('Rec','Lig','dG(kT)','solv','coul','ions','dG(kcal/mol)\n')
s = '%(rec)4s : %(lig)4s %(dG_kt)7.2f %(solv)7.2f %(coul)7.2f %(ions)7.2f %(dG_kcal)7.2f\n'
d = copy.copy(com['dG_delphi'])
d.update({'rec': com.rec_model.pdbCode, 'lig': com.lig_model.pdbCode})
r = t
r += s % d
return r
### MAIN ###
############
options = T.cmdDict({'ocom': 'delphi.complex', 'o': 'dg_delphi.out'})
try:
f_out = T.absfile(options['o'])
f_ocom = T.absfile(options['ocom'])
options['autocap'] = 'autocap' in options
options['debug'] = 'debug' in options
options['verbose'] = 'v' in options
if 'nice' in options: options['nice'] = int(options['nice'])
for key in [
'indi', 'exdi', 'salt', 'ionrad', 'prbrad', 'bndcon', 'scale',
'perfil'
p.add( points[i] )
## Legend
curves.reverse()
p.add( B.PlotKey( .70, .85, curves ) )
return p
###############
## MAIN
###############
if __name__ == '__main__':
options = T.cmdDict( defOptions() )
if not 'i' in options:
_use()
## Load result tree and dict with protocols
dat = T.load( options['i'] )
title = 't' in options
p = dat['protocols']
r = Reporter( dat, p )
if 'eps' in options:
p = r.plot_ens( ['dS', 'dS_sep', 'dS_rigid', 'dS_cross',
Options:
-o .. one or several project folders (default: current)
-? or -help .. this help screen
Default options:
"""
for key, value in o.items():
print "\t-",key, "\t",value
sys.exit(0)
if __name__ == '__main__':
options = T.cmdDict({'o':[ os.getcwd() ]})
if '?' in options or 'help' in options:
_use( options )
folders = T.toList( options['o'] )
if not os.path.exists( folders[0] +'/templates'):
print 'Current directory is not a valid modeling folder.'
_use( options )
T.flushPrint( "Creating folders and links...\n" )
for f in folders:
sv = VS(outFolder=f)
sv.go(f)
"""
identify options that have to be passed on to blastall
"""
result = {}
def_keys = defaultOptions().keys() + ['psi']
for k, v in options.items():
if not k in def_keys:
result[ k ] = v
return result
### MAIN ###
options = tools.cmdDict( defaultOptions() )
outFolder = tools.absfile( options['o'] )
f_target = tools.absfile( options['q'] )
f_target = f_target or outFolder + SequenceSearcher.F_FASTA_TARGET
if not (f_target and os.path.exists( f_target ) ):
_use( defaultOptions() )
if '?' in options or 'help' in options:
_use( defaultOptions() )
seq_db = options['db']
e = float( options['e'] )
aln = int( options['aln'])
clustLim = int( options['limit'])
simCut = float( options['simcut'] )
if len(todo) > 0:
msg = "\n%i out of %i complexes are to be updated\n\n"
t.flushPrint(msg % (len(todo), len(cl)))
return cl
else:
t.flushPrint("\nList contains no data that can be updated\n")
###########################
# MAIN
###########################
if len(sys.argv) < 3:
_use()
options = t.cmdDict(defaultOptions())
## ## current keys used for scoring
## scoreKeys = ['eProsa', 'ePairScore', 'foldX', 'cons_ent', 'cons_max']
## load docking solutions
t.flushPrint("\nLoading complex list %s ... " % t.absfile(options['i']))
complex_lst = t.load(options['i'])
t.flushPrint("done\n")
## validate and expand list of keys to be calculated
force = []
if options.has_key('f'):
raw_force = t.toList(options['f'])
## check that the key is valid
Options:
-d [str], list of project directory
-s show the structure final.pdb im PyMol
"""
for key, value in o.items():
print "\t-",key, "\t",value
sys.exit(0)
if __name__ == '__main__':
options = T.cmdDict()
f = os.getcwd()
if '?' in options or 'help' in options:
_use( options )
if not os.path.exists(f + VS.F_RESULT_FOLDER) and not options.has_key('d'):
print 'Current directory is not a valid modeling project folder.'
