def angleTertiaryAmine (atomNitrogen, atomCounterIon, listAtomLigand):
"""Calcul for nitrogen and counter ion angles
in: atom nitrogen, atom Counter Ions
out: list of 3 angles"""
matrix = atomNitrogen["connect"]
if len(matrix) < 4:
print "Atom does not 3 bonds !!"
return
else:
carbon1 = retrieveAtom.serial(matrix[1], listAtomLigand)
carbon2 = retrieveAtom.serial(matrix[2], listAtomLigand)
carbon3 = retrieveAtom.serial(matrix[3], listAtomLigand)
distanceNitrogenCounterIon = distanceTwoatoms(atomNitrogen, atomCounterIon)
distanceCarbon1CounterIon = distanceTwoatoms(atomCounterIon, carbon1)
distanceCarbon2CounterIon = distanceTwoatoms(atomCounterIon, carbon2)
distanceCarbon3CounterIon = distanceTwoatoms(atomCounterIon, carbon3)
distanceNitrogenCarbon1 = distanceTwoatoms(atomNitrogen, carbon1)
distanceNitrogenCarbon2 = distanceTwoatoms(atomNitrogen, carbon2)
distanceNitrogenCarbon3 = distanceTwoatoms(atomNitrogen, carbon3)
angle1 = degrees(acos((distanceNitrogenCarbon1 * distanceNitrogenCarbon1 + distanceNitrogenCounterIon * distanceNitrogenCounterIon - distanceCarbon1CounterIon * distanceCarbon1CounterIon) / (2 * distanceNitrogenCarbon1 * distanceNitrogenCounterIon)))
angle2 = degrees(acos((distanceNitrogenCarbon2 * distanceNitrogenCarbon2 + distanceNitrogenCounterIon * distanceNitrogenCounterIon - distanceCarbon2CounterIon * distanceCarbon2CounterIon) / (2 * distanceNitrogenCarbon2 * distanceNitrogenCounterIon)))
angle3 = degrees(acos((distanceNitrogenCarbon3 * distanceNitrogenCarbon3 + distanceNitrogenCounterIon * distanceNitrogenCounterIon - distanceCarbon3CounterIon * distanceCarbon3CounterIon) / (2 * distanceNitrogenCarbon3 * distanceNitrogenCounterIon)))
return [angle1, angle2, angle3]
def retrieveAtomConnected(atom, listAtom):
"""retrieve list atom connected
in: atom, list atoms
out: list atoms connected"""
listAtom = []
atom = retrieveAtom.serial(int(atom), listAtom)
connectMatrix = atom['connect']
for i in connectMatrix:
listAtom.append(retrieveAtom.serial(i, listAtom))
return listAtom
def connectMatrixSerialToConnectMatrixElement(connectMatrixSerial, listAtom):
'''transform Connect matrix with serial
in: connect matrix serial, list atom
out: list -> matrix connect element'''
link = []
for serial in connectMatrixSerial:
try : link.append(retrieveAtom.serial(int(serial), listAtom)["element"])
except : pass
return link
def AngleSecondaryFromLig(atomN, atom_neighbor, l_atom_lig):
"""Calcul for nitrogen and neighbor
in: atom nitrogen, atom neighbor
out: angle between muddle of 2 cabones and N and neigbbor"""
l_connect = atomN["connect"]
if len(l_connect) < 3:
print "Atom does not 2 bonds !!"
return
else:
atomC1 = retrieveAtom.serial(l_connect[1], l_atom_lig)
atomC2 = retrieveAtom.serial(l_connect[2], l_atom_lig)
angle1 = Angle3Atoms (atomC1, atomN, atom_neighbor)
angle2 = Angle3Atoms (atomC2, atomN, atom_neighbor)
return [angle1, angle2]
def appendAtomConnect(atom, listRetrive, atomLigand):
listSerial = []
for atomRetrieve in listRetrive :
listSerial.append(atomRetrieve["serial"])
for serialAtom in atom["connect"] :
if not serialAtom in listSerial :
atom = retrieveAtom.serial(serialAtom, atomLigand)
if atom != 0 :
listRetrive.append(atom)
def coplanar (atom, l_atom_ligand):
"""Calculate the orthogonal distance between nitrogen atom of tertiary amine and plan with 3 carbons connect
in : - atom of nitrogen -> dictionnary
- all atom of ligand -> list of atom dictionnary
out : - distance -> float"""
matrix = atom["connect"]
if len(matrix) < 4:
print "Atom does not 3 bonds !!"
