pKaTool/pKacalc_interface.py
def really_getgroups(self):
        """Divide the files listed into protein and ligand, and initialise the routines"""
        proteins=[]
        ligands=[]
        for file,ftype in self.files_included:
            if ftype=='Protein':
                proteins.append(file)
            else:
                ligands.append(file)
        #
        # Right now we can only deal with one file of each type
        #
        pdbfile=proteins[0]
        if len(ligands)>0:
            ligandfile=ligands[0]
        else:
            ligandfile=None
        #
        # Now get the groups
        #
        if self.pdb2pKa_path.get()=="":
            tkMessageBox.showerror('PDB2pKa missing',
                                   'You did not specify the path to PDB2pKa')
            return
        import sys
        sys.path.append('/home/nielsen/lib/pdb2pqr_develop/pKa')
        import pka
        myProtein, myRoutines, myForcefield,apbs_setup, ligand_titratable_groups=pka.pre_init(pdbfile=pdbfile,ff='parse',ligand=ligandfile)
        print 'Return values from pdb2pqr pka'
        print myProtein
        print myRoutines
        print myForcefield
        print apbs_setup
        print ligand_titratble_groups
        groups=pka.pKaRoutines(myProtein, myRoutines, myForcefield,apbs_setup)
        print '-------'
        print groups
        return
Divide the files listed into protein and ligand, and initialise the routines
Divide the files listed into protein and ligand, and initialise the routines
Divide the files listed into protein and ligand and initialise the routines
def really_getgroups(self):
        proteins=[]
        ligands=[]
        for file,ftype in self.files_included:
            if ftype=='Protein':
                proteins.append(file)
            else:
                ligands.append(file)
         Right now we can only deal with one file of each type
        pdbfile=proteins[0]
        if len(ligands)>0:
            ligandfile=ligands[0]
        else:
            ligandfile=None
         Now get the groups
        if self.pdb2pKa_path.get()=="":
            tkMessageBox.showerror('PDB2pKa missing',
                                   'You did not specify the path to PDB2pKa')
            return
        import sys
        sys.path.append('/home/nielsen/lib/pdb2pqr_develop/pKa')
        import pka
        myProtein, myRoutines, myForcefield,apbs_setup, ligand_titratable_groups=pka.pre_init(pdbfile=pdbfile,ff='parse',ligand=ligandfile)
        print 'Return values from pdb2pqr pka'
        print myProtein
        print myRoutines
        print myForcefield
        print apbs_setup
        print ligand_titratble_groups
        groups=pka.pKaRoutines(myProtein, myRoutines, myForcefield,apbs_setup)
        print '-------'
        print groups
        return
def really_getgroups ( self ) : proteins = [ ] ligands = [ ] for file , ftype in self . files_included : if ftype == 'Protein' : proteins . append ( file ) else : ligands . append ( file ) pdbfile = proteins [ 0 ] if len ( ligands ) > 0 : ligandfile = ligands [ 0 ] else : ligandfile = None if self . pdb2pKa_path . get ( ) == "" : tkMessageBox . showerror ( 'PDB2pKa missing' , 'You did not specify the path to PDB2pKa' ) return import sys sys . path . append ( '/home/nielsen/lib/pdb2pqr_develop/pKa' ) import pka myProtein , myRoutines , myForcefield , apbs_setup , ligand_titratable_groups = pka . pre_init ( pdbfile = pdbfile , ff = 'parse' , ligand = ligandfile ) print 'Return values from pdb2pqr pka' print myProtein print myRoutines print myForcefield print apbs_setup print ligand_titratble_groups groups = pka . pKaRoutines ( myProtein , myRoutines , myForcefield , apbs_setup ) print '-------' print groups return
Divide the files listed into protein and ligand, and initialise the routines
Divide the files listed into protein and ligand and initialise the routines
"""Divide the files listed into protein and ligand, and initialise the routines""" # # Right now we can only deal with one file of each type # # # Now get the groups #
self