_use( options )
## Try to add project folders
## look for default cross-validation projects
d = []
if os.path.exists( f + VS.F_RESULT_FOLDER ):
d = [ f ]
-r receptor chain list (e.g. 0 1 )
-l ligand ~ (e.g. 2 )
-o output file
-lo,lr ligand, receptor model output file
Default options:
"""
for key, value in options.items():
print "\t-",key, "\t",value
sys.exit(0)
### MAIN ###
############
options = T.cmdDict( {'o':'ref.complex', 'lo':'lig.model', 'ro':'rec.model' } )
if len (sys.argv) < 3:
_use( options )
## create a reference complex
print "Loading..."
ref_com = PDBModel( options['c'] )
print "Removing water..."
ref_com.remove( lambda a: a['residue_name'] in ['TIP3','HOH','WAT'] )
## extract rec and lig chains
rec_chains = T.toIntList( options['r'] )
lig_chains = T.toIntList( options['l'] )
print "Extracting rec and lig..."
if len( sys.argv ) < 2:
print \
"""
Restart a distributed calculation.
Syntax: restartPVM.py -i |rst_file| [-a]
Options:
i .. restart file containing result of TrackingJobMaster.getRst()
a .. add hosts to PVM
"""
sys.exit(0)
## MAIN ##
use()
cmd = T.cmdDict()
T.flushPrint('Loading restart data...')
rst = T.load( cmd['i'] )
hosts = []
if 'a' in cmd:
hosts = [ h['host'] for h in rst['hosts'] ]
master = restart( rst, hosts=hosts )
T.flushPrint('Master initialized for restart.')
master.start()
o['o'] = 'entropy_result.dic'
## uncomment for testing
## o['step'] = 2
## o['start']= 100
## o['stop'] = 400
## o['ref'] = '~/interfaces/c15/com_wet/ref.complex'
## o['i'] = '~/interfaces/c15/rec_pcr_00/traj.dat+\
## ~/interfaces/c15/lig_pcr_00/traj.dat'
return o
##########
## MAIN ##
options = t.cmdDict( defOptions() )
if not ('i' in options ):
_use()
## convert command line parameters
for k in ['s','e','ss', 'se', 'step','fit_s', 'fit_e', 'nice','thin', 'ex_n',
'ex3', 'shift', 'border']:
if k in options:
options[k] = int( options[k] )
for k in ['debug', 'verbose', 'cast', 'split', 'shuffle', 'shift', 'heavy',
'solvent', 'protein']:
if k in options:
options[k] = 1
else:
## have too remove objects backvards not to change indexes
r.reverse()
for j in r:
d.remove(j)
if len(d)==0:
print 'Nothing to model. Exiting.'
sys.exit(0)
return d
if __name__ == '__main__':
## look for default cross-validation projects
options = T.cmdDict({'h':10, 'd':[], 'zfilter':TF.Z_CUTOFF,'idfilter':TF.ID_CUTOFF})
d=options['d'] or collect_project_folders( )
if (options['d'] is None) or ('help' in options or '?' in options):
_use( options )
folders = T.toList(options['d'])
hostNumber = int(options['h'])
fastaTarget = options.get('fta', None)
f_pir = options.get('pir', None)
template_folder = options.get('tf', None)
starting_model = int(options.get('sm', 1))
ending_model = int(options.get('em', 10))
ferror = options.get('fe', None)
windows = "w" in options
EnsembleTraj.py for details).
traj2ensemble.py -i |in_traj| -n |n_members| -o |out_traj| -pdb |PDBCode| ]
o - out file name (default: replace input file)
n - number of ensemble members to expect (default: 10)
pdb - PDB code to be stored in trajectory
"""
sys.exit(0)
##########
## MAIN ##
use()
o = T.cmdDict( {'n':10} )
f_in = T.absfile( o['i'] )
f_out = T.absfile( o.get('o', f_in) )
n = int( o['n'] )
T.flushPrint("Loading...")
t = T.load( f_in )
T.flushPrint("Converting %i frames..." % len(t) )
if isinstance(t, EnsembleTraj ):
T.flushPrint( "Nothing to be done!\n")
sys.exit(0)
t = traj2ensemble( t, n )
addFrameNames( t, trajIndex )
e = end or len( t )
if start or end or (step != 1):
t = t.takeFrames( range( start, e, step ) )
return t
############
### MAIN ###
use()
o = T.cmdDict( {'o':'traj_ensemble.dat'} )
out = T.absfile( o['o'] )
inLst = T.toList( o['i'] )
start = int( o.get('s','0') )
end = o.get( 'e', None )
if end:
end = int( end )
step = int( o.get('step',1) )
ref = o.get('ref',None)
if ref:
ref = PDBModel( T.absfile( ref ) )
if 'prot' in o:
ref = ref.compress( ref.maskProtein() )
if len( todo ) > 0:
msg = "\n%i out of %i complexes are to be updated\n\n"
t.flushPrint( msg%(len(todo), len(cl) ) )
return cl
else:
t.flushPrint( "\nList contains no data that can be updated\n" )
###########################
# MAIN
###########################
if len(sys.argv) < 3:
_use()
options = t.cmdDict( defaultOptions() )
## ## current keys used for scoring
## scoreKeys = ['eProsa', 'ePairScore', 'foldX', 'cons_ent', 'cons_max']
## load docking solutions
t.flushPrint( "\nLoading complex list %s ... " % t.absfile( options['i'] ) )
complex_lst = t.load( options['i'] )
t.flushPrint( "done\n" )
## validate and expand list of keys to be calculated
force = []
if options.has_key('f'):
raw_force = t.toList( options['f'] )
## check that the key is valid
they must have, at least, all the atoms that are in the reference.
Default options:
"""
for key, value in options.items():
print "\t-",key, "\t",value
sys.exit(0)
### MAIN ###
############
if len (sys.argv) < 3:
_use( {'o':'traj.dat'} )
options = tools.cmdDict( {'o':'traj.dat'} )
## get all PDBs and models directly from a directory (avoids shell limits)
if 'd' in options:
d = tools.absfile( options['d'] )
l = os.listdir( d )
l = [ x for x in l if x[-4:].upper() == '.PDB' or x[-6:] == '.MODEL' \
or x[-7:].upper() == '.PDB.GZ' ]
l = [ os.path.join( d, f ) for f in l ]
options['i'] = l
if 'e' in options:
t_class = EnsembleTraj
else:
t_class = Trajectory
Options:
-o .. one or several project folders (default: current)
-? or -help .. this help screen
Default options:
"""
for key, value in o.items():
print "\t-", key, "\t", value
sys.exit(0)
if __name__ == '__main__':
options = T.cmdDict({'o': [os.getcwd()]})
if '?' in options or 'help' in options:
_use(options)
folders = T.toList(options['o'])
if not os.path.exists(folders[0] + '/templates'):
print 'Current directory is not a valid modeling folder.'
_use(options)
T.flushPrint("Creating folders and links...\n")
for f in folders:
sv = VS(outFolder=f)
sv.go(f)
for j in r:
d.remove(j)
if len(d) == 0:
print 'Nothing to model. Exiting.'
