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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