Omega.py - Revision history

Frodo at 04:08, 14 February 2014

2014-02-14T04:08:28Z

← Older revision		Revision as of 04:08, 14 February 2014
Line 77:		Line 77:
	# Omega file with special no ring conformation parameters		# Omega file with special no ring conformation parameters
	SetMaxConfs(30)		SetMaxConfs(30)


			[[Category:Software]]
			[[Category:Manual]]

Oliv Eidam at 22:04, 29 April 2013

2013-04-29T22:04:50Z

← Older revision		Revision as of 22:04, 29 April 2013
Line 10:		Line 10:
	(=> if your ligand has no rings, copy and edit omega_noring.parm ($DOCK_BASE/data/omega_noring.parm)		(=> if your ligand has no rings, copy and edit omega_noring.parm ($DOCK_BASE/data/omega_noring.parm)

	2) Edit omega.parm in your favorite editor.		2) Edit and save omega.parm (using the same name) in your favorite editor.

	3) Run dbgen.csh with altered settings in omega.parm (has to be in directory where you run dbgen.csh):		3) Run dbgen.csh with altered settings in omega.parm (has to be in directory where you run dbgen.csh):
Line 71:		Line 71:
	SetSearchForceField('mmff94s_NoEstat')		SetSearchForceField('mmff94s_NoEstat')
	SetTorsionDrive(True)		SetTorsionDrive(True)


			===Example of omega_noring.parm===

			# Omega file with special no ring conformation parameters
			SetMaxConfs(30)

Oliv Eidam at 22:00, 29 April 2013

2013-04-29T22:00:25Z

Show changes

Oliv Eidam at 23:40, 26 April 2013

2013-04-26T23:40:07Z

← Older revision		Revision as of 23:40, 26 April 2013
Line 5:		Line 5:
	The easiest way to change the settings for Omega is to copy the default omega.py file into the directory where you want to generate ligand conformations using dbgen.csh.		The easiest way to change the settings for Omega is to copy the default omega.py file into the directory where you want to generate ligand conformations using dbgen.csh.

	Type:		1) Type:
	which omega.py		which omega.py

	Copy the output of the which command above into your current working directory:		2)Copy the output of the which command above into your current working directory:
	cp /raid3/software/dockenv/etc/omega.py .		cp /raid3/software/dockenv/etc/omega.py .

	Rename that file to omega.parm:		3) Rename that file to omega.parm:
	mv omega.py omega.parm		mv omega.py omega.parm

	Edit omega.parm in your favorite editor.		4) Edit omega.parm in your favorite editor.

	Run dbgen.csh with altered settings ~~for~~ omega:		5) Run dbgen.csh with altered settings in omega.parm (has to be in directory where you run dbgen.csh):
	dbgen.csh my_ligs.smi		dbgen.csh my_ligs.smi

Line 29:		Line 29:

	omega.SetRMSThreshold(0.80)		omega.SetRMSThreshold(0.80)

	omega.SetBuildForceField('mmff94s_NoEstat')		omega.SetBuildForceField('mmff94s_NoEstat')
	omega.SetSearchForceField('mmff94s_NoEstat')		omega.SetSearchForceField('mmff94s_NoEstat')

Oliv Eidam: Created page with "==Changing settings for Omega (OpenEye)== You may be interested to change the default settings for Omega (defined in omega.py) when generating conformations for docking. Maby..."

2013-04-26T22:42:30Z

Created page with "==Changing settings for Omega (OpenEye)== You may be interested to change the default settings for Omega (defined in omega.py) when generating conformations for docking. Maby..."

New page

==Changing settings for Omega (OpenEye)==

You may be interested to change the default settings for Omega (defined in omega.py) when generating conformations for docking. Mabye you want to increase the number of conformations sampled per ligand, or the force field used.<br>

The easiest way to change the settings for Omega is to copy the default omega.py file into the directory where you want to generate ligand conformations using dbgen.csh.

Type:
which omega.py

Copy the output of the which command above into your current working directory:
cp /raid3/software/dockenv/etc/omega.py .