sys.exit(0)
return d
if __name__ == '__main__':
## look for default cross-validation projects
options = T.cmdDict({
'h': 10,
'd': [],
'zfilter': TF.Z_CUTOFF,
'idfilter': TF.ID_CUTOFF
})
d = options['d'] or collect_project_folders()
if (options['d'] is None) or ('help' in options or '?' in options):
_use(options)
folders = T.toList(options['d'])
hostNumber = int(options['h'])
fastaTarget = options.get('fta', None)
f_pir = options.get('pir', None)
template_folder = options.get('tf', None)
starting_model = int(options.get('sm', 1))
ending_model = int(options.get('em', 10))
ferror = options.get('fe', None)
options = {}
options['q'] = tools.testRoot() + '/Mod/project/target.fasta'
options['o'] = tools.testRoot() + '/Mod/project'
options['log'] = '1'
options['view'] = '1'
return options
###########################
# MAIN
###########################
if len(sys.argv) < 3:
_use()
options = tools.cmdDict(options)
#options = testOptions()
outFolder = tools.absfile(options['o'])
f_target = tools.absfile(options['q'])
f_target = f_target or outFolder + SequenceSearcher.F_FASTA_TARGET
log = None
if 'log' in options:
log = LogFile(outFolder + '/modelling.log')
## databases used
seq_db = 'swissprot'
tmp_db = 'pdbaa'
###############
+ [ c.rec_model ]
if c.lig_model not in known_ligs:
stray_ligs[ c['model2']] = stray_ligs.get( c['model2'], []) \
+ [ c.lig_model ]
return stray_recs, stray_ligs
##############
## MAIN
##############
if __name__ == '__main__':
options = T.cmdDict({
'o': 'complexes_pooled.cl',
'mo': 'changed_models',
'ldic': 'pcr_lig/models.dic',
'rdic': 'pcr_rec/models.dic'
})
if len(sys.argv) < 2:
syntax()
fs = [T.absfile(f) for f in T.toList(options['i'])]
result = ComplexList()
rec_dic = T.load(T.absfile(options['rdic']))
lig_dic = T.load(T.absfile(options['ldic']))
for f in fs:
stray_recs[ c['model1']] = stray_recs.get( c['model1'], []) \
+ [ c.rec_model ]
if c.lig_model not in known_ligs:
stray_ligs[ c['model2']] = stray_ligs.get( c['model2'], []) \
+ [ c.lig_model ]
return stray_recs, stray_ligs
##############
## MAIN
##############
if __name__ == '__main__':
options = T.cmdDict( {'o':'complexes_pooled.cl',
'mo':'changed_models',
'ldic':'pcr_lig/models.dic',
'rdic':'pcr_rec/models.dic'} )
if len( sys.argv ) < 2:
syntax()
fs = [ T.absfile( f ) for f in T.toList( options['i'] ) ]
result = ComplexList()
rec_dic = T.load( T.absfile( options['rdic'] ) )
lig_dic = T.load( T.absfile( options['ldic'] ) )
for f in fs:
T.flushPrint('Loading %s ...' % f )
return l, replaced
def replace_import_statement(l, module, importas):
if importas == module:
importas = ''
else:
importas = ' as ' + importas
return l.replace('from ' + module + ' import *',
'import ' + module + importas)
options = t.cmdDict({'m': 'Numeric', 'as': 'N', 'e': ['Complex']})
module = options['m']
importas = options.get('as', module)
srcfiles = t.toList(options.get('i', None))
exclude = t.toList(options['e'])
try:
exec('import ' + module)
for fname in srcfiles:
fname = t.absfile(fname)
for j in r:
d.remove(j)
if len(d) == 0:
print 'Nothing to align. Exiting.'
