Errors importing sdf

Hi there,

we are having problems importing some chemdraw sdf files.  For example:

ChemDraw09240913002D

43 0 0 0 0 0 0 0 0 0999 V2000
-62.6711 -33.0532 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
-62.6711 -2.7518 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-37.8753 11.0092 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-11.7045 -2.7518 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
13.0794 11.0092 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
39.2521 -2.7518 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
64.0479 11.0092 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
64.0479 39.9455 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-65.4248 11.0092 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-33.7466 -12.3861 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-11.7045 9.6323 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
13.0794 -6.8805 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
43.3808 13.7748 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
72.3171 -11.0092 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
92.9724 -6.8805 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
88.8437 8.2574 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
39.2521 41.3224 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
18.5850 39.9455 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-36.5003 -33.0532 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
-13.0795 -34.4301 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
7.5620 -34.4301 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
25.4773 -34.4301 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
44.7577 -34.4301 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
62.6710 -34.4301 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
80.5745 -35.8050 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
98.4898 -35.8050 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
-79.2114 -37.1819 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
-98.4898 -34.4301 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
-6.1990 38.5706 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-26.8542 35.8050 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-46.1445 35.8050 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-68.1884 35.8050 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-66.8135 60.6008 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-36.5003 60.6008 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-18.5969 60.6008 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
-97.1129 -60.6008 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
-69.5653 -60.6008 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
-43.3927 -59.2259 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
-24.1024 -57.8490 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
4.8102 -57.8490 0.0000 Fe 0 1 0 0 0 0 0 2 0 0 0 0
13.0794 60.6008 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
40.6290 60.6008 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
70.9422 60.6008 0.0000 O 0 6 0 0 0 0 0 2 0 0 0 0
M CHG 8 1 3 2 -2 3 -2 4 -2 5 -2 6 -2 7 -2 8 -2
M CHG 8 9 -2 10 -2 11 -2 12 -2 13 -2 14 -2 15 -2 16 -2
M CHG 8 17 -2 18 -2 19 3 20 3 21 3 22 3 23 3 24 3
M CHG 8 25 3 26 3 27 3 28 3 29 -2 30 -2 31 -2 32 -2
M CHG 8 33 -2 34 -2 35 -2 36 3 37 3 38 3 39 3 40 3
M CHG 3 41 -2 42 -2 43 -2
M END

 

This seems to be something to do with the lines highlighted in red.  I wonder if you can advise.  We have a large number of compounds we need to import with this problem.

 

Thanks

Megan

Hi,

Can you please attach this file? Because in MOL format, the space and tabs are also important, and it was lost during the paste.

Thanks!

Peter

I have attached an example of the problem file here.

Thanks,

Megan

I've started to investigate the attached file. However, I can't reproduce any error yet.

Which version do you use? I tried with the latest Marvin 6.1.
What kind of problem did you faced with: Can't read the file, got error message, or the structure was incorrect?

Hi there,

There seems to be no error show when it loads, but there only seem to be a charge appearing, no iron or oxygen atoms appear at all.  I am using the latest version of the applet and have attached a screen grab of what we are getting

The example should contain a number of unconnected Fe and O atoms. The reason for this is the structure is undetermined but it was required that structure searches on the Fe and O to return the compound in the structure search, and molecular weights etc can be calculated etc.  So they have always been in the  structure table. We do need to be able to load and edit these files using chemAxon software.  We have a large number of them!

 I have attached a screen grab of the SDF being displayed in ChemDraw. 

Thanks for your help

Megan

 

 

 

 

For me, all of the atoms are imported, together with their charge, but the distance between the is too large. You can check it by calling a 2 dimensional clean (Structure>Clean2D).

As I can see from the figure you attached the atom should be far closer to each other after import, without doing cleaning. Can you confirm this? In this case there is a bug in our side, which will be fixed. 

Regard,
Peter

Hi Peter

Yes that seem to so do it!  Thanks so much! 

 I would like to have them viewable when they open in sketch and draw.  Can/should I clean all molecules, including ones without this problem, in our database using the MolHandler> clean? i.e

 MolHandler mh = new MolHandler();

        String molfile = ...;
        mh.setMolecule(molfile);
        mh.clean(false, ????);

if I use clean, what parameters would be best? I assume from your api that the always boolean should be set to false, but I am not sure about the second parameter, options.

Thanks again for all your help- the support chemaxon gives is fantastic!

Megan

 

 

I would suggest to use Cleaner.clean(Molecule mol , int dim, String opts) method. Here Molecule is your molecule object to clean, int is dimension, which should be 2 in this case. For opts, null is OK.

However, cleaning of a large set of large molecule can take a while. So, if speed is important, collect molecules where cleaning is important, and clean only them.

Please let us know, if you still have question!

Best Regards,
Peter

thanks for you help!