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

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

#include <EmbeddedFrag.h>

Public Types

enum  EAtomType { UNSPECIFIED = 0 , CISTRANS , RING }
 

Public Member Functions

 EmbeddedAtom ()
 
 EmbeddedAtom (const EmbeddedAtom &other)=default
 
 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 {0}
 
double angle {-1.0}
 the angle that is already takes at this atom, so any new atom attaching to More...
 
int nbr1 {-1}
 the first neighbor of this atom that form the 'angle' More...
 
int nbr2 {-1}
 the second neighbor of atom that from the 'angle' More...
 
int CisTransNbr {-1}
 is this is a cis/trans atom the neighbor of this atom that is involved in More...
 
bool ccw {true}
 <= PI/2 More...
 
int rotDir {0}
 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 {-1.0}
 
bool df_fixed {false}
 

Detailed Description

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

Definition at line 29 of file EmbeddedFrag.h.

Member Enumeration Documentation

◆ EAtomType

Enumerator
UNSPECIFIED 
CISTRANS 
RING 

Definition at line 31 of file EmbeddedFrag.h.

Constructor & Destructor Documentation

◆ EmbeddedAtom() [1/3]

RDDepict::EmbeddedAtom::EmbeddedAtom ( )
inline

Definition at line 33 of file EmbeddedFrag.h.

◆ EmbeddedAtom() [2/3]

RDDepict::EmbeddedAtom::EmbeddedAtom ( const EmbeddedAtom other)
default

◆ EmbeddedAtom() [3/3]

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

Definition at line 41 of file EmbeddedFrag.h.

Member Function Documentation

◆ operator=()

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

Definition at line 54 of file EmbeddedFrag.h.

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

◆ Reflect()

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

Definition at line 80 of file EmbeddedFrag.h.

References RDDepict::reflectPoint().

◆ Transform()

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

Definition at line 73 of file EmbeddedFrag.h.

References RDGeom::Transform2D::TransformPoint().

Member Data Documentation

◆ aid

unsigned int RDDepict::EmbeddedAtom::aid {0}

Definition at line 88 of file EmbeddedFrag.h.

◆ angle

double RDDepict::EmbeddedAtom::angle {-1.0}

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=().

◆ ccw

bool RDDepict::EmbeddedAtom::ccw {true}

<= PI/2

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

Definition at line 110 of file EmbeddedFrag.h.

Referenced by operator=().

◆ CisTransNbr

int RDDepict::EmbeddedAtom::CisTransNbr {-1}

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=().

◆ d_density

double RDDepict::EmbeddedAtom::d_density {-1.0}

Definition at line 133 of file EmbeddedFrag.h.

Referenced by operator=().

◆ df_fixed

bool RDDepict::EmbeddedAtom::df_fixed {false}

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=().

◆ loc

RDGeom::Point2D RDDepict::EmbeddedAtom::loc

Definition at line 118 of file EmbeddedFrag.h.

Referenced by operator=().

◆ nbr1

int RDDepict::EmbeddedAtom::nbr1 {-1}

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

Definition at line 96 of file EmbeddedFrag.h.

Referenced by operator=().

◆ nbr2

int RDDepict::EmbeddedAtom::nbr2 {-1}

the second neighbor of atom that from the 'angle'

Definition at line 99 of file EmbeddedFrag.h.

Referenced by operator=().

◆ neighs

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=().

◆ normal

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=().

◆ rotDir

int RDDepict::EmbeddedAtom::rotDir {0}

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: