Uses of Interface
toxTree.tree.rules.IAlertCounter

Packages that use IAlertCounter

Package	Description
mic.rules
michaelacceptors.rules
mutant.rules
toxtree.plugins.ames.rules
toxtree.plugins.dnabinding.rules
toxtree.plugins.func.rules
toxtree.plugins.proteinbinding.rules
toxtree.plugins.skinsensitisation.rules
toxTree.tree.rules	The package contains several generic implementations of IDecisionRule rules
verhaar.rules	The package contains implementations of IDecisionRule rules for VerhaarScheme decision tree.
verhaar.rules.helper

Uses of IAlertCounter in mic.rules

Classes in mic.rules that implement IAlertCounter

Modifier and Type	Class and Description
class	PB29
class	PB30
class	SA1
class	SA10
class	SA11 Aliphatic and aromatic aldehydes.
class	SA12 Quinones
class	SA13
class	SA14
class	SA15
class	SA16
class	SA18 TODO Reimplement PAH recognition in a more robust way, possibly by generalized Hueckel rule (Randic)
class	SA19 If the set of fused rings contains > 2 aromatic rings and > 1 heteroaromatic rings, the rule returns true.
class	SA2 SA2
class	SA21
class	SA22
class	SA23
class	SA24
class	SA25
class	SA26 Aromatic ring N-oxide.
class	SA27 Nitro aromatic (and more).
class	SA28 TODO - this is same as mutant.rules.SA28 -to reuse instead of copy
class	SA28bis Aromatic mono- and dialkylamine (with exceptions).
class	SA28ter Aromatic N-acyl amine.
class	SA29
class	SA3
class	SA30
class	SA32
class	SA33
class	SA34
class	SA35
class	SA36
class	SA4
class	SA5
class	SA6
class	SA7
class	SA8
class	SA9

Fields in mic.rules declared as IAlertCounter

Modifier and Type	Field and Description
protected IAlertCounter	SA26.alertsCounter

Uses of IAlertCounter in michaelacceptors.rules

Classes in michaelacceptors.rules that implement IAlertCounter

Modifier and Type	Class and Description
class	Rule1 TODO with StructureAlertAmbit [CH]#CC=O doesn't match COC(=O)C#C while C#CC=O matches COC(=O)C#C
class	Rule10A
class	Rule10B
class	Rule12A
class	Rule12B
class	Rule13A
class	Rule13B
class	Rule2
class	Rule3
class	Rule4A
class	Rule4B
class	Rule5
class	Rule6
class	Rule7
class	Rule8
class	Rule9A
class	Rule9B

Uses of IAlertCounter in mutant.rules

Classes in mutant.rules that implement IAlertCounter

Modifier and Type	Class and Description
class	SA1_gen
class	SA10_gen
class	SA11_gen Aliphatic and aromatic aldehydes.
class	SA12_gen Quinones
class	SA13_gen
class	SA14_gen
class	SA15_gen
class	SA16_gen
class	SA17_nogen
class	SA18_gen TODO Reimplement PAH recognition in a more robust way, possibly by generalized Hueckel rule (Randic)
class	SA19_gen If the set of fused rings contains > 2 aromatic rings and > 1 heteroaromatic rings, the rule returns true.
class	SA2_gen SA2_gen
class	SA20_nogen
class	SA21_gen
class	SA22_gen
class	SA23_gen
class	SA24_gen
class	SA25_gen
class	SA26_gen Aromatic ring N-oxide.
class	SA27_gen Nitro aromatic (and more).
class	SA28_gen [a;!$(a(a[A;!#1])(a[A;!#1]));!$(aa[CX3](=O)[OX2H1]);!$(aa[SX4](=[OX1])(=[OX1])([O-]));!$(aaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aaaaaa[SX4](=[OX1])(=[OX1])([O-]));!$(aN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]));!$(aaaaaN(CC[Cl,Br,F,I])(CC[Cl,Br,F,I]))]!@[$([NX3;v3]([#1,CX4,CX3])([#1,CX4,CX3])),$([NX3;v3]([OX2H])([#1,CX4,CX3])),$([NX3;v3]([#1,CX4])OC=O)]
class	SA28bis_gen Aromatic mono- and dialkylamine (with exceptions).
class	SA28ter_gen Aromatic N-acyl amine.
class	SA29_gen
class	SA3_gen
class	SA30_gen
class	SA31a_nogen TODO Verify how many level of recursive smarts are supported TODO verify what's wrong with matching c;R
class	SA31b_nogen
class	SA31c_nogen
class	SA37_gen
class	SA38_gen
class	SA39_gen_and_nogen
class	SA4_gen
class	SA40_nogen
class	SA41_nogen
class	SA42_nogen
class	SA43_nogen
class	SA44_nogen
class	SA45_nogen
class	SA46_nogen
class	SA47_nogen
class	SA48_nogen
class	SA49_nogen
class	SA5_gen
class	SA50_nogen
class	SA51_nogen
class	SA52_nogen
class	SA53_nogen
class	SA54_nogen
class	SA55_nogen
class	SA56_nogen
class	SA6_gen
class	SA7_gen
class	SA8_gen
class	SA9_gen