sys.exit(0)
return d
if __name__ == '__main__':
## look for default cross-validation projects
d = []
options = T.cmdDict({'h': 10, 'd': d})
d = options['d'] or collect_project_folders()
if (options['d'] is None) or ('help' in options or '?' in options):
_use(options)
folders = T.toList(options['d'])
hostNumber = int(options['h'])
pdbFolder = options.get('pdb', None)
fastaTemplates = options.get('ft', None)
fastaSequences = options.get('fs', None)
fastaTarget = options.get('fta', None)
ferror = options.get('fe', None)
show_output = 'w' in options
-amber rename CYX -> CYS, HID/HIE/HIP -> HIS, unwrap atom names
(this creates models with the same atom/res names as pdbs created
with ambpdb -p top.parm -aatm -bres < some.crd > some.pdb )
-s sort atoms alphabetically within residues
Default options:
"""
for key, value in o.items():
print "\t-",key, "\t",value
sys.exit(0)
if __name__ == '__main__':
options = T.cmdDict( {'h':10, 'c':5 } )
if len( sys.argv ) < 2:
_use( options )
hostNumber = int( options['h'] )
chunk = int( options['c'] )
windows = options.has_key('w')
amber = options.has_key('amber')
sort = options.has_key('s')
outFolder = None
if options.has_key('o'):
outFolder = T.absfile( options['o'] )
## get all PDBs and models directly from a directory (avoids shell limits)
return result
def test():
options = defOptions()
options['i'] = '/home/Bis/raik/data/tb/interfaces/c11/lig_pcr_00/traj.dat'
options['step'] = '3'
options['s'] = '0'
options['o'] = '~johan/dock/scripts'
options['ref'] = ''
return options
if __name__ == '__main__':
if len(sys.argv) < 2:
_use()
## options = test()
options = T.cmdDict(defOptions())
tc = load(options)
r = cluster(tc, options)
## r=rmsdLimitedClustering( tc, options )
if options.has_key('co'):
T.dump(tc, options['co'])
report(tc)
-d [str], list of project validation directories
-modlist str, the path to the 'PDBModels.list' from the
project directory
-ref str, the path to the 'reference.pdb' from
the project directory (known structure)
"""
for key, value in o.items():
print "\t-", key, "\t", value
sys.exit(0)
if __name__ == '__main__':
options = T.cmdDict()
f = os.getcwd()
if '?' in options or 'help' in options or 'h' in options:
_use(options)
if not os.path.exists(f + B.F_INPUT_FOLDER) and not options.has_key('d'):
print 'Current directory is not a valid modeling project folder.'
_use(options)
## Try to add project folders
## look for default cross-validation projects
d = []
if os.path.exists(f + VS.F_RESULT_FOLDER):
d = glob.glob(f + VS.F_RESULT_FOLDER + '/*')
options = {}
options['q'] = tools.testRoot()+ '/Mod/project/target.fasta'
options['o'] = tools.testRoot()+ '/Mod/project'
options['log'] = '1'
options['view'] = '1'
return options
###########################
# MAIN
###########################
if len(sys.argv) < 3:
_use()
options = tools.cmdDict( options )
#options = testOptions()
outFolder = tools.absfile( options['o'] )
f_target = tools.absfile( options['q'] )
f_target = f_target or outFolder + SequenceSearcher.F_FASTA_TARGET
log = None
if 'log' in options:
log = LogFile( outFolder + '/modelling.log' )
## databases used
seq_db = 'swissprot'
tmp_db = 'pdbaa'
- Ends of chains are assumed if the residue numbering jumps backward, if there
is a TER record or chain ID or segid change, or if there is a chain break.
- A chain break is assumed if there is an untypical gap in the chain of back-
bone atoms (see PDBModel.chainBreaks() ).
- The index of the first chain is 0.
- Original waters are deleted.
- As usual, options can also be put into a file and loaded with the -x option
Default options:
"""
for key, value in options.items():
print "\t-",key, "\t",value
#sys.exit(0)
options = t.cmdDict( {'o':'out.parm'} )
try:
f_out = options['o']
if 'ocrd' in options:
options['f_out_crd'] = options['ocrd']
if 'opdb' in options:
options['f_out_pdb'] = options['opdb']
if 'box' in options:
options['box'] = float( options['box'] )
options['cap'] = 'cap' in options
options['capN']= t.toIntList( options.get('capN',[]))
options['capC']= t.toIntList( options.get('capC',[]))
traj2ensemble.py -i |in_traj| -n |n_members| -o |out_traj| -pdb |PDBCode| ]
o - out file name (default: replace input file)
n - number of ensemble members to expect (default: 10)
pdb - PDB code to be stored in trajectory
"""
sys.exit(0)
##########
## MAIN ##
use()
o = T.cmdDict({'n': 10})
f_in = T.absfile(o['i'])
f_out = T.absfile(o.get('o', f_in))
n = int(o['n'])
T.flushPrint("Loading...")
