def angleGuanidium(central_atom, atom_check, l_atom_lig) :
l_N_temp = []
l_atom_connect_central, l_atom_element = retrieveAtom.atomConnect(l_atom_lig, central_atom["serial"])
for atom_N in l_atom_connect_central[1:] :
l_atom_connect_N, l_element_N = retrieveAtom.atomConnect(l_atom_lig, atom_N["serial"])
if l_element_N == ["N", "C"] :
if not l_atom_connect_N[0] in l_N_temp :
l_N_temp.append (deepcopy(l_atom_connect_N[0]))
if len(l_N_temp) == 2 :
at_considered = CenterPoint(l_N_temp[0], l_N_temp[-1])
elif len(l_N_temp) > 2 :
for N_temp in l_N_temp :
if distanceTwoatoms(central_atom, N_temp) > 3.0 :
del N_temp
if len(l_N_temp) == 2 :
at_considered = CenterPoint(l_N_temp[0], l_N_temp[-1])
else :
return "ERROR"
return [angleVector(central_atom, at_considered, atom_check)]
def imidazole(l_atom2, l_atom_lig):
"""search imidazole global
in: list atom connected of nitrogen, list atom ligand
out: boolean"""
connect1 = toolSubstructure.matrixElement(l_atom2)
# print connect1
# append first atom
if connect1 == ["N", "C", "C"]:
l_atom3, conect2 = retrieveAtom.atomConnect(l_atom_lig, l_atom2[1]["serial"])
l_atom32, conect22 = retrieveAtom.atomConnect(l_atom_lig, l_atom2[2]["serial"])
# sort list to reduce if condition
conect2.sort ()
conect22.sort ()
if conect2 == ["C", "C", "N", "N"] or conect2 == ["C", "N", "N"]:
l_serial_check = [l_atom2[0]["serial"], l_atom3[0]["serial"]]
if imidazoleATOM3(l_atom3, l_serial_check, l_atom_lig)[0] == 1:
# print "l344"
return [1, l_serial_check]
elif conect22 == ["C", "C", "N", "N"] or conect22 == ["C", "N", "N"]:
l_serial_check = [l_atom2[0]["serial"], l_atom32[0]["serial"]]
if imidazoleATOM3(l_atom32, l_serial_check, l_atom_lig)[0] == 1:
# print "l350"
return [1, l_serial_check]
return [0, []]
def angleAcidCarboxylic(central_atom, atom_check, l_atom_lig) :
l_atom_connect, matrix_connect = retrieveAtom.atomConnect(l_atom_lig, central_atom["serial"])
l_O_temp = []
for atom_connect in l_atom_connect[1:] :
l_temp_connect, connect_matrix = retrieveAtom.atomConnect(l_atom_lig, atom_connect["serial"])
if connect_matrix == ["O", "C"] :
l_O_temp.append (atom_connect)
at_considered = CenterPoint(l_O_temp[0], l_O_temp[1])
return [angleVector(central_atom, at_considered, atom_check)]
def riboseFromADPRiboseAtom3 (serialAtom3, listAtomLigand, serialInit, serialPrevious) :
"""search ribose atom3
in: list atom connected of nitrogen, list atom ligand
out: boolean"""
listAtomConnect3, connect3 = retrieveAtom.atomConnect(listAtomLigand , serialAtom3)
for atom in listAtomConnect3 :
if atom["element"] == "O" :
listAtomConnectO, connectO = retrieveAtom.atomConnect(listAtomLigand, atom["serial"])
if connectO != ["O", "C"] :
return 0
for atom in listAtomConnect3 :
if atom["element"] == "C" and atom["serial"] != serialPrevious and atom["serial"] != serialAtom3:
atomConnect4, connectAtom4 = retrieveAtom.atomConnect(listAtomLigand, atom["serial"])
if connectAtom4 == ["C", "O", "C", "C"] or connectAtom4 == ["C", "C", "O", "C"] or connectAtom4 == ["C", "C", "C", "O"] :
if riboseFromADPRiboseAtom4 (atom["serial"], listAtomLigand, serialInit, serialAtom3) == 1 :
return 1
return 0
def globalNeighbors(distance, l_atom_ligand, pdb, struct_global_neighbor):
"""Retrieve neighbor in sphere
in : distance arroud atom, atom in ligand, name of pdb
out : list of atoms"""
for atom in l_atom_ligand:
groupAtom, conect = retrieveAtom.atomConnect(l_atom_ligand, atom["serial"])
