caddsuite_linux_x86_64: CADDSuite/data/OpenBabel/SMARTS

annotate CADDSuite/data/OpenBabel/SMARTS_InteLigand.txt @ 0:bac3c274238f

Migrated tool version 0.93 from old tool shed archive to new tool shed repository

author	marcel
date	Tue, 07 Jun 2011 16:43:30 -0400
parents
children

rev	line source
0 bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	1 #
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	2 # SMARTS Patterns for Functional Group Classification
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	3 #
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	4 # written by Christian Laggner
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	5 # Copyright 2005 Inte:Ligand Software-Entwicklungs und Consulting GmbH
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	6 #
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	7 # Released under the Lesser General Public License (LGPL license)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	8 # see http://www.gnu.org/copyleft/lesser.html
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	9 # Modified from Version 221105
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	10 #####################################################################################################
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	11
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	12 # General Stuff:
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	13 # These patters were written in an attempt to represent the classification of organic compounds
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	14 # from the viewpoint of an organic chemist.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	15 # They are often very restrictive. This may be generally a good thing, but it also takes some time
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	16 # for filtering/indexing large compound sets.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	17 # For filtering undesired groups (in druglike compounds) one will want to have more general patterns
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	18 # (e.g. you don't want any halide of any acid, neither aldehyde nor formyl esters and amides, ...).
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	19 #
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	20
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	21 # Part I: Carbon
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	22 # ==============
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	23
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	24
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	25 # I.1: Carbon-Carbon Bonds
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	26 # ------------------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	27
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	28 # I.1.1 Alkanes:
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	29
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	30 Primary_carbon: [CX4H3][#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	31
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	32 Secondary_carbon: [CX4H2]([#6])[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	33
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	34 Tertiary_carbon: [CX4H1]([#6])([#6])[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	35
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	36 Quaternary_carbon: [CX4]([#6])([#6])([#6])[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	37
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	38
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	39 # I.1.2 C-C double and Triple Bonds
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	40
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	41 Alkene: [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	42 # sp2 C may be substituted only by C or H -
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	43 # does not hit ketenes and allenes, nor enamines, enols and the like
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	44
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	45 Alkyne: [CX2]#[CX2]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	46 # non-carbon substituents (e.g. alkynol ethers) are rather rare, thus no further discrimination
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	47
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	48 Allene: [CX3]=[CX2]=[CX3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	49
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	50
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	51 # I.2: One Carbon-Hetero Bond
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	52 # ---------------------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	53
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	54
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	55 # I.2.1 Alkyl Halogenides
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	56
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	57 Alkylchloride: [ClX1][CX4]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	58 # will also hit chloromethylethers and the like, but no chloroalkenes, -alkynes or -aromats
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	59 # a more restrictive version can be obtained by modifying the Alcohol string.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	60
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	61 Alkylfluoride: [FX1][CX4]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	62
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	63 Alkylbromide: [BrX1][CX4]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	64
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	65 Alkyliodide: [IX1][CX4]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	66
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	67
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	68 # I.2.2 Alcohols and Ethers
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	69
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	70 Alcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	71 # nonspecific definition, no acetals, aminals, and the like
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	72
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	73 Primary_alcohol: [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	74
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	75 Secondary_alcohol: [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	76
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	77 Tertiary_alcohol: [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	78
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	79 Dialkylether: [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	80 # no acetals and the like; no enolethers
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	81
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	82 Dialkylthioether: [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	83 # no acetals and the like; no enolethers
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	84
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	85 Alkylarylether: [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	86 # no acetals and the like; no enolethers
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	87
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	88 Diarylether: [c][OX2][c]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	89
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	90 Alkylarylthioether: [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	91
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	92 Diarylthioether: [c][SX2][c]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	93
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	94 Oxonium: [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	95 # can't be aromatic, thus O and not #8
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	96
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	97 # I.2.3 Amines
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	98
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	99 Amine: [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	100 # hits all amines (prim/sec/tert/quart), including ammonium salts, also enamines, but not amides, imides, aminals, ...
