Greg,
Does writing V3000 format work too? How do you trigger V3000 write-out
instead of V2000?
I never know RDKit can work with V3000!
Thanks,
Igor
On Wed, Aug 21, 2013 at 7:43 AM, Greg Landrum <[email protected]>wrote:
> Hi Toby,
>
> On Wed, Aug 21, 2013 at 12:10 PM, Toby Wright <[email protected]>wrote:
>
>>
>> I'm trying to read the data lines from an SD file where the CTAB is in
>> V3000 format. If the file "v3000propIssue.sdf" contains the following:
>> testMol
>>
>>
>> 0 0 0 0 0 999 V3000
>> M V30 BEGIN CTAB
>> M V30 COUNTS 1 0 0 0 0
>> M V30 BEGIN ATOM
>> M V30 1 C 0 0 0 0
>> M V30 END ATOM
>> M V30 END CTAB
>> M END
>> > <TestProp>
>> 42
>>
>> $$$$
>>
>> then it is read by an SDMolSupplier it loads correctly (as shown by the
>> Debug) apart from the data lines which are not converted to RDKit
>> properties as the following interactive code snippet show:
>>
>> >>> import rdkit
>> >>> from rdkit import Chem
>> >>> mol = Chem.SDMolSupplier("v3000propIssue.sdf").next()
>> [10:59:33] ERROR: Problems encountered parsing data fields
>> [10:59:33] ERROR: moving to the begining of the next molecule
>> >>> mol.HasProp("_Name")
>> 1
>> >>> mol.HasProp("TestProp")
>> 0
>>
>
> That's a bug (and an embarrassing one). Looks like I've never tested the
> use of v3000 mol files in SDFs. They certainly should work though.
>
> I'll get it fixed.
>
> -greg
>
>
>
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