def main(self, pdb1, pdb2, chains1, chains2):
import Numeric, math, os
import quakes
instance_quakes = quakes.quakes()
import sys
sys.path.append('/home/people/tc/python/Protool/')
import geometry
instance_geometry = geometry.geometry()
pdbs = [pdb1,pdb2]
##
## parse coordinates to dictionary
##
d_noncoordinates = {}
d_coordinates = {}
for pdb in pdbs:
## read pdb file
fd = open('%s%s.pdb' %(self.pdbpath, pdb),'r')
lines = fd.readlines()
fd.close()
## parse pdb file
d_noncoords = instance_quakes.parse_pdbnoncoordinatesections(lines, pdb)
d_coords = instance_quakes.parse_pdbcoordinatesection(lines, pdb)
d_noncoordinates[pdb] = d_noncoords
d_coordinates[pdb] = d_coords
##
## convert dictionary of coordinates to list of coordinates
##
coordinates1 = []
coordinates2 = []
d_alignATOMseq = {}
for i in range(len(chains1)):
chain1 = chains1[i]
chain2 = chains2[i]
d_res_nos1, d_res_nos2, l1, l2, ATOMseq1, ATOMseq2 = instance_quakes.alignATOMseq(d_coordinates, d_noncoordinates, pdb1, pdb2, chain1, chain2)
d_alignATOMseq[chain2] = {}
d_alignATOMseq[chain2]['d_res_nos1'] = d_res_nos1
d_alignATOMseq[chain2]['d_res_nos2'] = d_res_nos2
d_alignATOMseq[chain2]['l1'] = l1
d_alignATOMseq[chain2]['l2'] = l2
coords1, coords2, rescount = instance_quakes.ATOMrecords2coordinates(d_coordinates, pdb1, pdb2, chain1, chain2, d_res_nos1, d_res_nos2, l1, l2, ATOMseq1, ATOMseq2)
coordinates1 += coords1
coordinates2 += coords2
##
## align coordinates
##
rmsd = instance_geometry.superpose(coordinates1,coordinates2)
tv1 = instance_geometry.fitcenter
rm = instance_geometry.rotation
tv2 = instance_geometry.refcenter
##
## calculate RMSD of transformed coordinates of individual residues
##
lines1 = []
lines2 = []
atom_no = 0
for i in range(len(chains1)):
chain1 = chains1[i]
chain2 = chains2[i]
for SEQRESpos1 in range(l2,len(ATOMseq1)+l2):
SEQRESpos2 = SEQRESpos1+l1-l2
res_no1 = d_res_nos1[SEQRESpos1]['res_no']
res_no2 = d_res_nos2[SEQRESpos2]['res_no']
if res_no1 == '-' or res_no2 == '-':
continue
iCode1 = d_res_nos1[SEQRESpos1]['iCode']
iCode2 = d_res_nos2[SEQRESpos2]['iCode']
if res_no1 not in d_coordinates[pdb1]['chains'][chain1]['residues'].keys():
continue
if res_no2 not in d_coordinates[pdb2]['chains'][chain2]['residues'].keys():
continue
if 'REMARK' in d_coordinates[pdb1]['chains'][chain1]['residues'][res_no1]['d_iCodes'][iCode1].keys():
continue
if 'REMARK' in d_coordinates[pdb2]['chains'][chain2]['residues'][res_no2]['d_iCodes'][iCode2].keys():
continue
d_resname = {
pdb1:{'chain':chain1,'res_no':res_no1,'iCode':iCode1},
pdb2:{'chain':chain2,'res_no':res_no2,'iCode':iCode2},
}
for pdb in d_resname.keys():
chain = d_resname[pdb]['chain']
res_no = d_resname[pdb]['res_no']
iCode = d_resname[pdb]['iCode']
res_name = d_coordinates[pdb]['chains'][chain]['residues'][res_no]['d_iCodes'][iCode]['res_name']
