def optimize2(self):
a = symgen.symgen()
symorganics = []
processing = []
optimum = []
original = []
originalcount = 0
optimumcount = 0
maxcounts = []
newx = 0
newy = 0
newz = 0
nflag = 0
verbose = 0
numorg = float(len(self.organics))
count = 0
counter = 0
checkcounter = 0
file = open(self.root + 'optimize_organic.log', 'w')
curres = 0
flag = 0
curror = ""
currch = ""
currpdb = ""
hold = ""
print "Optimizing individual organic/ligand symmetries - Please wait."
changemade = 0
for o in self.organics:
count = count + 1
counter = counter + 1
if(counter % 10 == 0):
disp = float(count / numorg) * 100
# print "Optimizing individual organic symmetries - %.1f%% complete. "%disp
counter = 0
if((o['res num'] == curres) and (o['res name'] == curror) and (o['chain'] == currch)):
processing.append(o)
hold = o
else: #process data and start a new list
if (flag == 1):
changemade = 0
hold = o
tproc = []
tproc.append(o)
curres = o['res num']
curror = o['res name']
currch = o['chain']
symmorganics = a.varpass2(processing)
opcount = []
for i in range(1000):
opcount.append(0)
best = 0
counter = 0
bestpos = 0
for i in symmorganics:
checkcounter = 0
for j in i:
checkcount = 0
for pdb in self.pdbs:
if (pdb == currpdb):
#print '---'
#print "%s%s"%(o['res name'],o['res num'])
checkcount = pdb.compare(j)
opcount[checkcounter] = opcount[checkcounter] + checkcount
checkcounter += 1
maxpos = 0
mypos = 0
maxcount = 0
for i in opcount:
if(i > maxcount):
maxpos = mypos
maxcount = i
mypos += 1
for i in symmorganics:
optimum.append(i[maxpos])
pcount = 0
for i in processing:
j = optimum[pcount]
if maxcount == 0:
file.write(str(i.pdb) + " " + i['res name'] + ' ' + i['atom name'] + " %d No Change Made\n" % i['res num'])
file.write("****WARNING**** THIS ATOM MAKES NO PROTEIN CONTACTS ****WARNING****\n\n")
else:
if((str(j[4]) == "[0, 0, 0]" and j[3] == "x,y,z")):
if(verbose):
file.write(str(i.pdb) + " " + i['res name'] + ' ' + i['atom name'] + " %d No Change Made\n\n" % i['res num'])
else:
file.write(str(i.pdb) + " " + i['res name'] + ' ' + i['atom name'] + " %d Optimization Results" % i['res num'])
file.write("\nOriginal Position: %.3f %.3f %.3f" % (i.position()[0], i.position()[1], i.position()[2]))
file.write("\nOriginal Contacts: %d" % i.howclose())
file.write("\nOptimized Position: %.3f %.3f %.3f" % (j[0], j[1], j[2]))
file.write("\nOptimized Symmetry UC: " + str(j[4]))
file.write("\nOptimized Operator: " + j[3])
file.write("\nOptimized Contacts: %d\n\n" % maxcount)
if maxcount > 0:
i.optimum_update(j)
pcount += 1
optimum = []
currpdb = o.pdb
processing = []
processing.append(tproc[0])
else:
flag = 1
optimum = []
processing = []
processing.append(o)
curres = o['res num']
curror = o['res name']
currch = o['chain']
currpdb = o.pdb
changemade = 0
o = hold
symmorganics = a.varpass2(processing)
opcount = []
for i in range(1000):
opcount.append(0)
for i in symmorganics:
checkcounter = 0
for j in i:
checkcount = 0
for pdb in self.pdbs:
if (pdb == currpdb):
checkcount = pdb.compare(j)
opcount[checkcounter] = opcount[checkcounter] + checkcount
checkcounter += 1
maxpos = 0
mypos = 0
maxcount = 0
for i in opcount:
if(i > maxcount):
maxpos = mypos
maxcount = i
mypos += 1
for i in symmorganics:
optimum.append(i[maxpos])
pcount = 0
for i in processing:
j = optimum[pcount]
if maxcount == 0:
file.write(str(i.pdb) + " " + i['res name'] + ' ' + i['atom name'] + " %d No Change Made\n" % i['res num'])
file.write("****WARNING**** THIS ATOM MAKES NO PROTEIN CONTACTS ****WARNING****\n\n")
else:
if((str(j[4]) == "[0, 0, 0]" and j[3] == "x,y,z")):
if(verbose):
file.write(str(i.pdb) + " " + i['res name'] + ' ' + i['atom name'] + " %d No Change Made\n\n" % i['res num'])
else:
file.write(str(i.pdb) + " " + i['res name'] + ' ' + i['atom name'] + " %d Optimization Results" % i['res num'])
file.write("\nOriginal Position: %.3f %.3f %.3f" % (i.position()[0], i.position()[1], i.position()[2]))
file.write("\nOriginal Contacts: %d" % i.howclose())
file.write("\nOptimized Position: %.3f %.3f %.3f]" % (j[0], j[1], j[2]))
file.write("\nOptimized Symmetry UC: " + str(j[4]) + ']')
file.write("\nOptimized Operator: " + j[3] + ']')
file.write("\nOptimized Contacts: %d\n\n" % maxcount)
if maxcount > 0:
i.optimum_update(j)
pcount += 1
optimum = []
processing = []
file.close()
def optimize2(self):
a = symgen.symgen()
symorganics = []
processing = []
optimum = []
original = []
originalcount = 0
optimumcount = 0
maxcounts = []
newx = 0
newy = 0
newz = 0
nflag = 0
verbose = 0
numorg = float(len(self.organics))
count = 0
counter = 0
checkcounter = 0
file = open(self.root + 'optimize_organic.log', 'w')
curres = 0
flag = 0
curror = ""
currch = ""
currpdb = ""
hold = ""
print "Optimizing individual organic/ligand symmetries - Please wait."
