Relevant commit:
https://github.com/cdk/cdk/commit/20d57ed9e92e187e3ef3f356d4236534bff0bce2
You can actually control the that set from an option if IIRC so you a work
around in 1.5.14 might be to add those to the ignore. I can remember though
if this might also remove the title line - there were some other commit
around then for example null is now blank.
John
On 26 June 2017 at 09:51, John Mayfield <[email protected]> wrote:
> Use version 2.0 :-)
>
> On 26 June 2017 at 08:31, Tim Dudgeon <[email protected]> wrote:
>
>> Here's what I see:
>>
>> IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
>> SmilesParser parser = new SmilesParser(bldr);
>> IAtomContainer mol1 = parser.parseSmiles("CCO");
>> IAtomContainer mol2 = parser.parseSmiles("CCO ethanol");
>> SDFWriter sdf = new SDFWriter(System.out);
>> sdf.write(mol1);
>> sdf.write(mol2);
>>
>> Outputs:
>>
>>
>> CDK 0626170823
>>
>> 3 2 0 0 0 0 0 0 0 0999 V2000
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>> 1 2 1 0 0 0 0
>> 2 3 1 0 0 0 0
>> M END
>> > <cdk:Title>
>> null
>>
>> $$$$
>> ethanol
>> CDK 0626170823
>>
>> 3 2 0 0 0 0 0 0 0 0999 V2000
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>> 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>> 1 2 1 0 0 0 0
>> 2 3 1 0 0 0 0
>> M END
>> > <cdk:Title>
>> ethanol
>>
>> $$$$
>>
>> Note that for mol1 no title is set but a property named cdk:Title is
>> output with a value of "null".
>> For mol2 the title is set and output correctly, but the property
>> cdk:Title is also output.
>> This is with version 1.5.14.
>>
>> Tim
>>
>>
>>
>> On 25/06/2017 15:40, John Mayfield wrote:
>>
>> I'm planning on rewriting the CTab readers to fix issues like the
>> cdk:Remark nastyness but the title lines should still be working.
>>
>> IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
>>> SmilesParser smipar = new SmilesParser(bldr);
>>> IAtomContainer mol = smipar.parseSmiles("CCO ethanol");
>>> new MDLV2000Writer(System.out).write(mol);
>>> System.out.println("//");
>>> try (SDFWriter sdf = new SDFWriter(System.out)) {
>>> sdf.write(mol);
>>> }
>>
>>
>> Result:
>>
>> ethanol
>>>
>>> CDK 0625171540
>>>
>>>
>>>> 3 2 0 0 0 0 0 0 0 0999 V2000
>>>
>>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>>> 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>>> 1 2 1 0 0 0 0
>>>
>>> 2 3 1 0 0 0 0
>>>
>>> M END
>>>
>>> //
>>>
>>> ethanol
>>>
>>> CDK 0625171540
>>>
>>>
>>>> 3 2 0 0 0 0 0 0 0 0999 V2000
>>>
>>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>>> 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
>>>
>>> 1 2 1 0 0 0 0
>>>
>>> 2 3 1 0 0 0 0
>>>
>>> M END
>>>
>>> $$$$
>>>
>>>
>> How are you using them Tim?
>>
>> John
>>
>> On 24 June 2017 at 17:19, Tim Dudgeon <[email protected]> wrote:
>>
>>> One possibility might be to use the value of IChemObject.getID() for the
>>> title line.
>>> Not sure if that would be a good or a bad idea. But I tried it and it
>>> doesn't work.
>>>
>>> Another thing I noticed is that CDK has a bad habit of adding an empty
>>> cdk:Remark property for no particular reason.
>>> But if you know about this then you can remove it before exporting so
>>> its not a major problem.
>>>
>>> Tim
>>>
>>>
>>>
>>> On 24/06/2017 15:45, Egon Willighagen wrote:
>>>
>>>> Mmm... I'd consider that a regression, as that was the intended
>>>> behavior...
>>>>
>>>> John, do you agree we should restore that behavior, or do you have a
>>>> better solution?
>>>>
>>>> Egon
>>>>
>>>>
>>>> On Sat, Jun 24, 2017 at 4:23 PM, Tim Dudgeon <[email protected]>
>>>> wrote:
>>>>
>>>>> Hi All,
>>>>>
>>>>> I'm needing to write the title line (the first line in the record) for
>>>>> MDL
>>>>> formats.
>>>>> I'm using SDFWriter.write(mol) to write out the SD file.
>>>>> I've found that you can do this be setting the property
>>>>> CDKConstants.TITLE
>>>>> (which has a value of "cdk:Title") of the IAtomContainer to the value
>>>>> you
>>>>> want in the title line , but you also get this written as a SD file
>>>>> property, which is not what I want.
>>>>>
>>>>> Is there a way of better controlling this?
>>>>>
>>>>> Tim
>>>>>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
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>>>>>
>>>>
>>>>
>>>>
>>>
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>>
>>
>>
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>
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