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	101
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	102 # the following amines include also the protonated forms
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	103
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	104 Primary_aliph_amine: [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	105
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	106 Secondary_aliph_amine: [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	107
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	108 Tertiary_aliph_amine: [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	109
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	110 Quaternary_aliph_ammonium: [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	111
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	112 Primary_arom_amine: [NX3H2+0,NX4H3+]c
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	113
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	114 Secondary_arom_amine: [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	115
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	116 Tertiary_arom_amine: [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	117
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	118 Quaternary_arom_ammonium: [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	119
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	120 Secondary_mixed_amine: [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	121
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	122 Tertiary_mixed_amine: [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	123
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	124 Quaternary_mixed_ammonium: [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	125
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	126 Ammonium: [N+;!$([N]~[!#6]);!$(N=);!$([N]~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	127 # only C and H substituents allowed. Quaternary or protonated amines
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	128 # NX4+ or Nv4+ is not recognized by Daylight's depictmatch if less than four C are present
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	129
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	130
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	131 # I.2.4 Others
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	132
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	133 Alkylthiol: [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	134
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	135 Dialkylthioether: [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	136
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	137 Alkylarylthioether: [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	138
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	139 Disulfide: [SX2D2][SX2D2]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	140
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	141 1,2-Aminoalcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	142 # does not hit alpha-amino acids, enaminoalcohols, 1,2-aminoacetals, o-aminophenols, etc.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	143
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	144 1,2-Diol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	145 # does not hit alpha-hydroxy acids, enolalcohols, 1,2-hydroxyacetals, 1,2-diphenols, etc.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	146
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	147 1,1-Diol: [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	148
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	149 Hydroperoxide: [OX2H][OX2]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	150 #does not neccessarily have to be connected to a carbon atom, includes also hydrotrioxides
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	151
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	152 Peroxo: [OX2D2][OX2D2]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	153
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	154 Organolithium_compounds: [LiX1][#6,#14]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	155
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	156 Organomagnesium_compounds: [MgX2][#6,#14]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	157 # not restricted to Grignard compounds, also dialkyl Mg
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	158
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	159 Organometallic_compounds: [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	160 # very general, includes all metals covalently bound to carbon
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	161
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	162
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	163 # I.3: Two Carbon-Hetero Bonds (Carbonyl and Derivatives)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	164 # ----------------------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	165
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	166 # I.3.1 Double Bond to Hetero
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	167
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	168 Aldehyde: [$([CX3H][#6]),$([CX3H2])]=[OX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	169 # hits aldehydes including formaldehyde
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	170
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	171 Ketone: [#6][CX3](=[OX1])[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	172 # does not include oxo-groups connected to a (hetero-) aromatic ring
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	173
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	174 Thioaldehyde: [$([CX3H][#6]),$([CX3H2])]=[SX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	175
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	176 Thioketone: [#6][CX3](=[SX1])[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	177 # does not include thioxo-groups connected to a (hetero-) aromatic ring
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	178
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	179 Imine: [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	180 # nitrogen is not part of an amidelike strukture, nor of an aromatic ring, but can be part of an aminal or similar
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	181
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	182 Immonium: [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	183
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	184 Oxime: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	185
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	186 Oximether: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	187 # ether, not ester or amide; does not hit isoxazole
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	188
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	189
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	190 # I.3.2. Two Single Bonds to Hetero
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	191
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	192 Acetal: [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	193 # does not hit hydroxy-methylesters, ketenacetals, hemiacetals, orthoesters, etc.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	194
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	195 Hemiacetal: [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	196
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	197 Aminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	198 # Ns are not part of an amide or similar. v3 ist to exclude nitro and similar groups
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	199
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	200 Hemiaminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	201
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	202 Thioacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	203
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	204 Thiohemiacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	205
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	206 Halogen_acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	207 # hits chloromethylenethers and other reactive alkylating agents
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	208
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	209 Acetal_like: [NX3v3,SX2,OX2;!$(C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(C=[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	210 # includes all of the above and other combinations (S-C-N, hydrates, ...), but still no aminomethylenesters and similar
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	211
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	212 Halogenmethylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	213 # also reactive alkylating agents. Acid does not have to be carboxylic acid, also S- and P-based acids allowed
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	214
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	215 NOS_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(*=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(C=[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	216 # Same as above, but N,O or S instead of halogen. Ester/amide allowed only on one side
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	217
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	218 Hetero_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(*=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(C=[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	219 # Combination of the last two patterns
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	220
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	221 Cyanhydrine: [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	222
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	223
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	224 # I.3.3 Single Bond to Hetero, C=C Double Bond (Enols and Similar)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	225
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	226 Chloroalkene: [ClX1][CX3]=[CX3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	227
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	228 Fluoroalkene: [FX1][CX3]=[CX3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	229
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	230 Bromoalkene: [BrX1][CX3]=[CX3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	231
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	232 Iodoalkene: [IX1][CX3]=[CX3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	233
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	234 Enol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	235 # no phenols
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	236
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	237 Endiol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	238 # no 1,2-diphenols, ketenacetals, ...
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	239
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	240 Enolether: [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	241 # finds also endiodiethers, but not enolesters, no aromats
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	242
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	243 Enolester: [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	244
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	245
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	246 Enamine: [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	247 # does not hit amines attached to aromatic rings, nor may the nitrogen be aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	248
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	249 Thioenol: [SX2H][CX3;$([H1]),$(C[#6])]=[CX3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	250
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	251 Thioenolether: [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	252
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	253
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	254 # I.4: Three Carbon-Hetero Bonds (Carboxyl and Derivatives)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	255 # ------------------------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	256
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	257 Acylchloride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	258
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	259 Acylfluoride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	260
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	261 Acylbromide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	262
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	263 Acyliodide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	264
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	265 Acylhalide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	266 # all of the above
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	267
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	268
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	269 # The following contains all simple carboxylic combinations of O, N, S, & Hal -
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	270 # - acids, esters, amides, ... as well as a few extra cases (anhydride, hydrazide...)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	271 # Cyclic structures (including aromats) like lactones, lactames, ... got their own
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	272 # definitions. Structures where both heteroatoms are part of an aromatic ring
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	273 # (oxazoles, imidazoles, ...) were excluded.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	274
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	275 Carboxylic_acid: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	276 # includes carboxylate anions
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	277
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	278 Carboxylic_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	279 # does not hit anhydrides or lactones
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	280
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	281 Lactone: [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	282 # may also be aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	283
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	284 Carboxylic_anhydride: [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	285 # anhydride formed by two carboxylic acids, no mixed anhydrides (e.g. between carboxylic acid and sulfuric acid); may be part of a ring, even aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	286
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	287 Carboxylic_acid_derivative: [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	288 # includes most of the structures of I.4 and many more, also 1,3-heteroaromatics such as isoxazole
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	289
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	290 Carbothioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	291 # hits both tautomeric forms, as well as anions
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	292
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	293 Carbothioic_S_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	294
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	295 Carbothioic_S_lactone: [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	296 # may also be aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	297
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	298 Carbothioic_O_ester: [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	299
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	300 Carbothioic_O_lactone: [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	301
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	302 Carbothioic_halide: [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	303
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	304 Carbodithioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	305
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	306 Carbodithioic_ester: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	307
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	308 Carbodithiolactone: [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	309
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	310
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	311 Amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	312 # does not hit lactames
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	313
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	314 Primary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	315
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	316 Secondary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	317
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	318 Tertiary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	319
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	320 Lactam: [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	321 # cyclic amides, may also be aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	322
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	323 Alkyl_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	324 # may be part of a ring, even aromatic. only C allowed at central N. May also be triacyl amide
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	325
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	326 N_hetero_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	327 # everything else than H or C at central N
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	328
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	329 Imide_acidic: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1])
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	330 # can be deprotonated
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	331
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	332 Thioamide: [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	333 # does not hit thiolactames
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	334
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	335 Thiolactam: [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	336 # cyclic thioamides, may also be aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	337
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	338
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	339 Oximester: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	340 # may also be part of a ring / aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	341
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	342 Amidine: [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	343 # only basic amidines, not as part of aromatic ring (e.g. imidazole)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	344
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	345 Hydroxamic_acid: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	346
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	347 Hydroxamic_acid_ester: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	348 # does not hit anhydrides of carboxylic acids withs hydroxamic acids
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	349
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	350
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	351 Imidoacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	352 # not cyclic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	353
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	354 Imidoacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	355 # the enamide-form of lactames. may be aromatic like 2-hydroxypyridine
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	356
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	357 Imidoester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	358 # esters of the above structures. no anhydrides.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	359
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	360 Imidolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	361 # no oxazoles and similar
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	362
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	363 Imidothioacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	364 # not cyclic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	365
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	366 Imidothioacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	367 # the enamide-form of thiolactames. may be aromatic like 2-thiopyridine
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	368
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	369 Imidothioester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	370 # thioesters of the above structures. no anhydrides.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	371
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	372 Imidothiolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	373 # no thioxazoles and similar
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	374
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	375 Amidine: [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	376 # only basic amidines, not substituted by carbonyl or thiocarbonyl, not as part of a ring
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	377
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	378 Imidolactam: [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	379 # one of the two C~N bonds is part of a ring (may be aromatic), but not both - thus no imidazole
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	380
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	381 Imidoylhalide: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	382 # not cyclic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	383
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	384 Imidoylhalide_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	385 # may also be aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	386
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	387 # may be ring, aromatic, substituted with carbonyls, hetero, ...
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	388 # (everything else would get too complicated)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	389
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	390 Amidrazone: [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	391 # hits both tautomers. as above, it may be ring, aromatic, substituted with carbonyls, hetero, ...
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	392
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	393
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	394 Alpha_aminoacid: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	395 # N may be alkylated, but not part of an amide (as in peptides), ionic forms are included
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	396 # includes also non-natural aminoacids with double-bonded or two aliph./arom. substituents at alpha-C
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	397 # N may not be aromatic as in 1H-pyrrole-2-carboxylic acid
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	398
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	399 Alpha_hydroxyacid: [OX2H][C][CX3](=[OX1])[OX2H,OX1-]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	400
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	401 Peptide_middle: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	402 # finds peptidic structures which are neither C- nor N-terminal. Both neighbours must be amino-acids/peptides
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	403
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	404 Peptide_C_term: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	405 # finds C-terminal amino acids
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	406
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	407 Peptide_N_term: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	408 # finds N-terminal amino acids. As above, N may be substituted, but not part of an amide-bond.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	409
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	410
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	411 Carboxylic_orthoester: [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	412 # hits also anhydride like struktures (e. g. HC(OMe)2-OC=O residues)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	413
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	414 Ketene: [CX3]=[CX2]=[OX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	415
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	416 Ketenacetal: [#7X2,#8X3,#16X2;$([#6,#14])][#6X3]([#7X2,#8X3,#16X2;$([#6,#14])])=[#6X3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	417 # includes aminals, silylacetals, ketenesters, etc. C=C DB is not aromatic, everything else may be
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	418
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	419 Nitrile: [NX1]#[CX2]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	420 # includes cyanhydrines
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	421
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	422 Isonitrile: [CX1-]#[NX2+]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	423
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	424
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	425 Vinylogous_carbonyl_or_carboxyl_derivative: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	426 # may be part of a ring, even aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	427
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	428 Vinylogous_acid: [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	429
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	430 Vinylogous_ester: [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	431
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	432 Vinylogous_amide: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	433
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	434 Vinylogous_halide: [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	435
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	436
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	437
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	438 # I.5: Four Carbon-Hetero Bonds (Carbonic Acid and Derivatives)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	439 # -----------------------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	440
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	441 Carbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	442 # may be part of a ring, even aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	443
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	444 Carbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	445
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	446 Carbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	447 # unstable
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	448
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	449 Carbonic_acid_derivatives: [!#6][#6X3](=[!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	450
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	451
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	452 Thiocarbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	453 # may be part of a ring, even aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	454
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	455 Thiocarbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	456
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	457 Thiocarbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	458
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	459
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	460 Urea:[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	461 # no check whether part of imide, biuret, etc. Aromatic structures are only hit if
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	462 # both N share no double bonds, like in the dioxo-form of uracil
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	463
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	464 Thiourea: [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	465
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	466 Isourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	467 # O may be substituted. no check whether further amide-like bonds are present. Aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	468 # structures are only hit if single bonded N shares no additional double bond, like in
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	469 # the 1-hydroxy-3-oxo form of uracil
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	470
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	471 Isothiourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	472
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	473 Guanidine: [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	474 # also hits guanidinium salts. v3 and v4 to avoid nitroamidines
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	475
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	476 Carbaminic_acid: [NX3]C(=[OX1])[O;X2H,X1-]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	477 # quite unstable, unlikely to be found. Also hits salts
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	478
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	479 Urethan: [#7X3][#6](=[OX1])[#8X2][#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	480 # also hits when part of a ring, no check whether the last C is part of carbonyl
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	481
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	482 Biuret: [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	483
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	484 Semicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	485
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	486 Carbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	487
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	488 Semicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	489
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	490 Carbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	491
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	492 Thiosemicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	493
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	494 Thiocarbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	495
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	496 Thiosemicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	497
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	498 Thiocarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	499
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	500
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	501 Isocyanate: [NX2]=[CX2]=[OX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	502
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	503 Cyanate: [OX2][CX2]#[NX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	504
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	505 Isothiocyanate: [NX2]=[CX2]=[SX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	506
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	507 Thiocyanate: [SX2][CX2]#[NX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	508
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	509 Carbodiimide: [NX2]=[CX2]=[NX2]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	510
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	511 Orthocarbonic_derivatives: [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	512 # halogen allowed just once, to avoid mapping to -OCF3 and similar groups (much more
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	513 # stable as for example C(OCH3)4)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	514
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	515
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	516 # I.6 Aromatics
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	517 # -------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	518
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	519 # I know that this classification is not very logical, arylamines are found under I.2 ...