changemade = 0
for o in self.organics:
count = count + 1
counter = counter + 1
if (counter % 10 == 0):
disp = float(count / numorg) * 100
# print "Optimizing individual organic symmetries - %.1f%% complete. "%disp
counter = 0
if ((o['res num'] == curres) and (o['res name'] == curror)
and (o['chain'] == currch)):
processing.append(o)
hold = o
else: #process data and start a new list
if (flag == 1):
changemade = 0
hold = o
tproc = []
tproc.append(o)
curres = o['res num']
curror = o['res name']
currch = o['chain']
symmorganics = a.varpass2(processing)
opcount = []
for i in range(1000):
opcount.append(0)
best = 0
counter = 0
bestpos = 0
for i in symmorganics:
checkcounter = 0
for j in i:
checkcount = 0
for pdb in self.pdbs:
if (pdb == currpdb):
#print '---'
#print "%s%s"%(o['res name'],o['res num'])
checkcount = pdb.compare(j)
opcount[checkcounter] = opcount[
checkcounter] + checkcount
checkcounter += 1
maxpos = 0
mypos = 0
maxcount = 0
for i in opcount:
if (i > maxcount):
maxpos = mypos
maxcount = i
mypos += 1
for i in symmorganics:
optimum.append(i[maxpos])
pcount = 0
for i in processing:
j = optimum[pcount]
if maxcount == 0:
file.write(
str(i.pdb) + " " + i['res name'] + ' ' +
i['atom name'] +
" %d No Change Made\n" % i['res num'])
file.write(
"****WARNING**** THIS ATOM MAKES NO PROTEIN CONTACTS ****WARNING****\n\n"
)
else:
if ((str(j[4]) == "[0, 0, 0]"
and j[3] == "x,y,z")):
if (verbose):
file.write(
str(i.pdb) + " " + i['res name'] +
' ' + i['atom name'] +
" %d No Change Made\n\n" %
i['res num'])
else:
file.write(
str(i.pdb) + " " + i['res name'] + ' ' +
i['atom name'] +
" %d Optimization Results" % i['res num'])
file.write(
"\nOriginal Position: %.3f %.3f %.3f" %
(i.position()[0], i.position()[1],
i.position()[2]))
file.write("\nOriginal Contacts: %d" %
i.howclose())
file.write(
"\nOptimized Position: %.3f %.3f %.3f" %
(j[0], j[1], j[2]))
file.write("\nOptimized Symmetry UC: " +
str(j[4]))
file.write("\nOptimized Operator: " + j[3])
file.write("\nOptimized Contacts: %d\n\n" %
maxcount)
if maxcount > 0:
i.optimum_update(j)
pcount += 1
optimum = []
currpdb = o.pdb
processing = []
processing.append(tproc[0])
else:
flag = 1
optimum = []
processing = []
processing.append(o)
curres = o['res num']
curror = o['res name']
currch = o['chain']
currpdb = o.pdb
changemade = 0
o = hold
symmorganics = a.varpass2(processing)
opcount = []
for i in range(1000):
opcount.append(0)
for i in symmorganics:
checkcounter = 0
for j in i:
checkcount = 0
for pdb in self.pdbs:
if (pdb == currpdb):
checkcount = pdb.compare(j)
opcount[checkcounter] = opcount[checkcounter] + checkcount
checkcounter += 1
maxpos = 0
mypos = 0
maxcount = 0
for i in opcount:
if (i > maxcount):
maxpos = mypos
maxcount = i
mypos += 1
for i in symmorganics:
optimum.append(i[maxpos])
pcount = 0
for i in processing:
j = optimum[pcount]
if maxcount == 0:
file.write(
str(i.pdb) + " " + i['res name'] + ' ' + i['atom name'] +
" %d No Change Made\n" % i['res num'])
file.write(
"****WARNING**** THIS ATOM MAKES NO PROTEIN CONTACTS ****WARNING****\n\n"
)
else:
if ((str(j[4]) == "[0, 0, 0]" and j[3] == "x,y,z")):
if (verbose):
file.write(
str(i.pdb) + " " + i['res name'] + ' ' +
