def convert_PEAT_to_classic(operations): operations=get_single_operations(operations) newops=[] import string, Protool PI=Protool.structure() for operation in operations: resid=get_resid_from_mut(operation) old=PI.three_to_one[get_oldrestyp_from_mut(operation)] new=PI.three_to_one[get_newrestyp_from_mut(operation)] resnum=get_resnum_from_mut(operation) resnum=string.lstrip(resnum,'0') classic='%s%s%s' %(old,resnum.strip(),new) newops.append(classic) classicops=string.join(newops,'+') return classicops
def convert_PEAT_to_classic(operations): operations = get_single_operations(operations) newops = [] import string, Protool PI = Protool.structure() for operation in operations: resid = get_resid_from_mut(operation) old = PI.three_to_one[get_oldrestyp_from_mut(operation)] new = PI.three_to_one[get_newrestyp_from_mut(operation)] resnum = get_resnum_from_mut(operation) resnum = string.lstrip(resnum, '0') classic = '%s%s%s' % (old, resnum.strip(), new) newops.append(classic) classicops = string.join(newops, '+') return classicops
def __init__(self, pdbfiles): """Calculate a score for sequence-local contacts""" import Protool self.X = Protool.structure() for pdbfile in pdbfiles: xs = [] ys = [] labels = [] count = 0 PI = self.get_PDB(pdbfile) seq = PI.PirSeq(PI.sequence) window = 4 * [None] residues = 4 * [None] for residue, type in PI.sequence[:3]: window.append(type) residues.append(residue) for residue, type in PI.sequence[3:]: window.append(type) window = window[1:] # residues.append(residue) residues = residues[1:] # print window if window[3] in ["ASP", "GLU"]: # ,'LYS','HIS','ARG']: # print window score = self.score_window(window) print residues[3], window[3], score xs.append(count) labels.append(residues[3] + ":%s" % window[3]) ys.append(score) count = count + 1 # # Plot a bar chart # import pylab pylab.bar(xs, ys) import numpy xs = numpy.array(xs) pylab.xticks(xs + 0.5, labels, rotation="vertical", size="x-small") pylab.title("dpKa values") pylab.show() return
def __init__(self, pdbfiles): """Calculate a score for sequence-local contacts""" import Protool self.X = Protool.structure() for pdbfile in pdbfiles: xs = [] ys = [] labels = [] count = 0 PI = self.get_PDB(pdbfile) seq = PI.PirSeq(PI.sequence) window = 4 * [None] residues = 4 * [None] for residue, type in PI.sequence[:3]: window.append(type) residues.append(residue) for residue, type in PI.sequence[3:]: window.append(type) window = window[1:] # residues.append(residue) residues = residues[1:] #print window if window[3] in ['ASP', 'GLU']: #,'LYS','HIS','ARG']: #print window score = self.score_window(window) print residues[3], window[3], score xs.append(count) labels.append(residues[3] + ':%s' % window[3]) ys.append(score) count = count + 1 # # Plot a bar chart # import pylab pylab.bar(xs, ys) import numpy xs = numpy.array(xs) pylab.xticks(xs + 0.5, labels, rotation='vertical', size='x-small') pylab.title('dpKa values') pylab.show() return