public class Molecule
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static int |
RENDER_MODE_BALLS_N_STICKS |
static int |
RENDER_MODE_COLORED_STICKS |
static int |
RENDER_MODE_COVALENT |
static int |
RENDER_MODE_POLYGON |
static int |
RENDER_MODE_VAN_DER_WAALS |
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 |
---|---|
float |
calculateRadius()
returns the radius the Molecule on the x/z plane.
|
Atom[] |
getAlignedAtomCopies()
returns a copy of all atoms of the molecule.
|
javax.media.j3d.BoundingBox |
getBounds()
returns the BoundingBox of the molecule.
|
javax.vecmath.Point3f |
getCenterPoint()
Deprecated.
the equivalent method getPosition() should be used instead
|
int |
getDomainIdentifier()
Returns the ID-number of the microdomain that this molecule is assigned
to
|
int |
getLayerID()
Returns the ID-number of the Layer that this molecule is assigned to
|
float |
getMaxRadius_XZ()
Compares the widht (x) and the height (z) of the molecule's current
boundingbox and returns the largest of these two values
|
Atom[] |
getOriginalAtoms()
Returns the list of all actual Atom instances.
|
Molecule_3D |
getOriginalMolecule()
returns the original Molecule_3D of this wrapper molecule.
|
javax.vecmath.Point3f |
getPosition()
returns the position of the molecule in the membrane
|
javax.vecmath.Matrix3f |
getRotationMatrix()
returns the current rotation matrix of this molecule.
|
javax.vecmath.Point3f[] |
getTrianglePoints()
returns the scaled points of the triangles that build up the shape of the
molecule.
|
java.lang.String |
getType()
returns the PDB code of the molecule
|
java.awt.geom.Rectangle2D.Double |
getXZBounds()
Determines the BoundingBox of the molecule and returns a rectangle that
represents the bounds on the x/z plane
|
float |
getYTranslation()
returns the translation on the y-axis.
|
void |
rotX(float angle)
rotates the molecule around the x-axis
|
void |
rotY(float angle)
rotates the molecule around the y-axis
|
void |
rotZ(float angle)
rotates the molecule around the z-axis
|
void |
setPosition(javax.vecmath.Point3f newpoint)
sets the position of the molecule.
|
void |
setRotationMatrix(javax.vecmath.Matrix3f newmatrix)
sets the rotation matrix.
|
void |
setYTranslation(float translation)
sets the y translation NOTE: If this molecule is already added to the
membrane model this will immediately move the molecule.
|
void |
updateGeometry()
Updates the geometry of this Molecule.
|
public static final int RENDER_MODE_POLYGON
public static final int RENDER_MODE_COVALENT
public static final int RENDER_MODE_VAN_DER_WAALS
public static final int RENDER_MODE_COLORED_STICKS
public static final int RENDER_MODE_BALLS_N_STICKS
public Molecule(Molecule_3D original, MembranePackingAlgorithm algo)
public java.lang.String getType()
@Deprecated public javax.vecmath.Point3f getCenterPoint()
public javax.vecmath.Point3f getPosition()
public javax.vecmath.Matrix3f getRotationMatrix()
public Atom[] getAlignedAtomCopies()
public float getMaxRadius_XZ()
public float calculateRadius()
public javax.media.j3d.BoundingBox getBounds()
public java.awt.geom.Rectangle2D.Double getXZBounds()
public javax.vecmath.Point3f[] getTrianglePoints()
public void setRotationMatrix(javax.vecmath.Matrix3f newmatrix)
newmatrix
- the
new rotation matrix that represents the rotation of the
molecule relative to the PDB file coordinatespublic void setPosition(javax.vecmath.Point3f newpoint)
newpoint
- the
new position of the molecule in the membrane spacepublic void rotX(float angle)
angle
- the
angle in degreespublic void rotY(float angle)
angle
- the
angle in degreespublic void rotZ(float angle)
angle
- the
angle in degreespublic Molecule_3D getOriginalMolecule()
public float getYTranslation()
public void setYTranslation(float translation)
translation
- the
desired y-value of the molecule's positionpublic int getDomainIdentifier()
public int getLayerID()
public void updateGeometry()
public Atom[] getOriginalAtoms()