d_atoms = d_coordinates[pdb]['chains'][chain]['residues'][res_no]['d_iCodes'][iCode]['atoms']
d_resname[pdb]['res_name'] = res_name
d_resname[pdb]['d_atoms'] = d_atoms
res_name1 = d_resname[pdb1]['res_name']
res_name2 = d_resname[pdb2]['res_name']
d_atoms1 = d_resname[pdb1]['d_atoms']
d_atoms2 = d_resname[pdb2]['d_atoms']
## print pdb1, pdb2, chain1, chain2, res_no1, res_no2, res_name1, res_name2
##
## calculate rmsd for the atoms of the residue
##
SS = []
for atom_name in d_atoms1.keys():
if atom_name not in d_atoms2.keys():
continue
coordinate1 = d_atoms1[atom_name]['coordinate']
coordinate2 = Numeric.matrixmultiply(rm, d_atoms2[atom_name]['coordinate']-tv1)+tv2
SS += [sum((coordinate2-coordinate1)**2)]
RMSD = math.sqrt(sum(SS)/len(SS))
occupancy = bfactor = RMSD/rmsd
##
## append atoms and coordinates to lines
##
for atom_name in d_atoms1.keys():
if atom_name not in d_atoms2.keys():
continue
coordinate1 = d_atoms1[atom_name]['coordinate']
coordinate2 = d_atoms2[atom_name]['coordinate']
x1 = coordinate1[0]; y1 = coordinate1[1]; z1 = coordinate1[2]
x2 = coordinate2[0]; y2 = coordinate2[1]; z2 = coordinate1[2]
atom_no += 1
altloc = ''
charge = ''
if 'H' in atom_name:
element = 'H'
else:
element = atom_name[0]
lines1 += [
'%6s%5i %4s%1s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2s\n'
%('ATOM'.ljust(6), atom_no, atom_name.ljust(4), altloc, res_name1.ljust(3), chain1, res_no1, iCode1, x1, y1, z1, occupancy, bfactor, element.rjust(2), charge.rjust(2))
]
lines2 += [
'%6s%5i %4s%1s%3s %1s%4i%1s %8.3f%8.3f%8.3f%6.2f%6.2f %2s%2s\n'
%('ATOM'.ljust(6), atom_no, atom_name.ljust(4), altloc, res_name2.ljust(3), chain2, res_no2, iCode2, x2, y2, z2, occupancy, bfactor, element.rjust(2), charge.rjust(2))
]
fd = open('%s%s.pdb' %(self.path_out,pdb1),'w')
fd.writelines(lines1)
fd.close()
fd = open('%s%s.pdb' %(self.path_out,pdb2),'w')
fd.writelines(lines2)
fd.close()
for pdb in pdbs:
## write rasmol script
lines = [
'rasmol -nodisplay %s%s.pdb << EOF\n' %(self.path_out,pdb),
'color temperature\n',
'spacefill\n',
'write %s%s.ppm\n' %(self.path_tmp,pdb),
'exit\n',
]
## write rasmol script to file
fd = open('%s%srasmol.src' %(self.path_tmp,pdb),'w')
fd.writelines(lines)
fd.close()
## execute rasmol script
os.system('source %s%srasmol.src' %(self.path_tmp,pdb))
## convert rasmol output
os.system('convert %s%s.ppm -resize x80 %s%s.gif' %(self.path_tmp,pdb, self.path_out,pdb))
## clean up
os.system('rm %s%s.ppm' %(self.path_tmp,pdb))
## clean up
os.system('rm %s%srasmol.src' %(self.path_tmp,pdb))
os.system
return
def rmsd2bfactor(
pdb1,
pdb2,
biomolecule1,
biomolecule2,
rmsd,
d_coordinates,
d_header,
tv1,
rm,
tv2,
l_equivalent_chains,
bmchains1,
bmchains2,
d_chains_intrapdb_sequence_identical,
d_chains_interpdb_sequence_similar,
d_ATOMseq,
path_pdb,
):
print 'rmsd2bfactor'
biomolecule1 = str(biomolecule1).zfill(2)
biomolecule2 = str(biomolecule2).zfill(2)
