Modifier and Type | Field and Description |
---|---|
Molecule_3D |
MoleculeProfile.mol |
Modifier and Type | Method and Description |
---|---|
void |
MoleculeEditor.applyProfile(Molecule_3D[] molsToApplyTo,
MoleculeProfile profile) |
static boolean |
Molecule_Profile_IO.existsProfile(Molecule_3D mol,
java.lang.String name,
java.lang.String pdbCode) |
static java.lang.String[] |
Molecule_Profile_IO.getAllProfileNames(Molecule_3D mol,
java.lang.String pdbCode) |
static java.io.File[] |
Molecule_Profile_IO.getAllProfiles(Molecule_3D mol,
java.lang.String pdbCode) |
static MoleculeProfile |
Molecule_Profile_IO.readDefaultProfile(Molecule_3D mol) |
static MoleculeProfile |
Molecule_Profile_IO.readProfile(Molecule_3D mol,
java.lang.String name,
java.lang.String code) |
static void |
Molecule_Profile_IO.saveProfile(Molecule_3D mol,
java.lang.String name) |
Constructor and Description |
---|
MoleculeEditor(Molecule_3D mol,
boolean applyable,
Engine engine,
java.lang.String currentProfile,
java.lang.Double standardStereoValue) |
Modifier and Type | Class and Description |
---|---|
class |
Lipid_3D
An extended version of a molecule.
|
class |
Protein_3D
An extended version of a molecule.
|
Modifier and Type | Method and Description |
---|---|
Molecule_3D |
Molecule_3D.copy(boolean cloneAlignment,
boolean resetAtomPositions)
Creates a new Protein / Lipid and copies all of its data.
|
Molecule_3D[] |
MembraneModel.getAllMoleculesInMembrane() |
Molecule_3D[] |
MembraneModel.getAllMoleculesInMembrane(boolean interimSortByType) |
Molecule_3D[] |
MembraneModel.getAllMoleculesInMembrane(int domainID,
int layerID) |
Molecule_3D[] |
MembraneModel.getAllMoleculesInMembraneSortedBySide() |
Molecule_3D[] |
MembraneModel.getAllMoleculesInMembraneSortedByType() |
Molecule_3D |
MembraneModel.getFirstMoleculeThatHasFile(java.io.File file,
int group,
int modelnumber)
Returns the first Molecule found that has the passed file in the
specified group of molecules
|
Modifier and Type | Method and Description |
---|---|
java.util.Vector<Molecule_3D> |
MembraneModel.getCurrentIntersections(boolean withBorderCheck) |
Modifier and Type | Method and Description |
---|---|
void |
MembraneModel.deleteMolecule(Molecule_3D mol)
deletes the passed Molecule of any kind
|
boolean |
Molecule_3D.equalsType(Molecule_3D other) |
boolean |
MembraneModel.isMoleculeStillIn(Molecule_3D mol)
Tests, if the passed protein is currently in the model
|
Modifier and Type | Method and Description |
---|---|
static Molecule_3D |
DataPool.DNDBridge.getCurrentMolecule()
Returns the current Protein
|
Modifier and Type | Method and Description |
---|---|
java.util.Vector<Molecule_3D> |
Engine.MembraneOperations.getCurrentSelection() |
Modifier and Type | Method and Description |
---|---|
void |
Engine.MembraneOperations.alignSingleProtein(Molecule_3D proToAlign) |
void |
Engine.MembraneOperations.alignSingleProteinPlus(Molecule_3D proToAlign) |
static float |
DataPool.AtomValues.calculateAtomicMass(Molecule_3D mol) |
void |
Engine.MembraneOperations.openMoleculeEditorFromCV(Molecule_3D mol) |
static void |
DataPool.DNDBridge.overwriteCurrentMolecule(Molecule_3D current)
Overwrites the current Protein
|
void |
Engine.MembraneOperations.pickMolecules(Molecule_3D[] proPicked) |
void |
Engine.MembraneOperations.selectFromCV(Molecule_3D mol,
int type) |
void |
Engine.MembraneOperations.startModelChange(Molecule_3D mol) |
Modifier and Type | Field and Description |
---|---|
Molecule_3D |
Hud.currentMoleculeAligning |
Modifier and Type | Method and Description |
---|---|
Molecule_3D[] |
IntersectManager.getCollisionObjects()
Returns the list of Objects, that have collided during the last run of a
test.
|
Modifier and Type | Method and Description |
---|---|
java.util.Vector<Molecule_3D> |
PickNDragManager.getSelected()
Returns the currently selected proteins
|
java.util.Vector<Molecule_3D> |
Membrane3D.getSelectedMolecules()
Returns the selected Proteins from the PNDmanager
|
Modifier and Type | Method and Description |
---|---|
static void |
Atom_Creator_3D.addBalls(Molecule_3D mol,
Atom_3D[] atoms,
boolean fullSize,
java.awt.Color selectionColor,
int radiusMode,
boolean opmAtoms) |
void |
Membrane3D.addMolecule(Molecule_3D mol,
boolean rebuildAxis)
adds a Molecule to the 3d view if the boolean is set, the axis of the 3D
modell will be repainted.
|
void |
CameraMode.forwardButton(int bt,
Molecule_3D ref) |
int[] |
IntersectManager.intercects_Molecule_Border_In_Detail(Molecule_3D mol,
java.awt.Dimension membraneSize)
An enhanced version of the molecule_border-test.