atom = buildAtom(distance, groupAtom[0], pdb, "global", l_atom_ligand)
struct_global_neighbor.append(atom)
def riboseFromADPRiboseAtom4 (serial, listAtomLigand, serialInit, serialPrevious) :
"""search ribose atom4
in: list atom connected of nitrogen, list atom ligand
out: boolean"""
listAtomC, connectC = retrieveAtom.atomConnect(listAtomLigand, serial)
for atom in listAtomC[1:] :
if atom["element"] == "O" :
listAtomConnectO, connectO = retrieveAtom.atomConnect(listAtomLigand, atom["serial"])
if connectO != ["O", "C"] :
return 0
for atom in listAtomC :
if atom["serial"] != serial and atom["serial"] != serialPrevious :
for serial in atom["connect"] :
if serial == serialInit :
return 1
return 0
def riboseFromADPRibose (listAtomLigand):
"""search ribose global
in: list atom connected of nitrogen, list atom ligand
out: boolean"""
for atom in listAtomLigand :
if atom["element"] == "O" :
listAtomConnectO, connectO = retrieveAtom.atomConnect(listAtomLigand, atom["serial"])
if connectO == ["O", "C", "C"] :
serialInit = atom["serial"]
listAtomConnectC1, connectC1 = retrieveAtom.atomConnect(listAtomLigand, atom["connect"][1])
listAtomConnectC2, connectC2 = retrieveAtom.atomConnect(listAtomLigand, atom["connect"][2])
if "C" in connectC1[1:] :
if riboseFromADPRiboseAtom2(listAtomConnectC1, listAtomLigand, serialInit) == 1 :
return 1
if "C" in connectC2[1:] :
if riboseFromADPRiboseAtom2(listAtomConnectC2, listAtomLigand, serialInit) == 1 :
return 1
return 0
def acidCarboxylic(l_C2, l_atom_lig) :
l_serial = []
connectO1 = toolSubstructure.matrixElement(l_C2)
if connectO1 != ["O", "C"] :
return [0, []]
else :
l_serial.append (l_C2[0]["serial"])
l_connect3, connectC2 = retrieveAtom.atomConnect(l_atom_lig, l_C2[1]["serial"])
connectC2.sort()
if connectC2 == ["C", "C", "O", "O"] :
l_serial.append (l_connect3[0]["serial"])
for atom3 in l_connect3[1:] :
if atom3["element"] == "O" and not atom3["serial"] in l_serial:
l_O2, connectO2 = retrieveAtom.atomConnect(l_atom_lig, atom3["serial"])
if connectO2 == ["O", "C"] :
l_serial.append (atom3["serial"])
else :
return [0, []]
elif atom3["element"] == "C" and not atom3["serial"] in l_serial :
l_atomC4, connectC4 = retrieveAtom.atomConnect(l_atom_lig, atom3["serial"])
# print connectC4, "Check"
connectC4_unique = sorted(set(connectC4),key=connectC4.index)
# print connectC4_unique
if connectC4_unique != ["C"] :
return [0, []]
else :
for atom_conex in l_atomC4[1:] :
if toolSubstructure.checkSingleBond(l_atomC4[0], atom_conex) == 0 :
return [0, []]
# check 3 atom and not a hydroxyl group
if len (l_serial) == 3 :
return [1, l_serial]
return [0, []]
def interestGroup (max_distance, l_atom_lig, name_PDB, d_stock_neighbor, more_flex = 0):
"""Search different groups
in : ligands in namePDB
out : major nitrogen in the group of different structures
change distance max for Guanidium + 1.5
imidazole + 1.1
and acid carboxylic + 1.3
append more flex to GPCR study"""
l_serialN = ListSerialElement(l_atom_lig, "N")
l_serialO = ListSerialElement(l_atom_lig, "O")
# different d_stock_neighbor
for serialN in l_serialN:
l_atom_connectN, conect = retrieveAtom.atomConnect(l_atom_lig, serialN)
# check every substructure
if imidazole(l_atom_connectN, l_atom_lig)[0] == 1:
implementNeighborStruct (max_distance + 1.5, l_atom_connectN, name_PDB, l_atom_lig, "IMD", d_stock_neighbor)
elif Guanidium(l_atom_connectN, l_atom_lig)[0] == 1:
implementNeighborStruct (max_distance + 1.1, l_atom_connectN, name_PDB, l_atom_lig, "GAI", d_stock_neighbor)
