A B C D E F G H I J L M N O P R S T U V W X

R

RULE_NAME - Static variable in class uk.ac.ed.simulator_pdb.model.TemplateFile

radius - Variable in class uk.ac.ed.simulator_pdb.model.PDBFile.AminoAcid

radius - Variable in class uk.ac.ed.simulator_pdb.model.PDBFile.Cluster

readInstanceFile(File) - Method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.NeuroMLHandler

readPDBFile(File) - Method in class uk.ac.ed.simulator_pdb.model.pdb_handler.PDBHandler

readTemplateFile(File) - Method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.NeuroMLHandler

recalculateCentreOfMass() - Method in class uk.ac.ed.simulator_pdb.model.SimObjectTemplate

remove(InstanceFile) - Method in class uk.ac.ed.simulator_pdb.InstanceTreeView

remove(Object) - Method in class uk.ac.ed.simulator_pdb.TreeView

removeBondSite(SimBondSite) - Method in class uk.ac.ed.simulator_pdb.model.SimObjectTemplate

removeCluster(SimCluster) - Method in class uk.ac.ed.simulator_pdb.Java3DView

removeCluster(SimCluster) - Method in class uk.ac.ed.simulator_pdb.model.SimulatorModel

removeFileListener(InstanceBuilderModel.FileListener) - Method in class uk.ac.ed.simulator_pdb.model.InstanceBuilderModel

removeFileListener(TemplateBuilderModel.FileListener) - Method in class uk.ac.ed.simulator_pdb.model.TemplateBuilderModel

removeIfClause(String) - Method in class uk.ac.ed.simulator_pdb.model.SimRuleTemplate

removeInstance(SimObject) - Method in class uk.ac.ed.simulator_pdb.model.InstanceFile

removeInstance(SimParticle) - Method in class uk.ac.ed.simulator_pdb.model.InstanceFile

removeInstance(SimBond) - Method in class uk.ac.ed.simulator_pdb.model.InstanceFile

removeInstance(SimRule) - Method in class uk.ac.ed.simulator_pdb.model.InstanceFile

removeInstanceFile(InstanceFile) - Method in class uk.ac.ed.simulator_pdb.model.InstanceBuilderModel

removeInstanceListener(InstanceFile.InstanceFileListener) - Method in class uk.ac.ed.simulator_pdb.model.InstanceFile

removeInstanceListener(InstanceFileObject.InstanceFileObjectListener) - Method in class uk.ac.ed.simulator_pdb.model.InstanceFileObject

removeLikelyhood(SimRuleTemplate.Likelyhood) - Method in class uk.ac.ed.simulator_pdb.model.SimRuleTemplate

removeObject(SimObject) - Method in class uk.ac.ed.simulator_pdb.Java3DView

removeObject(SimObject) - Method in class uk.ac.ed.simulator_pdb.model.SimCluster

removeObjectTemplateListener(SimObjectTemplate.SimObjectTemplateListener) - Method in class uk.ac.ed.simulator_pdb.model.SimObjectTemplate

removePDBFile(PDBFile) - Method in class uk.ac.ed.simulator_pdb.model.TemplateBuilderModel

removePDBFileListener(PDBFile.PDBListener) - Method in class uk.ac.ed.simulator_pdb.model.PDBFile

removeRuleTemplate(SimRuleTemplate) - Method in class uk.ac.ed.simulator_pdb.model.SimBondTemplate

removeSelectedObjectListener(InstanceBuilderModel.SelectedObjectListener) - Method in class uk.ac.ed.simulator_pdb.model.InstanceBuilderModel

removeSelectedObjectListener(TemplateBuilderModel.SelectedObjectListener) - Method in class uk.ac.ed.simulator_pdb.model.TemplateBuilderModel

removeSimulationListener(SimulatorModel.SimulationListener) - Method in class uk.ac.ed.simulator_pdb.model.SimulatorModel

removeSubParticle(SimSubParticle) - Method in class uk.ac.ed.simulator_pdb.model.SimObjectTemplate

removeTemplate(TemplateFileObject) - Method in class uk.ac.ed.simulator_pdb.model.PDBFile

removeTemplateFile(TemplateFile) - Method in class uk.ac.ed.simulator_pdb.model.TemplateBuilderModel

removeTemplateFileListener(TemplateFile.TemplateFileListener) - Method in class uk.ac.ed.simulator_pdb.model.TemplateFile

removeTemplateFileObject(TemplateFileObject) - Method in class uk.ac.ed.simulator_pdb.model.TemplateFile

removeTemplateListener(TemplateFileObject.TemplateFileObjectListener) - Method in class uk.ac.ed.simulator_pdb.model.TemplateFileObject

renderBond(SimBond) - Method in class uk.ac.ed.simulator_pdb.Java3DView

renderBondSite(SimBondSite) - Method in class uk.ac.ed.simulator_pdb.Java3DView

renderBoundingBox() - Method in class uk.ac.ed.simulator_pdb.Java3DView

renderCluster(SimCluster) - Method in class uk.ac.ed.simulator_pdb.Java3DView

renderObject(SimObject) - Method in class uk.ac.ed.simulator_pdb.Java3DView

renderObjectTemplate(SimObjectTemplate) - Method in class uk.ac.ed.simulator_pdb.Java3DView

renderPDBFile(PDBFile) - Method in class uk.ac.ed.simulator_pdb.Java3DView

renderParticle(SimParticle) - Method in class uk.ac.ed.simulator_pdb.Java3DView

renderParticleTemplate(SimParticleTemplate) - Method in class uk.ac.ed.simulator_pdb.Java3DView

renderSubParticle(SimSubParticle) - Method in class uk.ac.ed.simulator_pdb.Java3DView

renderer - Variable in class uk.ac.ed.simulator_pdb.TreeView

reset() - Method in class uk.ac.ed.simulator_pdb.model.SimulatorModel

revalidate() - Method in class uk.ac.ed.simulator_pdb.model.PDBFile

root - Variable in class uk.ac.ed.simulator_pdb.TreeView