I'm using the org.openscience.smsd (external) code.
My question is should I switch to the older (deprecated)
org.openscience.cdk.smsd classes?
Tim
On 28/08/2019 12:47, John Mayfield wrote:
Which SMSD are you using? I don't have control over the downstream one.
On Wed, 28 Aug 2019 at 10:16, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
Unfortunately other parts of my code are using new features such
as IAtomContainer.atoms() so whilst switching to the legacy
IAtomContainer avoids the alignment problem it looks to be a no go
as a solution.
Would switching to the legacy classes in the
org.openscience.cdk.smsd package be an option or do I just need to
wait for the problem to be fixed?
On 28/08/2019 08:15, John Mayfield wrote:
Okay code is likely adding atoms/bonds in the wrong order, will
fix it.
On Tue, 27 Aug 2019 at 18:18, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
Hi John,
Yes, turning off AtomContainer2 avoids the error.
On 27/08/2019 16:31, John Mayfield wrote:
Hmm odd, in legacy so expected but tests seem okay. Can you
try turning off AtomContainer2,
https://github.com/cdk/cdk/wiki/AtomContainer2
On Tue, 27 Aug 2019 at 14:19, Tim Dudgeon
<tdudgeon...@gmail.com <mailto:tdudgeon...@gmail.com>> wrote:
Hi folks,
I'm getting a NPE from
AtomAtomMapping.getCommonFragmentAsSMILES() in certain
cases.
An example is below - the two structures differ only for
a Cl <-> Br change.
This is using the org.openscience.smsd.AtomAtomMapping,
org.openscience.smsd.Isomorphism and
org.openscience.smsd.tools.ExtAtomContainerManipulator
classes.
Not sure if those guys are active on this list?
IAtomContainer query
=smilesParser.parseSmiles('BrC1CCC(Cc2ccccc2)C1')
IAtomContainer target
=smilesParser.parseSmiles('ClC1CCC(Cc2ccccc2)C1')
StructureDiagramGenerator sdg =new StructureDiagramGenerator()
sdg.generateCoordinates(query)
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(query)
ExtAtomContainerManipulator.aromatizeMolecule(query)
ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(target)
ExtAtomContainerManipulator.aromatizeMolecule(target)
Isomorphism comparison =new Isomorphism(query, target,
Algorithm.DEFAULT,true,false,false)
AtomAtomMapping mapping = comparison.getFirstAtomMapping()
String mcsSmiles = mapping.getCommonFragmentAsSMILES()
The error I get is:
java.lang.NullPointerException
at
org.openscience.cdk.silent.AtomContainer2.getAtomRefUnsafe(AtomContainer2.java:172)
at
org.openscience.cdk.silent.AtomContainer2.getBond(AtomContainer2.java:612)
at
org.openscience.smsd.AtomAtomMapping.getCommonFragment(AtomAtomMapping.java:332)
at
org.openscience.smsd.AtomAtomMapping.getCommonFragmentAsSMILES(AtomAtomMapping.java:371)
at
org.squonk.fragnet.depict.ChemUtilsSpec.alignMolecule2(ChemUtilsSpec.groovy:81)
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