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
