RDKit
Open-source cheminformatics and machine learning.
RDDepict::EmbeddedAtom Class Reference

Class that contains the data for an atoms that has alredy been embedded. More...

#include <EmbeddedFrag.h>

Public Types

enum  EAtomType { UNSPECIFIED = 0, CISTRANS, RING }
 

Public Member Functions

 EmbeddedAtom ()
 
 EmbeddedAtom (unsigned int aid, const RDGeom::Point2D &pos)
 
EmbeddedAtomoperator= (const EmbeddedAtom &other)
 
void Transform (const RDGeom::Transform2D &trans)
 
void Reflect (const RDGeom::Point2D &loc1, const RDGeom::Point2D &loc2)
 

Public Attributes

unsigned int aid
 
double angle
 the angle that is already takes at this atom, so any new atom attaching to More...
 
int nbr1
 the first neighbor of this atom that form the 'angle' More...
 
int nbr2
 the second neighbor of atom that from the 'angle' More...
 
int CisTransNbr
 is this is a cis/trans atom the neighbor of this atom that is involved in More...
 
bool ccw
 <= PI/2 More...
 
int rotDir
 useful only on atoms that are degree >= 4 More...
 
RDGeom::Point2D loc
 
RDGeom::Point2D normal
 a zig-zag manner More...
 
RDKit::INT_VECT neighs
 and these are the atom IDs of the neighbors that still need to be embedded More...
 
double d_density
 
bool df_fixed
 

Detailed Description

Class that contains the data for an atoms that has alredy been embedded.

Definition at line 28 of file EmbeddedFrag.h.

Member Enumeration Documentation

Enumerator
UNSPECIFIED 
CISTRANS 
RING 

Definition at line 30 of file EmbeddedFrag.h.

Constructor & Destructor Documentation

RDDepict::EmbeddedAtom::EmbeddedAtom ( )
inline

Definition at line 32 of file EmbeddedFrag.h.

RDDepict::EmbeddedAtom::EmbeddedAtom ( unsigned int  aid,
const RDGeom::Point2D pos 
)
inline

Definition at line 45 of file EmbeddedFrag.h.

Member Function Documentation

EmbeddedAtom& RDDepict::EmbeddedAtom::operator= ( const EmbeddedAtom other)
inline

Definition at line 58 of file EmbeddedFrag.h.

References angle, ccw, CisTransNbr, d_density, df_fixed, loc, nbr1, nbr2, neighs, normal, and rotDir.

void RDDepict::EmbeddedAtom::Reflect ( const RDGeom::Point2D loc1,
const RDGeom::Point2D loc2 
)
inline

Definition at line 80 of file EmbeddedFrag.h.

References RDDepict::reflectPoint().

void RDDepict::EmbeddedAtom::Transform ( const RDGeom::Transform2D trans)
inline

Definition at line 73 of file EmbeddedFrag.h.

References RDGeom::Transform2D::TransformPoint().

Member Data Documentation

unsigned int RDDepict::EmbeddedAtom::aid

Definition at line 88 of file EmbeddedFrag.h.

double RDDepict::EmbeddedAtom::angle

the angle that is already takes at this atom, so any new atom attaching to

atom with have to fall in the available part

Definition at line 93 of file EmbeddedFrag.h.

Referenced by operator=().

bool RDDepict::EmbeddedAtom::ccw

<= PI/2

which direction do we rotate this normal to add the next bond if ccw is true we rotate counter cloack wise, otherwise rotate clock wise,

Definition at line 110 of file EmbeddedFrag.h.

Referenced by operator=().

int RDDepict::EmbeddedAtom::CisTransNbr

is this is a cis/trans atom the neighbor of this atom that is involved in

cis/trans system - defaults to -1

Definition at line 104 of file EmbeddedFrag.h.

Referenced by operator=().

double RDDepict::EmbeddedAtom::d_density

Definition at line 133 of file EmbeddedFrag.h.

Referenced by operator=().

bool RDDepict::EmbeddedAtom::df_fixed

if set this atom is fixed: further operations on the fragment may not move it.

Definition at line 137 of file EmbeddedFrag.h.

Referenced by operator=().

RDGeom::Point2D RDDepict::EmbeddedAtom::loc

Definition at line 118 of file EmbeddedFrag.h.

Referenced by operator=().

int RDDepict::EmbeddedAtom::nbr1

the first neighbor of this atom that form the 'angle'

Definition at line 96 of file EmbeddedFrag.h.

Referenced by operator=().

int RDDepict::EmbeddedAtom::nbr2

the second neighbor of atom that from the 'angle'

Definition at line 99 of file EmbeddedFrag.h.

Referenced by operator=().

RDKit::INT_VECT RDDepict::EmbeddedAtom::neighs

and these are the atom IDs of the neighbors that still need to be embedded

Definition at line 127 of file EmbeddedFrag.h.

Referenced by operator=().

RDGeom::Point2D RDDepict::EmbeddedAtom::normal

a zig-zag manner

this is a normal vector to one of the bonds that added this atom it provides the side on which we want to add a new bond to this atom, this is only relevant when we are dealing with non ring atoms. We would

Definition at line 124 of file EmbeddedFrag.h.

Referenced by operator=().

int RDDepict::EmbeddedAtom::rotDir

useful only on atoms that are degree >= 4

rotation direction around this atom when adding new atoms, we determine this for the first neighbor and stick to this direction after

Definition at line 116 of file EmbeddedFrag.h.

Referenced by operator=().


The documentation for this class was generated from the following file: