The Molecular Graphics Laboratory Forum

I am trying to run the script prepare_flexreceptor4.py in the following way:

prepare_flexreceptor4.py -r protein.pdbqt -s GLU345 -v

However I get a Python error:

set verbose to True
read protein.pdbqt
names_by_chain= ['GLU345']
processing res_names_by_chain= GLU345
Traceback (most recent call last):
File "/usr/people/douglas/programs/mgltools_i86Linux2_1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py", line 128, in <module>
res_names.split('_')
NameError: name 'res_names' is not defined

Is this a possible bug? I have MGL tools 1.5.4.

This is a bug in prepare_flexreceptor4.py which was corrected 10/2009.

You can obtain the corrected version by updating MGLToolsPckgs.
To do so, from the ADT GUI click on Help->Update.

Best wishes,
Ruth

Hi Ruth,

I did as you suggested and the update seemed to work (updated 1.5.4 rev28 to 1.5.4 rev30) but I still got the error. I did "ls -l prepare_flexreceptor4.py" and the timestamp had not been changed.

I tried downloading MGLTools manually and copying the prepare_flexreceptor4.py from the download to the correct location (/MGLToolsPckgs/AutoDockTools/Utilities24/) but still got the error.

This is the header from the file I just downloaded today:
$Header: /opt/cvs/python/packages/share1.5/AutoDockTools/Utilities24/prepare_flexreceptor4.py,v 1.5.2.1 2009/07/17 16:55:53 rhuey Exp $

I should point out that I never had any trouble setting up flexible recopter docking using the GUI, only when using the prepare_flexreceptor4.py script from the command line.

Looking in the script this section seems to be the culprit (although I can't be sure because I don't know Python):



This instance of res_names is the first place it appears in the script - it doesn't appear to get assigned any values anywhere.

What OS are you using?
Apparently the update mechanism failed and we need to repair it!

Nonetheless, I can send you the file as an attachment to an email
OR
it should be possible for you to make a minor cautious** text edit to prepare_flexreceptor4.py to get it working.
[**Since python is white-space delimited]

Note these lines (which are lines 129 + 130 in my version) in particular:
if res_names_by_chain.find(':')==-1:
res_names = res_names_by_chain.split('_')

Here is the content of prepare_flexreceptor4.py after the update on my linux computer:
#!/usr/bin/env python
#
#
#
# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/Utilities24/prepare_flexreceptor4.py,v 1.5.2.2 2009/10/09 18:17:08 rhuey Exp $
#
import os

from MolKit import Read
from MolKit.protein import ProteinSet, ResidueSet
from MolKit.molecule import BondSet
from MolKit.stringSelector import CompoundStringSelector

from AutoDockTools.MoleculePreparation import AD4FlexibleReceptorPreparation



if __name__ == '__main__':
import sys
import getopt


def usage():
"Print helpful, accurate usage statement to stdout."
print "Usage: prepare_flexreceptor4.py -r receptor_filename -s list_of_names_of_residues_to_move"
print " Description of command..."
print " -r receptor_filename (.pdbqt)"
print " -s specification for flex residues"
print " Use underscores to separate residue names:"
print " ARG8_ILE84 "
print " Use commas to separate 'full names' which uniquely identify residues:"
print " hsg1:A:ARG8_ILE84,hsg1:B:THR4 "
print " [syntax is molname:chainid:resname]"
print " Optional parameters:"
print " [-v] verbose output"
print " [-N] type(s) of bonds to disallow: "
print " [-P] pairs of atom names bonds between which to disallow: "
print " [-g pdbqt_filename] (rigid output filename)"
print " [-x pdbqt_filename] (flexible output filename)"

# process command arguments
try:
opt_list, args = getopt.getopt(sys.argv[1:], 'r:vs:N:P:g:x:h')
except getopt.GetoptError, msg:
print 'prepare_flexreceptor4.py: %s' %msg
usage()
sys.exit(2)

# initialize required parameters
#-r: ligand
receptor_filename = None
#-s: residues_to_move
residues_to_move = None
# optional parameters
verbose = None
#-N: type of bonds to disallow
disallow = ""
#-P: pairs of atom names bonds between which to disallow
disallowed_pairs = ""
#-g : rigid output filename
rigid_filename = None
#-x : flexible output filename
flexres_filename = None

#'r:vs:N:g:x:h'
for o, a in opt_list:
#print "o=", o, " a=", a
if o in ('-r', '--r'):
receptor_filename = a
if verbose: print 'set receptor_filename to ', a
if o in ('-v', '--v'):
verbose = True
if verbose: print 'set verbose to', True
if o in ('-s', '--s'):
residues_to_move = a
if verbose: print 'set residues_to_move to ', a
if o in ('-N', '--N'):
disallow = a
if verbose: print 'set disallow to ', a
if o in ('-P', '--P'):
disallowed_pairs = a
if verbose: print 'set disallowed_pairs to ', a
if o in ('-g', '--g'):
rigid_filename = a
if verbose: print 'set rigid_filename to ', a
if o in ('-x', '--'):
flexres_filename = a
if verbose: print 'set flexres_filename to ', a
if o in ('-h', '--'):
usage()
sys.exit()


if not receptor_filename:
print 'prepare_flexreceptor4: receptor filename must be specified!\n'
usage()
sys.exit()

