pKa/find_simple.py
def desolvation():
    """Find correlation between desolvation and acc"""
    import os
    dirs=os.listdir('data')
    xs=[]
    ys=[]
    for dir in dirs:
        print 'Processing %s' %dir
        #
        # find the PDB file
        #
        realdir=os.path.join(os.getcwd(),'data',dir)
        files=os.listdir(realdir)
        for file in files:
            realfile=os.path.join(realdir,file)
            if file[-4:]=='.pdb':
                import pKa.pKaTool.pKaIO
                X=pKa.pKaTool.pKaIO.pKaIO(realfile)
                X.assess_status()
                if X.calculation_completed==1:
                    #
                    # Hurra, the calc is complete. Load the desolvation energies
                    #
                    PBEdesolv=X.read_desolv()
                    #
                    # Now calculate the desolvation energies with Protool
                    #
                    P=Protool.structureIO()
                    P.readpdb(realfile)
                    P.get_titratable_groups()
                    P.calculate_desolvation()
                    #
                    #
                    x=[]
                    y=[]
                    for residue in PBEdesolv.keys():
                        if P.desolv.has_key(residue):
                            x.append(P.desolv[residue])
                            y.append(PBEdesolv[residue])
                    xs.append(x)
                    ys.append(y)
    plotit(xs,ys,'Desolvation',dirs)
    return
Find correlation between desolvation and acc
Find correlation between desolvation and acc
Find correlation between desolvation and acc
def desolvation():
    import os
    dirs=os.listdir('data')
    xs=[]
    ys=[]
    for dir in dirs:
        print 'Processing %s' %dir
         find the PDB file
        realdir=os.path.join(os.getcwd(),'data',dir)
        files=os.listdir(realdir)
        for file in files:
            realfile=os.path.join(realdir,file)
            if file[-4:]=='.pdb':
                import pKa.pKaTool.pKaIO
                X=pKa.pKaTool.pKaIO.pKaIO(realfile)
                X.assess_status()
                if X.calculation_completed==1:
                     Hurra, the calc is complete. Load the desolvation energies
                    PBEdesolv=X.read_desolv()
                     Now calculate the desolvation energies with Protool
                    P=Protool.structureIO()
                    P.readpdb(realfile)
                    P.get_titratable_groups()
                    P.calculate_desolvation()
                    x=[]
                    y=[]
                    for residue in PBEdesolv.keys():
                        if P.desolv.has_key(residue):
                            x.append(P.desolv[residue])
                            y.append(PBEdesolv[residue])
                    xs.append(x)
                    ys.append(y)
    plotit(xs,ys,'Desolvation',dirs)
    return
def desolvation ( ) : import os dirs = os . listdir ( 'data' ) xs = [ ] ys = [ ] for dir in dirs : print 'Processing %s' % dir realdir = os . path . join ( os . getcwd ( ) , 'data' , dir ) files = os . listdir ( realdir ) for file in files : realfile = os . path . join ( realdir , file ) if file [ - 4 : ] == '.pdb' : import pKa . pKaTool . pKaIO X = pKa . pKaTool . pKaIO . pKaIO ( realfile ) X . assess_status ( ) if X . calculation_completed == 1 : PBEdesolv = X . read_desolv ( ) P = Protool . structureIO ( ) P . readpdb ( realfile ) P . get_titratable_groups ( ) P . calculate_desolvation ( ) x = [ ] y = [ ] for residue in PBEdesolv . keys ( ) : if P . desolv . has_key ( residue ) : x . append ( P . desolv [ residue ] ) y . append ( PBEdesolv [ residue ] ) xs . append ( x ) ys . append ( y ) plotit ( xs , ys , 'Desolvation' , dirs ) return
Find correlation between desolvation and acc
Find correlation between desolvation and acc
"""Find correlation between desolvation and acc""" # # find the PDB file # # # Hurra, the calc is complete. Load the desolvation energies # # # Now calculate the desolvation energies with Protool # # #