return
else:
point = [float(retrieveAtom.serial(matrix[0], l_atom_ligand)["x"]), float(retrieveAtom.serial(matrix[0], l_atom_ligand)["y"]), float(retrieveAtom.serial(matrix[0], l_atom_ligand)["z"])]
d = symbols("d")
atom1 = retrieveAtom.serial(matrix[1], l_atom_ligand)
atom2 = retrieveAtom.serial(matrix[2], l_atom_ligand)
atom3 = retrieveAtom.serial(matrix[3], l_atom_ligand)
point1 = [float(atom1["x"]), float(atom1["y"]), float(atom1["z"])]
point2 = [float(atom2["x"]), float(atom2["y"]), float(atom2["z"])]
point3 = [float(atom3["x"]), float(atom3["y"]), float(atom3["z"])]
v1 = [point3[0] - point1[0], point3[1] - point1[1], point3[2] - point1[2]]
v2 = [point2[0] - point1[0], point2[1] - point1[1], point2[2] - point1[2]]
a = v1[1] * v2[2] - v1[2] * v2[1]
b = v1[2] * v2[0] - v1[0] * v2[2]
c = v1[0] * v2[1] - v1[1] * v2[0]
d = float(solve(a * point1[0] + b * point1[1] + c * point1[2] - d, d)[0])
nominator = abs(a * point[0] + b * point[1] + c * point[2] - d)
denominator = (a ** 2 + b ** 2 + c ** 2) ** (1 / 2)
distance = nominator / denominator
return distance
def cycleOnlyTestCarbon(serialFirst, serialTest, serialPrevious, atomLigand, test, flagNitrogen) :
atomTest = retrieveAtom.serial(serialTest, atomLigand)
if serialFirst == atomTest["serial"] and test == 0:
return 1
if atomTest == 0 :
return 0
if atomTest ["element"] != "C" and test != 0 and serialFirst != serialTest:
return 0
for conect in atomTest["connect"] :
atomSecond = retrieveAtom.serial(conect , atomLigand)
if atomSecond == 0 :
return 0
elif atomSecond["element"] == "N" :
flagNitrogen = flagNitrogen + 1
if flagNitrogen > 3 :
return 0
else :
continue
elif atomSecond["element"] != "C" :
return 0
if test == 0 :
return 0
for serialConnect in atomTest["connect"][1:] :
if serialConnect != serialPrevious :
if cycleOnlyTestCarbon(serialFirst, serialConnect, serialTest, atomLigand, test - 1, flagNitrogen) == 1 :
return 1
return 0
def controlLenCNBond (listAtomLigand, listDistance):
"""For each CN bond in list atom ligand, retrieve distance between C and N
in: list atom ligand, list distance retrieve
out: append in list ligand the distance"""
for atom in listAtomLigand:
if atom["element"] == "N":
matrixConnect = atom["connect"]
for serial in matrixConnect:
atomConect = retrieveAtom.serial(serial, listAtomLigand)
if atomConect != 0 and atomConect["element"] == "C":
distance = calcul.distanceTwoatoms(atom, atomConect)
listDistance.append(distance)
def cycle3(serialFirst, serialTest, serialPrevious, atomLigand, test) :
atomTest = retrieveAtom.serial(serialTest, atomLigand)
if atomTest == 0 :
return 0
if serialFirst in atomTest["connect"] and serialFirst != serialTest and serialFirst != serialPrevious :
return 1
if test == 0 :
return 0
for serialConnect in atomTest["connect"][1:] :
if serialConnect != serialPrevious :
if cycle3(serialFirst, serialConnect, serialTest, atomLigand, test - 1) == 1 :
return 1
return 0
def anglePrimaryAmine(atomNitrogen, atomCounterIon, atomLigands):
"""Calcul for nitrogen and counter ion angles
in: atom nitrogen, atom Counter Ions
out: list of 2 angles"""
matrix = atomNitrogen["connect"]
if len(matrix) < 2:
print "Atom does not 1 bonds !!"
return
else:
carbon1 = retrieveAtom.serial(matrix[1], atomLigands)
distanceNitrogenCounterIon = distanceTwoatoms(atomNitrogen, atomCounterIon)
distanceCarbon1CounterIon = distanceTwoatoms(atomCounterIon, carbon1)
distanceNitrogenCarbon1 = distanceTwoatoms(atomNitrogen, carbon1)
angle1 = degrees(acos((distanceNitrogenCarbon1 * distanceNitrogenCarbon1 + distanceNitrogenCounterIon * distanceNitrogenCounterIon - distanceCarbon1CounterIon * distanceCarbon1CounterIon) / (2 * distanceNitrogenCarbon1 * distanceNitrogenCounterIon)))
return [angle1]
atomLigand = loadFile.ligandInPDBConnectMatrixLigand(pdb, ligand)
writePDBfile.globalStruct(ligand + "_" + pdb + ".pdb", atomLigand)
nbAtom = len(atomLigand)
# print atomLigand
searchPDB.cycleGlobal(atomLigand)
# print atomLigand
listResult = []
for atom in atomLigand :
if atom["element"] == "N" or atom["element"] == "O" or atom["element"] == "C": # impact point
if atom["cycle"] == 1 :
cycleRetrieve = retrieveAtom.cycle(atom, atomLigand)
listResult.append(cycleRetrieve)
continue
for serialAtom in atom["connect"] :
atomRetrieve = retrieveAtom.serial(serialAtom, atomLigand)
if atomRetrieve == 0 :
continue
if atomRetrieve["cycle"] == 1 :
cycleRetrieve = retrieveAtom.cycle(atom, atomLigand)
listResult.append(cycleRetrieve)
continue
tool.checkListResult(listResult)
nbStruct = 1
for element in listResult :
writePDBfile.globalStruct(ligand + "_" + pdb + "_" + str(nbStruct) + ".pdb", element)
nbStruct = nbStruct + 1
j = j + 1