Standardizer adds additional empty lines to an SDFile

Standardizer adds additional empty lines to an SDFile. The result is that these SDFiles cannot be read anymore by KNIME SDFile reader.

I have no idea why this happens. I assume this is a bug.

This problem does not occur if one uses the KNIME nodes of www.infocom.co.jp.

Alex

See attached pictures.

The problem seems to be a line with too many charcters.

I enclose a subset of the input and output file. When I copy in Ultredit the section of the input file, I get a file with an extra line before AUXINFO. I edited the copied section, so it looks again like the input file, see attachments.

Alex

I'm not sure I get what is the error. The "INCHI" SDF field in the input file "edited input file for standardizer.sdf" contains an InChi string in format

>  <INCHI>

InChI=1/C26H28N2O5S/c1-26(2,3)15-11-12-17-20(14-15)34-24(28-22(29)19-10-7-13-33-19)21(17)23(30)27-18-9-6-5-8-16(18)25(31)32-4/h5-10,13,15H,11-12,14H2,1-4H3,(H,27,30)(H,28,29)



AuxInfo=1/1/N:29,30,31,32,33,34,25,27,28,21,22,15,24,14,16,9,4,11,12,3,1,8,5,2,13,19,10,7,20,18,23,26,17,6/E:(1,2,3)/rA:34CCCCCSNCCNCCCCCCOOCOCCOCCOCCCCCCCC/rB:d-1;;s1d-3;s1;s2s3;s2;s7;;s5;d-9s10;s8;s9;s3;s4;s14;s12;d5;s16;d8;d+12;s15s16;d13;s17;s21d-24;s13;s9;s11;s19;s19;s19;s26;d-27;d-28s33;/rC:-.6426,-.0698,0;.1619,-1.3829,0;-2.168,-2.7576,0;-2.9392,-1.3829,0;-.2459,1.4333,0;-.6091,-2.7519,0;1.6984,-1.3662,0;3.0396,-.6061,0;-.2459,4.5344,0;1.0673,2.2101,0;1.0673,3.7466,0;4.3639,.1929,0;-1.548,3.8472,0;-2.9392,-4.0762,0;-4.4871,-1.4109,0;-4.4648,-4.0986,0;5.7274,-.4051,0;-1.0282,2.7745,0;-5.2356,-5.4398,0;3.7828,-1.9306,0;4.4534,1.7183,0;-5.2356,-2.7576,0;-2.6374,2.6123,0;6.7276,.8187,0;5.9229,2.0534,0;-2.861,4.5846,0;-.2459,5.9872,0;2.3915,4.5344,0;-5.9902,-6.7751,0;-3.8668,-6.194,0;-6.7276,-5.0373,0;-2.9559,6.1214,0;1.0673,6.7751,0;2.3915,5.9872,0;







>  <SMILES>

There is an empty line after the "InChi" part, and there are three empty lines after the "AuxInfo" part. 

Is this INCHI string altered by Standardizer in KNIME? We cannot reproduce any error in Standardizer command line or desktop application.

Please clarify the error, and provide us information about your

• operating system


• Java version


• KNIME version


• JChem KNIME extension version.

The Standardizer does not change the InChI. The problem is that you get an extra empty line when you copy the line starting with InChI and the line starting with AUX from an SDFile to another file. This happens with an editor like UltraEdit. Similar, when you send a SDFile through the Standardizer you get in the end this extra line. The result is that you have a line with data, but no field name and you cannot read this SDFile anymore in some programs, like KNIME version 2.10.0 64 bit Windows 8.1.

I can copy the InChi Line and the Aux line from an email into UltrAEdit and I don't get the extra line.

I have an old definition documentation of the MDL CT File and there it states that the fileds cannot have more than 200 charcters, see: A [Data] value may extend over multiple lines containing up to 200 characters each. A blank line terminates each data item.

This seems not to be a ChemAxon problem, but one should be aware of the issue.

Alex

Thank you for the notification, this restriction for maximum line length in property fields avoided our attention. We'll add this as an incompatibility note to our documentation.

We don't know whether we will fix this as until now it haven't caused any compatibility issue with other chemistry products.

Best regards,

Peter