Re: [Cdk-user] CDK - issue with stereochemistry

[Yannick .Djoumbou]

Hi John,

Thanks for the quick response. My concern is that I would like to
preprocess the structures correctly so that no matter how the molecule was
originally stored and what tools was used (OpenBabel, CDK, JChem/MarVin), I
return one unique representation. Afterwards the molecule is subjected to
another tool that uses CDK for transformations.
BTW, I add the explicit hydrogens because most of the smarts string and
smirks strings I use later on contain them, and I noticed that I have to do
so in order for pattern matching or transformations to work.

Also, if I understood correctly, I have many lines that I should remove?
Which ones?

Thanks,

On Wed, Jun 7, 2017 at 2:12 PM, John Mayfield 
wrote:

> SmilesParser smipar = new SmilesParser(SilentChemObjectBuilder.getInstance
>> ());
>> System.out.println(SmartsPattern.create("c1c1")
>> .matches(smipar.parseSmiles("C1=CC=CC=C1")));
>
>
> Too many carbons in the SMILES...
>
> On 7 June 2017 at 21:11, John Mayfield 
> wrote:
>
>> You don't need to do any of this.
>>
>> - From your wording, it sounds like you store aromatic bonds in molfiles,
>> do not do this. ChemAxon know this is bad, they should warn on write (like
>> everyone else). Yes I know people use it but two wrongs don't make a right.
>>
>> - SINGLE_OR_DOUBLE is defunct do not use it... will get round to
>> deprecating that at some point. If you must...do it:
>> *if (bond.isAromatic() && bond.getOrder() == IBond.Order.UNSET)*
>>
>> - High level SMARTS matching automatically sets the aromaticity to be
>> correct (Daylight's - which incidentally you're not using here anyways :-D):
>>
>> SmilesParser smipar = new 
>> SmilesParser(SilentChemObjectBuilder.getInstance());
>> System.out.println(SmartsPattern.create("c1c1")
>> 
>> .matches(smipar.parseSmiles("C1=CC=CC=CC1")));
>>
>>
>>
>> John
>>
>> On 7 June 2017 at 20:58, Yannick .Djoumbou  wrote:
>>
>>> Thanks John,
>>>
>>> Because of the variety of sources from molecules, including the ones
>>> generated by JChem (which handles aromatic bonds differently from most), I
>>> decided to add a function that preprocesses molecules. here is the code.
>>> Please let me know if this is OK.
>>>
>>> I basically percieve the atoms, ckeck the bonds, and make sure that the
>>> aromatic bonds (which are represented in ChemAxon with 4 - query bonds) are
>>> set appropriately. I then aromatize the structure (as I want to run them
>>> against SMIRKS/SMARTS patterns that might include various representations
>>> of rings).  Subsequently, I convert implicit hydrogens to explicit
>>> hydrogens and generate coordinates for the new atoms.
>>>
>>> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
>>>Aromaticity aromaticity = new Aromaticity( ElectronDonation.cdk(),
>>> Cycles.cdkAromaticSet());
>>> for (IBond bond : molecule.bonds()) {
>>> if (bond.getFlag(CDKConstants.SINGLE_OR_DOUBLE)) {
>>> bond.setFlag(CDKConstants.ISAROMATIC, true);
>>> bond.getAtom(0).setFlag(CDKConstants.ISAROMATIC, true);
>>> bond.getAtom(1).setFlag(CDKConstants.ISAROMATIC, true);
>>> }
>>> }
>>> aromaticity.apply(molecule);
>>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
>>> StructureDiagramGenerator sdg = new StructureDiagramGenerator();
>>> sdg.setMolecule(molecule);
>>> sdg.generateCoordinates();
>>> IAtomContainer layedOutMol = sdg.getMolecule();
>>> return layedOutMol
>>>
>>> Thanks,
>>> Yannick
>>>
>>>
>>>
>>>
>>>
>>> On Wed, Jun 7, 2017 at 1:43 PM, John Mayfield <
>>> john.wilkinson...@gmail.com> wrote:
>>>
 I tried MarvinSketch before I posted that and all the same there too..
 let me know if you still think there is a problem.

 On 7 June 2017 at 18:13, Yannick .Djoumbou 
 wrote:

> Hi John,
>
> Thank you the fast response. I am using another viewer, which could
> have brought the confusion. This just means the issue in my code might 
> come
> from somewhere else.
>
> Thanks,
> Yannick
>
> On Tue, Jun 6, 2017 at 3:25 AM, John Mayfield <
> john.wilkinson...@gmail.com> wrote:
>
>> Hi Yannick,
>>
>> Please, please, please don't "add hydrogens" like this! The hydrogens
>> are already there and don't need to be added - this is just wasted effort
>> and worst of all the atom typing *might* change your structures
>> valence!! If for some reason you want to make hydrogens explicit just 
>> call
>> this method directly:
>>
>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule
>>> );
>>
>>
>> Anyways why do you think the stereochemistry is different? All your
>> SMILES are the same and the stereochemistry is preserved correctly - 
>> paste
>> them in here to see: https://cdkdepict-openche
>> m.rhcloud.com/depict.html
>>
>>
>> 

Re: [Cdk-user] CDK - issue with stereochemistry

[John Mayfield]

I tried MarvinSketch before I posted that and all the same there too.. let
me know if you still think there is a problem.