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	520
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	521 Phenol: [OX2H][c]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	522
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	523 1,2-Diphenol: [OX2H][c][c][OX2H]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	524
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	525 Arylchloride: [Cl][c]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	526
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	527 Arylfluoride: [F][c]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	528
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	529 Arylbromide: [Br][c]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	530
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	531 Aryliodide: [I][c]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	532
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	533 Arylthiol: [SX2H][c]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	534
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	535 Iminoarene: [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	536 # N may be substituted with H or C, but not carbonyl or similar
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	537 # aromatic atom is always C, not S or P (these are not planar when substituted)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	538
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	539 Oxoarene: [c]=[OX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	540
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	541 Thioarene: [c]=[SX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	542
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	543 Hetero_N_basic_H: [nX3H1+0]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	544 # as in pyrole. uncharged to exclude pyridinium ions
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	545
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	546 Hetero_N_basic_no_H: [nX3H0+0]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	547 # as in N-methylpyrole. uncharged to exclude pyridinium ions
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	548
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	549 Hetero_N_nonbasic: [nX2,nX3+]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	550 # as in pyridine, pyridinium
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	551
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	552 Hetero_O: [o]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	553
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	554 Hetero_S: [sX2]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	555 # X2 because Daylight's depictmatch falsely describes C1=CS(=O)C=C1 as aromatic
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	556 # (is not planar because of lonepair at S)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	557
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	558 Heteroaromatic: [a;!c]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	559
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	560
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	561 # Part II: N, S, P, Si, B
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	562 # =======================
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	563
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	564
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	565 # II.1 Nitrogen
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	566 # -------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	567
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	568 Nitrite: [NX2](=[OX1])[O;$([X2]),$([X1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	569 # hits nitrous acid, its anion, esters, and other O-substituted derivatives
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	570
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	571 Thionitrite: [SX2][NX2]=[OX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	572
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	573 Nitrate: [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	574 # hits nitric acid, its anion, esters, and other O-substituted derivatives
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	575
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	576 Nitro: [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	577 # hits nitro groups attached to C,N, ... but not nitrates
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	578
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	579 Nitroso: [NX2](=[OX1])[!#7;!#8]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	580 # no nitrites, no nitrosamines
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	581
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	582 Azide: [NX1]~[NX2]~[NX2,NX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	583 # hits both mesomeric forms, also anion
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	584
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	585 Acylazide: [CX3](=[OX1])[NX2]~[NX2]~[NX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	586
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	587 Diazo: [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	588
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	589 Diazonium: [#6][NX2+]#[NX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	590
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	591 Nitrosamine: [#7;!$(N*=O)][NX2]=[OX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	592
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	593 Nitrosamide: [NX2](=[OX1])N-*=O
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	594 # includes nitrososulfonamides
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	595
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	596 N-Oxide: [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	597 # Hits both forms. Won't hit azoxy, nitro, nitroso, or nitrate.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	598
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	599
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	600 Hydrazine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	601 # no hydrazides
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	602
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	603 Hydrazone: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	604
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	605 Hydroxylamine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	606 # no discrimination between O-, N-, and O,N-substitution
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	607
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	608
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	609 # II.2 Sulfur
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	610 # -----------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	611
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	612 Sulfon: [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	613 # can't be aromatic, thus S and not #16
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	614
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	615 Sulfoxide: [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	616
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	617 Sulfonium: [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	618 # can't be aromatic, thus S and not #16
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	619
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	620 Sulfuric_acid: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	621 # includes anions
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	622
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	623 Sulfuric_monoester: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	624
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	625 Sulfuric_diester: [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	626
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	627 Sulfuric_monoamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	628
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	629 Sulfuric_diamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	630
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	631 Sulfuric_esteramide: [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	632
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	633 Sulfuric_derivative: [SX4D4](=[!#6])(=[!#6])([!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	634 # everything else (would not be a "true" derivative of sulfuric acid, if one of the substituents were less electronegative
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	635 # than sulfur, but this should be very very rare, anyway)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	636
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	637
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	638
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	639 #### sulfurous acid and derivatives missing!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	640
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	641
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	642
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	643
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	644 Sulfonic_acid: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	645
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	646 Sulfonamide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	647
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	648 Sulfonic_ester: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	649
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	650 Sulfonic_halide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	651
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	652 Sulfonic_derivative: [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	653 # includes all of the above and many more
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	654 # for comparison: this is what "all sulfonic derivatives but not the ones above" would look like:
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	655 # [$([SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6;!O])[!#6]),$([SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[!$([FX1,ClX1,BrX1,IX1]);!$([#6]);!$([OX2H]);!$([OX1-]);!$([OX2][#6;!$(C=[O,N,S])]);!$([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	656
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	657
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	658 Sulfinic_acid: [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	659
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	660 Sulfinic_amide: [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	661