Fields in mutant.rules declared as IAlertCounter

Modifier and Type	Field and Description
protected IAlertCounter	SA20_nogen.alertsCounter
protected IAlertCounter	SA26_gen.alertsCounter

Uses of IAlertCounter in toxtree.plugins.ames.rules

Classes in toxtree.plugins.ames.rules that implement IAlertCounter

Modifier and Type	Class and Description
class	SA57_Ames
class	SA58_Ames
class	SA59_Ames
class	SA60_Ames
class	SA61_Ames
class	SA62_Ames
class	SA63_Ames
class	SA64_Ames
class	SA65_Ames
class	SA66_Ames
class	SA67_Ames
class	SA68_Ames
class	SA69_Ames

Fields in toxtree.plugins.ames.rules declared as IAlertCounter

Modifier and Type	Field and Description
protected IAlertCounter	SA26_gen.alertsCounter

Uses of IAlertCounter in toxtree.plugins.dnabinding.rules

Classes in toxtree.plugins.dnabinding.rules that implement IAlertCounter

Modifier and Type	Class and Description
class	DNABindingRule Parent class for all skin sens rules
class	SN1Rule SNAR

Uses of IAlertCounter in toxtree.plugins.func.rules

Classes in toxtree.plugins.func.rules that implement IAlertCounter

Modifier and Type	Class and Description
class	FG
class	FG1
class	FG10
class	FG11
class	FG12
class	FG13
class	FG14
class	FG15
class	FG16
class	FG17
class	FG18
class	FG19
class	FG2
class	FG20
class	FG21
class	FG22
class	FG23_1
class	FG23_2
class	FG23_3
class	FG23_4
class	FG23_5
class	FG23_6
class	FG23_7
class	FG23_8
class	FG23_LS
class	FG24_1
class	FG24_2
class	FG24_3
class	FG24_LS
class	FG25
class	FG26
class	FG27
class	FG28
class	FG29
class	FG3_1
class	FG3_2
class	FG3_LS
class	FG30
class	FG31_1
class	FG31_2
class	FG31_3
class	FG31_4
class	FG31_5
class	FG31_6
class	FG31_7
class	FG31_8
class	FG31_9
class	FG31_LS
class	FG32
class	FG33_1
class	FG33_2
class	FG33_3
class	FG33_4
class	FG33_5
class	FG33_6
class	FG33_7
class	FG33_8
class	FG33_LS
class	FG34_1
class	FG34_2
class	FG34_LS
class	FG35_1
class	FG35_10
class	FG35_11
class	FG35_12
class	FG35_13
class	FG35_2
class	FG35_3
class	FG35_4
class	FG35_5
class	FG35_6
class	FG35_7
class	FG35_8
class	FG35_9
class	FG35_LS
class	FG36
class	FG37_1
class	FG37_2
class	FG37_3
class	FG37_4
class	FG37_LS
class	FG38
class	FG39
class	FG4
class	FG4_1
class	FG4_2
class	FG4_LS
class	FG40
class	FG41_1
class	FG41_2
class	FG41_3
class	FG41_4
class	FG41_5
class	FG41_LS
class	FG42
class	FG43
class	FG44
class	FG45
class	FG46_1
class	FG46_2
class	FG46_LS
class	FG47
class	FG48_1
class	FG48_2
class	FG48_LS
class	FG49
class	FG5
class	FG50_1
class	FG50_2
class	FG50_3
class	FG50_LS
class	FG51_1
class	FG51_2
class	FG51_3
class	FG51_LS
class	FG52_1
class	FG52_2
class	FG52_3
class	FG52_LS
class	FG53_1
class	FG53_2
class	FG53_3
class	FG53_LS
class	FG54
class	FG55
class	FG56
class	FG57
class	FG58
class	FG59
class	FG6
class	FG60
class	FG61
class	FG62
class	FG63
class	FG64
class	FG65
class	FG66
class	FG67
class	FG68
class	FG69
class	FG7
class	FG70
class	FG71
class	FG72
class	FG73
class	FG74_1
class	FG74_2
class	FG74_3
class	FG74_4
class	FG74_5
class	FG74_6
class	FG74_7
class	FG74_LS
class	FG75_1
class	FG75_2
class	FG75_3
class	FG75_4
class	FG75_LS
class	FG76
class	FG77
class	FG78_1
class	FG78_2
class	FG78_3
class	FG78_4
class	FG78_LS
class	FG79_1
class	FG79_2
class	FG79_3
class	FG79_4
class	FG79_LS
class	FG8
class	FG80_1
class	FG80_2
class	FG80_LS
class	FG81_1
class	FG81_2
class	FG81_3
class	FG81_4
class	FG81_LS
class	FG82_1
class	FG82_2
class	FG82_3
class	FG82_4
class	FG82_LS
class	FG83_1
class	FG83_2
class	FG83_3
class	FG83_4
class	FG83_LS
class	FG84_1
class	FG84_2
class	FG84_LS
class	FG85
class	FG86
class	FG87
class	FG88
class	FG89
class	FG9
class	FG90

