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']