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	662 Sulfinic_ester: [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	663
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	664 Sulfinic_halide: [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	665
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	666 Sulfinic_derivative: [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	667
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	668 Sulfenic_acid: [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	669
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	670 Sulfenic_amide: [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	671
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	672 Sulfenic_ester: [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	673
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	674 Sulfenic_halide: [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	675
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	676 Sulfenic_derivative: [SX2;$([H1]),$([H0][#6])][!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	677
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	678
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	679 # II.3 Phosphorous
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	680 # ----------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	681
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	682 Phosphine: [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	683 # similar to amine, but less restrictive: includes also amide- and aminal-analogues
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	684
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	685 Phosphine_oxide: [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	686
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	687 Phosphonium: [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	688 # similar to Ammonium
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	689
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	690 Phosphorylen: [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	691
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	692
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	693 # conventions for the following acids and derivatives:
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	694 # acids find protonated and deprotonated acids
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	695 # esters do not find mixed anhydrides ( ...P-O-C(=O))
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	696 # derivatives: subtituents which go in place of the OH and =O are not H or C (may also be O,
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	697 # thus including acids and esters)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	698
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	699 Phosphonic_acid: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	700 # includes anions
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	701
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	702 Phosphonic_monoester: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	703
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	704 Phosphonic_diester: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	705
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	706 Phosphonic_monoamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	707
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	708 Phosphonic_diamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	709
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	710 Phosphonic_esteramide: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	711
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	712 Phosphonic_acid_derivative: [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	713 # all of the above and much more
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	714
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	715
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	716 Phosphoric_acid: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	717 # includes anions
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	718
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	719 Phosphoric_monoester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	720
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	721 Phosphoric_diester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	722
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	723 Phosphoric_triester: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	724
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	725 Phosphoric_monoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	726
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	727 Phosphoric_diamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	728
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	729 Phosphoric_triamide: [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	730
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	731 Phosphoric_monoestermonoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	732
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	733 Phosphoric_diestermonoamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	734
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	735 Phosphoric_monoesterdiamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	736
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	737 Phosphoric_acid_derivative: [PX4D4](=[!#6])([!#6])([!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	738
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	739
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	740 Phosphinic_acid: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	741
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	742 Phosphinic_ester: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	743
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	744 Phosphinic_amide: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	745
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	746 Phosphinic_acid_derivative: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	747
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	748
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	749 Phosphonous_acid: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	750
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	751 Phosphonous_monoester: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	752
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	753 Phosphonous_diester: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	754
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	755 Phosphonous_monoamide: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	756
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	757 Phosphonous_diamide: [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	758
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	759 Phosphonous_esteramide: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	760
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	761 Phosphonous_derivatives: [PX3;$([D2]),$([D3][#6])]([!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	762
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	763
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	764 Phosphinous_acid: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	765
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	766 Phosphinous_ester: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	767
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	768 Phosphinous_amide: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	769
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	770 Phosphinous_derivatives: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	771
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	772
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	773 # II.4 Silicon
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	774 # ------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	775
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	776 Quart_silane: [SiX4]([#6])([#6])([#6])[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	777 # four C-substituents. non-reactive, non-toxic, in experimental phase for drug development
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	778
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	779 Non-quart_silane: [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	780 # has 1-4 hydride(s), reactive. Daylight's depictmatch does not add hydrogens automatically to
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	781 # the free positions at Si, thus Hs had to be added implicitly
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	782
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	783 Silylmonohalide: [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	784 # reagents for inserting protection groups
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	785
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	786 Het_trialkylsilane: [SiX4]([!#6])([#6])([#6])[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	787 # mostly acid-labile protection groups such as trimethylsilyl-ethers
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	788
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	789 Dihet_dialkylsilane: [SiX4]([!#6])([!#6])([#6])[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	790
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	791 Trihet_alkylsilane: [SiX4]([!#6])([!#6])([!#6])[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	792
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	793 Silicic_acid_derivative: [SiX4]([!#6])([!#6])([!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	794 # four substituent which are neither C nor H
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	795
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	796
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	797 # II.5 Boron
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	798 # ----------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	799
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	800 Trialkylborane: [BX3]([#6])([#6])[#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	801 # also carbonyls allowed
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	802
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	803 Boric_acid_derivatives: [BX3]([!#6])([!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	804 # includes acids, esters, amides, ... H-substituent at B is very rare.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	805
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	806 Boronic_acid_derivative: [BX3]([!#6])([!#6])[!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	807 # # includes acids, esters, amides, ...