# elif diAmine(l_atom_connectN, l_atom_lig) == 1:
# implementNeighborStruct (max_distance, l_atom_connectN, name_PDB, l_atom_lig, "Diamine", d_dia_temp)
# elif pyridine(l_atom_connectN, l_atom_lig) == 1:
# implementNeighborStruct (max_distance, l_atom_connectN, name_PDB, l_atom_lig, "Pyridine", d_stock_neighbor)
elif cn(l_atom_connectN, l_atom_lig) == 1:
implementNeighborStruct (max_distance, l_atom_connectN, name_PDB, l_atom_lig, "I", d_stock_neighbor)
elif cnc(l_atom_connectN, l_atom_lig, more_flex = more_flex) == 1:
# print "l562 -> search PDB"
implementNeighborStruct (max_distance, l_atom_connectN, name_PDB, l_atom_lig, "II", d_stock_neighbor)
elif cncc(l_atom_connectN, l_atom_lig, more_flex = more_flex) == 1:
implementNeighborStruct (max_distance, l_atom_connectN, name_PDB, l_atom_lig, "III", d_stock_neighbor)
for serialO in l_serialO :
l_atom_connectO, conect = retrieveAtom.atomConnect(l_atom_lig, serialO)
if acidCarboxylic(l_atom_connectO, l_atom_lig)[0] == 1:
implementNeighborStruct (max_distance + 1.3, l_atom_connectO, name_PDB, l_atom_lig, "COO", d_stock_neighbor)
def interestStructure (l_atom_lig, more_flex = 0, debug = 0):
"""For one serial_nitrogen atom search substructure
in : list atom ligand
out : list of substructures found (list string)"""
l_serial_N = ListSerialElement (l_atom_lig, "N")
l_serial_O = ListSerialElement (l_atom_lig, "O")
if debug :
print l_serial_O
print l_serial_N
l_substruct = []
for serial_nitrogen in l_serial_N:
l_atom_connectN, connect = retrieveAtom.atomConnect(l_atom_lig, serial_nitrogen)
if imidazole(l_atom_connectN, l_atom_lig)[0] == 1:
l_substruct.append("IMD")
elif Guanidium(l_atom_connectN, l_atom_lig)[0] == 1 :
l_substruct.append("GAI")
# elif diAmine(l_atom_connectN, l_atom_lig) == 1 :
# l_substruct.append("Diamine")
# elif pyridine(l_atom_connectN, l_atom_lig) == 1 :
# l_substruct.append("Pyridine")
elif cn (l_atom_connectN, l_atom_lig) == 1:
l_substruct.append("I")
elif cnc(l_atom_connectN, l_atom_lig, more_flex = more_flex) == 1:
l_substruct.append("II")
elif cncc(l_atom_connectN, l_atom_lig, more_flex = more_flex) == 1:
l_substruct.append("III")
for serial_oxygen in l_serial_O:
l_atom_connectO, connect = retrieveAtom.atomConnect(l_atom_lig, serial_oxygen)
if acidCarboxylic(l_atom_connectO, l_atom_lig)[0] == 1:
l_substruct.append("COO")
return l_substruct
def riboseFromADPRiboseAtom2 (listAtomConnectC, listAtomLigand, serialInit) :
"""search ribose atom2
in: list atom connected of nitrogen, list atom ligand
out: boolean"""
for atom in listAtomConnectC :
if atom["element"] == "C" :
listAtomC3, connectC = retrieveAtom.atomConnect(listAtomLigand, atom["serial"])
if connectC == ["C", "O", "C", "C"] or connectC == ["C", "C", "O", "C"] or connectC == ["C", "C", "C", "O"] :
serialNext = listAtomC3[0]["serial"]
if riboseFromADPRiboseAtom3 (serialNext, listAtomLigand, serialInit, atom["serial"]) == 1 :
return 1
return 0
def CoplanarityIII (l_atom_lig) :
"""For each matrix connect N, C, C, C the coplanar distance
in: list atom in ligand, list distance coplar retrieve
out: append distance in list distance coplanar"""
l_out = []
l_serialN = searchPDB.ListSerialElement(l_atom_lig, "N")
for serialN in l_serialN:
l_atom_connect, conect_matrix = retrieveAtom.atomConnect(l_atom_lig, serialN)
if conect_matrix == ["N", "C", "C", "C"]:
dist = calcul.coplanar(l_atom_connect[0], l_atom_lig)
if dist != None :
