Uses of Interface
toxTree.tree.rules.IAlertCounter

Packages that use IAlertCounter
mic.rules   
michaelacceptors.rules   
mutant.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
 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
protected  IAlertCounter SA26.alertsCounter
           
 

Uses of IAlertCounter in michaelacceptors.rules
 

Classes in michaelacceptors.rules that implement IAlertCounter
 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
 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
protected  IAlertCounter SA26_gen.alertsCounter
           
protected  IAlertCounter SA20_nogen.alertsCounter
           
 

Uses of IAlertCounter in toxtree.plugins.dnabinding.rules
 

Classes in toxtree.plugins.dnabinding.rules that implement IAlertCounter
 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
 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
 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
 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
 class DefaultAlertCounter
           
 class StructureAlert
           
 class StructureAlertAmbit
           
 class StructureAlertCDK
           
 

Uses of IAlertCounter in verhaar.rules
 

Classes in verhaar.rules that implement IAlertCounter
 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
protected  IAlertCounter RuleLogPRange.alertsCounter
           
protected  IAlertCounter RuleIonicGroups.alertsCounter
           
protected  IAlertCounter Rule34.alertsCounter
           
protected  IAlertCounter Rule21.alertsCounter
           
protected  IAlertCounter Rule143.alertsCounter
           
protected  IAlertCounter Rule141.alertsCounter
           
protected  IAlertCounter Rule03.alertsCounter
           
 

Uses of IAlertCounter in verhaar.rules.helper
 

Classes in verhaar.rules.helper that implement IAlertCounter
 class RuleAnySubstructureCounter
           
 class RuleElementsCounter
           
 class RuleOnlyAllowedSubstructuresCounter
           
 

Fields in verhaar.rules.helper declared as IAlertCounter
protected  IAlertCounter RuleOnlyAllowedSubstructuresCounter.alertsCounter
           
protected  IAlertCounter RuleElementsCounter.alertsCounter
           
protected  IAlertCounter RuleAnySubstructureCounter.alertsCounter
           
 



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