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 <tdudgeon...@gmail.com> 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 <tdudgeon...@gmail.com>
>> 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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