public abstract class Molecule_3D
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
javax.media.j3d.TransformGroup |
additionalAtomInfoTG |
Atom_3D[] |
allAtomsSorted |
Atom_3D[] |
atoms |
com.sun.j3d.utils.behaviors.mouse.MouseRotate |
behavior |
java.util.Vector<Particle> |
currentCGParticles |
float |
maxAtomRadius |
Atom_3D[] |
opmAtoms |
Constraint_3D[] |
originalConstraints |
javax.vecmath.Point3f |
positionAfterReading |
Molecule |
teporaryMolecule |
int |
terCount |
Constructor and Description |
---|
Molecule_3D()
Creates a new molecule with a default matrix and all nessecary
capabilities set
|
Modifier and Type | Method and Description |
---|---|
void |
applyAtomPosition(int atomIndex,
javax.vecmath.Point3f newPosition)
Assigns a new Position to the Atom at the specified index.
|
void |
applyProfile(MoleculeProfile profile) |
float |
calculateRadius() |
void |
changeAndApplyModel(int newModel) |
void |
changeAndApplyModel(int newModel,
boolean updatePositionFactor) |
void |
coarseGrain(Particle newParticle) |
Molecule_3D |
copy(boolean cloneAlignment,
boolean resetAtomPositions)
Creates a new Protein / Lipid and copies all of its data.
|
void |
displayAdditionalInformation(Atom_3D atCursor,
float camDist) |
void |
displayOPMAtoms(boolean b) |
boolean |
equalsType(Molecule_3D other) |
java.util.Vector<Constraint_3D> |
getActiveConstraints() |
Atom_3D[] |
getAlignedAtoms() |
javax.media.j3d.BoundingBox |
getAlignedGeometricBounds()
Returns the current bounding box of this molecule.
|
Atom_3D[] |
getAlignedOPMAtoms() |
javax.vecmath.Point3f[] |
getAlignedTrianglePoints()
Returns the copy of the original trianglepoints of this object computed
to the correct alignment regarding to the translation and rotation of
this molecule.
|
int |
getAtomCount()
Returns the atomcount of this molecule
|
float |
getAtomicMass() |
Atom_3D[] |
getAtoms(boolean aligned,
boolean copy)
Returns a copy of all atoms for this instance in the right alignment.
|
java.lang.String |
getAuthor()
Returns the author of this pdb file
|
javax.media.j3d.BranchGroup |
getBranchGroup() |
int |
getChainCount()
Returns the count of chains in the underlying pdb file
|
java.lang.String[] |
getChainIDs()
Returns all chain ids used in the pdb file
|
java.awt.Color |
getColor()
Returns the currently used color for this object
|
java.lang.String |
getCurrentProfileName() |
java.lang.String |
getDate() |
int |
getDomainID() |
java.lang.String |
getHeader() |
Particle |
getHostParticle(Atom_3D atom) |
java.awt.Image |
getImageLarge() |
java.awt.Image |
getImageSmall() |
int |
getLayerID() |
javax.vecmath.Point3f |
getLower(boolean scaledToAngstrom)
Returns the lower corner of the current boundingbox.
|
int |
getModelcount() |
int |
getModelSet()
Returns the index of the model this molecule is constructed from.
|
com.sun.j3d.utils.behaviors.mouse.MouseRotate |
getMouseBehavior() |
float[] |
getOriginalAllAtomConstraintLenghts()
Deprecated.
|
float[] |
getOriginalAllAtomConstraintLengths() |
float |
getOriginalHeight() |
javax.vecmath.Point3f[] |
getOriginalTrianglePoints()
returns the original, unaligned trianglepoints
|
java.lang.String |
getPDBcode() |
java.io.File |
getPDBFile()
Returns the pdb file this molecule was created from
|
javax.vecmath.Matrix3f |
getPDBTMRotation()
Returns the molecule's PDBTM rotation matrix.
Returns a identity matrix by default. |
float |
getPDBTMTranslation()
Returns the y-coordinate of the molecule's bounding center after
transforming by the PPE.
Value 0 by default. |
javax.vecmath.Point3f |
getPosition()
Returns the Position of this instance in the membrane All values are
anstroms
|
int |
getRenderMode() |
javax.vecmath.Matrix3f |
getRotationMatrix()
returns the current rotation matrix of this molecule relative to the
coordinates of the pdb file this instance uses
|
javax.media.j3d.Shape3D |
getShape() |
java.lang.String |
getSOURCE() |
java.lang.String |
getTitle() |
javax.media.j3d.TransformGroup |
getTransformGroup() |
com.sun.j3d.utils.geometry.Box |
getUnrotatedBounds() |
javax.vecmath.Point3f |
getUpper(boolean scaledToAngstrom)
Returns the upper corner of the current boundingbox.
|
float |
getX() |
float |
getY() |
float |
getYTranslation()
Returns the current Y-height of this molecule in angstrom
|
float |
getZ() |
boolean |
isPicked()
Returns wether this protein is currently picked or not
|
boolean |
isPositionInAValidSpace()
Returns wether this protein has the valid position flag set or not
|
boolean |
isPositionisinavalidspace()
Deprecated.