l_out.append (str(dist))
return l_out
def imidazoleATOM5(l_atom5, l_serial_check, l_atom_lig):
"""Check the atom 5 in cercle of imidazole
in : atoms ligand in list, serial of first nitrogen, name of ligand
out : boolean"""
for atom5 in l_atom5 :
if atom5["element"] == "C" and not atom5["serial"] in l_serial_check:
l_atom6, conect5 = retrieveAtom.atomConnect(l_atom_lig, atom5["serial"])
# check connect atom4 IMD
conect5.sort()
if conect5 == ["C","C", "C", "N"] or conect5 == ["C","C", "N"] :
for atom6 in l_atom6 :
if atom6["element"] == "N" and atom6["serial"] in l_serial_check :
l_serial_check.append (l_atom6[0]["serial"])
return [1, l_serial_check]
return [0, l_serial_check]
def AngleNImd(atom_center, atom_check, l_atom_lig, debug = 0):
"""
based one central atom, take C between the two N
"""
for atom_lig in l_atom_lig :
l_atom2, connect1 = retrieveAtom.atomConnect(l_atom_lig, atom_lig["serial"])
if connect1 == ["N", "C", "C"] :
dist_N_center = distanceTwoatoms(l_atom2[0], atom_center)
if dist_N_center < 2.0 :
angle = Angle3Atoms(atom_check, atom_center, l_atom2[0])
return [angle]
return ["NA"]
def CenterImidazole (l_atom_in, l_atom_lig) :
atomN1 = deepcopy(l_atom_in[0])
for atom2 in l_atom_in[1:] :
l_atom3, connect2 = retrieveAtom.atomConnect(l_atom_lig, atom2["serial"])
connect2.sort ()
if connect2 == ["C", "C", "N", "N"] or connect2 == ["C", "N", "N"] :
for atom3 in l_atom3[1:] :
if atom3["element"] == "N" and atom3["serial"] != atomN1["serial"] :
center_atom = CenterPoint(atomN1, atom3)
return center_atom
print "ERROR"
return "ERROR"
def imidazoleATOM3(l_atom3, l_serial_check, l_atom_lig):
"""Check the atom3 3 in circle of imidazole
in : atoms ligand in list, serial of first nitrogen, name of ligand
out : boolean"""
for atom3 in l_atom3:
if atom3["element"] == "N":
if not atom3["serial"] in l_serial_check :
l_atom4, conect3 = retrieveAtom.atomConnect(l_atom_lig, atom3["serial"])
break
# print conect3, "CN1, l367"
if conect3 == ['N', 'C', 'C']:
l_serial_check.append (l_atom4[0]["serial"])
# print l_serial_check, "l370"
if imidazoleATOM4(l_atom4, l_serial_check, l_atom_lig)[0] == 1:
return [1, l_serial_check]
return [0, l_serial_check]
def CenterGuanidium (l_atom_connectN, l_atom_lig) :
l_atom_connect = []
for atom_connectN in l_atom_connectN :
l_atom_connect.append (atom_connectN["element"])
if l_atom_connect == ['N', 'C', 'C'] :
for C_atom in l_atom_connectN[1:] :
l_C_atom, l_connect = retrieveAtom.atomConnect(l_atom_lig, C_atom["serial"])
if l_connect == ["C", "N", "N", "N"] :
return deepcopy(l_C_atom[0])
if l_atom_connect == ["N", "C"] :
return deepcopy(l_atom_connectN[-1])
print "ERROR"
return "ERROR"
def BondLengthCandX (l_atom_lig, X_element) :
l_dist = []
l_serialX = searchPDB.ListSerialElement(l_atom_lig, str(X_element))
for serialX in l_serialX :
# print serialX
l_atom_connectX, connect = retrieveAtom.atomConnect(l_atom_lig, serialX)
i = 0
nb_connect = len (connect)
while i < nb_connect :
if len(l_atom_connectX) >= 2 :
dist = calcul.distanceTwoatoms(l_atom_connectX[0], l_atom_connectX[1])
# print dist
if dist != 100 :
l_dist.append (str(dist))
i = i + 1
return l_dist
def imidazoleATOM4(l_atom4, l_serial_check, l_atom_lig):
"""Check the atom4 4 in cercle of imidazole
in : atoms ligand in list, serial of first nitrogen, name of ligand
out : boolean"""
# print l_serial_check, "l387"
for atom4 in l_atom4:
if atom4["element"] == "C":
if not atom4["serial"] in l_serial_check :
