def __init__(self, trackGroup, ringModel, posScale, colorIndices):
NodePath.__init__(self)
self.assign(hidden.attachNewNode(\
base.localAvatar.uniqueName('ring-group')))
self.__period = trackGroup.period
self.__reverseFlag = trackGroup.reverseFlag
self.__tOffset = trackGroup.tOffset
self.__numRings = len(trackGroup.tracks)
self.__rings = []
self.__ringModels = []
for i in range(0,self.__numRings):
track = trackGroup.tracks[i]
tOffset = trackGroup.trackTOffsets[i]
ring = Ring.Ring(track,
tOffset,
posScale)
ring.reparentTo(self)
model = ringModel.copyTo(ring)
model.setColor(RingGameGlobals.ringColors[colorIndices[i]][1])
self.__rings.append(ring)
self.__ringModels.append(model)
def assign_ring_positions(self):
for ring in self.rings:
c1 = c2 = c3 = c4 = c5 = o5 = False
for atom in ring:
if not self.isO5(atom):
self.atoms[atom].set_axial(self.is_axial(atom))
if not c1 and self.isC1(atom):
self.atoms[atom].set_sugar_position("C1")
c1 = self.atoms[atom]
elif not c2 and self.isC2(atom):
self.atoms[atom].set_sugar_position("C2")
c2 = self.atoms[atom]
elif not c3 and self.isC3(atom):
self.atoms[atom].set_sugar_position("C3")
c3 = self.atoms[atom]
elif not c4 and self.isC4(atom):
self.atoms[atom].set_sugar_position("C4")
c4 = self.atoms[atom]
elif not c5 and self.isC5(atom):
self.atoms[atom].set_sugar_position("C5")
c5 = self.atoms[atom]
elif not o5 and self.isO5(atom):
self.atoms[atom].set_sugar_position("O5")
o5 = self.atoms[atom]
if c1 and c2 and c3 and c4 and c5 and o5:
self.Rings[self.ringHash(ring)] = Ring(c1, c2, c3, c4, c5, o5,
self.atoms)
else:
raise Exception
def test():
try:
dis = distance.distance()
print('Distance: %.2f cm' % dis)
if dis < LIMIT:
Ring.Ring()
time.sleep(0.2)
except KeyboardInterrupt:
print('User press CTRL+C, exit')
sys.exit()
def main():
message = "salut"
message2 = "toast"
message3 = "salut"
message4 = "bidon"
issue = "2"
userNumber = 3
id = 1
id2 = 2
G, g = buildG()
ring, userArray = Ring.myCreateRing(userNumber, g, G, q)
signature = Sign(message, issue, ring.pKeys, userArray[id], G, g,
userArray)
signature2 = Sign(message2, issue, ring.pKeys, userArray[id2], G, g,
userArray)
signature3 = Sign(message3, issue, ring.pKeys, userArray[id], G, g,
userArray)
signature4 = Sign(message4, issue, ring.pKeys, userArray[id], G, g,
userArray)
#TESTS
print("Verif of message and his signature : ")
print(Verify(issue, ring.pKeys, message, signature, G, g, userArray))
print("\nVerif of message2 and another signature : ")
print(Verify(issue, ring.pKeys, message2, signature, G, g, userArray))
print("\nVerif of message2 and his signature : ")
print(Verify(issue, ring.pKeys, message2, signature2, G, g, userArray))
print("\nTrace of different message by different people :")
print(
Trace(issue, ring.pKeys, g, G, message, signature, message2,
signature2))
print("\nTrace of same message by the same person :")
print(
Trace(issue, ring.pKeys, g, G, message, signature, message3,
signature3))
print("\nTrace of different message by the same person :")
print(
Trace(issue, ring.pKeys, g, G, message, signature, message4,
signature4))
import Ring
from itertools import permutations, combinations
