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view CADDSuite-1.5/data/OpenBabel/atomtyp.txt @ 16:1a24aef40d01 draft
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| author | marcel |
|---|---|
| date | Tue, 24 Jul 2012 11:10:07 -0400 |
| parents | ac342506cd4e |
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############################################################################## # # # Open Babel file: atomtyp.txt # # # # # # Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # # Some portions Copyright (c) 2001-2008 Geoffrey R. Hutchison # # Part of the Open Babel package, under the GNU General Public License (GPL)# # # # SMARTS patterns for atom typing (used by typer.cpp:OBAtomTyper) # # # # INTHYB: used to assign the internal hybridization values for atoms # # IMPVAL: used to assign the implicit valence of an atom # # EXTTYP: used to assign the external type of an atom for translation to # # package specific types (i.e. Sybyl Mol2) # # (these should correspond to INT type names in types.txt too.) # # # # The LAST PATTERN MATCHED is used to assign values with the corresponding # # INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed # # in the EXTRA DEFINITIONS section (to separate from original patterns.) # # # ############################################################################## INTHYB [D4] 3 #any 4-valent atom -- tetrahedral INTHYB [D5] 5 #any 5-valent atom -- trigbipy INTHYB [D6] 6 #any 6-valent atom -- oct INTHYB [C] 3 #sp3 carbon INTHYB [c,$(C=*)] 2 #sp2 carbon # INTHYB [$([#6]([#8D1])[#8D1])] 2 # Commented out after PR#3089597 INTHYB [$(C#*),$(C(=*)=*)] 1 #sp carbon INTHYB [N] 3 #sp3 nitrogen INTHYB [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen INTHYB [ND1,ND2,ND3]a 2 #sp2 nitrogen INTHYB [$(N#*),$([ND2](=*)=*)] 1 #sp nitrogen INTHYB [O] 3 #sp3 oxygen INTHYB [o,$(O=*),$(O[#6,#7,#8]=,:*)] 2 #sp2 oxygen INTHYB [$([#8D1][#6][#8D1])] 2 #sp2 oxygen INTHYB [$(O#*)] 1 #sp oxygen INTHYB [P] 3 #sp3 phosphorus INTHYB [#15;$([PD1]=*)] 2 #sp2 phosphorus INTHYB [PD5] 5 #sp3d phosphorus, as in PF5 INTHYB [Pv5] 5 #sp3d phosphorus, as in H3PO4 INTHYB [S] 3 #sp3 sulfur INTHYB [#16;s,$([SD1]=*)] 2 #sp2 sulfur INTHYB [SD6] 6 #sp3d2 sulfur, as in SF6 INTHYB [B] 2 #sp2 boron INTHYB [BD4] 3 #sp3 boron INTHYB [Al] 2 # typical sp2 Al (and family) INTHYB [Ga] 2 INTHYB [In] 2 INTHYB [Tl] 2 INTHYB [AlD4] 3 # sp3 Al INTHYB [Si] 3 # sp3 Si (and family) INTHYB [Pb] 3 INTHYB [Ge;!D5] 3 INTHYB [Sn;!D5] 3 INTHYB [AsD3] 3 # AsCl3 (AsCl5 handled by D5 above) INTHYB [SbD3] 3 # # SbD5, AsD5 are all trigbpy so are handled by D5 above INTHYB [BiD3] 3 # INTHYB [BiD5] 6 # BiF5 is square-pyr, not trigbpy INTHYB [se] 2 # aromatic sp2 Se INTHYB [Se] 3 # sp3 hybridization Se (and family) INTHYB [Te] 3 INTHYB [Po] 3 INTHYB [Be] 1 # Alkaline earth, like sp hybrids INTHYB [Mg] 1 INTHYB [Ca] 1 INTHYB [Sr] 1 INTHYB [Ba] 1 INTHYB [Ra] 1 #INTHYB [Pt] 4 # normally square planar #INTHYB [Pd] 4 #INTHYB [Cu] 4 #INTHYB [Ag] 4 #INTHYB [Au] 4 # #IMPLICIT VALENCE RULES # #IMPVAL [#3,#11,#19,#37,#55,#87] 1 # Alkali metals #IMPVAL [#4,#12,#20,#38,#56,#88] 2 # Alkaline earth IMPVAL [#5+] 2 IMPVAL [#5-] 4 IMPVAL [#5] 3 # Generic boron IMPVAL [$([#6+]=*)] 2 IMPVAL [$([#6+]#*)] 1 # just for InChI C2 IMPVAL [#6^3] 4 IMPVAL [#6^2] 3 IMPVAL [#6^1] 2 IMPVAL [#6^3+] 3 IMPVAL [#6^2+] 2 IMPVAL [#6^1+] 1 IMPVAL [#6^3-] 3 IMPVAL [#6^2-] 2 IMPVAL [#6^1-] 1 # isocyanides, CO (valence=1, bond order=3) IMPVAL [c+] 2 IMPVAL [N^3] 3 IMPVAL [N^3+] 4 IMPVAL [N^2] 3 #IMPVAL [N^2-,N^3-] 2 IMPVAL [ND1^1] 1 IMPVAL [ND2^1] 2 IMPVAL [$(N([OD1])*)] 3 IMPVAL [$(NC=O)] 3 #IMPVAL [$(n(c=O)c=O)] 3 # aromatic diimide IMPVAL [$(N(~[OD1])~[OD1])] 3 IMPVAL [$([Nr0]C=[Nr0])] 3 IMPVAL [$(N=*)] 2 #IMPVAL [$([Nr0]=C[Nr0])] 3 IMPVAL [$([Nr0]=C[Nr0])] 2 IMPVAL [$([N+r0]=C[Nr0])] 3 # patch from Steve Constable IMPVAL [$([#7D1-]=*)] 1 IMPVAL [N^1-] 1 # N2O [N-]=[N+]=O (valence=1, bondorder=2) IMPVAL [N-] 2 IMPVAL [n] 2 IMPVAL [n-] 2 IMPVAL [n+] 3 IMPVAL [$([#7-]=*)] 1 IMPVAL [$([#7+]#*)] 2 IMPVAL [$([#7+]=*)] 3 IMPVAL [$([#7+](=*)=*)] 2 IMPVAL [$([#8+]#*)] 1 IMPVAL [#8] 2 # Generic O IMPVAL [#8-] 1 IMPVAL [#8-2] 0 IMPVAL [#8+] 3 IMPVAL [$([#8]=*)] 1 IMPVAL [#8^1+] 1 # carbon monoxide IMPVAL [#9D0] 1 IMPVAL [#9D0-] 0 #[F-] IMPVAL [#13] 3 # generic Al IMPVAL [#14] 4 # regular sp3 Si IMPVAL [#14^2] 2 # silylenes IMPVAL [$([#14]=*)] 3 # e.g., Si=O IMPVAL [$([#14](=*)=*)] 0 # e.g., Si(=O)=O IMPVAL [$([#14+]#*)] 1 # just for InChI Si2 IMPVAL [$([#14-]#*)] 1 # just for InChI Si2 IMPVAL [#15D4] 4 IMPVAL [#15D3] 3 IMPVAL [#15D2] 3 IMPVAL [#15D1^3] 3 IMPVAL [#15D1^2] 3 IMPVAL [#15D0] 3 IMPVAL [$([#15]=[#6])] 2 IMPVAL [pD2] 2 IMPVAL [$([#15]=[#8])] 4 # phosphinate (double bond = one valence) IMPVAL [$([#15](=[#8])=[#8])] 3 # metaphosphate (double bond = one valence) IMPVAL [$([#15+](=[#8])([#8]))] 0 # R-P+O2 IMPVAL [#16] 2 #revised CM April 2008 IMPVAL [$([#16D1]=*)] 1 IMPVAL [$([#16D3](=O)(=O)-O)] 4 #e.g. O[S](=O)=O IMPVAL [$([#16D2](=O)-O)] 3 # e.g. O[S]=O IMPVAL [#16D1-] 1 IMPVAL [#17D0] 1 IMPVAL [#17D0-] 0 #[Cl-] IMPVAL [#31] 3 IMPVAL [#32] 4 IMPVAL [#33] 3 IMPVAL [as] 3 IMPVAL [#34] 2 IMPVAL [#35D0] 1 IMPVAL [#35D0-] 0 #[Br-] #IMPVAL [#49,#81] 3 # In, Tl, like Ga #IMPVAL [#50,#82] 4 # Sn, Pb, like Ge #IMPVAL [#51,#83] 3 # Sb, Bi, like As IMPVAL [#52] 2 IMPVAL [#53D0] 1 IMPVAL [#53D0-] 0 #[I-] # #EXTERNAL TYPE RULES # # Tinker OH hydrogens for MM2 # Fixes PR# 1839274 EXTTYP [#1][#8] HO EXTTYP [#7^3] N3 EXTTYP [#7X4] N3+ EXTTYP [#7^2] Npl EXTTYP [#7^1] N1 EXTTYP [$(N=*)] N2 EXTTYP [$([Nr0]C(=[Nr0])[Nr0])] Ng+ EXTTYP [$([Nr0]=C([Nr0])[Nr0])] Ng+ EXTTYP [$([ND1]=C[ND1])] Ng+ EXTTYP [$([ND1]C=[ND1])] Ng+ EXTTYP [$(N(O)*)] Nox EXTTYP [$(NC=[O,S])] Nam EXTTYP [$(N(~[OD1])~[OD1])] Ntr EXTTYP [n] Nar EXTTYP [#6^3] C3 EXTTYP [#6^2] C2 EXTTYP [$(C(=O)[OD1])] Cac EXTTYP [c] Car EXTTYP [#6^1] C1 EXTTYP [#6+] C+ EXTTYP [#6-] C- EXTTYP [#8^3] O3 EXTTYP [#8^2] O2 EXTTYP [$(Oa)] O2 #The following 2 lines used for correct Sybyl atom typing EXTTYP [$([OD2]C=[O,S])] O3 #ester oxygen EXTTYP [$(Oa)] O3 #aromatic ether EXTTYP [#8-] O- EXTTYP [$([#8D1]~[#6^2]~[#8D1])] O.co2 EXTTYP [#15] P EXTTYP [#15X4+] P3+ EXTTYP [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])] Pac EXTTYP [#15;$([#15D3](~[OD1])~[OD1])] Pac EXTTYP [#16] S3 EXTTYP [#16D3+,#16X3+] S3+ EXTTYP [#16;s,$([SD1]=*)] S2 EXTTYP [#16D4;$(S(=O)(=O))] So2 EXTTYP [#16D3;$(S(=O))] Sox EXTTYP [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])] Sac EXTTYP [#16;$([#16D3](~[OD1])~[OD1])] Sac EXTTYP [#5] B2 EXTTYP [#5D4] B3 ######################## Add Extra Definitions Here ########################## #INTHYB [U] 3 #INTHYB [W] 3 #INTHYB [Mo] 6 # for development #INTHYB [Cr] 5 # for development ############################# End Extra Definitions ##########################