t = T.load(f_in)
T.flushPrint("Converting %i frames..." % len(t))
if isinstance(t, EnsembleTraj):
T.flushPrint("Nothing to be done!\n")
sys.exit(0)
t = traj2ensemble(t, n)
return MS, AS, MS_sd, AS_sd
###########################
# MAIN
###########################
default = {'i':'1gxg_input.pdb',
'r':'~/GLY_pep/',
'l':'',
'mask':[0,1,0]}
if len (sys.argv) < 2:
_use( default )
options = T.cmdDict( default )
## where to run the calculation
base_folder = T.absfile( options['r'] )+'/'
## template gly-xxx-gly
template = os.path.abspath( options['i'] )
## label the result dictionaty files
label = '_' + options['l']
## mask to used to delete glycines
mask = [ int(i) for i in T.toList( options['mask'] )]
## create random prptides from template
#randomPeptides( template, base_folder )
t = '%4s : %4s %7s %7s %7s %7s %7s' %\
('Rec','Lig','dG(kT)','solv','coul','ions','dG(kcal/mol)\n')
s = '%(rec)4s : %(lig)4s %(dG_kt)7.2f %(solv)7.2f %(coul)7.2f %(ions)7.2f %(dG_kcal)7.2f\n'
d = copy.copy(com['dG_delphi'])
d.update( {'rec':com.rec_model.pdbCode, 'lig':com.lig_model.pdbCode} )
r = t
r += s % d
return r
### MAIN ###
############
options = T.cmdDict( {'ocom':'delphi.complex', 'o':'dg_delphi.out' } )
try:
f_out = T.absfile( options['o'] )
f_ocom = T.absfile( options['ocom'] )
options['autocap'] = 'autocap' in options
options['debug'] = 'debug' in options
options['verbose'] = 'v' in options
if 'nice' in options: options['nice'] = int( options['nice'] )
for key in ['indi', 'exdi', 'salt', 'ionrad', 'prbrad',
'bndcon', 'scale', 'perfil']:
if key in options: options[key] = float( options[key] )
replaced += 1
return l, replaced
def replace_import_statement( l, module, importas ):
if importas == module:
importas = ''
else:
importas = ' as ' + importas
return l.replace( 'from '+module+' import *', 'import '+module+importas)
options = t.cmdDict( {'m':'Numeric', 'as':'N', 'e':['Complex'] } )
module = options['m']
importas = options.get('as', module )
srcfiles = t.toList( options.get('i', None) )
exclude = t.toList( options['e'] )
try:
exec('import '+module)
for fname in srcfiles:
if len(sys.argv) < 2:
print \
"""
Restart a distributed calculation.
Syntax: restartPVM.py -i |rst_file| [-a]
Options:
i .. restart file containing result of TrackingJobMaster.getRst()
a .. add hosts to PVM
"""
sys.exit(0)
## MAIN ##
use()
cmd = T.cmdDict()
T.flushPrint('Loading restart data...')
rst = T.load(cmd['i'])
hosts = []
if 'a' in cmd:
hosts = [h['host'] for h in rst['hosts']]
master = restart(rst, hosts=hosts)
T.flushPrint('Master initialized for restart.')
master.start()
addFrameNames(t, trajIndex)
e = end or len(t)
if start or end or (step != 1):
t = t.takeFrames(range(start, e, step))
return t
############
### MAIN ###
use()
o = T.cmdDict({'o': 'traj_ensemble.dat'})
out = T.absfile(o['o'])
inLst = T.toList(o['i'])
start = int(o.get('s', '0'))
end = o.get('e', None)
if end:
end = int(end)
step = int(o.get('step', 1))
ref = o.get('ref', None)
if ref:
ref = PDBModel(T.absfile(ref))
if 'prot' in o:
ref = ref.compress(ref.maskProtein())
-? or help .. this help screen
Default options:
"""
for key, value in o.items():
print "\t-", key, "\t", value
sys.exit(0)
def defaultOptions():
return {'o': '.', 'log': None, 'h': None}
### MAIN ###
options = tools.cmdDict(defaultOptions())
outFolder = tools.absfile(options['o'])
host = options['h']
sap = not 'nosap' in options
log = None
if options['log']:
log = LogFile(outFolder + '/' + options['log'], 'a')
if not (os.path.exists(outFolder + '/templates')):
print 'Current directory is not a valid modeling folder (missing /templates).'
