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, []]
