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############################################################################## |
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# # |
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# Open Babel file: atomtyp.txt # |
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# # |
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# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # |
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# Some portions Copyright (c) 2001-2003 Geoffrey R. Hutchison # |
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# Part of the Open Babel package, under the GNU General Public License (GPL)# |
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# # |
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# SMARTS patterns for atom typing (used by typer.cpp:OBAtomTyper) # |
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# # |
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# INTHYB: used to assign the internal hybridization values for atoms # |
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# IMPVAL: used to assign the implicit valence of an atom # |
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# EXTTYP: used to assign the external type of an atom for translation to # |
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# package specific types (i.e. Sybyl Mol2) # |
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# (these should correspond to INT type names in types.txt too.) # |
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# # |
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# The LAST PATTERN MATCHED is used to assign values with the corresponding # |
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# INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed # |
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# in the EXTRA DEFINITIONS section (to separate from original patterns.) # |
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# # |
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############################################################################## |
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|
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INTHYB [C] 3 #sp3 carbon |
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INTHYB [c,$(C=*)] 2 #sp2 carbon |
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INTHYB [$([#6]([#8D1])[#8D1])] 2 #sp2 carbon |
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INTHYB [$(C#*),$(C(=*)=*)] 1 #sp carbon |
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INTHYB [N] 3 #sp3 nitrogen |
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INTHYB [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen |
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INTHYB [ND1,ND2,ND3]a 2 #sp2 nitrogen |
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INTHYB [$(N#*),$([ND2](=*)=*)] 1 #sp nitrogen |
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INTHYB [O] 3 #sp3 oxygen |
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INTHYB [o,$(O=*),$(O[#6,#7,#8]=,:*)] 2 #sp2 oxygen |
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INTHYB [$([#8D1][#6][#8D1])] 2 #sp2 oxygen |
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INTHYB [$(O#*)] 1 #sp oxygen |
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INTHYB [D4] 3 #any 4 valent atom |
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INTHYB [P] 3 #sp3 phosphorus |
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INTHYB [#15;$([PD1]=*)] 2 #sp2 phosphorus |
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INTHYB [S] 3 #sp3 sulfur |
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INTHYB [#16;s,$([SD1]=*)] 2 #sp2 sulfur |
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INTHYB [B] 2 #sp2 boron |
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INTHYB [BD4] 3 #sp3 boron |
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# |
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#IMPLICIT VALENCE RULES |
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# |
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IMPVAL [#6^3] 4 |
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IMPVAL [#6^2] 3 |
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IMPVAL [#6^1] 2 |
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IMPVAL [#6^3-] 3 |
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IMPVAL [#6^2-] 2 |
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IMPVAL [#6^1-] 1 #CM for isocyanides |
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IMPVAL [c+] 2 |
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IMPVAL [#8^3] 2 |
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IMPVAL [#8^2] 2 |
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IMPVAL [$([#8]=*)] 1 |
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IMPVAL [#8-] 1 |
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IMPVAL [$([#8D1]~[#7D3]~[#8D1])] 1 |
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IMPVAL [$([#8D1]~[#6]~[#8D1])] 1 |
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# This is from JOELib -- add H to acidic oxygens |
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IMPVAL [$([#8D1]-[#6]=[#8D1])] 2 |
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# But don't add an H for pH-corrected formal-charge = -1 oxygens |
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IMPVAL [$([#8D1-]-[#6]=[#8D1])] 1 |
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IMPVAL [N^3] 3 |
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IMPVAL [N^3+] 4 |
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IMPVAL [N^2] 3 |
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IMPVAL [N^2-,N^3-] 2 |
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IMPVAL [ND1^1] 1 |
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IMPVAL [ND2^1] 2 |
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IMPVAL [$(N([OD1])*)] 3 |
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IMPVAL [$(NC=O)] 3 |
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IMPVAL [$(N(~[OD1])~[OD1])] 3 |
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IMPVAL [$([Nr0]C=[Nr0])] 3 |
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IMPVAL [$(N=*)] 2 |
