def inputComplex(options):
if 'c' in options:
return T.load(T.absfile(options['c']))
m = PDBModel(T.absfile(options['i']))
## extract rec and lig chains
rec_chains = T.toIntList(options['r'])
lig_chains = T.toIntList(options['l'])
rec = m.takeChains(rec_chains)
lig = m.takeChains(lig_chains)
## create Protein complex
com = Complex(rec, lig)
return com
def table_ensemble(self, member=None, vpos=None, title=1):
"""
Tabulate different entropy components versus variable parameter.
d - dict, result of calculate()
vpos - int, report result for |i|th variable parameter value
title - 1|0, add title lines
"""
d = self.calculate(member)
s = ''
if title:
s += self.table_header()
vpos = T.toIntList(vpos or range(len(d['dS'])))
for i in vpos:
v = [
d[x][i] for x in [
'dS_rt', 'dS', 'dS_intra', 'dS_rigid', 'dS_cross',
'ddS_fake1'
]
]
s += "%4.0f %4.0f %5.0f %4.0f %4.0f %4.0f\n" % \
tuple( v )
return s
def inputComplex( options ):
if 'c' in options:
return T.load( T.absfile( options['c'] ) )
m = PDBModel( T.absfile( options['i'] ) )
## extract rec and lig chains
rec_chains = T.toIntList( options['r'] )
lig_chains = T.toIntList( options['l'] )
rec = m.takeChains( rec_chains )
lig = m.takeChains( lig_chains )
## create Protein complex
com = Complex( rec, lig )
return com
def table_ensemble( self, member=None, vpos=None, title=1 ):
"""
Tabulate different entropy components versus variable parameter.
d - dict, result of calculate()
vpos - int, report result for |i|th variable parameter value
title - 1|0, add title lines
"""
d = self.calculate( member )
s = ''
if title:
s += self.table_header()
vpos = T.toIntList( vpos or range( len( d['dS'] ) ) )
for i in vpos:
v = [ d[x][i] for x in ['dS_rt','dS', 'dS_intra', 'dS_rigid',
'dS_cross', 'ddS_fake1'] ]
s += "%4.0f %4.0f %5.0f %4.0f %4.0f %4.0f\n" % \
tuple( v )
return s
### 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..."
ref_rec = ref_com.takeChains( rec_chains )
ref_lig = ref_com.takeChains( lig_chains )
## create Protein complex
com = ProteinComplex( ref_rec, ref_lig )
print "Saving..."
ref_lig.saveAs( T.absfile( options['lo'] ) )
ref_rec.saveAs( T.absfile( options['ro'] ) )
T.dump( com, T.absfile( options['o']) )
]:
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:
options[k] = 0
for k in ['chains', 'ex1', 'ex2', 'ex']:
if k in options:
options[k] = t.toIntList(options[k])
if 'atoms' in options:
options['atoms'] = t.toList(options['atoms'])
if 'ex1' in options and 'ex2' in options:
options['ex'] = (options['ex1'], options['ex2'])
else:
options['ex'] = options.get('ex', options.get('ex1', None))
if 'log' in options:
options['log'] = LogFile(options['log'])
f_in = options['i']
del options['i']
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',[]))
options['hetatm'] = 'hetatm' in options
options['norun'] = 'norun' in options
options['debug'] = 'debug' in options
options['center'] = not 'nocenter' in options
if 'log' in options:
options['log'] = LogFile( options['log'] )
if 'norun' in options:
fbase = t.stripSuffix( t.absfile( options['i'] ) )
options['leap_in'] = options.get('leap_in', fbase+'_leap.in')
options['leap_pdb']= options.get('leap_pdb',fbase+'_forleap.pdb')
a = AmberParmBuilder( options['i'], **options )
## 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:
options[k] = 0
for k in ['chains','ex1', 'ex2', 'ex']:
if k in options:
options[k] = t.toIntList( options[k] )
if 'atoms' in options:
options['atoms'] = t.toList( options['atoms'] )
if 'ex1' in options and 'ex2' in options:
options['ex'] = ( options['ex1'], options['ex2'] )
else:
options['ex'] = options.get( 'ex', options.get('ex1', None) )
if 'log' in options:
options['log'] = LogFile( options['log'] )
f_in = options['i']
del options['i']
