RDKit
Open-source cheminformatics and machine learning.
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DepictUtils.h File Reference
#include <RDGeneral/types.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RWMol.h>
#include <GraphMol/ROMol.h>
#include <Geometry/Transform2D.h>
#include <Geometry/point.h>
#include <queue>

Go to the source code of this file.

Classes

struct  RDDepict::gtIIPair
 

Namespaces

 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

RDGeom::INT_POINT2D_MAP RDDepict::embedRing (const RDKit::INT_VECT &ring)
 Some utility functions used in generating 2D coordinates. More...
 
void RDDepict::transformPoints (RDGeom::INT_POINT2D_MAP &nringCor, const RDGeom::Transform2D &trans)
 
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. More...
 
void RDDepict::reflectPoints (RDGeom::INT_POINT2D_MAP &coordMap, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)
 Reflect a set of point through a the line joining two point. More...
 
RDGeom::Point2D RDDepict::reflectPoint (const RDGeom::Point2D &point, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)
 
RDKit::INT_VECT RDDepict::setNbrOrder (unsigned int aid, const RDKit::INT_VECT &nbrs, const RDKit::ROMol &mol)
 Set the neighbors yet to added to aid such that the atoms with the most subs fall on opposite sides. More...
 
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. More...
 
template<class T >
RDDepict::rankAtomsByRank (const RDKit::ROMol &mol, const T &commAtms, bool ascending=true)
 Sort a list of atoms by their CIP rank. More...
 
double RDDepict::computeSubAngle (unsigned int degree, RDKit::Atom::HybridizationType htype)
 computes a subangle for an atom of given hybridization and degree More...
 
int RDDepict::rotationDir (const RDGeom::Point2D &center, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2, double remAngle)
 computes the rotation direction between two vectors More...
 
RDGeom::Point2D RDDepict::computeNormal (const RDGeom::Point2D &center, const RDGeom::Point2D &other)
 computes and return the normal of a vector between two points More...
 
double RDDepict::computeAngle (const RDGeom::Point2D &center, const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)
 computes the rotation angle between two vectors More...
 
int RDDepict::pickFirstRingToEmbed (const RDKit::ROMol &mol, const RDKit::VECT_INT_VECT &fusedRings)
 pick the ring to embed first in a fused system More...
 
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 More...
 
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 More...
 
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. More...
 
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. More...
 

Variables

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