i['atom name'] +
" %d No Change Made\n\n" % i['res num'])
else:
file.write(
str(i.pdb) + " " + i['res name'] + ' ' +
i['atom name'] +
" %d Optimization Results" % i['res num'])
file.write(
"\nOriginal Position: %.3f %.3f %.3f" %
(i.position()[0], i.position()[1], i.position()[2]))
file.write("\nOriginal Contacts: %d" % i.howclose())
file.write("\nOptimized Position: %.3f %.3f %.3f]" %
(j[0], j[1], j[2]))
file.write("\nOptimized Symmetry UC: " + str(j[4]) + ']')
file.write("\nOptimized Operator: " + j[3] + ']')
file.write("\nOptimized Contacts: %d\n\n" % maxcount)
if maxcount > 0:
i.optimum_update(j)
pcount += 1
optimum = []
processing = []
file.close()
def __init__(self, pdb_filenames, root, err=1):
self.pdbs = []
totalnum = 0
for filename in pdb_filenames:
self.pdbs.append(PDB(filename, root + filename.split('/')[-1],watercheck=1))
self.pdbs.sort(key=str)
for i, pdb in enumerate(self.pdbs):
pdb.number = i
pdb.shortname = pdb.filename.split('/')[-1]
totalnum = i
self.waters = []
self.aa = []
self.organics = []
self.wList = []
self.max_x = -1000.2
self.max_y = -1000.3
self.max_z = -1000.4
self.min_x = 1000.2
self.min_y = 1000.3
self.min_z = 1000.4
self.rx = 0
self.ry = 0
self.rz = 0
self.lx = 0
self.ly = 0
self.lz = 0
self.cutoff = 5
shortest_distance = ('', Infinity)
for pdb in self.pdbs:
pdb.create_cell_table()
for atom in pdb:
if(atom['type'] == "ATOM" or atom['type'] == "HETATM"):
if(atom['res name'] in water_names):
self.waters.append(atom)
if(atom['res name'] in protein_names):
self.aa.append(atom)
if(atom['res name'] in organic_names):
self.organics.append(atom)
#Create Water Table
flag = 0
waters = []
#define boundaries
for atom in self.waters:
if(float(atom['x']) > self.max_x):
self.max_x = atom['x']
if(float(atom['y']) > self.max_y):
self.max_y = atom['y']
if(float(atom['z']) > self.max_z):
self.max_z = atom['z']
if(float(atom['x']) < self.min_x):
self.min_x = atom['x']
if(float(atom['y']) < self.min_y):
self.min_y = atom['y']
if(float(atom['z']) < self.min_z):
self.min_z = atom['z']
#define length of system
self.max_x = self.max_x + self.cutoff
self.max_y = self.max_y + self.cutoff
self.max_z = self.max_z + self.cutoff
self.min_x = self.min_x-self.cutoff
self.min_y = self.min_y-self.cutoff
self.min_z = self.min_z-self.cutoff
self.rx = self.max_x-self.min_x
self.ry = self.max_y-self.min_y
self.rz = self.max_z-self.min_z
#define how many cells per direction
self.lx = math.ceil(self.rx / self.cutoff)
self.ly = math.ceil(self.ry / self.cutoff)
self.lz = math.ceil(self.rz / self.cutoff)
#create and populate cell list
numcells = self.lx * self.ly * self.lz
cList = []
for i in xrange(int(numcells)):
cList.append([])
flag = 0
for atom in self.waters:
cx = math.floor((-self.min_x + atom['x']) / self.cutoff)
cy = math.floor((-self.min_y + atom['y']) / self.cutoff)
cz = math.floor((-self.min_z + atom['z']) / self.cutoff)
cID = cx * self.ly * self.lz + cy * self.lz + cz
cList[int(cID)].append(atom)
self.wList = cList
#End Water Table
count = 0
numwater = float(len(self.waters))
numorg = len(self.organics)
debug = 0
if(debug == 0):
#print "Calculating nearby contacts for waters."
