Last active
January 2, 2016 02:00
-
-
Save bougui505/e86aadf2d93c12b02b20 to your computer and use it in GitHub Desktop.
compute h-bonds with chimera. Launch it with chimera --nogui --script 'contacts.py structure.pdb'
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/usr/bin/env python | |
# -*- coding: utf-8 -*- | |
# for chimera 1.4 | |
from chimera import runCommand | |
import sys | |
rec_file = sys.argv[1] | |
basename = rec_file.split('/')[-1].split('.')[0] | |
#runCommand("open 0 receptor.pdb") | |
runCommand("open 0 %s"%rec_file) | |
runCommand("hbonds intramodel true distSlop 0.65 angleSlop 80 saveFile output/%s_hbonds.txt namingStyle serial"%basename) | |
runCommand("findclash #0 test #0 overlapCutoff 0 hbondAllowance 0 intraRes true saveFile output/%s_contacts.txt namingStyle serial"%basename) | |
runCommand("close 1") | |
runCommand("close 0") | |
#for ligNum in range(1, 1001): | |
#runCommand("open 1 ligand.%03d.pdb" % ligNum) | |
#runCommand("hbonds intramodel false saveFile ligand.%03d.hbonds" % | |
#ligNum) | |
#runCommand("close 1") |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment