RDKit: RDDepictor.h File Reference

| RDKit Open-source cheminformatics and machine learning.

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Classes | Namespaces | Functions | Variables
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 coordinate 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