|
boolean |
IntersectManager.intercects_Molecule_Border(Molecule_3D mol,
java.awt.Dimension membraneSize)
Tests, if a molecule is completely inside the defined membrane bounds
Returns false if not, no matter if the molecule intersects with the
border or if it is completely outside the range
|
boolean |
IntersectManager.intercects_Molecule_Earth(Molecule_3D mol)
Tests, if a molecule is inside the lower limit.
|
boolean |
IntersectManager.intercects_Molecule_Sky(Molecule_3D mol)
Tests, if a molecule is inside the upper limit.
|
boolean |
IntersectManager.intercectsBorderOrAnyMolecule(Molecule_3D mol,
boolean breakAfterFirstHit) |
boolean |
IntersectManager.intercectsBorderOrAnyMolecule(Molecule_3D mol,
int molID,
boolean breakAfterFirstHit,
java.util.HashSet<java.lang.String> hashMol2MolID) |
boolean |
IntersectManager.intercectsWithBorderOrAnyProtein(Molecule_3D mol,
boolean breakAfterFirstHit)
Tests, if a molecule collides with either the border or any Protein that
is already added to the membrane.
|
boolean |
IntersectManager.intersectsMoleculeAnyMolecules(Molecule_3D mol,
boolean breakAfterFirstHit)
Tests, if a molecule collides with any Molecule that is already added to
the membrane, inclusive lipids.
|
boolean |
IntersectManager.intersectsMoleculeAnyMolecules(Molecule_3D mol,
int molNumber,
boolean breakAfterFirstHit,
java.util.HashSet<java.lang.String> hashMol2MolIds)
Tests, if a molecule collides with any Molecule that is already added to
the membrane, inclusive lipids.
|
boolean |
IntersectManager.intersectsMoleculeAnyProtein(Molecule_3D mol,
boolean breakAfterFirstHit)
Tests, if a molecule collides with any Protein that is already added to
the membrane.
|
boolean |
IntersectManager.intersectsMoleculeMoleculesVector(Molecule_3D mol,
int molNumber,
java.util.Vector<?> molecules,
boolean breakAfterFirstHit,
java.util.HashSet<java.lang.String> hashMol2MolIDs)
Tests, if a molecule collides with any molecule in a list that also has
to be passed.
|
boolean |
IntersectManager.intersectsMoleculeMoleculesVector(Molecule_3D mol,
java.util.Vector<?> molecules,
boolean breakAfterFirstHit)
Tests, if a molecule collides with any molecule in a list that also has
to be passed.
|
void |
PickNDragManager.moveDNDObject(Molecule_3D current,
java.awt.Point loc)
Moves the passed Object to the passed mouse location on canvas (this time
while Drag and drop is active)
|
void |
Membrane3D.removeMoleculesFrom3D(Molecule_3D[] mols)
removes given proteins from the 3D model
|
void |
PickNDragManager.setPickedMolecules(Molecule_3D[] proPicked) |
static void |
Atom_Creator_3D.setUpMolecule(Molecule_3D mol,
int mode) |
Constructor and Description |
---|
SelectionBox(Molecule_3D mol,
int mode) |
Constructor and Description |
---|
EnterMatrixDialog(Molecule_3D currentMolecule,
java.awt.Point point)
Constucts a Frame and shows the passed inital Data in its textfields
|
Modifier and Type | Method and Description |
---|---|
Molecule_3D[] |
PropertiesView.getCurrentMolecules() |
Modifier and Type | Method and Description |
---|---|
void |
ComponentView.select(Molecule_3D mol,
int type) |
void |
PropertiesView.showProperties(Molecule_3D[] molecule)
displays properties of the passed molecules
|
void |
MembraneView.startSpecialMode(Molecule_3D mol,
int mode) |
Modifier and Type | Method and Description |
---|---|
java.util.Vector<Molecule_3D> |
MembraneViewListener.getCurrentSelection() |
Modifier and Type | Method and Description |
---|---|
void |
MembraneViewListener.alignSingleProtein(Molecule_3D molecule_3D) |
void |
MembraneViewListener.alignSingleProteinPlus(Molecule_3D molecule_3D) |
void |
MembraneViewListener.openMoleculeEditorFromCV(Molecule_3D mol) |
void |
MembraneViewListener.pickMolecules(Molecule_3D[] molecule_3Ds) |
void |
MembraneViewListener.selectFromCV(Molecule_3D mol,
int i) |
void |
MembraneViewListener.startModelChange(Molecule_3D mol) |
Modifier and Type | Method and Description |
---|---|
void |
PdbReader_3D.shapeIt(Molecule_3D mol) |
Modifier and Type | Method and Description |
---|---|
void |
MIFHandler.applyOPMAlignmentTo(Molecule_3D newProt)
This methods adjust the rotation and the position of the given
Protein to the actual membrane which it is placed into.
|
Modifier and Type | Method and Description |
---|---|
Molecule_3D |
Molecule.getOriginalMolecule()
returns the original Molecule_3D of this wrapper molecule.
|
Modifier and Type | Method and Description |
---|---|
static float |
MembranePackingAlgorithm.getTotalHeight(Molecule_3D lip)
NOT MEANT TO BE USED BY PLUGIN DEVELOPERS!
|
Constructor and Description |
---|
Molecule(Molecule_3D original,
MembranePackingAlgorithm algo)
Creates a new wrapper object of the given Molecule_3D
! NOT MEANT TO BE USED BY PLUGIN DEVELOPERS !
|
Modifier and Type | Method and Description |
---|---|
static java.awt.Image |
Cm2_Toolkit.Membrane_Image2D_Generator.createImage(Molecule_3D mol,
int prefX,
int prefY) |