Package psidev.psi.mi.jami.model

Interface CooperativeEffect

    • Field Detail

      • AFFECTED_INTERACTION

        static final String AFFECTED_INTERACTION
        Constant AFFECTED_INTERACTION="affected interaction"
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      • AFFECTED_INTERACTION_ID

        static final String AFFECTED_INTERACTION_ID
        Constant AFFECTED_INTERACTION_ID="MI:1150"
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      • NEGATIVE_EFFECT

        static final String NEGATIVE_EFFECT
        Constant NEGATIVE_EFFECT="negative cooperative effect"
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      • POSITIVE_EFFECT

        static final String POSITIVE_EFFECT
        Constant POSITIVE_EFFECT="positive cooperative effect"
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      • ALLOSTERIC_EFFECTOR

        static final String ALLOSTERIC_EFFECTOR
        Constant ALLOSTERIC_EFFECTOR="allosteric effector"
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      • ALLOSTERIC_EFFECTOR_ID

        static final String ALLOSTERIC_EFFECTOR_ID
        Constant ALLOSTERIC_EFFECTOR_ID="MI:1160"
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      • ALLOSTERIC_MOLECULE

        static final String ALLOSTERIC_MOLECULE
        Constant ALLOSTERIC_MOLECULE="allosteric molecule"
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      • ALLOSTERIC_MOLECULE_ID

        static final String ALLOSTERIC_MOLECULE_ID
        Constant ALLOSTERIC_MOLECULE_ID="MI:1159"
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      • ALLOSTERIC_K_RESPONSE

        static final String ALLOSTERIC_K_RESPONSE
        Constant ALLOSTERIC_K_RESPONSE="allosteric k-type response"
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      • ALLOSTERIC_K_RESPONSE_ID

        static final String ALLOSTERIC_K_RESPONSE_ID
        Constant ALLOSTERIC_K_RESPONSE_ID="MI:1162"
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      • ALLOSTERIC_V_RESPONSE

        static final String ALLOSTERIC_V_RESPONSE
        Constant ALLOSTERIC_V_RESPONSE="allosteric v-type response"
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      • ALLOSTERIC_V_RESPONSE_ID

        static final String ALLOSTERIC_V_RESPONSE_ID
        Constant ALLOSTERIC_V_RESPONSE_ID="MI:1163"
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      • HETEROTROPIC_ALLOSTERY

        static final String HETEROTROPIC_ALLOSTERY
        Constant HETEROTROPIC_ALLOSTERY="heterotropic allostery"
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      • HETEROTROPIC_ALLOSTERY_ID

        static final String HETEROTROPIC_ALLOSTERY_ID
        Constant HETEROTROPIC_ALLOSTERY_ID="MI:1168"
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      • HOMOTROPIC_ALLOSTERY

        static final String HOMOTROPIC_ALLOSTERY
        Constant HOMOTROPIC_ALLOSTERY="homotropic allostery"
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      • HOMOTROPIC_ALLOSTERY_ID

        static final String HOMOTROPIC_ALLOSTERY_ID
        Constant HOMOTROPIC_ALLOSTERY_ID="MI:1169"
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      • COOPERATIVE_EFFECT_VALUE

        static final String COOPERATIVE_EFFECT_VALUE
        Constant COOPERATIVE_EFFECT_VALUE="cooperative effect value"
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      • COOPERATIVE_EFFECT_VALUE_ID

        static final String COOPERATIVE_EFFECT_VALUE_ID
        Constant COOPERATIVE_EFFECT_VALUE_ID="MI:1152"
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      • ALLOSTERIC_DYNAMIC_CHANGE

        static final String ALLOSTERIC_DYNAMIC_CHANGE
        Constant ALLOSTERIC_DYNAMIC_CHANGE="allosteric change in dynamics"
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      • ALLOSTERIC_DYNAMIC_CHANGE_ID

        static final String ALLOSTERIC_DYNAMIC_CHANGE_ID
        Constant ALLOSTERIC_DYNAMIC_CHANGE_ID="MI:1166"
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      • ALTERED_PHYSICO_COMPATIBILITY