|
boolean |
isTransparent() |
boolean |
isUsingAtomColors()
Returns if the Molecule is displaying atom colors in Covalent or Van Der
Waals Mode.
|
void |
move() |
void |
recalculatePoints()
Allows to realign the trianglePoints and the boundingbox manually.
|
void |
restoreFromCoarseGrain(Particle oldParticle) |
void |
rotateCoarseGrainMembers() |
void |
setAtomicMass(float mass) |
void |
setAuthor(java.lang.String author)
Sets the author of the Ppdb file.
|
void |
setChainIDs(java.util.Set<java.lang.String> name)
Sets the characters of the chain ids used in the underlying pdb file.
|
void |
setColor(java.awt.Color color)
Sets the color for this object.
|
void |
setCurrentProfileName(java.lang.String currentProfileName) |
void |
setDate(java.lang.String date)
Sets the date
|
void |
setDomainID(int id) |
void |
setHeader(java.lang.String description)
Sets the description of the Protein.
|
void |
setLayerID(int id) |
void |
setModelcount(int modelcount) |
void |
setModelSet(int model)
Sets the model index this molecule was constructed from
|
void |
setMouseBehavior(com.sun.j3d.utils.behaviors.mouse.MouseRotate behavior) |
void |
setOriginalHeight(float height) |
void |
setPDBcode(java.lang.String bcode)
Sets the PDBcode
|
void |
setPDBFile(java.io.File pdbFile)
Sets this molecule's pdb file
|
void |
setPDBTMRotation(javax.vecmath.Matrix3f rotation)
Sets the PDBTM rotation matrix extracted from a PDBTM XML file.
Parameter rotation has to be not null. |
void |
setPDBTMTranslation(float center)
Sets the y-coordinate of the molecules bounding center after transforming
by the PPE.
Parameter center has to be a number. |
void |
setPickable(boolean pickable)
Sets the shape to pickable.
|
void |
setPicked(boolean b)
Sets this protein picked or unpicked.
|
void |
setPosition(float x,
float z)
Sets the Position of the instance of the Protein in the membrane
|
void |
setPosition(javax.vecmath.Point3f p) |
void |
setPositionIsInAValidSpace(boolean proteinRedAndTransparent)
Sets, wether this protein is in a valid space (that means not colliding
with anything) or not.
|
void |
setRenderMode(java.lang.Integer renderMode)
Sets and applies the specified render mode (see contants fields) if the
objects are currently live, else it does nothing.
|
void |
setRotationMatrix(javax.vecmath.Matrix3f rotationMatrix)
Sets the rotaion matrix for this object
|
void |
setSOURCE(java.lang.String source) |
void |
setTitle(java.lang.String title)
Sets the description of the Protein.
|
void |
setTransform(javax.media.j3d.Transform3D t3d) |
void |
setTransparent(boolean b)
This method sets the molecule into transparent mode.
|
void |
setTransparent(boolean transparent,
boolean pickable)
Sets the transparency and the picking value of the molecule.
|
void |
setTrianglePoints(javax.vecmath.Point3f[] point3fs)
Sets the triangle points for this object.
|
void |
setUnrotatedBounds(com.sun.j3d.utils.geometry.Box unrotatedBounds) |
void |
setUseAtomColors(boolean useAtomColors)
Sets if the Molecule should be displayed using atom colors in Covalent or
Van Der Waals Mode.
|
void |
setYTranslation(float translation)
Sets the current Y-translation in angstrom for this object.
