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 cn(listAtomConnectNitrogen, l_atom_lig):
"""search primary stAtom
in: list atom connected of nitrogen, list atom ligand
out: 1 or 0"""
stAtom = toolSubstructure.matrixElement(listAtomConnectNitrogen)
if stAtom == ["N", "C"] or stAtom == ["N", "C"]:
if toolSubstructure.checkSingleBond(listAtomConnectNitrogen[0], listAtomConnectNitrogen[1]) == 1:
if toolSubstructure.checkConectOnlyC(listAtomConnectNitrogen[1], l_atom_lig) == 1 :
return 1
return 0
def cnc(l_atom_connectN, l_atom_lig, more_flex = 0):
"""search secondary connect_element
in: list atom connected of nitrogen, list atom ligand
out: 1 or 0"""
connect_element = toolSubstructure.matrixElement(l_atom_connectN)
if connect_element == ["N", "C", "C"]:
# print "IN - NH2"
if more_flex == 1 : # more flexible control just connectivity
#if toolSubstructure.checkConectOnlyC(l_atom_connectN[1], l_atom_lig) == 1 and toolSubstructure.checkConectOnlyC(l_atom_connectN[2], l_atom_lig) == 1:
#if toolSubstructure.checkSingleBond(l_atom_connectN[0], l_atom_connectN[1]) == 1 and toolSubstructure.checkSingleBond(l_atom_connectN[0], l_atom_connectN[2]) == 1:
return 1
else :
if toolSubstructure.checkConectOnlyC(l_atom_connectN[1], l_atom_lig) == 1 and toolSubstructure.checkConectOnlyC(l_atom_connectN[2], l_atom_lig) == 1:
if toolSubstructure.checkSingleBond(l_atom_connectN[0], l_atom_connectN[1]) == 1 and toolSubstructure.checkSingleBond(l_atom_connectN[0], l_atom_connectN[2]) == 1:
return 1
return 0
def cncc(l_atom_connectN, l_atom_lig, more_flex = 0):
"""
Search tertiary amine in list of atom lig
- Append option
"""
connect_element = toolSubstructure.matrixElement(l_atom_connectN)
if connect_element == ["N", "C", "C", "C"]:
if more_flex == 1 :
#if toolSubstructure.checkCoplanar(l_atom_connectN[0], l_atom_lig) == 1:
# if toolSubstructure.checkSingleBond(l_atom_connectN[0], l_atom_connectN[1], d_min = 1.34) == 1 and toolSubstructure.checkSingleBond(l_atom_connectN[0], l_atom_connectN[2], d_min = 1.34) == 1 and toolSubstructure.checkSingleBond(l_atom_connectN[0], l_atom_connectN[3], d_min = 1.34) == 1:
return 1
else :
if toolSubstructure.checkConectOnlyC(l_atom_connectN[1], l_atom_lig) == 1 and toolSubstructure.checkConectOnlyC(l_atom_connectN[2], l_atom_lig) == 1 and toolSubstructure.checkConectOnlyC(l_atom_connectN[3], l_atom_lig) == 1:
if toolSubstructure.checkCoplanar(l_atom_connectN[0], l_atom_lig) == 1:
if toolSubstructure.checkSingleBond(l_atom_connectN[0], l_atom_connectN[1]) == 1 and toolSubstructure.checkSingleBond(l_atom_connectN[0], l_atom_connectN[2]) == 1 and toolSubstructure.checkSingleBond(l_atom_connectN[0], l_atom_connectN[3]) == 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 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, []]
