import sys
import math
sys.path.append('../..')
from MolecularSystem import System
x = System(None)
y = System(None)
z = System(None)
x.load_pdb('1KAW.pdb')
y.load_pdb('1L1OA.pdb')
z.load_pdb('1L1OB.pdb')
x.res_list = [8, 14, 32, 34, 57, 59, 71, 77, 79, 101, 109]
y.res_list = [25, 31, 41, 43, 53, 55, 63, 67, 69, 79, 84]
z.res_list = [74, 80, 92, 94, 104, 106, 120, 126, 128, 141, 146]
dsf = 0.2
for res_num1 in range(len(x.res_list)):
sum1 = 0.0
sum2 = 0.0
sum3 = 0.0
for res_num2 in range(0, len(x.res_list)):
#print x.ProteinList[0].residue_dict[x.res_list[res_num2]].res_number, x.ProteinList[0].residue_dict[x.res_list[res_num2]].central_atom.atom_number
#print y.ProteinList[0].residue_dict[y.res_list[res_num2]].res_number, y.ProteinList[0].residue_dict[y.res_list[res_num2]].central_atom.atom_number
#print z.ProteinList[0].residue_dict[z.res_list[res_num2]].res_number, z.ProteinList[0].residue_dict[z.res_list[res_num2]].central_atom.atom_number
#continue
dist1 = x.ProteinList[0].residue_dict[
x.res_list[res_num1]].central_atom.dist(
x.ProteinList[0].residue_dict[
x.res_list[res_num2]].central_atom)
dist2 = y.ProteinList[0].residue_dict[
y.res_list[res_num1]].central_atom.dist(
import sys
import os
sys.path.append('./Tools/Aligner')
import SequenceAligner
from MolecularSystem import System
list = os.listdir('.')
for pdb in list:
sys = System(pdb)
print pdb
for i in range(len(sys.ProteinList)-1):
for j in range(i+1,len(sys.ProteinList)):
a = SequenceAligner.SequenceAligner(0, 'global')
a.add_target(sys.ProteinList[i])
a.add_template(sys.ProteinList[j])
pid = a.align_sequences()
line = '%5.3f percent identity %s %s\n'%(pid, sys.ProteinList[i].chain_name, sys.ProteinList[j].chain_name)
print line