if not residues_to_move:
print 'prepare_flexreceptor4: residues to move must be specified!\n'
usage()
sys.exit()

extension = os.path.splitext(receptor_filename)[1]
if extension!=".pdbqt":
print 'prepare_flexreceptor4: receptor file must be in .pdbqt format\n'
usage()
sys.exit()

r = Read(receptor_filename)[0]
r.buildBondsByDistance()
if verbose: print 'read ', receptor_filename

all_res = ResidueSet()
# hsg1:A:ARG8_ILE82;hsg1:B:THR4
# ARG8_ILE84
names_by_chain = residues_to_move.split(',')
if verbose:
print "Specified flexres selection strings are:"
for strN in names_by_chain:
print " %s" %strN
#1. ['hsg1:A:ARG8_ILE82','hsg1:B:THR4']
# OR
#2. ARG8_ILE84
for res_names_by_chain in names_by_chain:
#check for ':'
if verbose: print "selecting ", res_names_by_chain
if res_names_by_chain.find(':')==-1:
# no ':' in selection string = simple case eg: ARG8_ILE84
res_names = res_names_by_chain.split('_')
if verbose: print "res_names=", res_names
for n in res_names:
if verbose: print "looking for ",n
res = r.chains.residues.get(lambda x: x.name==n)
if len(res):
all_res += res
if verbose: print " added ", res.name, " to ", all_res
else:
print "WARNING: no residue named " + n
else:
# 'hsg1:A:ARG8_ILE82'
# '1JFF_protein:A:THR179_GLU183,1JFF_protein:B:TRP21_ARG64_LEU275'
chainStart = res_names_by_chain.index(':')+1
molName = res_names_by_chain[:chainStart-1]
#if verbose: print "molName = ", molName, " chainStart=", chainStart
n = res_names_by_chain[chainStart:].replace("_", ",")
#if verbose: print "after comma replaced _ n is ", n, '\n'
selStr = molName + ":" + n
#if verbose: print "now selStr", selStr
# 'hsg1:A:ARG8,ILE82'
#res, msg = CompoundStringSelector().select(ProteinSet([r]), n)
res, msg = CompoundStringSelector().select(ProteinSet([r]), selStr)
#if verbose: print selStr, " selection =", res, " msg=", msg, '\n'
if len(res):
all_res += res
else:
print "no residue found using string ", selStr
#if verbose: print "built all_res=", all_res.full_name()
#check for duplicates
d = {}
for res in all_res: d[res] = 1
all_res = d.keys()
all_res = ResidueSet(all_res).uniq()
all_res.sort()
if verbose:
print "located ", len(all_res), " residues to format:"
for z in all_res: print " %s" %z.full_name()

#inactivate specified bonds
#disallowed_Pairs "CA_CB:CB_CG:C_CA"
all_bnds = BondSet()
#inactivate specified bonds
#disallowed_pairs "CA_CB:CB_CG:C_CA"
if len(disallowed_pairs):
bnd_pairs = disallowed_pairs.split(':')
for pair in bnd_pairs:
names = pair.split('_')
bnds = all_res.atoms.bonds[0].get(lambda x: x.atom1.name in names and x.atom2.name in names)
if len(bnds):
all_bnds += bnds

if verbose: print "beginning formatting ..."
fdp = AD4FlexibleReceptorPreparation(r, residues=all_res, rigid_filename=rigid_filename,
flexres_filename=flexres_filename,
non_rotatable_bonds=all_bnds)

if verbose: print "finished!"

# To execute this command type:
# prepare_flexreceptor4.py -l filename -r receptor_filename -s list_of_names_of_residues_to_move"







Would you please provide the information at the very top of your local copy of prepare_felxreceptor4.py which includes a revision number and a date?

Thanks a lot for your help,

I am using Fedora 8 to run the programs.

Please could you try downloading the package "mgltools_i86Linux2_1.5.4.tar.gz" from this page?:

http://mgltools.scripps.edu/downloads

When I extract the prepare_flexreceptor4.py file from it (on my Windows machine at home) this is the header:

#!/usr/bin/env python
#
#
#
# $Header: /opt/cvs/python/packages/share1.5/AutoDockTools/Utilities24/prepare_flexreceptor4.py,v 1.5.2.1 2009/07/17 16:55:53 rhuey Exp $
#

So although the automatic update did indeed fail there appears to be other problems.

Thanks for the message Douglas. Could you please run the following command to get the latest updates:

I've checked the file in downloads page and it indeed doesn't include the latest changes Ruth made. The GUI update (Help->Update) is supposed to download and install the latest changes from: http://mgltools.scripps.edu/downloads/t ... est-tested. The version number for prepare_flexreceptor4.py is 1.5.2.2 currently. Using cvs update command from above should do the job.

_________________
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Thanks Sargis. The cvs command seemed to successfully update the Python scripts.

However, now when I try to run prepare_receptor4.py, I get the following error:



This error is the same on all receptor pdbs I have tried prepare_receptor4.py on, all of which worked fine before I did the update.

If I revert to an older version of the script the problem goes away and everything runs as normal:

Hi Ruth/Sargis,

would you be able to check this error? Although reverting to the old version of prepare_receptr4.py works, I'd like to be using the newsest version.

So using this version of prepare_receptor4.py:


Using the following command:


I get the following error:


Could I please get some help with this?