|
void |
sortAtoms() |
java.lang.String |
toString()
Returns a string representation of this object for debugging
|
void |
updateAllBonds() |
void |
updateAtomColors() |
void |
updateGeometry()
Updates the Geometry (needs to be called after one or more
applyAtomPosition() calls)
|
void |
updateGeometry(boolean updatePositionFactor)
Updates the Geometry (needs to be called after one or more
applyAtomPosition() calls)
|
void |
updateVisualAtomPositionsOnly() |
public Molecule teporaryMolecule
public Atom_3D[] atoms
public Atom_3D[] allAtomsSorted
public float maxAtomRadius
public com.sun.j3d.utils.behaviors.mouse.MouseRotate behavior
public Constraint_3D[] originalConstraints
public java.util.Vector<Particle> currentCGParticles
public javax.vecmath.Point3f positionAfterReading
public Atom_3D[] opmAtoms
public int terCount
public final javax.media.j3d.TransformGroup additionalAtomInfoTG
public Molecule_3D()
public java.util.Vector<Constraint_3D> getActiveConstraints()
public java.lang.String getHeader()
public void setHeader(java.lang.String description)
public java.lang.String getTitle()
public void setTitle(java.lang.String title)
public java.lang.String getAuthor()
public void setAuthor(java.lang.String author)
public javax.vecmath.Point3f getPosition()
public float getX()
public float getY()
public float getZ()
public void setPosition(float x, float z)
public void move()
public void setTransform(javax.media.j3d.Transform3D t3d)
public java.lang.String getDate()
public void setDate(java.lang.String date)
public java.lang.String getPDBcode()
public void setPDBcode(java.lang.String bcode)
public java.lang.String getSOURCE()
public void setSOURCE(java.lang.String source)
source
- The SOURCE to set.public java.io.File getPDBFile()
public void setPDBFile(java.io.File pdbFile)
pdbFile
- public java.awt.Color getColor()
public void setColor(java.awt.Color color)
color
- public javax.vecmath.Matrix3f getRotationMatrix()
public void setRotationMatrix(javax.vecmath.Matrix3f rotationMatrix)
rotationMatrix
- public float getYTranslation()
public float getPDBTMTranslation()
0
by default.public javax.vecmath.Matrix3f getPDBTMRotation()
identity matrix
by default.public void setYTranslation(float translation)
translation
- public void setPDBTMTranslation(float center)
center
has to be a number.center
- public void setPDBTMRotation(javax.vecmath.Matrix3f rotation)
rotation
has to be not null.rotation
- public Molecule_3D copy(boolean cloneAlignment, boolean resetAtomPositions)
public java.lang.String toString()
toString
in class java.lang.Object
public void setTrianglePoints(javax.vecmath.Point3f[] point3fs)
point3fs
- public javax.vecmath.Point3f[] getOriginalTrianglePoints()
public void setOriginalHeight(float height)
public float getOriginalHeight()
public javax.vecmath.Point3f[] getAlignedTrianglePoints()
public Atom_3D[] getAlignedAtoms()
public javax.media.j3d.BoundingBox getAlignedGeometricBounds()
public javax.vecmath.Point3f getUpper(boolean scaledToAngstrom)
scaledToAngstrom
- public javax.vecmath.Point3f getLower(boolean scaledToAngstrom)
scaledToAngstrom
- public int getAtomCount()
public int getModelSet()
public void setModelSet(int model)
model
- public void recalculatePoints()
public int getChainCount()
public void setChainIDs(java.util.Set<java.lang.String> name)
name
- public java.lang.String[] getChainIDs()
public Atom_3D[] getAtoms(boolean aligned, boolean copy)
public void setDomainID(int id)
public int getDomainID()
public float getAtomicMass()
public void setAtomicMass(float mass)
public void setMouseBehavior(com.sun.j3d.utils.behaviors.mouse.MouseRotate behavior)
public com.sun.j3d.utils.behaviors.mouse.MouseRotate getMouseBehavior()
public javax.media.j3d.TransformGroup getTransformGroup()
public boolean equalsType(Molecule_3D other)
public float calculateRadius()
public void setRenderMode(java.lang.Integer renderMode)
public void updateAtomColors()
public int getLayerID()
public void setLayerID(int id)
public void updateGeometry(boolean updatePositionFactor)
boolean
- updatePositionFactor move the molecule to a newly generated positionpublic void updateGeometry()
public void updateVisualAtomPositionsOnly()
public int getRenderMode()
public void setPicked(boolean b)
b
- public void setPositionIsInAValidSpace(boolean proteinRedAndTransparent)
b
- @Deprecated public boolean isPositionisinavalidspace()
public boolean isPositionInAValidSpace()
public boolean isPicked()
public void setPickable(boolean pickable)
pickable
- public void setTransparent(boolean b)
b
- public void setTransparent(boolean transparent, boolean pickable)
transparent
- pickable
- public void applyAtomPosition(int atomIndex, javax.vecmath.Point3f newPosition)
atomIndex
- newPosition
- public void setPosition(javax.vecmath.Point3f p)
public javax.media.j3d.Shape3D getShape()
public javax.media.j3d.BranchGroup getBranchGroup()
public boolean isTransparent()
public boolean isUsingAtomColors()
public void setUseAtomColors(boolean useAtomColors)
useAtomColors
- public com.sun.j3d.utils.geometry.Box getUnrotatedBounds()
public void setUnrotatedBounds(com.sun.j3d.utils.geometry.Box unrotatedBounds)
public int getModelcount()
public void setModelcount(int modelcount)
public void changeAndApplyModel(int newModel, boolean updatePositionFactor)
public void changeAndApplyModel(int newModel)
public java.awt.Image getImageSmall()
public java.awt.Image getImageLarge()
public Atom_3D[] getAlignedOPMAtoms()
public void displayOPMAtoms(boolean b)
public void coarseGrain(Particle newParticle)
public void restoreFromCoarseGrain(Particle oldParticle)
public void updateAllBonds()
public void sortAtoms()
public java.lang.String getCurrentProfileName()
public void setCurrentProfileName(java.lang.String currentProfileName)
public void applyProfile(MoleculeProfile profile)
public void displayAdditionalInformation(Atom_3D atCursor, float camDist)
@Deprecated public float[] getOriginalAllAtomConstraintLenghts()
public float[] getOriginalAllAtomConstraintLengths()
public void rotateCoarseGrainMembers()