Rename that file to omega.parm:
mv omega.py omega.parm

Edit omega.parm in your favorite editor.

Run dbgen.csh with altered settings for omega:
dbgen.csh my_ligs.smi

==Increase ligand conformation sampling or change the type of force field==

An example of omega.py is shown at the bottom of this page. Settings you may want to consider changing are:

omega.SetEnergyWindow(12.5)

omega.SetMaxConfs(600)

omega.SetRMSThreshold(0.80)

omega.SetBuildForceField('mmff94s_NoEstat')
omega.SetSearchForceField('mmff94s_NoEstat')

*you could increase the energy window: e.g. omega.SetEnergyWindow(25.0)
=> There is no benchmarking of this setting that I am aware of...
*you could increase the number of output conformations: e.g. omega.SetMaxConfs(10000)
=> Molecules in ZINC have a cut a 600 conformations, which is certainly on the low side for flexible ligands
*you could lower the RMS threshold between the confs: e.g. omega.SetRMSThreshold(0.40)
=> This results in finer sampling of conformational space
*you could change the force field to included electrostatics: e.g. omega.SetBuildForceField('mmff94s') and omega.SetSearchForceField('mmff94s')
=> Internal benchmarkings on DUDE (by RGC) have shown that electrostatics improves enrichment for many targets.

===Example of omega.py===

#!/usr/bin/env python
import os
import sys
from openeye.oechem import *
from openeye.oeomega import *

def read_parm(parm):
if os.path.exists(parm):
f = open(parm, 'r')
for line in f:
line = line.strip()
if line and line[0] != '#':
eval('omega.%s' % line)
f.close()

def write_molecule(outfile, mol):
ofs = oemolostream(outfile)
OEWriteMolecule(ofs, mol)
ofs.close()

def set_defaults(omega):
# File Parameters
omega.SetCommentEnergy(True)
omega.SetIncludeInput(False)
omega.SetRotorOffset(True)
omega.SetSDEnergy(False)
omega.SetWarts(True)
# 3D Construction Parameters
omega.SetBuildForceField('mmff94s_NoEstat')
omega.SetCanonOrder(True)
omega.SetFixDeleteH(True)
omega.SetDielectric(1.0)
omega.SetExponent(1.0)
omega.SetFixRMS(0.15)
omega.SetFromCT(False)
omega.SetFixMaxMatch(1)
omega.SetFixUniqueMatch(True)
# Structure Enumeration Parameters
omega.SetEnumNitrogen(False)
omega.SetEnumRing(False)
# Torsion Driving Parameters
omega.SetEnergyWindow(12.5)
omega.SetMaxConfGen(100000)
omega.SetMaxConfs(600)
omega.SetMaxPoolSize(10000)
omega.SetMaxRotors(-1)
omega.SetMaxSearchTime(120.0)
omega.SetRangeIncrement(5)
omega.SetRMSThreshold(0.80)
omega.SetSearchForceField('mmff94s_NoEstat')
omega.SetTorsionDrive(True)

# Parse arguments here
parm_prefix = sys.argv[1]
infile = sys.argv[2]

parmfile = parm_prefix + ".parm"
noringparmfile = parm_prefix + "_noring.parm"

omega = OEOmega()
set_defaults(omega)

mol = OEMol()
inroot, inext = os.path.splitext(infile)
ifs = oemolistream(infile)
OEReadMolecule(ifs, mol)
ifs.close()
count, ringlist = OEDetermineRingSystems(mol)
rcf = open('ring_count', 'w')
rcf.write('%d\n' % count)
rcf.close()
if count == 0:
omega.SetMaxConfs(30)
read_parm(noringparmfile)
outfile = "%s.%d.mol2" % (inroot, count)
if omega(mol):
write_molecule(outfile, mol)
else:
read_parm(parmfile)
pred = OEPartPredAtom(ringlist)
for i in xrange(1, count+1):
pred.SelectPart(i)
outfile = "%s.%d.mol2" % (inroot, i)
molcopy = OEMol(mol)
if omega(molcopy, pred):
write_molecule(outfile, molcopy)