Copyright (C) 2015 Deepesh Nagarajan (1337deepesh@gmail.com)
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License http://www.gnu.org/licenses/ for more details.
This README file will guide you through an example 'Pocketanneal' usage:
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Enter the Pocketanneal directory through terminal cd Pocketanneal
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Run 'Format.sh' to add hydrogens & clean your input PROTEIN.pdb file: bash Format.sh -i example/protein_1dhi_A.pdb -o ~/Desktop/Pocketanneal_OUTPUT_01 -d database/
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After pre-processing, run Pocketanneal with these arguments: python Pocketanneal.py -P ~/Desktop/Pocketanneal_OUTPUT_01/output.pdb -p example/pocket_1dhi_A.pdb -d database -n 1000 -a 2 -o ~/Desktop/Pocketanneal_OUTPUT_02
A more detailed guide explaining every step can be found in: gedit Pocketanneal/example/example.sh
Install autodocktools:
**sudo apt-get install autodocktools**
On Ubuntu 16 onwards, you have to downgrade numpy:
**sudo pip install numpy==1.8**
This script runs on Python 2.7.12 (Ubuntu 16.04). Don't run on Python 3.
I can't make any guesses about how Pocketanneal will run on future Ubuntu versions.
Ignore this output on terminal (generated by autodock, makes no difference to the score output): *swig/python detected a memory leak of type 'BHtree ', no destructor found.
Python image libraries are in a state of flux. Simply comment out line 20 and line 995 in Pocketanneal.py if the Image library is giving you trouble. import Image, ImageDraw, ImageFont (Pocketanneal.py, line 26) grapher(XY_data, str(working_directory)+"/score_log.png", str(IP_database)) (Pocketanneal.py, line 995)
If you have any queries/suggestions, contact me: Deepesh Nagarajan: 1337deepesh@gmail.com
I will eventually leave my current position, so I can't guarantee indefinite support.