VENDOR:          http://joelib.sf.net
RELEASE_VERSION: $Revision: 1.8 $
RELEASE_DATE:    $Date: 2004/03/15 13:33:42 $

################################################################################
#	                    JOELib file: atomtyp.txt                           #
#                                                                              #
# 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)                             #
#                                                                              #
# 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                                             #
#                                                                              #
################################################################################

INTHYB	[C]				3	#sp3 carbon
INTHYB	[c,$(C=*)]			2	#sp2 carbon
INTHYB	[$([#6]([#8Q1])[#8Q1])]		2	#sp2 carbon
INTHYB	[$(C#*),$(C(=*)=*)]		1	#sp  carbon
INTHYB	[N]				3	#sp3 nitrogen
INTHYB	[n,$(N=*),$(N[#6,#7,#8]=,:,#*)]	2	#sp2 nitrogen
INTHYB	[$(N#*),$([NQ2](=*)=*)]		1	#sp  nitrogen
INTHYB	[O]				3	#sp3 oxygen
INTHYB	[o,$(O=*),$(O[#6,#7,#8]=,:*)]	2	#sp2 oxygen
INTHYB	[$([#8Q1][#6][#8Q1])]		2	#sp2 oxygen
INTHYB	[$(O#*)]			1	#sp  oxygen
INTHYB  [Q4]                            3       #any 4 valent atom

INTHYB	[P]				3	#sp3 phosphorus
INTHYB	[#15;$([PQ1]=*)]		2	#sp2 phosphorus
INTHYB	[S]				3	#sp3 sulfur
INTHYB	[#16;s,$([SQ1]=*)]		2	#sp2 sulfur
INTHYB	[B]				2	#sp2 boron
INTHYB	[BQ4]				3	#sp3 boron
#
#IMPLICIT VALENCE RULES
#
IMPVAL	[#6^3]			4
IMPVAL	[#6^2]			3
IMPVAL	[#6^1]			2
IMPVAL  [#6^3-]			3
IMPVAL  [#6^2-]			2
IMPVAL  [c+]                    2

IMPVAL	[#8^3]				2
IMPVAL	[#8^2]				2
IMPVAL	[$([#8]=*)]			1
IMPVAL	[#8-]				1
IMPVAL  [$([#8Q1]~[#7Q3]~[#8Q1])]	1
#IMPVAL	[$([#8Q1]~[#6]~[#8Q1])]		1
IMPVAL	[$([#8Q1]-[#6]=[#8Q1])]		2
IMPVAL	[$([#8-Q1]-[#6]=[#8Q1])]	1

IMPVAL	[N^3]			3
IMPVAL	[N^3+]			4
IMPVAL	[N^2]			3
IMPVAL  [N^2-,N^3-]		2
IMPVAL	[NQ1^1]			1
IMPVAL	[NQ2^1]			2
IMPVAL	[$(N([OQ1])*)]		3
IMPVAL	[$(NC=O)]		3
IMPVAL	[$(N(~[OQ1])~[OQ1])]	3
IMPVAL	[$([Nr0]C=[Nr0])]	3
IMPVAL	[$(N=*)]		2
#IMPVAL	[$([Nr0]=C[Nr0])]	2 #uncomment this line for cansmi testing
IMPVAL  [$([#7Q1-]=*)]          1
IMPVAL	[n]			2
IMPVAL	[n-]			2
IMPVAL  [n+]			3

IMPVAL	[#15Q4]			4
IMPVAL	[#15Q3]			3
IMPVAL	[#15Q2]			3
IMPVAL	[#15Q1^3]		3
IMPVAL	[#15Q1^2]		3
IMPVAL  [$([#15]=[#6])]         2
IMPVAL  [pQ2]			2

IMPVAL	[#16Q4]			4
IMPVAL	[#16Q3]			3
IMPVAL	[#16Q2]			2
IMPVAL	[$([#16Q1]-*)]		2
IMPVAL	[#16Q1^2]		1
IMPVAL  [s]                     2
IMPVAL  [#16Q1-]		1

IMPVAL  [#5]			3
IMPVAL  [as]			3
#
#EXTERNAL TYPE RULES
#
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	[$([Nr0]=C([Nr0])[Nr0])]	Ng+
EXTTYP	[$([NQ1]=C[NQ1])]		Ng+
EXTTYP	[$([NQ1]C=[NQ1])]		Ng+
EXTTYP	[$(N(O)*)]			Nox
EXTTYP	[$(NC=[O,S])]			Nam
EXTTYP	[$(N(~[OQ1])~[OQ1])]		Ntr
EXTTYP	[n]				Nar

EXTTYP	[#6^3]				C3
EXTTYP	[#6^2]				C2
EXTTYP	[$(C(=O)[OQ1])]			Cac
EXTTYP	[c]				Car
EXTTYP	[#6^1]				C1
EXTTYP	[#6+]				C+
EXTTYP	[#6-]				C-

EXTTYP	[#8^3]				O3
EXTTYP	[#8^2]				O2
EXTTYP  [$(Oa)]				O2
#Uncomment the following 2 lines for correct sybyl atom typing
EXTTYP	[$([OQ2]C=[O,S])]		O3	#ester oxygen
EXTTYP  [$(Oa)]                        O3      #aromatic ether
EXTTYP	[#8-]				O-
EXTTYP  [$([#8Q1]~[#6]~[#8Q1])]         Oco2

EXTTYP	[#15]					P
EXTTYP	[#15X4+]				P3+
EXTTYP	[#15;$([#15Q4](~[OQ1])(~[OQ1])~[OQ1])]	Pac
EXTTYP  [#15;$([#15Q3](~[OQ1])~[OQ1])]		Pac

EXTTYP	[#16]					S3
EXTTYP	[#16Q3+,#16X3+]				S3+
EXTTYP	[#16;s,$([SQ1]=*)]			S2
EXTTYP	[#16Q4;$(S(=O)(=O))]			So2
EXTTYP	[#16Q3;$(S(=O))]			Sox
EXTTYP	[#16;$([#16Q4](~[OQ1])(~[OQ1])~[OQ1])]	Sac
EXTTYP	[#16;$([#16Q3](~[OQ1])~[OQ1])]		Sac

EXTTYP	[#5]				B2
EXTTYP	[#5Q4]				B3

######################## Add Extra Definitions Here ##############################


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