n = 5
carrier = list(range(0, n))
print('carrier: ', carrier)
list_of_permutations = list(permutations(range(0, n)))
# all possible rows of the multiplication table (without the zero and one columns)
list_of_permutations1 = list(permutations(range(0, n), n - 2))
# choose n-1 distinct rows (it doesnt harm to order them with combinations instead of permutations)
for table_plus in combinations(list_of_permutations, n):
def plus(x, y):
return table_plus[x][y]
Ring.__init__(carrier, 0, 1, plus,
plus) # the 2nd plus is redundant for now
# any structure generated so far satisfies Ring.has_minus() because we use permutations
if Ring.has_zero() and Ring.plus_is_associative():
# choose n-2 distinct rows (the first two rows are determined by the properties of zero and one)
for table_mult in permutations(list_of_permutations1, n - 2):
def mult(x, y):
if x == 0:
return 0
elif y == 0:
return 0
elif x == 1:
return y
elif y == 1:
return x
else:
def Set_Up_FF(self, run_orca=True, local=True):
if run_orca:
print "Setting up Orca input script"
# Write Orca Input File
File_Name = self.Name + ".inp"
File = open(File_Name, 'w')
File.write(
'! RKS B3LYP 6-31+G** NormalSCF Opt NOSOSCF CHELPG PAL8\n\n')
File.write('*xyz 0 1\n')
for Atom_Obj in self.Atom_List:
File.write('%s %.5f %.5f %.5f\n' %
(Atom_Obj.Element, Atom_Obj.Position[0],
Atom_Obj.Position[1], Atom_Obj.Position[2]))
File.write('*')
File.close()
Finished = False
File_Out = self.Name + ".out"
if local:
#Run subprocess on local machine
os.system('mkdir Orca')
os.system('mv %s ./Orca' % File_Name)
os.chdir('./Orca')
File_Out = self.Name + ".out"
try:
File = open(File_Out, 'r')
except:
os.system(
'/usr/local/share/orca_3_0_0_macosx_openmpi165/orca %s > %s'
% (File_Name, File_Out)) # Run Orca Job
else:
print "Running Orca Geometry Optimization on Comet"
cmd = "mkdir " + Configure.Comet_Path % self.Name
subprocess.call(["ssh", Configure.Comet_Login, cmd])
subtemp = Configure.Template_Path + "sub_orca_temp"
submit = "submit_orca"
Path = Configure.Comet_Path % self.Name
# Write submit script
with open(subtemp) as f:
template = f.read()
s = template.format(Comet_Path=Path,
Orca_Path=Configure.Orca_Path,
name=self.Name)
with open(submit, "w") as f:
f.write(s)
# Copy Files over to Comet
os.system(Configure.c2c % (submit, self.Name))
os.system(Configure.c2c % (File_Name, self.Name))
# Run job
os.system(Configure.c2l % (self.Name, File_Out))
try:
File = open(File_Out, 'r')
except:
subprocess.call([
"ssh", Configure.Comet_Login,
Configure.SBATCH % (self.Name, submit)
])
i = 0
while not Finished:
os.system(Configure.c2l % (self.Name, File_Out))
try:
File = open(File_Out, 'r')
File_Lines = File.readlines()
print File_Lines[-1]
if File_Lines[-1].split(
' ')[0] == "TOTAL" or self.UnConverged:
Finished = True
else:
print "Not Finished"
i += 10
print "Sleeping process", i, "Minutes"
time.sleep(600)
except:
print "Sleeping process", i, "miniutes"
time.sleep(600)
i += 10
else:
os.chdir('./Orca')
File_Out = self.Name + ".out"
# Extract info from Orca output file
Orca_File = open(File_Out, 'r')
File_Lines = Orca_File.readlines()
print "Extracting Redundant Coordinates..."