##
## append secondary structure information
##
d_lines_ss = {
pdb1: [],
pdb2: [],
}
for pdb in d_lines_ss:
##
## read lines
##
fd = open(
'%s/%s/pdb%s.ent' % (path_pdb, pdb.lower()[1:3], pdb.lower()), 'r')
## fd = open('C:\Users\Tommy Carstensen\Downloads\pdb\%s.pdb' %(pdb.lower(),),'r')
lines = fd.readlines()
fd.close()
for line in lines:
record = line[:6].strip()
if record in [
'HELIX',
'SHEET',
'TURN',
]:
d_lines_ss[pdb] += line
chains1 = l_equivalent_chains[0]
chains2 = l_equivalent_chains[1]
if len(chains1) != len(chains2):
print pdb1, pdb2
print chains1, chains2
notexpected
##
## parse coordinates for the specific combinations of chain1 and chain2
##
instance_quakes = quakes.quakes()
(
coordinates1,
coordinates2,
residue_count,
d_lines,
l_RMSDs,
d_coordinates1,
d_coordinates2,
) = instance_quakes.prepare_coords_for_alignment(
pdb1,
pdb2,
chains1,
chains2,
d_chains_intrapdb_sequence_identical,
d_chains_interpdb_sequence_similar,
d_coordinates,
d_ATOMseq,
rmsd=rmsd,
tv1=tv1,
rm=rm,
tv2=tv2,
)
##
## append lines by model to final lines
##
pdblines1 = d_lines_ss[pdb1]
pdblines2 = d_lines_ss[pdb2]
for model in d_lines[pdb1].keys():
pdblines1 += [
'MODEL %4s \n'
% (model)
]
pdblines1 += d_lines[pdb1][model]
pdblines1 += [
'ENDMDL \n'
]
for model in d_lines[pdb2].keys():
pdblines2 += [
'MODEL %4s \n'
% (model)
]
pdblines2 += d_lines[pdb2][model]
pdblines2 += [
'ENDMDL \n'
]
fd = open(
'pdb/%s/%s%s%s%s.pdb' % (pdb1[1], pdb1, str(biomolecule1).zfill(2),
pdb2, str(biomolecule2).zfill(2)), 'w')
fd.writelines(pdblines1)
fd.close()
fd = open(
'pdb/%s/%s%s%s%s.pdb' % (pdb2[1], pdb2, str(biomolecule2).zfill(2),
pdb1, str(biomolecule1).zfill(2)), 'w')
fd.writelines(pdblines2)
fd.close()
##
## gif thumbnails
##
d_biomolecules = {pdb1: biomolecule1, pdb2: biomolecule2}
for pdb in d_biomolecules.keys():
print 'gif thumbnail', pdb
biomolecule = d_biomolecules[pdb]
if pdb == pdb1:
prefix = pdb1 + str(biomolecule1).zfill(2) + pdb2 + str(
biomolecule2).zfill(2)
if pdb == pdb2:
prefix = pdb2 + str(biomolecule2).zfill(2) + pdb1 + str(
biomolecule1).zfill(2)
## write rasmol script
lines = [
'rasmol -nodisplay pdb/%s/%s.pdb <<EOF\n' % (pdb[1], prefix),
'color temperature\n',
'wireframe 0\n',
'cartoon\n',
'write ppm/%s.ppm\n' % (prefix),
'exit\n',
]
## write rasmol script to file
fd = open('src/%srasmol.src' % (prefix), 'w')
fd.writelines(lines)
fd.close()
## execute rasmol script
os.system('source src/%srasmol.src > log/%srasmol.log' %
(prefix, prefix))
## convert rasmol output
os.system('convert ppm/%s.ppm -resize x80 gif/%s/%s.gif' %
(prefix, pdb[1], prefix))
## clean up
os.remove('ppm/%s.ppm' % (prefix))
os.remove('log/%srasmol.log' % (prefix))
os.remove('src/%srasmol.src' % (prefix))
return
def rmsd2bfactor(
pdb1, pdb2, biomolecule1, biomolecule2, rmsd, d_coordinates, d_header,
tv1, rm, tv2,
l_equivalent_chains, bmchains1, bmchains2,