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#IMPVAL [$([Nr0]=C[Nr0])] 3 |
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IMPVAL [$([Nr0]=C[Nr0])] 2 |
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IMPVAL [$([#7D1-]=*)] 1 |
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IMPVAL [n] 2 |
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IMPVAL [n-] 2 |
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IMPVAL [n+] 3 |
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IMPVAL [#9D0] 1 |
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IMPVAL [#9D0-] 0 #[F-] |
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IMPVAL [#15D4] 4 |
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IMPVAL [#15D3] 3 |
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IMPVAL [#15D2] 3 |
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IMPVAL [#15D1^3] 3 |
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IMPVAL [#15D1^2] 3 |
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IMPVAL [#15D0] 3 |
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IMPVAL [$([#15]=[#6])] 2 |
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IMPVAL [pD2] 2 |
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IMPVAL [$([#15]=[#8])] 4 # phosphinate (double bond = one valence) |
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IMPVAL [#16D4] 4 |
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IMPVAL [#16D3] 3 |
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IMPVAL [#16D2] 2 |
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IMPVAL [$([#16D1]-*)] 2 |
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IMPVAL [#16D1^2] 1 |
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IMPVAL [s] 2 |
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IMPVAL [#16D1-] 1 |
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IMPVAL [#16D0] 2 |
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IMPVAL [#17D0] 1 |
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IMPVAL [#17D0-] 0 #[Cl-] |
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IMPVAL [#35D0] 1 |
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IMPVAL [#35D0-] 0 #[Br-] |
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IMPVAL [#53D0] 1 |
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IMPVAL [#53D0-] 0 #[I-] |
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IMPVAL [#5] 3 |
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IMPVAL [as] 3 |
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# |
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#EXTERNAL TYPE RULES |
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# |
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EXTTYP [#7^3] N3 |
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EXTTYP [#7X4+] N3+ |
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EXTTYP [#7^2] Npl |
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EXTTYP [#7^1] N1 |
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EXTTYP [$(N=*)] N2 |
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EXTTYP [$([Nr0]C(=[Nr0])[Nr0])] Ng+ |
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EXTTYP [$([Nr0]=C([Nr0])[Nr0])] Ng+ |
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EXTTYP [$([ND1]=C[ND1])] Ng+ |
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EXTTYP [$([ND1]C=[ND1])] Ng+ |
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EXTTYP [$(N(O)*)] Nox |
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EXTTYP [$(NC=[O,S])] Nam |
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EXTTYP [$(N(~[OD1])~[OD1])] Ntr |
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EXTTYP [n] Nar |
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EXTTYP [#6^3] C3 |
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EXTTYP [#6^2] C2 |
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EXTTYP [$(C(=O)[OD1])] Cac |
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EXTTYP [c] Car |
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EXTTYP [#6^1] C1 |
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EXTTYP [#6+] C+ |
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EXTTYP [#6-] C- |
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EXTTYP [#8^3] O3 |
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EXTTYP [#8^2] O2 |
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EXTTYP [$(Oa)] O2 |
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#The following 2 lines used for correct Sybyl atom typing |
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EXTTYP [$([OD2]C=[O,S])] O3 #ester oxygen |
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EXTTYP [$(Oa)] O3 #aromatic ether |
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EXTTYP [#8-] O- |
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EXTTYP [$([#8D1]~[#6]~[#8D1])] O.co2 |
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EXTTYP [#15] P |
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EXTTYP [#15X4+] P3+ |
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EXTTYP [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])] Pac |
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EXTTYP [#15;$([#15D3](~[OD1])~[OD1])] Pac |
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EXTTYP [#16] S3 |
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EXTTYP [#16D3+,#16X3+] S3+ |
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EXTTYP [#16;s,$([SD1]=*)] S2 |
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EXTTYP [#16D4;$(S(=O)(=O))] So2 |
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EXTTYP [#16D3;$(S(=O))] Sox |
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EXTTYP [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])] Sac |
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EXTTYP [#16;$([#16D3](~[OD1])~[OD1])] Sac |
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EXTTYP [#5] B2 |
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EXTTYP [#5D4] B3 |
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######################## Add Extra Definitions Here ########################## |
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############################# End Extra Definitions ########################## |
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