Mercurial > repos > marcel > caddsuite_mac10_6
diff CADDSuite-1.6/data/OpenBabel/atomtyp.txt @ 8:dbb480e39d95 draft
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| author | marcel |
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| date | Sat, 15 Dec 2012 13:15:46 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite-1.6/data/OpenBabel/atomtyp.txt Sat Dec 15 13:15:46 2012 -0500 @@ -0,0 +1,259 @@ +############################################################################## +# # +# 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 ########################## +