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

A

ADD - Static variable in class uk.ac.ed.simulator_pdb.model.SimRuleTemplate

AMINO_ACIDS - Static variable in class uk.ac.ed.simulator_pdb.model.PDBFile

ANGSTROMS_PER_METRE - Static variable in class uk.ac.ed.simulator_pdb.model.Constants

APPROVE_OPTION - Static variable in class uk.ac.ed.simulator_pdb.View.ChooserDialog

ATOMS - Static variable in class uk.ac.ed.simulator_pdb.model.PDBFile

action - Variable in class uk.ac.ed.simulator_pdb.model.neuroml_handler.XMLSimRuleTemplate

addAtom(PDBFile.Atom) - Method in class uk.ac.ed.simulator_pdb.model.PDBFile.AminoAcid

addAtom(SimParticleTemplate, Vector3d, int) - Method in class uk.ac.ed.simulator_pdb.model.PDBFile

addBond(SimBond) - Method in class uk.ac.ed.simulator_pdb.model.SimObject

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

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

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

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

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

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

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

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

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

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

addInstanceFile(InstanceFile) - Method in class uk.ac.ed.simulator_pdb.TreeView

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

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

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

addLikelyhood(double, double) - Method in class uk.ac.ed.simulator_pdb.model.SimRuleTemplate

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

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

addPDBFile(PDBFile) - Method in class uk.ac.ed.simulator_pdb.TreeView

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

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

addParticle(SimParticle) - Method in class uk.ac.ed.simulator_pdb.model.SimObject

addRule(SimRule) - Method in class uk.ac.ed.simulator_pdb.model.SimBond

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

addRuleTemplateIds - Variable in class uk.ac.ed.simulator_pdb.model.neuroml_handler.XMLSimBondTemplate

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

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

addSimBondSite(SimBondSite) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimBondSite(SimBondSite, DefaultMutableTreeNode) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimBondTemplate(SimBondTemplate) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimBondTemplate(SimBondTemplate, DefaultMutableTreeNode) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimObject(SimObject) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimObject(SimObject, DefaultMutableTreeNode) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimObjectTemplate(SimObjectTemplate, DefaultMutableTreeNode) - Method in class uk.ac.ed.simulator_pdb.TemplateTreeView

addSimObjectTemplate(SimObjectTemplate) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimObjectTemplate(SimObjectTemplate, DefaultMutableTreeNode) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimParticleTemplate(SimParticleTemplate) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimParticleTemplate(SimParticleTemplate, DefaultMutableTreeNode) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimRuleTemplate(SimRuleTemplate) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimRuleTemplate(SimRuleTemplate, DefaultMutableTreeNode) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimSubParticle(SimSubParticle) - Method in class uk.ac.ed.simulator_pdb.TreeView

addSimSubParticle(SimSubParticle, DefaultMutableTreeNode) - Method in class uk.ac.ed.simulator_pdb.TreeView

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

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

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

addTemplateFile(TemplateFile) - Method in class uk.ac.ed.simulator_pdb.TemplateTreeView

addTemplateFile(TemplateFile) - Method in class uk.ac.ed.simulator_pdb.TreeView

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

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

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

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

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

addTo(TemplateFile) - Method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.XMLSimBondTemplate

addTo(TemplateFile) - Method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.XMLSimLandscapeTemplate

addTo(InstanceFile, TemplateFile[]) - Method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.XMLSimObject

addTo(TemplateFile) - Method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.XMLSimObjectTemplate

addTo(TemplateFile) - Method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.XMLSimParticleTemplate

addTo(TemplateFile) - Method in class uk.ac.ed.simulator_pdb.model.neuroml_handler.XMLSimRuleTemplate

adjustOrientation(Matrix4d, Matrix4d) - Method in class uk.ac.ed.simulator_pdb.model.SimLandscapeTemplate

adjustPosition(Matrix4d, Matrix4d) - Method in class uk.ac.ed.simulator_pdb.model.SimLandscapeTemplate

adjustTransformationMatrix(Matrix4d, Matrix4d) - Method in class uk.ac.ed.simulator_pdb.model.SimLandscapeTemplate

alignForBonding(Matrix4d, Matrix4d, double) - Method in class uk.ac.ed.simulator_pdb.SimulationJava3DController

alignForBonding(SimBond, SimBond) - Method in class uk.ac.ed.simulator_pdb.SimulationJava3DController

alpha - Variable in class uk.ac.ed.simulator_pdb.model.neuroml_handler.XMLSimParticleTemplate

amino_acids - Variable in class uk.ac.ed.simulator_pdb.model.PDBFile

atoms - Variable in class uk.ac.ed.simulator_pdb.model.PDBFile