On 7 June 2017 at 18:13, Yannick .Djoumbou  wrote:

> Hi John,
>
> Thank you the fast response. I am using another viewer, which could have
> brought the confusion. This just means the issue in my code might come from
> somewhere else.
>
> Thanks,
> Yannick
>
> On Tue, Jun 6, 2017 at 3:25 AM, John Mayfield  > wrote:
>
>> Hi Yannick,
>>
>> Please, please, please don't "add hydrogens" like this! The hydrogens are
>> already there and don't need to be added - this is just wasted effort and
>> worst of all the atom typing *might* change your structures valence!! If
>> for some reason you want to make hydrogens explicit just call this method
>> directly:
>>
>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
>>
>>
>> Anyways why do you think the stereochemistry is different? All your
>> SMILES are the same and the stereochemistry is preserved correctly - paste
>> them in here to see: https://cdkdepict-openchem.rhcloud.com/depict.html
>>
>>
>> [image: Inline images 1]
>>
>
>
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Re: [Cdk-user] CDK - issue with stereochemistry

[Yannick .Djoumbou]

Hi John,

Thank you the fast response. I am using another viewer, which could have
brought the confusion. This just means the issue in my code might come from
somewhere else.

Thanks,
Yannick

On Tue, Jun 6, 2017 at 3:25 AM, John Mayfield 
wrote:

> Hi Yannick,
>
> Please, please, please don't "add hydrogens" like this! The hydrogens are
> already there and don't need to be added - this is just wasted effort and
> worst of all the atom typing *might* change your structures valence!! If
> for some reason you want to make hydrogens explicit just call this method
> directly:
>
> AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);
>
>
> Anyways why do you think the stereochemistry is different? All your SMILES
> are the same and the stereochemistry is preserved correctly - paste them in
> here to see: https://cdkdepict-openchem.rhcloud.com/depict.html
>
>
> [image: Inline images 1]
>
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Re: [Cdk-user] CDK - issue with stereochemistry

[John Mayfield]

Hi Yannick,

Please, please, please don't "add hydrogens" like this! The hydrogens are
already there and don't need to be added - this is just wasted effort and
worst of all the atom typing *might* change your structures valence!! If
for some reason you want to make hydrogens explicit just call this method
directly:

AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);


Anyways why do you think the stereochemistry is different? All your SMILES
are the same and the stereochemistry is preserved correctly - paste them in
here to see: https://cdkdepict-openchem.rhcloud.com/depict.html


[image: Inline images 1]
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[Cdk-user] CDK - issue with stereochemistry

[Yannick .Djoumbou]

Hi all,

I have an issue handling stereochemistry with CDK. I am using CDK-1.5.13. I
have the following molecule:

Mol 1: [H][C@@]1(O)[C@@H](CO)O[C@@]([H])(OC2CCC3CCC(=O)OC3C2)[C@
]([H])(O)[C@H]1O

I am using the following code to add implicit hydrogens and further convert
them into explicit ones. The resulting structure serves as input for
another function.

 AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);

CDKHydrogenAdder.getInstance(molecule
.getBuilder()).addImplicitHydrogens(molecule);

AtomContainerManipulator.convertImplicitToExplicitHydrogens(molecule);


Unfortunately, the stereochemistry in structure that results from this code
is messed up. This is what I get in return:

Mol2: [H][C@@]1(O[H])[C@@](C(O[H])([H])[H])(O[C@
@]([H])(OC2(C(C(C3(C(C(C(=O)OC3(C2([H])[H])[H])([H])[H])([H])[H])[H])([H])[H])([H])[H])[H])[C@
]([H])(O[H])[C@]1(O[H])[H])[H]

But what I think should be returned is

Mol3: [H]OC([H])([H])[C@@]1([H])O[C@
@]([H])(OC2([H])C([H])([H])C([H])([H])C3([H])C([H])([H])C([H])([H])C(=O)OC3([H])C2([H])[H])[C@
]([H])(O[H])[C@@]([H])(O[H])[C@]1([H])O[H]

Is there a reason for the change of stereochemical information? How to fix
the code in order to obtain the Mol3 structure?


Thank you so much for your help.

Best,

Yannick
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