Hi,
>> But, is not possible put the name for each molecule that appear in the sdf
>> file?
> I can see that this would be useful, but at present the molecule title
> cannot be used as the output file name with babel or obabel.
>
> It would probably be possible using a simple Python script.
>
Sure, probably the best way, IMHO.
Or split the sdf (output files should be the molecule name) (with e.g.
SplitSDFiles.pl from Mayachemtools; I have my own very basic perl
script too if you want to give it a try), and convert to mol2.
Or convert the multi sdf to multi mol2, and split the mol2 (I have a
basic perl script for that too - it should take less that one day for
1 million molecule, if I remember well, on my own PC).
Or split the sdf with obabel, rename the file (I have a tcl script if
the name is in a sdf field, or perl script which need an input file
with mol names).
But all that stuff was before I knew pybel, which can do it in one shoot:
#!/usr/bin/python
import pybel
for mol in pybel.readfile("sdf", "tmp.sdf"):
filename = mol.OBMol.GetTitle()
filename = filename + ".mol2"
output = open(filename,"w") # erase existing file, if any
output.write(mol.write("mol2"))
output.close()
That's it.
Comments welcome, I'm always eager to learn how do it better, as
scripting is not my biggest skill :)
Regards,
Pascal
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