l_atom5, conect4 = retrieveAtom.atomConnect(l_atom_lig, atom4["serial"])
conect4.sort ()
if conect4 == ["C", "C", "C", "N"] or conect4 == ["C", "C", "N"] :
l_serial_check.append (l_atom5[0]["serial"])
imd, l_serial_check = imidazoleATOM5(l_atom5, l_serial_check, l_atom_lig)
# print l_serial_check, imd
if imd == 1:
return [1, l_serial_check]
else :
l_serial_check.remove(l_atom5[0]["serial"])
return [0, l_serial_check]
def Guanidium(l_at_connect_N, l_atom_lig):
"""search Guanidium
in: list atom connected of nitrogen, list atom ligand
out: 1 or 0"""
connectN1 = toolSubstructure.matrixElement(l_at_connect_N)
nb_NH = 0
l_atom_out = []
# atom lateral
if connectN1 == ["N", "C"] :
l_at_connect_c, connectC = retrieveAtom.atomConnect(l_atom_lig , l_at_connect_N[1]["serial"])
if connectC == ["C", "N", "N", "N"] :
l_atom_out.append (deepcopy(l_at_connect_c[0])) # append C
groupAtomN1, conect_N1 = retrieveAtom.atomConnect(l_atom_lig , int (l_at_connect_c[0]["connect"][1]))
groupAtomN2, conect_N2 = retrieveAtom.atomConnect(l_atom_lig , int (l_at_connect_c[0]["connect"][2]))
groupAtomN3, conect_N3 = retrieveAtom.atomConnect(l_atom_lig , int (l_at_connect_c[0]["connect"][3]))
l_conect = [conect_N1, conect_N2, conect_N3]
l_group_atom = [groupAtomN1, groupAtomN2, groupAtomN3]
i = 0
while i < 3 :
if l_conect[i] == ["N", "C"] :
nb_NH = nb_NH + 1
i = i + 1
elif l_conect[i] == ["N", "C", "C"]:
if l_group_atom[i][1]["serial"] != l_at_connect_c[0]["serial"] :
l_atom_out.append (deepcopy(l_group_atom[i][1]))
elif l_group_atom[i][2]["serial"] != l_at_connect_c[0]["serial"] :
l_atom_out.append (deepcopy(l_group_atom[i][2]))
else :
print "ERROR l158"
return [0, []]
i = i + 1
else :
return [0, []]
# check number primary connectN1 -> case GAI not take, change ?
if nb_NH == 2 :
l_atom_out.append (deepcopy(groupAtomN1[0]))
l_atom_out.append (deepcopy(groupAtomN2[0]))
l_atom_out.append (deepcopy(groupAtomN3[0]))
else :
return [0, []]
# atom central structure
elif connectN1 == ["N", "C", "C"] :
for at_conect in l_at_connect_N[1:] :
l_group_at, conect_N = retrieveAtom.atomConnect(l_atom_lig , at_conect["serial"])
if conect_N == ["C", "N", "N", "N"] :
l_c_central = l_group_at
l_atom_out.append (deepcopy(l_c_central[0]))
for group_at in l_group_at[1:] :
l_goup_N, connect_N = retrieveAtom.atomConnect(l_atom_lig , group_at["serial"])
if connect_N == ["N", "C"] :
nb_NH = nb_NH + 1
else :
l_atom_out.append (deepcopy(l_group_at[0]))
if nb_NH >= 2 and len (l_atom_out) >= 2 :
l_atom_out.append (deepcopy(l_c_central[1]))
l_atom_out.append (deepcopy(l_c_central[2]))
l_atom_out.append (deepcopy(l_c_central[3]))
else :
return [0, []]
if len (l_atom_out) != 5 :
return [0,[]]
else :
# append 2 carbons
l_C, connectC = retrieveAtom.atomConnect(l_atom_lig , l_atom_out[0]["serial"])
if connectC == ["C", "N", "N", "N"] :
l_serial = [l_atom_out[1]["serial"], l_atom_out[0]["serial"]]
atomC1 = l_atom_out[1]
else :
l_serial = [l_atom_out[0]["serial"], l_atom_out[1]["serial"]]
atomC1 = l_atom_out[0]
# distance between C2 and N
d1 = calcul.distanceTwoatoms(atomC1, l_atom_out[2])
d2 = calcul.distanceTwoatoms(atomC1, l_atom_out[3])
d3 = calcul.distanceTwoatoms(atomC1, l_atom_out[4])
l_dist = [d1, d2, d3]
l_dist.sort ()
for dist in l_dist :
if dist == d1 :
l_serial.append (l_atom_out[2]["serial"])
elif dist == d2 :
l_serial.append (l_atom_out[3]["serial"])
else :
l_serial.append (l_atom_out[4]["serial"])
return [1,l_serial]
return [0, []]