RDKit
Open-source cheminformatics and machine learning.
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RDDepict::Compute2DCoordParameters Struct Reference

#include <RDDepictor.h>

Public Member Functions

 Compute2DCoordParameters ()=default
 

Public Attributes

const RDGeom::INT_POINT2D_MAPcoordMap
 
bool canonOrient = false
 
bool clearConfs = true
 
unsigned int nFlipsPerSample = 0
 
unsigned int nSamples = 0
 the number of samples
 
int sampleSeed = 0
 seed for the random sampling process
 
bool permuteDeg4Nodes = false
 
bool forceRDKit = false
 
bool useRingTemplates = false
 

Detailed Description

Definition at line 71 of file RDDepictor.h.

Constructor & Destructor Documentation

◆ Compute2DCoordParameters()

RDDepict::Compute2DCoordParameters::Compute2DCoordParameters ( )
default

Member Data Documentation

◆ canonOrient

bool RDDepict::Compute2DCoordParameters::canonOrient = false

canonicalize the orientation so that the long axes align with the x-axis etc.

Definition at line 77 of file RDDepictor.h.

◆ clearConfs

bool RDDepict::Compute2DCoordParameters::clearConfs = true

clear all existing conformations on the molecule before adding the 2D coordinates instead of simply adding to the list

Definition at line 79 of file RDDepictor.h.

◆ coordMap

const RDGeom::INT_POINT2D_MAP* RDDepict::Compute2DCoordParameters::coordMap
Initial value:
=
nullptr

a map of int to Point2D, between atom IDs and their locations. This is the container the user needs to fill if he/she wants to specify coordinates for a portion of the molecule, defaults to 0

Definition at line 72 of file RDDepictor.h.

◆ forceRDKit

bool RDDepict::Compute2DCoordParameters::forceRDKit = false

use RDKit to generate coordinates even if preferCoordGen is set to true

Definition at line 89 of file RDDepictor.h.

◆ nFlipsPerSample

unsigned int RDDepict::Compute2DCoordParameters::nFlipsPerSample = 0

the number of rotatable bonds that are flipped at random for each sample

Definition at line 82 of file RDDepictor.h.

◆ nSamples

unsigned int RDDepict::Compute2DCoordParameters::nSamples = 0

the number of samples

Definition at line 84 of file RDDepictor.h.

◆ permuteDeg4Nodes

bool RDDepict::Compute2DCoordParameters::permuteDeg4Nodes = false

try permuting the drawing order of bonds around atoms with four neighbors in order to improve the depiction

Definition at line 86 of file RDDepictor.h.

◆ sampleSeed

int RDDepict::Compute2DCoordParameters::sampleSeed = 0

seed for the random sampling process

Definition at line 85 of file RDDepictor.h.

◆ useRingTemplates

bool RDDepict::Compute2DCoordParameters::useRingTemplates = false

whether to use ring system templates for generating initial coordinates

Definition at line 91 of file RDDepictor.h.


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