Convert sdf file to multiple mol files

Hi everybody,





I try to convert a sdf file containing thousands of compounds into multiple mol file (with for example an automatic number file name).


I read the help file but there's only the function to convert multiple mol files to a unique sdf file.





Have you got any idea for doing this type of conversion ?





Thanks !





Alex

Try the attached example.

Thank you for your help,





I used perl scripts in order to do this type of conversion but I'll try your script.





Alexandre

Hi,


thats what I call redundant or duplicate work.


I tried to find "sdf2mol" (SDF to mol) on the internet but only could find


one reference to a (non-existing) python file.





I remember that I could convert SDF files to mol and jpeg


and png etc with SDF-toolkit, OpenBabel or any perl or


python script. But I tried and either could not find it or


bring it to work. So I started to code for some minutes and


then came across other examples here and there was the


code already :-)





Long explanation short story.


This sdf2mol converts a single SD file (SDF) or SMI file (SMILES) to multiple mol, pdf, png etc. files





So this code is also a SDF2png, SDF2bmp, SDF2mol, SDF2pdf, SDF2cml


SMI2mol, SMI2png, SMI2pdf, SMI2cml.


So virtually all formats molconvert also supports.





SDF2mol converts large SDF or SMILES files into multiple single mol files or pictures





usage: SDF2mol inputname outputname format


example: SDF2mol C6H6.sdf C6H6mol mol


example: SDF2mol C6H6.smi C6H6pic png


example: SDF2mol C6H6.sdf C6H6out mol:-H





/* The input file format is guessed automatically or specified as an import option


* to the constructor. Many different formats are supported like


* "mol", "rgf", "sdf", "rdf", "csmol", "csrgf", "cssdf", "csrdf", "cml", "mrv",


* "smiles", "cxsmiles", "pdb", "xyz" "sybyl", "mol2", "pdb", "xyz"


* Output molecule formats: mol, rgf, sdf, rdf, csmol, csrgf, cssdf, csrdf, cml,


* Output Graphics formats: emf, jpeg, msbmp, pdf, png, pov, ppm, svg.


* Other formats: gzip, base64. (See -Ho)


* MolImporter can also import gzip compressed and base64 encoded structures.


*/





/*


* Basic export options





a, +a, +a_gen General aromatization. Example: "XXX:a"


a_bas Basic aromatization. Example: "XXX:a_bas"


-a Dearomatize. Example: "XXX:-a"


H or +H Add explicit Hydrogen atoms. Example: "XXX:H"


-H Remove explicit Hydrogen atoms. Example: "XXX:-H"





Here, XXX can be any molecule or image format like


mol, sdf, rdf, rgf, rxn, csmol, cssdf, csrdf, csrgf, csrxn,


smiles, cxsmiles, abbrevgroup, mrv, cml, jpeg, png, ppm or svg, msbmp


but aromatization options have no effect on formats which


do not store bond orders like cube, pdb and xyz.


*/





See the attached sdf2mol.java and sdf2mol.bat and


sdf2mol.jar. So if you want to create a mol file


use SDF2mol.bat C6H6-cdk.smi C6H6mol mol


or if you want to create multiple pictures (png,jpeg,bmp)


use SDF2mol.bat c6h6-cdk.smi c6h6 png





The output print should be like that:


SDF2mol 2007 v1.0 - CPUs:8


Number of molecules in C6H6-cdk.smi: 217


Created 217 new mol files. Thank you for using SDF2mol!





Kind regards


Tobias

Thank you!

Hi,


I just found out that some of the options for converting pictures,


like SDF2png or SDF2JPG do not work with SDF2MOL (creates 0 length pictures).

Code:

sdf2mol input.sdf  outputname "png:w300,#ffffff,-a,-H" sdf2mol  input.sdf outputname  "jpeg:q100,w300,#ffffff,-a,-H"

It only works without options

Code:

sdf2mol input.sdf  outputname png sdf2mol  input.sdf outputname  jpeg

Or 1) converting to mol and 2) converting to png, JPG with options


(like different colors, width, background)

Code:

(1) sdf2mol input.sdf  outputname mol (2) create a windows batchfile doconvert.bat for %%f in (*.mol) do molconvert "png:w300,#ffffff,-a,-H" %%f -o %%f.png

This will convert all the pictures with the possible and correct options.


This mode works good for most purposes.





Tobias

The error is in your code.


You should parse format string. Skip export options (":w300,#ffffff,-a,-H") from the file name extension:

Code:

int x = format.indexOf(":"); String ext = (x > -1)? format.substring(0,x) : format; localfilename =  outputname+ "-" + (molcounter)+ "." + ext;

Hi Tamas,


once you know its easy :-) I did it the easy way (form me) but I also updated the code, works fine, thank you. So here it is, see attachement.


Tobias

Hello there,





This topic seems to be the close enough to my query. I have to send an email to a superior who does not have instant jchem nor want to install it. Intuitively he asks for a pdf, and I naively thought I could just chose my default print to pdf option that is available on my mac. There is a print to file option, but for some reason this results in a ps (post script) file being sent to my printer rather than to file in the location I specified.





Does anyone have solutions? I would like an exact representation of the grid view.





Thanks for your help

It seems to be an InstantJChem issue. By printing MarvinView tables, there are "Preview" and "PDF" options (beside the "Print" button) on the Print panel.


(To tell the truth, your question is not too close to the original topic. InstantJChem uses a totally different renderer for tables than Marvin.)


I forward your questions to the IJC team.

We will look at the print to file and/or PDF situation in Instant JChem.


But without that working I don't think there are any options for getting an exact representation of what you see in IJC. You could of course export the data to a SD file or similar, but would require the recipient of the file being able to view it.

TobiasKind wrote:

Hi Tamas, once you know its easy :-) I did it the easy way (form me) but I also updated the code, works fine, thank you. So here it is, see attachement. Tobias

How to convert skc file or TGF file to sdf file or RXn file

Hi,

Presently the SKC import feature is not available in Marvin; it is planned for version 5.3 coming this Autumn.

Best regards,

Akos

I tried to use sdf2mol according to Tobias instruction and get this error:

Number of molecules in C:\Compounds.sdf: 15
Exception in thread "main" java.lang.NoSuchMethodError: chemaxon.formats.MolExporter.write(Lchemaxon/struc/Molecule;)V
        at examples.sdf2mol.main(sdf2mol.java:190)

I am using JChem 5.5

Hi,

it is better to simply use the molconvert tool from command line like this:

molconvert mol inputfile.sdf -o outpufilename.mol -m

Is this suitable for you, or you need a Java solution?

Regards,
Istvan