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228 lines
9.1 KiB
Plaintext
228 lines
9.1 KiB
Plaintext
# original source: http://tripod.nih.gov/files/patty.rules, copied July 2015
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#
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# CAT CATION, used for basic functionality; i.e., protonated
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# ANI ANION, used for acidic functionality; i.e., de-protonated
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#
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# POL POLAR, atom is neither an ANION nor a CATION and has a LP
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# and a polar H, or (due to tautomerization) can be a donor
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# or an acceptor.
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#
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# DON DONOR, an atom that is none of the above and has a polar H.
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# ACC ACCEPTOR, an atom that is none of the above and has an LP.
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#
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# HYD HYRDOPHOBIC, an atom that is none of the above and is an
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# accessible atom that has hydrophobic functionality
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#
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# OTH OTHER, an atom that falls in none of the above classes.
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* OTH # Default Rule
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[#8] ACC # O
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[#7] DON # N
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[#6,#14] HYD # C, Si
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[#16] HYD # S
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[#34] HYD # Se
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[#16] HYD # P
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[#33] HYD # As
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[#9D1,#17D1,#35D1,#53D1,#85D1] HYD # halogens
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[#9D0,#17D0,#35D0,#53D0,#85D0] ANI
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[OHD1] POL # hydroxide
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[OH2] POL # water (NEW)
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[#1] HYD # H
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[#1][#7] DON
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[NH0]#* ACC # :N# (sp)
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[ND2](*)=* ACC # =N- (sp2)
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[nH0] ACC # aomatic N - (sp2)
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[NH;D1]=* POL # HN=X
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[ND1]=* POL # N=N= (azide)
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[#7,#15,#33;D4] CAT # quaternary N,P,As
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# any nonconjugated sp3 N is a basic amine (except next
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# to conjugated a N)
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[#7D1]-* CAT
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[#7D2](-*)-* CAT
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[#7D3](-*)(-*)-* CAT
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[#7v4] CAT
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[#7D3]-N-*=* OTH
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[#7D3](-*)(-*)-N-*#* OTH
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# conjugated N's
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[#7D1]-*=* DON
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[#7D1]-*:* DON
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[#7D1]-*#* DON
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[#7H;D2]-*=* DON
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[#7H;D2]-*:* DON
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[#7H;D2]-*#* DON
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[#7;D3]-*=* OTH # conj & buried
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[#7;D3]-*:* OTH #
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[#7;D3](*=*)(-&!@*)*:* OTH
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[#7;D3]-*#* OTH
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# amidine
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#
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# N+H2
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# //
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# CH3--C--:NH2
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[#7D1]-C(-[#6])=[#7D1] CAT
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[#7D1]=C(-[#6])-[#7D1] CAT
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# changed to #7D1
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[#7D1]-C(-S)=[#7D1] CAT
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[#7D1]=C(-S)-[#7D1] CAT
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# guanidinium
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N-C(=N)-N CAT
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N=C(-N)-N CAT
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# nitro
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[OD1]-N=[OD1] ACC
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[OD1]=N-[OD1] ACC
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# trisubstituted sp2 amines are cations with exceptions
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[#7,#15,#33;D3]=* CAT
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N([OD1])=[OD1] OTH
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# disbustituted sp amines and exceptions
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[N+;D2](=*)=* CAT # diazonium -[N+]#
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[N+;D2]#* CAT # #N-
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[N+;D2]#[CX1] OTH # isonitrile -N#C:
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[CX1]#[N+;D2] ACC # isonitrile :C#N-
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# trisubstituted oxygens, sulfurs and exceptions
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[#8,#16;D3] CAT # -O(-*)(-*)
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[#8,#16;D3](=*) CAT # =O-
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S=[#8,#16;X1] OTH # dative sulfoxides
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*-[#8,#16;X1] OTH # oxides,sulfides
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# misc anions
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[SD1]a ANI
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# phosphate/arsenate monoanion and S equialents
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#
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# O O
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# | |
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# P--O (-) and --P--O (-)
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# /
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[#8,#16,#34;X1]~[#15,#33;D3]~[#8,#16,#34;D1] ANI
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[#8,#16,#34;D1]~[#15,#33;D3]~[#8,#16,#34;X1] ANI
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[#8,#16,#34;X1]~[#15,#33;D4]~[#8,#16,#34;D1] ANI
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[#8,#16,#34;D1]~[#15,#33;D4]~[#8,#16,#34;X1] ANI
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[#15,#33;D3]([#8,#16,#34;X1])~[#8,#16,#34;D1] OTH
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[#15,#33;D3]([#8,#16,#34;D1])~[#8,#16,#34;X1] OTH
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[#15,#33;D4]([#8,#16,#34;X1])~[#8,#16,#34;D1] OTH
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[#15,#33;D4]([#8,#16,#34;D1])~[#8,#16,#34;X1] OTH
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# sulfite and selenite anion and S equivalents
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#
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# O O
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# | |
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# S--O (-) and O--S--O (-)
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# / |
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[#8,#16,#34;X1]~[#8,#16,#34;D3]~[#8,#16,#34;D1] ANI