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	808
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	809 Borohydride: [BH1,BH2,BH3,BH4]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	810 # at least one H attached to B
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	811
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	812 Quaternary_boron: [BX4]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	813 # mostly borates (negative charge), in complex with Lewis-base
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	814
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	815
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	816
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	817 # Part III: Some Special Patterns
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	818 # ===============================
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	819
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	820
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	821 # III.1 Chains
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	822 # ------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	823
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	824 # some simple chains
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	825
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	826
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	827
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	828 # III.2 Rings
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	829 # -----------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	830
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	831 Aromatic: a
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	832
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	833 Heterocyclic: [!#6;!R0]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	834 # may be aromatic or not
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	835
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	836 Epoxide: [OX2r3]1[#6r3][#6r3]1
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	837 # toxic/reactive. may be annelated to aromat, but must not be aromatic itself (oxirane-2,3-dione)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	838
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	839 NH_aziridine: [NX3H1r3]1[#6r3][#6r3]1
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	840 # toxic/reactive according to Maybridge's garbage filter
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	841
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	842 Spiro: [D4R;$((@)(@)(@)@*)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	843 # at least two different rings can be found which are sharing just one atom.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	844 # these two rings can be connected by a third ring, so it matches also some
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	845 # bridged systems, like morphine
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	846
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	847 Annelated_rings: [R;$((@)(@)@);!$([R2;$((@)(@)(@)@)])]@[R;$((@)(@)@);!$([R2;$((@)(@)(@)@)])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	848 # two different rings sharing exactly two atoms
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	849
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	850 Bridged_rings: [R;$((@)(@)@);!$([D4R;$((@)(@)(@)@)]);!$([R;$((@)(@)@);!$([R2;$((@)(@)(@)@)])]@[R;$((@)(@)@);!$([R2;$((@)(@)(@)@*)])])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	851 # part of two or more rings, not spiro, not annelated -> finds bridgehead atoms,
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	852 # but only if they are not annelated at the same time - otherwise impossible (?)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	853 # to distinguish from non-bridgehead annelated atoms
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	854
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	855 # some basic ring-patterns (just size, no other information):
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	856
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	857
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	858
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	859
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	860
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	861 # III.3 Sugars and Nucleosides/Nucleotides, Steroids
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	862 # --------------------------------------------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	863
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	864 # because of the large variety of sugar derivatives, different patterns can be applied.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	865 # The choice of patterns and their combinations will depend on the contents of the database
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	866 # e.g. natural products, nucleoside analoges with modified sugars, ... as well as on the
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	867 # desired restriction
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	868
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	869
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	870 Sugar_pattern_1: [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	871 # 5 or 6-membered ring containing one O and at least one (r5) or two (r6) oxygen-substituents.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	872
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	873 Sugar_pattern_2: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	874 # 5 or 6-membered ring containing one O and an acetal-like bond at postion 2.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	875
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	876 Sugar_pattern_combi: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	877 # combination of the two above
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	878
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	879 Sugar_pattern_2_reducing: [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	880 # 5 or 6-membered cyclic hemi-acetal
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	881
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	882 Sugar_pattern_2_alpha: [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	883 # 5 or 6-membered cyclic hemi-acetal
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	884
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	885 Sugar_pattern_2_beta: [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	886 # 5 or 6-membered cyclic hemi-acetal
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	887
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	888 ##Poly_sugar_1: ([OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)].[OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)])
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	889 # pattern1 occours more than once (in same molecule, but moieties don't have to be adjacent!)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	890
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	891 ##Poly_sugar_2: ([OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)].[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)])
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	892 # pattern2 occours more than once (in same molecule, but moieties don't have to be adjacent!)
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	893
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	894
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	895 # III.4 Everything else...
