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Input .mol files from a directory
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Filmon

Joined: 15 Dec 2014
Posts: 1

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Link to postPosted: Mon Jan 12, 2015 4:13 pmPost subject: Input .mol files from a directory Reply with quote

Hi, I am trying to calculate protonation of a list of compounds from .mol files. 

I have the following command with works perfectly:

cxcalc -N ih majormicrospecies -H 7.3 compound.mol | cxcalc formalcharge formula

and the output is:

1, -2, compound formula (id, formal charge and formula respectively).

The problem is the input file for multiple .mol file. I have over 100 compounds in a directory. How can i read and calculate each file by providing the directory name as input? so i get a list of output file as follows:

 

1, -2, compound formula (id, formal charge and formula respectively)

2, 0, compound formula 

3, 1, compound formula

etc….

 

Many thanks in advance.

 

László
ChemAxon personnel
Joined: 14 Jan 2011
Posts: 78

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Link to postPosted: Tue Jan 13, 2015 3:12 pmPost subject: Reply with quote

Dear Filmon,

You can fuse all files into an sdf with molconvert:

molconvert sdf *.mol -o molecules.sdf
cxcalc -N ih majormicrospecies -H 7.3 molecules.sdf | cxcalc formalcharge formula

Or a one-step solution:

cxcalc -N ih majormicrospecies -H 7.3 *.mol | cxcalc formalcharge formula

Best regards,
Laszlo 

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