# get.adjacency.matrix: Get adjacency matrix for a molecule. In rcdk: Interface to the 'CDK' Libraries

## Description

The adjacency matrix for a molecule with N non-hydrogen atoms is an N \times N matrix where the element [i,j] is set to 1 if atoms i and j are connected by a bond, otherwise set to 0.

## Usage

 1 get.adjacency.matrix(mol) 

## Arguments

 mol A jobjRef object with Java class IAtomContainer

## Value

A N \times N numeric matrix

## Author(s)

Rajarshi Guha rajarshi.guha@gmail.com

## See Also

get.connection.matrix

## Examples

 1 2 m <- parse.smiles("CC=C")[[1]] get.adjacency.matrix(m) 

### Example output

Loading required package: rcdklibs
Loading required package: rJava
[,1] [,2] [,3]
[1,]    0    1    0
[2,]    1    0    1
[3,]    0    1    0


rcdk documentation built on March 13, 2020, 1:30 a.m.