.. _PhysiCell_java_CancerImmune_ImmuneCellRule_java:

ImmuneCellRule.java
===================

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.. code-block:: console

    import ru.biosoft.physicell.biofvm.VectorUtil;
    import ru.biosoft.physicell.core.Cell;
    import ru.biosoft.physicell.core.CellFunctions.CustomCellRule;
    import ru.biosoft.physicell.core.Model;
    import ru.biosoft.physicell.core.Phenotype;
    import ru.biosoft.physicell.core.RandomGenerator;

    public class ImmuneCellRule extends CustomCellRule
    {
        private RandomGenerator rng;

        public ImmuneCellRule(Model model)
        {
            rng = model.getRNG();
        }
        public void execute(Cell pCell, Phenotype phenotype, double dt)
        {
            int attach_lifetime_i = pCell.customData.findVariableIndex( "attachment_lifetime" );

            if( phenotype.death.dead == true )
            {
                // the cell death functions don't automatically turn off custom functions, since those are part of mechanics. 
                // Let's just fully disable now. 
                pCell.functions.customCellRule = null;
                return;
            }

            // if I'm docked
            if( pCell.state.numberAttachedCells() > 0 )
            {
                // attempt to kill my attached cell
                Cell attached = pCell.state.attachedCells.iterator().next();///[0];
                boolean detachMe = false;

                if( attemptApoptosis( pCell, attached, dt ) )
                {
                    triggerApoptosis( pCell, attached );
                    detachMe = true;
                }

                // decide whether to detach 
                if( rng.checkRandom( dt / ( pCell.customData.get( attach_lifetime_i ) + 1e-15 ) ) )
                    detachMe = true;

                // if I dettach, resume motile behavior 
                if( detachMe )
                {
                    Cell.detachCells( pCell, attached );
                    phenotype.motility.isMotile = true;
                }
                return;
            }

            // I'm not docked, look for cells nearby and try to docked if this returns non-NULL, we're now attached to a cell 
            if( checkNeighborsForAttachment( pCell, dt ) != null )
            {
                phenotype.motility.isMotile = false;
                return;
            }
            phenotype.motility.isMotile = true;
        }

        static boolean triggerApoptosis(Cell pAttacker, Cell pTarget)
        {
            if( pTarget.phenotype.death.dead )
                return false;
            pTarget.startDeath( pTarget.phenotype.death.findDeathModelIndex( "apoptosis" ) );
            return true;
        }

        boolean attemptApoptosis(Cell pAttacker, Cell pTarget, double dt)
        {
            int oncoproteinIndex = pTarget.customData.findVariableIndex( "oncoprotein" );
            int killRateIndex = pAttacker.customData.findVariableIndex( "kill_rate" );

            double oncoproteinSaturation = pAttacker.customData.get( "oncoprotein_saturation" ); // 2.0; 
            double oncoproteinThreshold = pAttacker.customData.get( "oncoprotein_threshold" ); // 0.5; // 0.1; 
            double oncoproteinDifference = oncoproteinSaturation - oncoproteinThreshold;

            double targetOconoprotein = pTarget.customData.get( oncoproteinIndex );
            if( targetOconoprotein < oncoproteinThreshold )
                return false;

            double scale = ( targetOconoprotein - oncoproteinThreshold ) / oncoproteinDifference;
            scale = Math.min( scale, 1.0 );

            if( rng.checkRandom( pAttacker.customData.get( killRateIndex ) * scale * dt ) )
                return true;
            return false;
        }

        public Cell checkNeighborsForAttachment(Cell pAttacker, double dt)
        {
            for( Cell nearbyCell : pAttacker.cells_in_my_container() )
            {
                if( nearbyCell != pAttacker )// don't try to kill yourself 
                {
                    if( attemptAttachment( pAttacker, nearbyCell, dt ) )
                        return nearbyCell;
                }
            }
            return null;
        }

        boolean attemptAttachment(Cell pAttacker, Cell pTarget, double dt)
        {
            double oncoprotein_saturation = pAttacker.customData.get( "oncoprotein_saturation" );
            double oncoprotein_threshold = pAttacker.customData.get( "oncoprotein_threshold" );
            double maxAttachmentDistance = pAttacker.customData.get( "max_attachment_distance" );
            double minAttachmentDistance = pAttacker.customData.get( "min_attachment_distance" );
            double targetOncoprotein = pTarget.customData.get( "oncoprotein" );
            if( targetOncoprotein > oncoprotein_threshold && !pTarget.phenotype.death.dead )
            {
                double distance = VectorUtil.dist( pTarget.position, pAttacker.position );
                if( distance > maxAttachmentDistance )
                    return false;

                double attachRate = pAttacker.customData.get( "attachment_rate" );
                double scale = ( targetOncoprotein - oncoprotein_threshold ) / ( oncoprotein_saturation - oncoprotein_threshold );
                double distanceScale = ( maxAttachmentDistance - distance ) / ( maxAttachmentDistance - minAttachmentDistance );
                attachRate *= Math.min( scale, 1.0 ) * Math.min( distanceScale, 1.0 );
                if( rng.checkRandom( attachRate * dt ) )
                    Cell.attachcCells( pAttacker, pTarget );
                return true;//TODO: should we return true only if attached successfully?
            }
            return false;
        }
    }