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[#8,#16,#34;D1]~[#8,#16,#34;D3]~[#8,#16,#34;X1] ANI
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[#8,#16,#34;X1]~[#8,#16,#34;D4](~[#8,#16,#34;D1])~[#8,#16,#34;X1] ANI
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[#8,#16,#34;D1]~[#8,#16,#34;D4](~[#8,#16,#34;X1])~[#8,#16,#34;X1] ANI
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# muscimol anion (first O is ANI, N is ACC)
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#
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# *--* *--*
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# / | / |
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# (-) O-C O or O=C O
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# \\ / \ /
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# N: :N (-)
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[#8D1][#6]1=[#7][#8]**1 ANI
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[#7]1=[#6]([#8D1])**[#8]1 ANI
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[#8]=[#6]1[#7][#8]**1 ANI
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[#7]1[#6](=O)**[#8]1 ANI
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# tetrazole anion (all Ns are ANI)
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#
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# :N--N: (-) :N--N:
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# # || / ||
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# :N C or :N C (aromatic)
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# \ / \\ /
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# N: (-) N:
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[nD2]1[nD2][nD2][nD2]c1 ANI
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[nD2]1[nD2][nD2]c[nD2]1 ANI
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[nD2]1[nD2]c[nD2][nD2]1 ANI
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[nD2]1c[nD2][nD2][nD2]1 ANI
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# diaminopyrimidine (ring Ns are POL)
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#
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# *==*
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# / \
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# :N C--NH2 (aromatic)
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# \\ #
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# C--N:
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# /
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# NH2
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[nD2]1c(N)[nD2]c(N)aa1 POL
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[nD2]1c(N)aa[nD2]c1(N) POL
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# make imidazole Ns both POL
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#
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# C==C C==C
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# / | / |
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# :N NH or HN N: (aromatic)
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# \\ / \ #
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# C C
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#
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#
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n1cncc1 POL
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# stabilized sulfonamides and phosphonamides
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#
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# O
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# |
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# a--S--NH2
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# |
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# O
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[ND1]~[SD4](a)(~[#8,#16,#34;D1])(~[#8,#16,#34;D1]) POL
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[ND1]~[PD4](a)(~[#8,#16,#34;D1])(~[#8,#16,#34;D1]) POL
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[#8,#16,#34;D1]~[SD4](a)(~[#8,#16,#34;D1])~[ND1] ACC
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[#8,#16,#34;D1]~[PD4](a)(~[#8,#16,#34;D1])~[ND1] ACC
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[#8,#16,#34;D1]~[SD4](a)(~[#8,#16,#34;D1])~[ND2] ANI
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[#8,#16,#34;D1]~[PD4](a)(~[#8,#16,#34;D1])~[ND2] ANI
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[ND2]~[SD4](a)(~[#8,#16,#34;D1])(~[#8,#16,#34;D1]) ANI
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# carbonyl-hydroxide tautaumers
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#
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# !O !O
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# | |
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# C C
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# / \\/ \\
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# OH X O
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[OH]C(*)=*C=O POL
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O=C*=C(*)[OH] POL
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O=C-*:[#6](*)[OH] POL
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# carboxylates and S equivalents
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#
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# O
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# #
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# -C
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# \
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# O (-)
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[#8,#16,#34;D1]C=[#8,#16,#34] ANI
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[#8,#16,#34]=C[#8,#16,#34;D1] ANI
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# *==*
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# / \
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# * C==O (aromatic)
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# \\ /
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# C--C And 4 Cs away
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# /
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# OH
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[OH]c1cc(=O)aaa1 POL
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O=c1cc([OH])aaa1 POL
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[OH]c1ccc(=O)aa1 POL
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O=c1ccc([OH])aa1 POL
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# special ionizations of adjacent keto/enols
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[OD1]C=CC(=O)[O]* ANI
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[OD1]C=CC(=O)[N]* ANI
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O=C-CC(=O)[O]* ANI
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O=C-CC(=O)[N]* ANI
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OC=C-C(=O)C=CO ANI
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OC-C=C(-O)C=CO ANI
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# planar buried C bonded to electronegative atom
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[#6D3](=*)-[#7,#8] OTH
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[#6D3](:*)(:*)[#7,#8] OTH
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[#6D3](-*)(:*):[#7,#8] OTH
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[#6D3]=[#7,#8] OTH
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[#6D2](#*)-[#7,#8] OTH
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[#6D2](*)#[#7,#8] OTH
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[#6D2](=*)=[#7,#8] OTH
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[#16D2](#*)-[#7,#8] OTH # buried sp S
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[#16D2](*)#[#7,#8] OTH
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[#16D2](=*)=[#7,#8] OTH
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# misc fixups
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[ND2](=*)=* OTH # sp buried
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[ND2](*)#* OTH
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[#7,#15,#33;D4]=[S,O] OTH
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[ND3]P(=O) OTH
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[OD1]-n ACC
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n-[OD1] OTH
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