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	896 # ------------------------
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	897
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	898 Conjugated_double_bond: =[]=,#,:[]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	899
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	900 Conjugated_tripple_bond: #[]=,#,:[]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	901
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	902 Cis_double_bond: /[D2]=[D2]\
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	903 # only one single-bonded substituent on each DB-atom. no aromats.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	904 # only found when character of DB is explicitely stated.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	905
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	906 Trans_double_bond: /[D2]=[D2]/
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	907 # analog
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	908
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	909 Mixed_anhydrides: [$(=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	910 # should hits all combinations of two acids
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	911
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	912 Halogen_on_hetero: [FX1,ClX1,BrX1,IX1][!#6]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	913
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	914 Halogen_multi_subst: [F,Cl,Br,I;!$([X1]);!$([X0-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	915 # Halogen which is not mono-substituted nor an anion, e.g. chlorate.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	916 # Most of these cases should be also filtered by Halogen_on_hetero.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	917
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	918 Trifluoromethyl: [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1])
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	919 # C with three F attached, connected to anything which is not another halogen
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	920
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	921 C_ONS_bond: [#6]~[#7,#8,#16]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	922 # probably all drug-like molecules have at least one O, N, or S connected to a C -> nice filter
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	923
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	924 ## Mixture: ().()
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	925 # two or more seperate parts, may also be salt
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	926 # component-level grouping is not yet supported in Open Babel Version 2.0
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	927
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	928
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	929 Charged: [!+0]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	930
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	931 Anion: [-1,-2,-3,-4,-5,-6,-7]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	932
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	933 Kation: [+1,+2,+3,+4,+5,+6,+7]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	934
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	935 Salt: ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7])
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	936 # two or more seperate components with opposite charges
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	937
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	938 ##Zwitterion: ([-1,-2,-3,-4,-5,-6,-7].[+1,+2,+3,+4,+5,+6,+7])
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	939 # both negative and positive charges somewhere within the same molecule.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	940
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	941 1,3-Tautomerizable: [$([#7X2,OX1,SX1]=[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]=),$([#7X3,OX2,SX2;!H0]:n)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	942 # 1,3 migration of H allowed. Includes keto/enol and amide/enamide.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	943 # Aromatic rings must stay aromatic - no keto form of phenol
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	944
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	945 1,5-Tautomerizable: [$([#7X2,OX1,SX1]=,:*=,:[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]==),$([#7X3,OX2,SX2;!H0]=,:*:n)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	946
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	947 Rotatable_bond: [!$(#)&!D1]-!@[!$(#)&!D1]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	948 # taken from http://www.daylight.com/support/contrib/smarts/content.html
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	949
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	950 Michael_acceptor: [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	951 # the classical case: C=C near carbonyl, nitrile, nitro, or similar
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	952 # Oxo-heteroaromats and similar are not included.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	953
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	954 Dicarbodiazene: [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1])
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	955 # Michael-like acceptor, see Mitsunobu reaction
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	956
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	957 # H-Bond_donor:
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	958
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	959 # H-Bond_acceptor:
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	960
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	961 # Pos_ionizable:
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	962
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	963 # Neg_ionizable:
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	964
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	965 # Unlikely_ions:
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	966 # O+,N-,C+,C-, ...
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	967
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	968 CH-acidic: [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$([S,O,N;H1,H2]);!$([+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	969 # C-H alpha to carbony, nitro or similar, C is not double-bonded, only C, H, S,P=O and nitro substituents allowed.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	970 # pentadiene is included. acids, their salts, prim./sec. amides, and imides are excluded.
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	971 # hits also CH-acidic_strong
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	972
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	973 CH-acidic_strong: [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$([S,O,N;H1,H2]);!$([+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$([S,O,N;H1,H2]);!$([+0][S,O;X1-])]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	974 # same as above (without pentadiene), but carbonyl or similar on two or three sides
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	975
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	976 Chiral_center_specified: [$([@](~)(~)()),$([@H]()()),$([@](~)()),$([@H](~)~)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	977 # Hits atoms with tetrahedral chirality, if chiral center is specified in the SMILES string
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	978 # depictmach does not find oxonium, sulfonium, or sulfoxides!
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	979
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	980 # Chiral_center_unspecified: [$([@?](~)(~)()),$([@?H]()()),$([@?](~)()),$([@?H](~)~)]
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	981 # Hits atoms with tetrahedral chirality, if chiral center is not specified in the SMILES string
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	982 # "@?" (unspecified chirality) is not yet supported in Open Babel Version 2.0
bac3c274238f Migrated tool version 0.93 from old tool shed archive to new tool shed repository marcel parents: diff changeset	983

Mercurial > repos > marcel > caddsuite_linux_x86_64

annotate CADDSuite/data/OpenBabel/SMARTS_InteLigand.txt @ 0:bac3c274238f