DepictUtils.h File Reference

#include <RDGeneral/export.h>
#include <RDGeneral/types.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RWMol.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/Substruct/SubstructUtils.h>
#include <Geometry/Transform2D.h>
#include <Geometry/Transform3D.h>
#include <Geometry/point.h>
#include <queue>

Go to the source code of this file.

Classes
struct	RDDepict::gtIIPair

Namespaces
namespace	RDDepict

Typedefs
typedef std::vector< const RDGeom::Point2D * >	RDDepict::VECT_C_POINT
typedef std::pair< int, int >	RDDepict::PAIR_I_I
typedef std::vector< PAIR_I_I >	RDDepict::VECT_PII
typedef std::priority_queue< PAIR_I_I, VECT_PII, gtIIPair >	RDDepict::PR_QUEUE
typedef std::pair< double, PAIR_I_I >	RDDepict::PAIR_D_I_I
typedef std::list< PAIR_D_I_I >	RDDepict::LIST_PAIR_DII
typedef std::pair< int, int >	RDDepict::INT_PAIR
typedef std::vector< INT_PAIR >	RDDepict::INT_PAIR_VECT
typedef INT_PAIR_VECT::const_iterator	RDDepict::INT_PAIR_VECT_CI
typedef std::pair< double, INT_PAIR >	RDDepict::DOUBLE_INT_PAIR

Functions
RDKIT_DEPICTOR_EXPORT RDGeom::INT_POINT2D_MAP	RDDepict::embedRing (const RDKit::INT_VECT &ring)
	Some utility functions used in generating 2D coordinates.
RDKIT_DEPICTOR_EXPORT void	RDDepict::transformPoints (RDGeom::INT_POINT2D_MAP &nringCor, const RDGeom::Transform2D &trans)
RDKIT_DEPICTOR_EXPORT RDGeom::Point2D	RDDepict::computeBisectPoint (const RDGeom::Point2D &rcr, double ang, const RDGeom::Point2D &nb1, const RDGeom::Point2D &nb2)
	Find a point that bisects the angle at rcr.
RDKIT_DEPICTOR_EXPORT void	RDDepict::reflectPoints (RDGeom::INT_POINT2D_MAP &coordMap, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)
	Reflect a set of point through the line joining two point.
RDKIT_DEPICTOR_EXPORT RDGeom::Point2D	RDDepict::reflectPoint (const RDGeom::Point2D &point, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)
RDKIT_DEPICTOR_EXPORT RDKit::INT_VECT	RDDepict::setNbrOrder (unsigned int aid, const RDKit::INT_VECT &nbrs, const RDKit::ROMol &mol)
RDKIT_DEPICTOR_EXPORT RDKit::INT_VECT	RDDepict::findNextRingToEmbed (const RDKit::INT_VECT &doneRings, const RDKit::VECT_INT_VECT &fusedRings, int &nextId)
	From a given set of rings find the ring the largest common elements with other rings.
template<class T >
RDKIT_DEPICTOR_EXPORT T	RDDepict::rankAtomsByRank (const RDKit::ROMol &mol, const T &commAtms, bool ascending=true)
	Sort a list of atoms by their CIP rank.
double	RDDepict::computeSubAngle (unsigned int degree, RDKit::Atom::HybridizationType htype)
	computes a subangle for an atom of given hybridization and degree
int	RDDepict::rotationDir (const RDGeom::Point2D &center, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2, double remAngle)
	computes the rotation direction between two vectors
RDGeom::Point2D	RDDepict::computeNormal (const RDGeom::Point2D &center, const RDGeom::Point2D &other)
	computes and return the normal of a vector between two points
double	RDDepict::computeAngle (const RDGeom::Point2D &center, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)
	computes the rotation angle between two vectors
RDKIT_DEPICTOR_EXPORT int	RDDepict::pickFirstRingToEmbed (const RDKit::ROMol &mol, const RDKit::VECT_INT_VECT &fusedRings)
	pick the ring to embed first in a fused system
RDKIT_DEPICTOR_EXPORT RDKit::INT_VECT	RDDepict::getRotatableBonds (const RDKit::ROMol &mol, unsigned int aid1, unsigned int aid2)
	find the rotatable bonds on the shortest path between two atoms we will ignore ring atoms, and double bonds which are marked cis/trans
RDKIT_DEPICTOR_EXPORT RDKit::INT_VECT	RDDepict::getAllRotatableBonds (const RDKit::ROMol &mol)
	find all the rotatable bonds in a molecule we will ignore ring atoms, and double bonds which are marked cis/trans
RDKIT_DEPICTOR_EXPORT void	RDDepict::getNbrAtomAndBondIds (unsigned int aid, const RDKit::ROMol *mol, RDKit::INT_VECT &aids, RDKit::INT_VECT &bids)
	Get the ids of the atoms and bonds that are connected to aid.
RDKIT_DEPICTOR_EXPORT INT_PAIR_VECT	RDDepict::findBondsPairsToPermuteDeg4 (const RDGeom::Point2D &center, const RDKit::INT_VECT &nbrBids, const VECT_C_POINT &nbrLocs)
	Find pairs of bonds that can be permuted at a non-ring degree 4 atom.
int	RDDepict::getAtomDepictRank (const RDKit::Atom *at)
	returns the rank of the atom for determining draw order
RDKIT_DEPICTOR_EXPORT bool	RDDepict::hasTerminalRGroupOrQueryHydrogen (const RDKit::ROMol &query)
RDKIT_DEPICTOR_EXPORT std::unique_ptr< RDKit::RWMol >	RDDepict::prepareTemplateForRGroups (RDKit::RWMol &templateMol)
RDKIT_DEPICTOR_EXPORT void	RDDepict::reducedToFullMatches (const RDKit::RWMol &reducedQuery, const RDKit::RWMol &molHs, std::vector< RDKit::MatchVectType > &matches)
RDKIT_DEPICTOR_EXPORT bool	RDDepict::invertWedgingIfMolHasFlipped (RDKit::ROMol &mol, const RDGeom::Transform3D &trans)

Variables
RDKIT_DEPICTOR_EXPORT double	RDDepict::BOND_LEN
RDKIT_DEPICTOR_EXPORT double	RDDepict::COLLISION_THRES
RDKIT_DEPICTOR_EXPORT double	RDDepict::BOND_THRES
RDKIT_DEPICTOR_EXPORT double	RDDepict::ANGLE_OPEN
RDKIT_DEPICTOR_EXPORT unsigned int	RDDepict::MAX_COLL_ITERS
RDKIT_DEPICTOR_EXPORT double	RDDepict::HETEROATOM_COLL_SCALE
RDKIT_DEPICTOR_EXPORT unsigned int	RDDepict::NUM_BONDS_FLIPS