RDKit
Open-source cheminformatics and machine learning.
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>

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Classes

class  RDDepict::DepictException
 

Namespaces

namespace  RDKit
 Std stuff.
 
namespace  RDDepict
 

Functions

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)
 Generate 2D coordinates (a depiction) for a molecule. More...
 
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. More...
 
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), bool acceptFailure=false, 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. More...
 
RDKIT_DEPICTOR_EXPORT void RDDepict::generateDepictionMatching2DStructure (RDKit::ROMol &mol, const RDKit::ROMol &reference, const RDKit::MatchVectType &refMatchVect, int confId=-1, bool forceRDKit=false)
 Compute 2D coordinates where a piece of the molecule is constrained to have the same coordinates as a reference. More...
 
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. More...
 
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. More...
 
RDKIT_DEPICTOR_EXPORT double RDDepict::normalizeDepiction (RDKit::ROMol &mol, int confId=-1, int canonicalize=1, double scaleFactor=-1.0)
 Normalizes the 2D depiction. More...
 

Variables

RDKIT_DEPICTOR_EXPORT bool RDDepict::preferCoordGen