for i in range(len(File_Lines)):
Line = File_Lines[i].strip('\n').split()
#print Line
Found = False
try:
if Line[0] == "Redundant" and self.UnConverged:
Redundant = True
j = i + 6
k = 0
while Redundant:
R_Line = File_Lines[j]
R_Line = R_Line.split()
print R_Line
try:
if int(R_Line[0].strip('.')) >= 1:
j = j + 1
Type = R_Line[1].split('(')[0]
k += 1
# Extract Bonds
if Type == "B":
Master_ID = int(R_Line[2].split(',')[0])
Slave_ID = int(R_Line[3].split(')')[0])
req = float(R_Line[-1])
self.Atom_List[Master_ID].Bond_List.append(
self.Atom_List[Slave_ID])
self.Atom_List[Slave_ID].Bond_List.append(
self.Atom_List[Master_ID])
self.Bond_List.append(
Bond.Bond(self.Atom_List[Master_ID],
self.Atom_List[Slave_ID],
req))
# Extract Angles
if Type == "A":
Master_ID = int(R_Line[3].split(',')[0])
Slave1_ID = int(R_Line[2].split(',')[0])
Slave2_ID = int(R_Line[4].split(')')[0])
Angle_Eq = float(R_Line[-1])
self.Angle_List.append(
Angle.Angle(self.Atom_List[Master_ID],
self.Atom_List[Slave1_ID],
self.Atom_List[Slave2_ID],
Angle_Eq))
if Type == "D":
Master1_ID = int(R_Line[3].split(',')[0])
Master2_ID = int(R_Line[4].split(',')[0])
Slave1_ID = int(R_Line[2].split(',')[0])
Slave2_ID = int(R_Line[5].split(')')[0])
Dihedral_Eq = float(R_Line[-1])
self.Dihedral_List.append(
Dihedral.Dihedral(
self.Atom_List[Master1_ID],
self.Atom_List[Master2_ID],
self.Atom_List[Slave1_ID],
self.Atom_List[Slave2_ID],
Dihedral_Eq))
except:
Redundant = False
Found = True
print k
if Found:
break
elif Line[0] == "Redundant" and (
File_Lines[i + 2].strip('\n').split()[1]
== "Optimized"):
print "Found redundant internal coordinates"
Redundant = True
j = i + 7
while Redundant:
R_Line = File_Lines[j]
R_Line = R_Line.split()
try:
if int(R_Line[0].strip('.')) >= 1:
j = j + 1
Type = R_Line[1].split('(')[0]
# Extract Bonds
if Type == "B":
Master_ID = int(R_Line[2].split(',')[0])
Slave_ID = int(R_Line[3].split(')')[0])
req = float(R_Line[-1])
self.Atom_List[Master_ID].Bond_List.append(
self.Atom_List[Slave_ID])
self.Atom_List[Slave_ID].Bond_List.append(
self.Atom_List[Master_ID])
self.Bond_List.append(
Bond.Bond(self.Atom_List[Master_ID],
self.Atom_List[Slave_ID],
req))
# Extract Angles
if Type == "A":
Master_ID = int(R_Line[3].split(',')[0])
Slave1_ID = int(R_Line[2].split(',')[0])
Slave2_ID = int(R_Line[4].split(')')[0])
Angle_Eq = float(R_Line[-1])
self.Angle_List.append(
Angle.Angle(self.Atom_List[Master_ID],
self.Atom_List[Slave1_ID],
self.Atom_List[Slave2_ID],
Angle_Eq))
if Type == "D":
Master1_ID = int(R_Line[3].split(',')[0])
Master2_ID = int(R_Line[4].split(',')[0])
Slave1_ID = int(R_Line[2].split(',')[0])
Slave2_ID = int(R_Line[5].split(')')[0])
Dihedral_Eq = float(R_Line[-1])
self.Dihedral_List.append(
Dihedral.Dihedral(
self.Atom_List[Master1_ID],
self.Atom_List[Master2_ID],
self.Atom_List[Slave1_ID],
self.Atom_List[Slave2_ID],
Dihedral_Eq))
except:
Redundant = False
if Line[0] == "CHELPG" and len(
Line) == 2 and not self.UnConverged:
for j in range(self.N):
Chelp_Line = File_Lines[i + 2 + j].split()
index = int(Chelp_Line[0])
charge = float(Chelp_Line[3])
self.Atom_List[index].Charge = charge
if Line[0] == "CARTESIAN" and Line[2] == "(ANGSTROEM)":
for j in range(self.N):
XYZ_Line = File_Lines[i + 2 + j].split()
Position_Temp = np.array([
float(XYZ_Line[1]),
float(XYZ_Line[2]),
float(XYZ_Line[3])
],
dtype=float)
self.Atom_List[j].Position = Position_Temp
except:
continue
print "Redundant Internal Coordinates and ChelpG partial charges Extracted"
print "Bond_List = ", len(self.Bond_List)
if not run_orca:
os.chdir('..')
if local:
os.chdir('..')
