[Dock-fans] Need some help with my dataset

Trent E. Balius tbalius at aol.com
Thu Aug 10 15:22:21 PDT 2017

 Hi Ribas,

I would suggest writing a python (or your favorite computer language) script to do this.

Have it read in the mol2 file and write out a csv file.
All of the information in viewdock is in the mol2 file.  

You could even do this with grep, awk, and paste.

Do something like this:

>> grep "######    Name:"  mol.mol2  | awk '{print $3}' > name.txt
>> grep "######    GridScore:" mol.mol2 | awk '{print #3' > score.txt

 >> grep "######    Int_energy:" mol.mol2 | awk '{print #3' > int_en.txt

>> paste -d, name.txt score.txt int_en.txt > file.csv

I did not check that this works.

Then open this csv in Excel. 

I hope that this helps,


Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius



-----Original Message-----
From: José Ribamar dos Santos Ferreira Júnior <zeribajr at usp.br>
To: dock-fans <dock-fans at docking.org>
Sent: Thu, Aug 10, 2017 1:18 pm
Subject: [Dock-fans] Need some help with my dataset


I have a colleague with whom I work, she did some docking simulations with several molecules and showed me the results in Chimera (https://www.cgl.ucsf.edu/chimera/). She later asked me to transport to an excel plan the data from about 400.000 molecules docked. I´m doing this by hand and sent an email to Chimera developers that told me there is no way to transport this information directly to an excel file. Could someone, please, help me with this problem? Does DOCK has a way to put molecules information directly into a worksheet. The information I need is molecule name; Grid Score;  Int_energy; number of hydrogen bonds, and residues interacting with the receptor. Thank you in advance.



José Ribamar dos Santos Ferreira Júnior
Universidade de São Paulo
Escola de Artes, Ciências e Humanidades
Laboratório de Biotecnologia
Av. Arlindo Béttio, 1000 - Ermelino Matarazzo
Bloco A3, piso térreo, Ala 2
São Paulo - SP
CEP 03828-000
Fone: 11-3091-8873

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