_use(defaultOptions())
if '?' in options or 'help' in options:
_use(defaultOptions())
return MS, AS, MS_sd, AS_sd
###########################
# MAIN
###########################
default = {'i':'1gxg_input.pdb',
'r':'~/GLY_pep/',
'l':'',
'mask':[0,1,0]}
if len (sys.argv) < 2:
_use( default )
options = T.cmdDict( default )
## where to run the calculation
base_folder = T.absfile( options['r'] )+'/'
## template gly-xxx-gly
template = os.path.abspath( options['i'] )
## label the result dictionaty files
label = '_' + options['l']
## mask to used to delete glycines
mask = [ int(i) for i in T.toList( options['mask'] )]
## create random prptides from template
#randomPeptides( template, base_folder )
r.reverse()
for j in r:
d.remove(j)
if len(d)==0:
print 'Nothing to align. Exiting.'
sys.exit(0)
return d
if __name__ == '__main__':
## look for default cross-validation projects
d = []
options = T.cmdDict({'h':10, 'd':d})
d=options['d'] or collect_project_folders( )
if (options['d'] is None) or ('help' in options or '?' in options):
_use( options )
folders = T.toList(options['d'])
hostNumber = int(options['h'])
pdbFolder = options.get('pdb', None)
fastaTemplates = options.get('ft', None)
fastaSequences = options.get('fs', None)
fastaTarget = options.get('fta', None)
ferror = options.get('fe',None)
show_output = 'w' in options
o['o'] = 'entropy_result.dic'
## uncomment for testing
## o['step'] = 2
## o['start']= 100
## o['stop'] = 400
## o['ref'] = '~/interfaces/c15/com_wet/ref.complex'
## o['i'] = '~/interfaces/c15/rec_pcr_00/traj.dat+\
## ~/interfaces/c15/lig_pcr_00/traj.dat'
return o
##########
## MAIN ##
options = t.cmdDict(defOptions())
if not ('i' in options):
_use()
## convert command line parameters
for k in [
's', 'e', 'ss', 'se', 'step', 'fit_s', 'fit_e', 'nice', 'thin', 'ex_n',
'ex3', 'shift', 'border'
]:
if k in options:
options[k] = int(options[k])
for k in [
'debug', 'verbose', 'cast', 'split', 'shuffle', 'shift', 'heavy',
'solvent', 'protein'
Default options:
"""
for key, value in options.items():
print "\t-", key, "\t", value
sys.exit(0)
### MAIN ###
############
if len(sys.argv) < 3:
_use({'o': 'traj.dat'})
options = tools.cmdDict({'o': 'traj.dat'})
## get all PDBs and models directly from a directory (avoids shell limits)
if 'd' in options:
d = tools.absfile(options['d'])
l = os.listdir(d)
l = [ x for x in l if x[-4:].upper() == '.PDB' or x[-6:] == '.MODEL' \
or x[-7:].upper() == '.PDB.GZ' ]
l = [os.path.join(d, f) for f in l]
options['i'] = l
if 'e' in options:
t_class = EnsembleTraj
else:
t_class = Trajectory
-amber rename CYX -> CYS, HID/HIE/HIP -> HIS, unwrap atom names
(this creates models with the same atom/res names as pdbs created
with ambpdb -p top.parm -aatm -bres < some.crd > some.pdb )
-s sort atoms alphabetically within residues
Default options:
"""
for key, value in o.items():
print "\t-", key, "\t", value
sys.exit(0)
if __name__ == '__main__':
options = T.cmdDict({'h': 10, 'c': 5})
if len(sys.argv) < 2:
_use(options)
hostNumber = int(options['h'])
chunk = int(options['c'])
windows = options.has_key('w')
amber = options.has_key('amber')
sort = options.has_key('s')
outFolder = None
if options.has_key('o'):
outFolder = T.absfile(options['o'])
## get all PDBs and models directly from a directory (avoids shell limits)