print "Optimized XYZ Coordinates:\n"
for Atom_Obj in self.Atom_List:
# Finds OPLS Types and Classes
print Atom_Obj.Atom_ID, Atom_Obj.Element, Atom_Obj.Position, sorted(
[Atomobj.Element for Atomobj in Atom_Obj.Bond_List])
print "----------------------------------"
# Find all the ring units in the molecule and add them to the ring list
self.Ring_List = Ring.create_rings(self.Atom_List)
return
def __init__(self, master, ser=""):
#create base path for storing files, temperature curves, etc:
if not os.path.exists(self.basePath):
#os.chdir('/home/pi/Desktop/')
os.mkdir(self.basePath)
os.chown(self.basePath, 1000, 1000)
#create dictionary to store all classes that will be used
usedClasses = dict()
##create the mainframe
frame = tk.Frame()
frame.grid(row=0, column=0, rowspan=1, columnspan=1)
row1Frame = tk.Frame(master=frame, bd=2, relief="ridge")
row2Frame = tk.Frame(master=frame, bd=2, relief="ridge")
row3Frame = tk.Frame(master=frame, bd=2, relief="ridge")
row4Frame = tk.Frame(master=frame, bd=2, relief="ridge")
if serialAvail == True:
# for Arduino Uno from RPi
#self.ser = serial.Serial('/dev/ttyACM0', 115200)
# for Arduino Nano from RPi
self.ser = serial.Serial('/dev/ttyUSB0', 9600)
# ser = serial.Serial('/dev/ttyUSB0', 4800,timeout=0.05)
##show the pieces of the GUI
##depending on which flags are on (see above):
###CAMERA###
if self.cameraFlag == 1:
import Camera
self.frameCam = tk.Frame(master=row2Frame, bd=3)
self.frameCam.pack(side="top")
self.Camera = Camera.Camera(parent=self.frameCam,
label="CAMERA",
basePath=self.basePath)
usedClasses["camera"] = self.Camera
else:
usedClasses["camera"] = 0
###LED1###
if self.led1Flag == 1:
import LED
self.frameLed1 = tk.Frame(row1Frame, bd=3)
self.frameLed1.grid(row=0, column=0, sticky="NW")
self.LED1 = LED.LED(parent=self.frameLed1, label="LED 1",
onAdd=self.led1OnAdd, offAdd=self.led1OffAdd,
zapDurAdd=self.led1ZapDurAdd, ser=self.ser,
#prot=self.prot,
#protFrame=self.frameProt,
)
led1Off = self.led1OffAdd
self.ser.write(led1Off.encode('utf-8'))
# usedClasses["led1"] = self.LED1
usedClasses["led1"] = 1
#print (self.LED1)
else:
usedClasses["led1"] = 0
###LED2###
if self.led2Flag == 1:
import LED
self.frameLed2 = tk.Frame(row1Frame, bd=3)
self.frameLed2.grid(row=0, column=1, sticky="NW")
self.LED2 = LED.LED(parent=self.frameLed2, label="LED 2",
onAdd=self.led2OnAdd, offAdd=self.led2OffAdd,
zapDurAdd=self.led2ZapDurAdd, ser=self.ser,
#prot=self.prot, protFrame=self.frameProt,
)
led2Off = self.led2OffAdd
self.ser.write(led2Off.encode('utf-8'))
# usedClasses["led2"] = self.LED2
usedClasses["led2"] = 1
else:
usedClasses["led2"] = 0
###MATRIX###
if self.matrixFlag == 1:
import Matrix
self.frameMatrix = tk.Frame(row1Frame, bd=3)
self.frameMatrix.grid(row=0, column=2, sticky="W",)
self.Matrix = Matrix.Matrix(parent=self.frameMatrix, label="MATRIX",
pat3Add=self.matPat3Add,pat4Add=self.matPat4Add, offAdd=self.matOffAdd,
pat1Add=self.matPat1Add, pat2Add=self.matPat2Add,
brightAdd=self.matBrightAdd,
ser=self.ser
)
matOff = self.matOffAdd
self.ser.write(matOff.encode('utf-8'))
usedClasses["matrix"] = 1#self.Matrix
else:
usedClasses["matrix"] = 0
###RING###
if self.ringFlag == 1:
