Use version 2.0 :-)
On 26 June 2017 at 08:31, Tim Dudgeon <tdudgeon...@gmail.com> 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 <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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>
>
>
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