        static final String ALTERED_PHYSICO_COMPATIBILITY
        Constant ALTERED_PHYSICO_COMPATIBILITY="altered physicochemical compatibility"
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      • ALTERED_PHYSICO_COMPATIBILITY_ID

        static final String ALTERED_PHYSICO_COMPATIBILITY_ID
        Constant ALTERED_PHYSICO_COMPATIBILITY_ID="MI:1172"
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      • COMPOSITE_BINDING

        static final String COMPOSITE_BINDING
        Constant COMPOSITE_BINDING="composite binding site formation"
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      • COMPOSITE_BINDING_ID

        static final String COMPOSITE_BINDING_ID
        Constant COMPOSITE_BINDING_ID="MI:1171"
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      • ALLOSTERIC_STRUCTURE_CHANE

        static final String ALLOSTERIC_STRUCTURE_CHANE
        Constant ALLOSTERIC_STRUCTURE_CHANE="allosteric change in structure"
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      • ALLOSTERIC_STRUCTURE_CHANE_ID

        static final String ALLOSTERIC_STRUCTURE_CHANE_ID
        Constant ALLOSTERIC_STRUCTURE_CHANE_ID="MI:1165"
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      • PRE_ORGANIZATION

        static final String PRE_ORGANIZATION
        Constant PRE_ORGANIZATION="configurational pre-organization"
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      • EFFECT_OUTCOME

        static final String EFFECT_OUTCOME
        Constant EFFECT_OUTCOME="cooperative effect outcome"
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    • Method Detail

      • getCooperativityEvidences

        <T extends CooperativityEvidence> Collection<T> getCooperativityEvidences()
        Collection of experimental methods and publications from which this cooperative effect has been inferred. The collection cannot be null, if the CooperativeEffect does not have any cooperativityEvidences, this method should return an empty collection.
        Type Parameters:
        T - a T object
        Returns:
        Collection of experimental methods and publications

      • getAffectedInteractions

        <T extends ModelledInteraction> Collection<T> getAffectedInteractions()
        Collection of model interactions affected by this model interaction. The collection cannot be null, if the CooperativeEffect does not have any affectedInteractions, this method should return an empty collection.
        Type Parameters:
        T - a T object
        Returns:
        collection of model interactions affected by this model interaction

      • getAnnotations

        <T extends Annotation> Collection<T> getAnnotations()
        The Collection of annotations describing the cooperativeEffect. The Collection cannot be null. If the cooperativeEffect does not have any annotations, the method should return an empty Collection. Ex: comments, cautions, ...
        Type Parameters:
        T - a T object
        Returns:
        the annotations

      • getOutCome

        CvTerm getOutCome()
        For an interaction that has a cooperative effect on a subsequent interaction, this term indicates whether this effect is positive or negative, i.e. whether the subsequent interaction is augmented or diminished. It is a controlled vocabulary term and cannot be null.
        Returns:
        cooperative effect outcome

      • setOutCome

        void setOutCome​(CvTerm effect)
        Sets the cooperative effect outcome
        Parameters:
        effect - : cooperative effect outcome
        Throws:
        IllegalArgumentException - when effect is null

      • getResponse

        CvTerm getResponse()
        This term describes the cooperative effect on the interactions. It could be a pre-assembly response or an allosteric response. The pre-assembly response describes the way in which preformation of a molecular complex has a non-allosteric cooperative effect on subsequent interactions of its components. The allosteric response describes the effect of an allosteric binding event. It specifies which properties of the allosteric molecule are altered, i.e. whether the interaction alters either (a) binding or (b) catalytic properties of the allosteric molecule at a site distinct from the allosteric site. The response is a controlled vocabulary term and can be null if it is not known. Ex: binding site hiding, allosteric k-type response, ...
        Returns:
        the response

      • setResponse

        void setResponse​(CvTerm response)
        Sets the response.
        Parameters:
        response - : the allosteric or pre-assembly response