converting an entire sdf file into png images

How do I convert an entire sdf file into png images of molecules as a batch program?

Please, see the attached example.

what is the syntax for invoking the convert2image.java file?





Is it possible to provide a quick example?

Code:

java -classpath .:marvinbeans/lib/MarvinBeans.jar test.image.Convert2image "png:w300,h300" input.sdf

By the way, if you call the application without parameter, the help of the application will be printed.

I have created a binary package for this application.


If you are not familiar in Java compiling use this package instead of the Java source.


You can download it from the following URL (the further description about it is available there):


http://www.chemaxon.com/forum/viewpost6728.html#6728

I have a microsoft access database of structures stored as blob fields imported from an sdf file using the jchem manager.





Is there a script avialable to convert the structures into png or jpeg images as a batch program so that the name of the output image file is the same as the cd_id of each structure record in the database?





Alternatively is it possible to adapt the convert2image script so that the name of the output image file starts from 1 and increments as it reads and creates the image files from the sdf file? e.g 1.png, 2.png etc as opposed to the current format of mols1.sdf.png, mols1.sdf_1.png etc?

If you want to generate output file name from the value of an SD field, you can do it by the following way:

Code:

Molecule mol; // the current molecule String outputfile; // the name of the image file ... String fieldname = "cd_id" // the name of the property field String fieldvalue = mol.getProperty(fieldname); if(fieldvalue != null) {     outputfile = fieldvalue+".png"; }

You can use and modify freely the code of Convert2Image example.


We are planning to create a more sophisticated example for batch conversion in the future.

Is there a working example of the convert2image script with the above code for generating output file names from the value of an sd field?





I have tried to edit the convert2image file but unsure where the above code needs to go? Its been a while since i did any Java programming! Any help would be greatly appreciated :-)

I have updated the application. You can find it on the same place (among Contributed softwares). Its help is already available there.


http://www.chemaxon.com/forum/viewpost6728.html#6728


In the current version, there is a new option: an SD field can be specified to create output file name from the field's current value.