18#include <boost/smart_ptr.hpp>
35 const char *
what() const noexcept
override {
return _msg.c_str(); }
78 bool canonOrient = false,
bool clearConfs = true,
79 unsigned int nFlipsPerSample = 0,
unsigned int nSamples = 0,
80 int sampleSeed = 0,
bool permuteDeg4Nodes = false,
bool forceRDKit = false);
136 bool canonOrient = true,
bool clearConfs = true,
double weightDistMat = 0.5,
137 unsigned int nFlipsPerSample = 3,
unsigned int nSamples = 100,
138 int sampleSeed = 25,
bool permuteDeg4Nodes = true,
bool forceRDKit = false);
175 RDKit::ROMol &mol, const
RDKit::ROMol &reference,
int confId = -1,
176 const
RDKit::ROMol *referencePattern =
177 static_cast<const
RDKit::ROMol *>(
nullptr),
178 bool acceptFailure = false,
bool forceRDKit = false,
179 bool allowOptionalAttachments = false);
207 RDKit::ROMol &mol, const
RDKit::ROMol &reference,
209 bool forceRDKit = false);
236 RDKit::ROMol &mol, const
RDKit::ROMol &reference,
int confId = -1,
237 RDKit::ROMol *referencePattern =
nullptr,
bool acceptFailure = false,
238 bool forceRDKit = false);
257 bool minimizeRotation = false);
287 int canonicalize = 1,
288 double scaleFactor = -1.0);
DepictException(const char *msg)
~DepictException() noexcept override=default
DepictException(const std::string msg)
const char * what() const noexcept override
#define RDKIT_DEPICTOR_EXPORT
boost::shared_array< double > DOUBLE_SMART_PTR
RDKIT_DEPICTOR_EXPORT void 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 referen...
RDKIT_DEPICTOR_EXPORT double normalizeDepiction(RDKit::ROMol &mol, int confId=-1, int canonicalize=1, double scaleFactor=-1.0)
Normalizes the 2D depiction.
RDKIT_DEPICTOR_EXPORT unsigned int 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.
RDKIT_DEPICTOR_EXPORT void 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 mult...
RDKIT_DEPICTOR_EXPORT RDKit::MatchVectType 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...
RDKIT_DEPICTOR_EXPORT unsigned int 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 bool preferCoordGen
std::map< int, Point2D > INT_POINT2D_MAP
std::vector< std::pair< int, int > > MatchVectType
used to return matches from substructure searching, The format is (queryAtomIdx, molAtomIdx)