That doesn't help. They are not implicit hydrogens, they are real
(explicit) ones.
So presumably they would need to be deleted and then implicit ones
adding back?
Tim
On 22/06/2016 11:42, John M wrote:
Well you can just zero all the counts,
for (IAtom atom : mol.atoms())
atom.setImplicitHydrogenCount(0);
but you can still store contracted forms in mol2 so it's not a general
solution,
John
Regards,
John W May
john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com>
On 22 June 2016 at 11:20, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
Yes, that's right. They are there in the mol2 file.
Strange that you need to "add" them again!
Tim
On 22/06/2016 11:10, John M wrote:
Or actually if the hydrogens are explicit in the input they are
preserved. Looking this up briefly looks to be the case.
Regards,
John W May
john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com>
On 22 June 2016 at 10:52, John M <john.wilkinson...@gmail.com
<mailto:john.wilkinson...@gmail.com>> wrote:
Hmm,
That shouldn't be the case - if you use the
ImplicitHydrogenAdder, this would only be if you then
'convertImplicitToExplicit'.
John
Regards,
John W May
john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com>
On 22 June 2016 at 10:41, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
The bit I didn't like was when I added the implicit
hydrogens and then exported to smiles then the smiles
contains all those hydrogens (as
Explicit/Expanded/Sprouted in your terminology). So to me
it looks like it added explicit hydrogens.
Tim
On 22/06/2016 10:08, John M wrote:
Sorry could be my bad wording, there are really three
'levels' of hydrogens representation. This isn't that
confusing but the terminology is often misnamed in
toolkits/formats. Even there where i said explicit I
should have said labelled or something similar:
Implicit/Undefined -> defined by valence rules -> CCO
Labelled/Contracted/Suppressed -> explicitly stated in
format -> [CH3][CH2][OH]
Explicit/Expanded/Sprouted -> explicit nodes ->
C][H])([H])([H])C([H])([H])O[H]
When CDK says 'ImplicitHydrogenAdder' it's not adding
implicit hydrogens per say but rather taken a molecule
with some unknown hydrogen counts (implicit) it sets the
value of these explicitly. They are still contracted on
the parent atoms. You can take always expand these and
make them explicit nodes in the graph if so desired
(AtomContainerManipulator.convertImplicitHydrogensToExplicit)
or something similar. The reverse is
'suppressExplicitHydrogens', also for legacy reason
'removeExplicitHydrogens' but doesn't actually remove
them so the 'suppress' name is preffered.
John
Regards,
John W May
john.wilkinson...@gmail.com
<mailto:john.wilkinson...@gmail.com>
On 22 June 2016 at 09:55, Tim Dudgeon
<tdudgeon...@gmail.com <mailto:tdudgeon...@gmail.com>>
wrote:
John
Thanks for that. Adding implicit hydrogens does
indeed resolve the problem.
But does this mean that for formats like this you
MUST add IMPLICIT hydrogens everywhere (there's no
way for them to be explicit)? That's ugly!
Tim
On 21/06/2016 19:04, John M wrote:
SMILES, InChI, Molfile have explicit valence models
and thus their hydrogens are set automatically on
read. For other formats you need to add them. The
CDK doesn't do this by valence counting but rather
through more expensive atom typing. Very clunky:
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHydrogenAdder.getInstance(mol.getBuilder()).addImplicitHydrogens(mol);
If someone can point at the Tripos Mol2 valence
model, am happy to add it. Should be easy right as
they encode the atom types in the format?
John
Regards,
John W May
john.wilkinson...@gmail.com
<mailto:john.wilkinson...@gmail.com>
On 21 June 2016 at 17:22, Tim Dudgeon
<tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
I'm having difficulty reading Mol2 format
files. Code is:
def is = new
FileInputStream("../../data/testfiles/ligand.mol2")
def reader = new Mol2Reader(is)
def file = reader.read(new ChemFile())
def mol =
ChemFileManipulator.getAllAtomContainers(file).get(0)
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol)
def out = new ByteArrayOutputStream()
def writer = new SMILESWriter(out)
writer.writeAtomContainer(mol)
println new String(out.toByteArray())
The file appears to be a valid mol2 format
file, but when I try to write it out as smiles
it blows up with:
java.lang.NullPointerException: One or more
atoms had an undefined number of implicit hydrogens
at
com.google.common.base.Preconditions.checkNotNull(Preconditions.java:229)
at
org.openscience.cdk.smiles.CDKToBeam.toBeamAtom(CDKToBeam.java:195)
at
org.openscience.cdk.smiles.CDKToBeam.toBeamGraph(CDKToBeam.java:145)
at
org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:369)
at
org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:325)
at
org.openscience.cdk.io.SMILESWriter.writeAtomContainer(SMILESWriter.java:179)
What am I missing?
Tim
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