This is for marking the molecule as 2D (i.e. having 2D coordinates
associated with it). After reading a SMILES it should be marked as 0D.
- Noel
On 18 June 2013 19:48, Craig James <cja...@emolecules.com> wrote:
> (forgot to cc list the first time...)
>
>
> On Tue, Jun 18, 2013 at 10:34 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
>>
>> I understand where the expected output is coming from, but where's the
>> 'wrong' output coming from?
>
>
> Sorry for not making that clear ... the "expected" output is from obabel,
> and the "wrong" output is from my C++ program.
>
>>
>>
>> You have pmol_conv_ich->SetInAndOutFormats("inchi", "inchi");
>>
>> This does mean you are reading one of those InChIs and roundtripping
>> it? Or are you reading the SMILES somewhere else and using this
>> OBConversion object?
>
>
> The latter ... there's a separate OBConversion object with in/out formats of
> "smi".
>
> OK, I think I found the problem. In my code that parses the SMILES I found
> this:
>
> pmol->SetDimension(2); // workaround for OpenBabel bug: discards
> // chirality if this isn't set.
>
> This must have been put in there a long time ago, and I have no idea if it's
> still relevant or not. If I take it out, the InChI strings are created
> properly.
>
> However, I can't find any meaningful documentation about what SetDimension()
> is supposed to do or how it's used. I suspect I had to add SetDimension()
> because of this code in canon.cpp:
>
> // Determine stereochemistry from coordinates if needed
> if (!mol->HasChiralityPerceived()) {
> switch (mol->GetDimension()) {
> case 2:
> mol->DeleteData(OBGenericDataType::StereoData);
> TetrahedralFrom2D(mol, stereoUnits);
> CisTransFrom2D(mol, stereoUnits);
> break;
> case 3:
> mol->DeleteData(OBGenericDataType::StereoData);
> TetrahedralFrom3D(mol, stereoUnits);
> CisTransFrom3D(mol, stereoUnits);
> break;
> default:
> TetrahedralFrom0D(mol, stereoUnits);
> CisTransFrom0D(mol, stereoUnits);
> break;
> }
> }
>
> ... but who knows? I'll have to dig into it a bit more...
>
> Thanks,
> Craig
>
>
>
>>
>> - Noel
>>
>> On 18 June 2013 16:45, Craig James <cja...@emolecules.com> wrote:
>> > I'm getting different InChI strings from obabel than when I invoke the
>> > InChI
>> > format directly from C++ code. It looks like it has to do with options
>> > ...
>> > but my code isn't setting any I/O options for the InChI writer. Here's
>> > the
>> > output from my test program:
>> >
>> > ERROR: incorrect InChI:
>> > expected:
>> >
>> > 'InChI=1S/C15H17NO5/c1-10(14(18)20-2)16-13(17)9-6-11-4-7-12(8-5-11)15(19)21-3/h4-10H,1-3H3,(H,16,17)/b9-6+/t10-/m0/s1'
>> > got:
>> >
>> > 'InChI=1S/C15H17NO5/c1-10(14(18)20-2)16-13(17)9-6-11-4-7-12(8-5-11)15(19)21-3/h4-10H,1-3H3,(H,16,17)'
>> > SMILES is: 'COC(=O)[C@@H](NC(=O)/C=C/c1ccc(cc1)C(=O)OC)C
>> >
>> > The "expected" string is from "obabel -i smi -o inchi". Note that it
>> > seems
>> > to be stereo information that differs between the two.
>> >
>> > The C++ code I'm using is pretty simple:
>> >
>> > OBConversion *pmol_conv_ich = NULL;
>> > pmol_conv_ich = new OBConversion();
>> > pmol_conv_ich->SetInAndOutFormats("inchi", "inchi");
>> > ...
>> > string inchi = pmol_conv_ich->WriteString(pmol, true);
>> >
>> > I don't set any options on pmol_conf_ich. The SMILES shown above is
>> > from
>> > the same pmol OBMol object.
>> >
>> > Why is this output different from obabel's output?
>> >
>> > Thanks,
>> > Craig
>> >
>> >
>> >
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>
>
>
>
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