import Ring
self.frameRing = tk.Frame(row1Frame, bd=3)
self.frameRing.grid(row=1, column=0, sticky="NW",
columnspan=3, rowspan=1)
self.Ring = Ring.Ring(parent=self.frameRing, label="RING",
ringOnAdd=self.ringOnAdd,
ringOffAdd=self.ringOffAdd,
ringZapAdd=self.ringZapAdd,
redAdd=self.ringRedAdd,
greenAdd=self.ringGreenAdd,
blueAdd=self.ringBlueAdd,
allAdd=self.ringAllAdd,
rotAdd=self.ringRotAdd,
ser=self.ser)
ringOff=self.ringOffAdd
self.ser.write(ringOff.encode('utf-8'))
usedClasses["ring"] = 1#self.Ring
else:
usedClasses["ring"] = 0
###PELTIER###
if self.peltierFlag == 1:
import Peltier
self.framePelt = tk.Frame(row4Frame, bd=3)
self.framePelt.pack(side="left")
self.Peltier = Peltier.Peltier(parent=self.framePelt,
label="PELTIER",
onAdd=self.peltOnAdd,
offAdd=self.peltOffAdd,
tempAdd=self.peltTempAdd,
basePath=self.basePath,
ser=self.ser)
peltOff = self.peltOffAdd
self.ser.write(peltOff.encode('utf-8'))
usedClasses["peltier"] = 1#self.Peltier
else:
usedClasses["peltier"] = 0
###Auto Focus###
if self.autofocusFlag == 1:
import AutoFocus
self.frameAuto = tk.Frame(row4Frame, bd=3)
self.frameAuto.pack(side="left")
self.AutoFocus = AutoFocus.AutoFocus(parent=self.frameAuto,
label="Focus",
velAdd=self.autoFocusAdd,
ser=self.ser)
servoOff=str(self.autoFocusAdd)+"*"+ str(0)+"*"
self.ser.write(servoOff.encode('utf-8'))
###Protocol###
if self.protocolFlag == 1:
import Protocol
self.frameProt = tk.Frame(master=row3Frame,
bd=3,
relief="ridge")
self.frameProt.pack(side="top")
self.Protocol = Protocol.Protocol(parent = self.frameProt,
usedClasses=usedClasses,
basePath = self.basePath+"/protocol/",
label="Protocols",ser=self.ser,
timingAdd=self.timeAdd)
# print(self.timeAdd)
#self.prot = True
#self.protocol = Protocol(parent=self.frameProt, ser=self.ser)
else:
self.frameProt = ""
self.prot = False
##mock up###
if self.mockupFlag == 1:
import Mock_up
self.frameMock = tk.Frame(row4Frame, bd=3)
self.frameMock.pack(side="left")
self.Mockup= Mock_up.Mock_up(parent=self.frameMock,
label="mock_up",
ser=self.ser)
###QUIT###
if self.quitFlag == 1:
self.frameQuit = tk.Frame(master=row4Frame)
self.frameQuit.pack(side="right")
#self.frameQuit.grid(row=5, column=2, sticky="NW")
self.quitAPP(parent=self.frameQuit)
#draw all frames on screen
row4Frame.grid(row=5, column=0, sticky="NWE", columnspan=1)
row1Frame.grid(row=1, column=0, sticky="NWE", columnspan=1)
row3Frame.grid(row=1, column=2, sticky="NWE")
row2Frame.grid(row=0, column=0, sticky="NWE", columnspan=1)
# Max length genome for any individual in intial population
maxInitGenomeLen = 50
# Max length gemone for any individual at any time.
maxLenGenome = 50
# Maximum number of generation to evolve the population over
maxGenerations = 1000
# Print Genomes?
debugGenomes = True
numDebugGenomes = 5
# Initialize the population...
print "Initializing the population"
population = []
for i in range(popSize):
# Add the individual to the population and their starting fitness of zero. Form of [fitness, genome]
population.append([0, Ring.Ring([random.choice(['C','D'])] + \
[RandomBase() for i in range(random.randint(0,maxInitGenomeLen))])]) # Sets the rest of the player.
print "Beginning Evolution!"