for w in self.waters:
count = count + 1
for pdb in self.pdbs:
if (pdb == w.pdb):
w.setclose(pdb.compare(w.position()))
for o in self.organics:
for pdb in self.pdbs:
if (pdb == o.pdb):
o.setclose(pdb.compare(o.position()))
self.root = root + self.stamp
if(not os.path.exists(self.root)):
os.makedirs(self.root)
self.master = Analyzer.Cluster_List()
self.master_org = Analyzer.Ocluster_List()
self.master_path = self.root + 'master.html'
self.orgmaster_path = self.root + 'org.html'
self.err = self.start_err = 1.0
self.orgerr = 1.0
self.centers = []
def __init__(self, pdb_filenames, root, err=1):
self.pdbs = []
totalnum = 0
for filename in pdb_filenames:
self.pdbs.append(
PDB(filename, root + filename.split('/')[-1], watercheck=1))
self.pdbs.sort(key=str)
for i, pdb in enumerate(self.pdbs):
pdb.number = i
pdb.shortname = pdb.filename.split('/')[-1]
totalnum = i
self.waters = []
self.aa = []
self.organics = []
self.wList = []
self.max_x = -1000.2
self.max_y = -1000.3
self.max_z = -1000.4
self.min_x = 1000.2
self.min_y = 1000.3
self.min_z = 1000.4
self.rx = 0
self.ry = 0
self.rz = 0
self.lx = 0
self.ly = 0
self.lz = 0
self.cutoff = 5
shortest_distance = ('', Infinity)
for pdb in self.pdbs:
pdb.create_cell_table()
for atom in pdb:
if (atom['type'] == "ATOM" or atom['type'] == "HETATM"):
if (atom['res name'] in water_names):
self.waters.append(atom)
if (atom['res name'] in protein_names):
self.aa.append(atom)
if (atom['res name'] in organic_names):
self.organics.append(atom)
#Create Water Table
flag = 0
waters = []
#define boundaries
for atom in self.waters:
if (float(atom['x']) > self.max_x):
self.max_x = atom['x']
if (float(atom['y']) > self.max_y):
self.max_y = atom['y']
if (float(atom['z']) > self.max_z):
self.max_z = atom['z']
if (float(atom['x']) < self.min_x):
self.min_x = atom['x']
if (float(atom['y']) < self.min_y):
self.min_y = atom['y']
if (float(atom['z']) < self.min_z):
self.min_z = atom['z']
#define length of system
self.max_x = self.max_x + self.cutoff
self.max_y = self.max_y + self.cutoff
self.max_z = self.max_z + self.cutoff
self.min_x = self.min_x - self.cutoff
self.min_y = self.min_y - self.cutoff
self.min_z = self.min_z - self.cutoff
self.rx = self.max_x - self.min_x
self.ry = self.max_y - self.min_y
self.rz = self.max_z - self.min_z
#define how many cells per direction
self.lx = math.ceil(self.rx / self.cutoff)
self.ly = math.ceil(self.ry / self.cutoff)
self.lz = math.ceil(self.rz / self.cutoff)
#create and populate cell list
numcells = self.lx * self.ly * self.lz
cList = []
for i in xrange(int(numcells)):
cList.append([])
flag = 0
for atom in self.waters:
cx = math.floor((-self.min_x + atom['x']) / self.cutoff)
cy = math.floor((-self.min_y + atom['y']) / self.cutoff)
cz = math.floor((-self.min_z + atom['z']) / self.cutoff)
cID = cx * self.ly * self.lz + cy * self.lz + cz
cList[int(cID)].append(atom)
self.wList = cList
#End Water Table
count = 0
numwater = float(len(self.waters))
numorg = len(self.organics)
debug = 0
if (debug == 0):
#print "Calculating nearby contacts for waters."
for w in self.waters:
count = count + 1
for pdb in self.pdbs:
if (pdb == w.pdb):
w.setclose(pdb.compare(w.position()))
for o in self.organics:
for pdb in self.pdbs:
if (pdb == o.pdb):
o.setclose(pdb.compare(o.position()))
self.root = root + self.stamp
if (not os.path.exists(self.root)):
os.makedirs(self.root)
self.master = Analyzer.Cluster_List()
self.master_org = Analyzer.Ocluster_List()
self.master_path = self.root + 'master.html'
self.orgmaster_path = self.root + 'org.html'
self.err = self.start_err = 1.0
self.orgerr = 1.0
self.centers = []