protein
Class Protein

java.lang.Object
  protein.Protein

public class Protein
extends java.lang.Object

Author:

User

Constructor Summary

Protein(java.lang.String PDBcode)

Method Summary

void	addProteinPositions(int[] positions)
void	completeScaling() Scales the protein by applying the matrix to the original Coordinates.
int	get_Line_quantity()
int	get_xz_percentage()
int	getAtom_count() returns the amount of the atom_coordinates
java.lang.String	getCISPEP()
java.lang.String	getCOMPD()
java.lang.String	getComponent()
java.util.Vector[]	getCoordinates()
java.lang.String	getCoordinatesAsString()
java.lang.String	getDate()
java.lang.String	getDBREF()
java.util.Vector	getDescription()
java.lang.String	getECN()
int[]	getExtremePointsIndex()
java.lang.String	getFilepath()
java.lang.String	getFORMUL()
java.lang.String	getHELIX()
java.lang.String	getHET()
java.lang.String	getHETNAM()
java.lang.String	getHYDBND()
double	getLength()
java.lang.String	getLINK()
double[]	getlipid_extreme_y()
java.lang.String	getMetabolite()
int	getModel_count()
java.lang.String	getMODRES()
java.lang.String	getName()
java.lang.String	getNodeName()
java.util.Vector[]	getOriginalCoordinates()
java.lang.String	getPDBcode()
java.awt.Color	getProteinColor()
java.util.Vector	getProteinPositions()
int	getQuantity()
float	getRatio()
int	getResidueSequenceCount()
java.util.Vector[]	getrotatedCoordinatesforWriter(int degree)
javax.vecmath.Matrix3f	getRotationMatrix() Return an instance of the rotationMatrix.
void	getRotationMatrix(javax.vecmath.Matrix3f givenRotation) Returns the rotationMatrix of the protein and writes it to the given Matrix3f.
java.lang.String	getSEQRES()
java.lang.String	getSHEET()
double[]	getSize()
int[]	getSizeByLipids()
java.lang.String	getSLTBRG()
java.lang.String	getSOURCE()
java.lang.String	getSSBOND()
java.lang.String	getSubcomponent()
java.lang.String	getSuperAtom()
java.lang.String	getTURN()
double	getxz_area()
float	getYTranslation() Returns the yTranslation of the protein.
float	getYTranslation4Jmol() Returns the yTranslation of the protein for Jmol, multiplicated by 2.8.
boolean	isModified()
boolean	isSelfmade()
java.util.Vector	lipidFillingInCube()
void	lipidScaling(javax.vecmath.Matrix3f matrix)
void	scaleProteintoNull() Scaling of the Coordinates.
void	set_Line_quantity(int rest)
void	setAtom_count(int atom_count) sets the amount of the atom coordinates
void	setCISPEP(java.lang.String cispep)
void	setCOMPD(java.lang.String compd)
void	setComponent(java.lang.String component)
void	setCoordinates(java.util.Vector[] coordinates) Sets the Coordinates.
void	setDate(java.lang.String date)
void	setDBREF(java.lang.String dbref)
void	setDescription(java.util.Vector description) Sets the description of the Protein.
void	setECN(java.lang.String ecn) Sets the description of the Protein.
void	setFilepath(java.lang.String filepath)
void	setFORMUL(java.lang.String formul)
void	setHELIX(java.lang.String helix)
void	setHET(java.lang.String het)
void	setHETNAM(java.lang.String hetnam)
void	setHYDBND(java.lang.String hydbnd)
void	setLength() Sets the maximal length of the protein
void	setLINK(java.lang.String link)
void	setMetabolite(java.lang.String metabolite) Sets the Metabolite of the Protein in the membrane
void	setModel_count(int model_count)
void	setModified(boolean modified)
void	setMODRES(java.lang.String modres)
void	setName(java.lang.String name) Sets the description of the Protein.
void	setNodeName(java.lang.String nodeName) Sets the name of a node.
void	setOriginalCoordinates(java.util.Vector[] givenCoordinates) The originalCoordinates to set.
void	setPDBcode(java.lang.String bcode) Sets the PDBcode
void	setProteinColor(java.awt.Color proteinColor)
void	setProteinPositions(java.util.Vector proteinPositions) Sets the ProteinPosition of the instances of the Protein in the membrane
void	setQuantity(int quantity) sets the quantity of the protein
void	setRatio(float ratio) sets the ratio of the protein in the membrane model
void	setResidueSequenceCount(int residueSequenceCount)
void	setRotationMatrix(javax.vecmath.Matrix3f givenRotation) Sets the rotationMatrix of the protein.
void	setSelfmade(boolean selfmade) Sets boolean if Protein is selfmade
void	setSEQRES(java.lang.String seqres)
void	setSHEET(java.lang.String sheet)
void	setSize() Sets the size of the Protein.
void	setSize2(double[] size)
void	setSLTBRG(java.lang.String sltbrg)
void	setSOURCE(java.lang.String source)
void	setSSBOND(java.lang.String ssbond)
void	setSubcomponent(java.lang.String subcomponent)
void	setSuperAtom(java.lang.String superAtom)
void	setTURN(java.lang.String turn)
void	setxz_area() The xz_area to set.
void	setxz_area(double xz_area)
void	setYTranslation(float translation) Sets the yTranslation of the protein.
void	setYTranslationLoad(float translation) Sets the yTranslation of the protein which ist used when loading the protein for the first time into the program.
void	startup() computes relevant values of the protein based on the Coordinates: scaleProteintoNull(), setExtremePointsIndex(), setSize(), setxz_area(), lipidFillingInCube().
void	startupLipid() computes relevant values of the lipid-Protein based on the Coordinates: scaleProteintoNull(), setExtremePointsIndex(), setSize()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Protein