# Evolve until the halt criteria is met.
for j in range(maxGenerations):
# Reset fitness scores for this round
for individual in population:
individual[0] = 0.0
# Mutate some survivors
for individual in population:
for base in range(len(individual[1])):
if random.random() < mutationChance:
individual[1][base] = RandomBase()
def Set_Up_FF(self, run_orca=True, local= True):
if run_orca:
print "Setting up Orca input script"
# Write Orca Input File
File_Name = self.Name + ".inp"
File = open(File_Name, 'w')
File.write('! RKS B3LYP 6-31+G** NormalSCF Opt NOSOSCF CHELPG PAL8\n\n')
File.write('*xyz 0 1\n')
for Atom_Obj in self.Atom_List:
File.write('%s %.5f %.5f %.5f\n' % ( Atom_Obj.Element, Atom_Obj.Position[0], Atom_Obj.Position[1],Atom_Obj.Position[2]))
File.write('*')
File.close()
Finished = False
File_Out = self.Name + ".out"
if local:
#Run subprocess on local machine
os.system('mkdir Orca')
os.system('mv %s ./Orca' % File_Name)
os.chdir('./Orca')
File_Out = self.Name + ".out"
try:
File = open(File_Out,'r')
except:
os.system('/usr/local/share/orca_3_0_0_macosx_openmpi165/orca %s > %s' %(File_Name, File_Out)) # Run Orca Job
else:
print "Running Orca Geometry Optimization on Comet"
cmd = "mkdir " + Configure.Comet_Path % self.Name
subprocess.call(["ssh", Configure.Comet_Login, cmd])
subtemp = Configure.Template_Path + "sub_orca_temp"
submit = "submit_orca"
Path = Configure.Comet_Path % self.Name
# Write submit script
with open(subtemp) as f:
template = f.read()
s = template.format(Comet_Path=Path, Orca_Path = Configure.Orca_Path, name = self.Name )
with open(submit ,"w") as f:
f.write(s)
# Copy Files over to Comet
os.system( Configure.c2c % (submit, self.Name))
os.system( Configure.c2c % (File_Name, self.Name))
# Run job
os.system( Configure.c2l % (self.Name, File_Out))
try:
File = open(File_Out,'r')
except:
subprocess.call(["ssh",Configure.Comet_Login, Configure.SBATCH % (self.Name, submit)])
i = 0
while not Finished:
os.system( Configure.c2l % (self.Name, File_Out))
try:
File = open(File_Out,'r')
File_Lines = File.readlines()
print File_Lines[-1]
if File_Lines[-1].split(' ')[0] == "TOTAL" or self.UnConverged:
Finished = True
else:
print "Not Finished"
i += 10
print "Sleeping process", i, "Minutes"
time.sleep(600)
except:
print "Sleeping process", i, "miniutes"
time.sleep(600)
i += 10
else:
os.chdir('./Orca')
File_Out = self.Name + ".out"
# Extract info from Orca output file
Orca_File = open(File_Out, 'r')
File_Lines = Orca_File.readlines()
print "Extracting Redundant Coordinates..."
for i in range(len(File_Lines)):
Line = File_Lines[i].strip('\n').split()
#print Line
Found = False
try:
if Line[0] == "Redundant" and self.UnConverged:
Redundant = True
j = i + 6
k = 0
while Redundant:
R_Line = File_Lines[j]
R_Line = R_Line.split()
print R_Line
try:
if int(R_Line[0].strip('.')) >= 1:
j = j + 1
Type = R_Line[1].split('(')[0]
k += 1
# Extract Bonds
if Type == "B":
Master_ID = int(R_Line[2].split(',')[0])
Slave_ID = int(R_Line[3].split(')')[0])
req = float(R_Line[-1])
self.Atom_List[Master_ID].Bond_List.append(self.Atom_List[Slave_ID])
self.Atom_List[Slave_ID].Bond_List.append(self.Atom_List[Master_ID])
self.Bond_List.append( Bond.Bond(self.Atom_List[Master_ID], self.Atom_List[Slave_ID], req))
# Extract Angles
if Type == "A":
Master_ID = int(R_Line[3].split(',')[0])
Slave1_ID = int(R_Line[2].split(',')[0])
Slave2_ID = int(R_Line[4].split(')')[0])
Angle_Eq = float(R_Line[-1])
