction) for a molecule.
RDKIT_DEPICTOR_EXPORT unsigned int	RDDepict::compute2DCoordsMimicDistMat (RDKit::ROMol &mol, const DOUBLE_SMART_PTR *dmat=nullptr, bool canonOrient=true, bool clearConfs=true, double weightDistMat=0.5, unsigned int nFlipsPerSample=3, unsigned int nSamples=100, int sampleSeed=25, bool permuteDeg4Nodes=true, bool forceRDKit=false)
	Compute the 2D coordinates such the interatom distances mimic those in a distance matrix.
RDKIT_DEPICTOR_EXPORT void	RDDepict::generateDepictionMatching2DStructure (RDKit::ROMol &mol, const RDKit::ROMol &reference, const RDKit::MatchVectType &refMatchVect, int confId=-1, const ConstrainedDepictionParams &params=ConstrainedDepictionParams())
	Compute 2D coordinates where a piece of the molecule is constrained to have the same coordinates as a reference. Correspondences between reference and molecule atom indices are determined by refMatchVect.
RDKIT_DEPICTOR_EXPORT void	RDDepict::generateDepictionMatching2DStructure (RDKit::ROMol &mol, const RDKit::ROMol &reference, const RDKit::MatchVectType &refMatchVect, int confId, bool forceRDKit)
	Overload.
RDKIT_DEPICTOR_EXPORT RDKit::MatchVectType	RDDepict::generateDepictionMatching2DStructure (RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, const RDKit::ROMol *referencePattern=static_cast< const RDKit::ROMol * >(nullptr), const ConstrainedDepictionParams &params=ConstrainedDepictionParams())
	Compute 2D coordinates constrained to a reference; the constraint can be hard (default) or soft.
RDKIT_DEPICTOR_EXPORT RDKit::MatchVectType	RDDepict::generateDepictionMatching2DStructure (RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId, const RDKit::ROMol *referencePattern, bool acceptFailure, bool forceRDKit=false, bool allowOptionalAttachments=false)
	Compute 2D coordinates where a piece of the molecule is constrained to have the same coordinates as a reference.
RDKIT_DEPICTOR_EXPORT void	RDDepict::generateDepictionMatching3DStructure (RDKit::ROMol &mol, const RDKit::ROMol &reference, int confId=-1, RDKit::ROMol *referencePattern=nullptr, bool acceptFailure=false, bool forceRDKit=false)
	Generate a 2D depiction for a molecule where all or part of it mimics the coordinates of a 3D reference structure.
RDKIT_DEPICTOR_EXPORT void	RDDepict::straightenDepiction (RDKit::ROMol &mol, int confId=-1, bool minimizeRotation=false)
	Rotate the 2D depiction such that the majority of bonds have an angle with the X axis which is a multiple of 30 degrees.
RDKIT_DEPICTOR_EXPORT double	RDDepict::normalizeDepiction (RDKit::ROMol &mol, int confId=-1, int canonicalize=1, double scaleFactor=-1.0)
	Normalizes the 2D depiction.

Variables
RDKIT_DEPICTOR_EXPORT bool	RDDepict::preferCoordGen