Uses of IAlertCounter in toxtree.plugins.proteinbinding.rules

Classes in toxtree.plugins.proteinbinding.rules that implement IAlertCounter

Modifier and Type	Class and Description
class	ProteinBindingRule Parent class for all skin sens rules

Uses of IAlertCounter in toxtree.plugins.skinsensitisation.rules

Classes in toxtree.plugins.skinsensitisation.rules that implement IAlertCounter

Modifier and Type	Class and Description
class	AcylTransferRule Acyl transfer
class	MichaelAcceptorRule Michael acceptors
class	ShiffBaseRule Shiff base
class	SkinSensitisationRule Parent class for all skin sens rules
class	SN2Rule SN2
class	SNARRule SNAR

Uses of IAlertCounter in toxTree.tree.rules

Classes in toxTree.tree.rules that implement IAlertCounter

Modifier and Type	Class and Description
class	DefaultAlertCounter
class	StructureAlert
class	StructureAlertAmbit
class	StructureAlertCDK

Uses of IAlertCounter in verhaar.rules

Classes in verhaar.rules that implement IAlertCounter

Modifier and Type	Class and Description
class	Rule01 Consists only of C,H,N,O,S,halogens (exluding I).
class	Rule03 Have a molecular mass (MW) not more than 600 Daltons.
class	Rule11 Does not contain I.
class	Rule13 Contain only C&H.
class	Rule14 Contain only C,H and halogen.
class	Rule141 Acyclic compound NOT containing halogen at beta-positions from unsaturations (e.g.
class	Rule142 Monocyclic compounds substituted with halogens.
class	Rule143 Monocyclic compounds that are unsubstituted or substituted with acyclic structures containing only C&H or complying with rule Rule141.
class	Rule144 Polycyclic compounds that are unsubstituted or substituted with acyclic structures containing only C&H or complying with Rule141.
class	Rule15 Contain only C,H,O.
class	Rule16 Contain only C,H,N.
class	Rule161 Aliphatic secondary or tertiary amines.
class	Rule17 Contain only C,H,O and halogen.
class	Rule21 Non- or weakly acidic phenols.
class	Rule22 Anilines with one nitro substituent and/or one to three chlorine substituents, and/or alkyl substituents.
class	Rule23 Be mononitroaromatics with one or two chlorine substituents and/or alkyl substituents.
class	Rule25 Pyridines with one or two chlorine substituents and/or alkyl substituents.
class	Rule4 Compounds acting by a specific mechanism.
class	RuleIonicGroups Uses QueryAssociationBond ro verify if the query compound has an ionic bond.
class	RuleLogPRange 0 <= LogP <= 6.

Fields in verhaar.rules declared as IAlertCounter

Modifier and Type	Field and Description
protected IAlertCounter	RuleLogPRange.alertsCounter
protected IAlertCounter	Rule03.alertsCounter
protected IAlertCounter	Rule34.alertsCounter
protected IAlertCounter	RuleIonicGroups.alertsCounter
protected IAlertCounter	Rule21.alertsCounter
protected IAlertCounter	Rule141.alertsCounter
protected IAlertCounter	Rule143.alertsCounter

Uses of IAlertCounter in verhaar.rules.helper

Classes in verhaar.rules.helper that implement IAlertCounter

Modifier and Type	Class and Description
class	RuleAnySubstructureCounter
class	RuleElementsCounter
class	RuleOnlyAllowedSubstructuresCounter

Fields in verhaar.rules.helper declared as IAlertCounter

Modifier and Type	Field and Description
protected IAlertCounter	RuleOnlyAllowedSubstructuresCounter.alertsCounter
protected IAlertCounter	RuleElementsCounter.alertsCounter
protected IAlertCounter	RuleAnySubstructureCounter.alertsCounter