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

 get.connection.matrix R Documentation

## Get connection matrix for a molecule.

### Description

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

### Usage

get.connection.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

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