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