conversion of mol file to pdb

Question

[khushgee0]

How to convert whole folder containing .mol file to .pdb format in one run?

Answer 1

[GouthamAtla]

You can try openbabel to convert.

http://openbabel.org/wiki/Tutorial:Basic_Usage

It offers a tons of file format conversions.

Answer 2

[wdiwdi]

This is easily done with a small script by means of the Cactvs Cheminformatics Toolkit (visit www.xemistry.com/academic for free academic packages). This gives you more opportunities to control what exactly is happening in the translation than running a turnkey application.

Minimal Tcl script:

foreach f [glob *.mol] {
        molfile loop $f eh {
                molfile write [file rootname $f].pdb $eh
        }
}

Minimal Python script:

import glob,os
for f in glob.glob('*.mol'):
        for e in Molfile(f):
                Molfile.Write(os.path.splitext(f)[0]+'.pdb',e)

(these scripts allow for multi-record SDF with a misleading suffix in addition to single-record simple Molfiles)