d_chains_intrapdb_sequence_identical, d_chains_interpdb_sequence_similar,
d_ATOMseq,
path_pdb,
):
print 'rmsd2bfactor'
biomolecule1 = str(biomolecule1).zfill(2)
biomolecule2 = str(biomolecule2).zfill(2)
##
## append secondary structure information
##
d_lines_ss = {
pdb1:[],
pdb2:[],
}
for pdb in d_lines_ss:
##
## read lines
##
fd = open('%s/%s/pdb%s.ent' %(path_pdb, pdb.lower()[1:3], pdb.lower()),'r')
## fd = open('C:\Users\Tommy Carstensen\Downloads\pdb\%s.pdb' %(pdb.lower(),),'r')
lines = fd.readlines()
fd.close()
for line in lines:
record = line[:6].strip()
if record in ['HELIX','SHEET','TURN',]:
d_lines_ss[pdb] += line
chains1 = l_equivalent_chains[0]
chains2 = l_equivalent_chains[1]
if len(chains1) != len(chains2):
print pdb1, pdb2
print chains1, chains2
notexpected
##
## parse coordinates for the specific combinations of chain1 and chain2
##
instance_quakes = quakes.quakes()
(
coordinates1, coordinates2, residue_count, d_lines, l_RMSDs,
d_coordinates1, d_coordinates2,
) = instance_quakes.prepare_coords_for_alignment(
pdb1,pdb2,chains1,chains2,
d_chains_intrapdb_sequence_identical,
d_chains_interpdb_sequence_similar,
d_coordinates,d_ATOMseq,
rmsd=rmsd, tv1=tv1, rm=rm, tv2=tv2,
)
##
## append lines by model to final lines
##
pdblines1 = d_lines_ss[pdb1]
pdblines2 = d_lines_ss[pdb2]
for model in d_lines[pdb1].keys():
pdblines1 += ['MODEL %4s \n' %(model)]
pdblines1 += d_lines[pdb1][model]
pdblines1 += ['ENDMDL \n']
for model in d_lines[pdb2].keys():
pdblines2 += ['MODEL %4s \n' %(model)]
pdblines2 += d_lines[pdb2][model]
pdblines2 += ['ENDMDL \n']
fd = open('pdb/%s/%s%s%s%s.pdb' %(pdb1[1], pdb1, str(biomolecule1).zfill(2), pdb2, str(biomolecule2).zfill(2)), 'w')
fd.writelines(pdblines1)
fd.close()
fd = open('pdb/%s/%s%s%s%s.pdb' %(pdb2[1], pdb2, str(biomolecule2).zfill(2), pdb1, str(biomolecule1).zfill(2)), 'w')
fd.writelines(pdblines2)
fd.close()
##
## gif thumbnails
##
d_biomolecules = {pdb1:biomolecule1,pdb2:biomolecule2}
for pdb in d_biomolecules.keys():
print 'gif thumbnail', pdb
biomolecule = d_biomolecules[pdb]
if pdb == pdb1:
prefix = pdb1+str(biomolecule1).zfill(2)+pdb2+str(biomolecule2).zfill(2)
if pdb == pdb2:
prefix = pdb2+str(biomolecule2).zfill(2)+pdb1+str(biomolecule1).zfill(2)
## write rasmol script
lines = [
'rasmol -nodisplay pdb/%s/%s.pdb <<EOF\n' %(pdb[1], prefix),
'color temperature\n',
'wireframe 0\n',
'cartoon\n',
'write ppm/%s.ppm\n' %(prefix),
'exit\n',
]
## write rasmol script to file
fd = open('src/%srasmol.src' %(prefix),'w')
fd.writelines(lines)
fd.close()
## execute rasmol script
os.system('source src/%srasmol.src > log/%srasmol.log' %(prefix,prefix))
## convert rasmol output
os.system('convert ppm/%s.ppm -resize x80 gif/%s/%s.gif' %(prefix,pdb[1],prefix))
## clean up
os.remove('ppm/%s.ppm' %(prefix))
os.remove('log/%srasmol.log' %(prefix))
os.remove('src/%srasmol.src' %(prefix))
return
