PerceiveCDKAtomTypes.code.md

PerceiveCDKAtomTypes.groovy

Source code

The source code may use or refer to content in a local workspace. This Bioclipse workspace used can be found on GitHub.

Bioclipse 2.6

mol = cdk.fromSMILES("CCO")
cdx.perceiveCDKAtomTypes(mol)
print cdx.perceiveCDKAtomTypes(mol)

Bacting

To run this code, you first need to install Bacting (Groovy) or pyBacting (Python).

@Grab(group='io.github.egonw.bacting', module='managers-cdk', version='0.1.2')
@Grab(group='io.github.egonw.bacting', module='managers-cdkdebug', version='0.1.2')

workspaceRoot = "../ws"
cdk = new net.bioclipse.managers.CDKManager(workspaceRoot);
cdx = new net.bioclipse.managers.cdkdebug.CDKDebugManager(workspaceRoot);

mol = cdk.fromSMILES("CCO")
cdx.perceiveCDKAtomTypes(mol)
print cdx.perceiveCDKAtomTypes(mol)

Output

1:C.sp3
2:C.sp3
3:O.sp3