annotate CADDSuite/data/OpenBabel/atomtyp.txt @ 3:ff6df146c0d5

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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  [Ge]                      3
INTHYB  [Sn]                      3
INTHYB  [Pb]                      3
INTHYB  [As]                      3       # sp3 hybridization As (and family)
INTHYB  [Sb]                      3
INTHYB  [Bi]                      3

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]                      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 # 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 [$([#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 ##########################