self.Angle_List.append( Angle.Angle(self.Atom_List[Master_ID], self.Atom_List[Slave1_ID], self.Atom_List[Slave2_ID], Angle_Eq))
if Type == "D":
Master1_ID = int(R_Line[3].split(',')[0])
Master2_ID = int(R_Line[4].split(',')[0])
Slave1_ID = int(R_Line[2].split(',')[0])
Slave2_ID = int(R_Line[5].split(')')[0])
Dihedral_Eq = float(R_Line[-1])
self.Dihedral_List.append(Dihedral.Dihedral(self.Atom_List[Master1_ID],self.Atom_List[Master2_ID], self.Atom_List[Slave1_ID], self.Atom_List[Slave2_ID], Dihedral_Eq))
except:
Redundant = False
Found = True
print k
if Found:
break
elif Line[0] == "Redundant" and (File_Lines[i+2].strip('\n').split()[1] == "Optimized"):
print "Found redundant internal coordinates"
Redundant = True
j = i + 7
while Redundant:
R_Line = File_Lines[j]
R_Line = R_Line.split()
try:
if int(R_Line[0].strip('.')) >= 1:
j = j + 1
Type = R_Line[1].split('(')[0]
# Extract Bonds
if Type == "B":
Master_ID = int(R_Line[2].split(',')[0])
Slave_ID = int(R_Line[3].split(')')[0])
req = float(R_Line[-1])
self.Atom_List[Master_ID].Bond_List.append(self.Atom_List[Slave_ID])
self.Atom_List[Slave_ID].Bond_List.append(self.Atom_List[Master_ID])
self.Bond_List.append( Bond.Bond(self.Atom_List[Master_ID], self.Atom_List[Slave_ID], req))
# Extract Angles
if Type == "A":
Master_ID = int(R_Line[3].split(',')[0])
Slave1_ID = int(R_Line[2].split(',')[0])
Slave2_ID = int(R_Line[4].split(')')[0])
Angle_Eq = float(R_Line[-1])
self.Angle_List.append( Angle.Angle(self.Atom_List[Master_ID], self.Atom_List[Slave1_ID], self.Atom_List[Slave2_ID], Angle_Eq))
if Type == "D":
Master1_ID = int(R_Line[3].split(',')[0])
Master2_ID = int(R_Line[4].split(',')[0])
Slave1_ID = int(R_Line[2].split(',')[0])
Slave2_ID = int(R_Line[5].split(')')[0])
Dihedral_Eq = float(R_Line[-1])
self.Dihedral_List.append(Dihedral.Dihedral(self.Atom_List[Master1_ID],self.Atom_List[Master2_ID], self.Atom_List[Slave1_ID], self.Atom_List[Slave2_ID], Dihedral_Eq))
except:
Redundant = False
if Line[0] == "CHELPG" and len(Line) == 2 and not self.UnConverged:
for j in range(self.N):
Chelp_Line = File_Lines[i+2+j].split()
index = int(Chelp_Line[0])
charge = float(Chelp_Line[3])
self.Atom_List[index].Charge = charge
if Line[0] == "CARTESIAN" and Line[2] == "(ANGSTROEM)":
for j in range(self.N):
XYZ_Line = File_Lines[i+2+j].split()
Position_Temp = np.array( [float(XYZ_Line[1]) ,float(XYZ_Line[2]) ,float(XYZ_Line[3])], dtype = float)
self.Atom_List[j].Position = Position_Temp
except:
continue
print "Redundant Internal Coordinates and ChelpG partial charges Extracted"
print "Bond_List = ", len(self.Bond_List)
if not run_orca:
os.chdir('..')
if local:
os.chdir('..')
print "Optimized XYZ Coordinates:\n"
for Atom_Obj in self.Atom_List:
# Finds OPLS Types and Classes
print Atom_Obj.Atom_ID, Atom_Obj.Element, Atom_Obj.Position, sorted([ Atomobj.Element for Atomobj in Atom_Obj.Bond_List ])
print "----------------------------------"
# Find all the ring units in the molecule and add them to the ring list
self.Ring_List = Ring.create_rings(self.Atom_List)
return
color="b",
linestyle='None',
ms=10.0)
ContourPlt.plot(KD1,
KD2,
marker="o",
color="cyan",
linestyle='None',
ms=10.0)
plt.draw()
if ShowRingCurve:
import Ring as RingData
Ring = RingData.Ring3()
PlotA0 = "MaxFrac"
def UpdateAxes():
global KD1, KD2
if ShowRingCurve:
global Ring
RingKD = np.sqrt(KD1 * KD2)
Ring.SetKD(RingKD)
Ring.SetDeg(Deg)
RingConc = A0Range[A0Target]
Ring.SetConc0(RingConc)