public Protein(java.lang.String PDBcode)

Method Detail

startup

public void startup()

computes relevant values of the protein based on the Coordinates: scaleProteintoNull(), setExtremePointsIndex(), setSize(), setxz_area(), lipidFillingInCube(). Important if Cordinates are modified, then dependent values have to be re-computed

See Also:

scaleProteintoNull, setExtremePointsIndex, setSize, setxz_area, lipidFillingInCube

startupLipid

public void startupLipid()

computes relevant values of the lipid-Protein based on the Coordinates: scaleProteintoNull(), setExtremePointsIndex(), setSize()

See Also:

scaleProteintoNull, setExtremePointsIndex, setSize

getlipid_extreme_y

public double[] getlipid_extreme_y()

Returns:

Returns [double min, double max] of the y-values that are inside the bilayer membrane

getCoordinates

public java.util.Vector[] getCoordinates()

Returns:

Returns the Coordinates. Coordinates consists of 4 Vectors containing the atom names, x-values, y-values and z-values

getCoordinatesAsString

public java.lang.String getCoordinatesAsString()

Returns:

Returns the Coordinates as String

setCoordinates

public void setCoordinates(java.util.Vector[] coordinates)

Sets the Coordinates.

Parameters:

coordinates - Coordinates consists of 4 Vectors containing the atom names, x-values, y-values and z-values

getDescription

public java.util.Vector getDescription()

Returns:

Returns the description of the Protein.

setDescription

public void setDescription(java.util.Vector description)

Sets the description of the Protein.

getECN

public java.lang.String getECN()

Returns:

Returns the ECN of the Protein.

setECN

public void setECN(java.lang.String ecn)

Sets the description of the Protein.

getName

public java.lang.String getName()

Returns:

Returns the name of the Protein.

setName

public void setName(java.lang.String name)

Sets the description of the Protein.

getProteinPositions

public java.util.Vector getProteinPositions()

Returns:

Returns the ProteinPosition of the instances of the Protein in the membrane

addProteinPositions

public void addProteinPositions(int[] positions)

Parameters:

positions - The positions to add Adds ProteinPosition of the Protein.

setProteinPositions

public void setProteinPositions(java.util.Vector proteinPositions)

Sets the ProteinPosition of the instances of the Protein in the membrane

getMetabolite

public java.lang.String getMetabolite()

Returns:

Returns the Metabolite of the Protein

setMetabolite

public void setMetabolite(java.lang.String metabolite)

Sets the Metabolite of the Protein in the membrane

isModified

public boolean isModified()

Returns:

True if Protein is modified

setModified

public void setModified(boolean modified)

Parameters:

modified - Sets boolean if Protein is modified

isSelfmade

public boolean isSelfmade()

Returns:

Returns boolean if Protein is selfmade

setSelfmade

public void setSelfmade(boolean selfmade)

Sets boolean if Protein is selfmade

Parameters:

selfmade - True if selfmade

getDate

public java.lang.String getDate()

Returns:

Returns the date

setDate

public void setDate(java.lang.String date)

Parameters:

date - The date to be set Sets the date

getPDBcode

public java.lang.String getPDBcode()

Returns:

Returns the PDBcode

setPDBcode

public void setPDBcode(java.lang.String bcode)

Sets the PDBcode

getQuantity

public int getQuantity()

Returns:

the quantity of the protein

setQuantity

public void setQuantity(int quantity)

sets the quantity of the protein

getRatio

public float getRatio()

Returns:

the ratio of the protein in the membrane model

setRatio

public void setRatio(float ratio)

sets the ratio of the protein in the membrane model

setSize2

public void setSize2(double[] size)

setSize

public void setSize()

Sets the size of the Protein. It will be calculated by the Coordinates

getSize

public double[] getSize()

Returns:

Returns the size

getSizeByLipids

public int[] getSizeByLipids()

Returns:

Returns the size of the Protein how many lipids have to be replaced on the membrane. Calculation depends on Coordinates and given BilayerType of the membrane

getExtremePointsIndex

public int[] getExtremePointsIndex()

Returns:

Returns the extremePointsIndex. The array contains the atom indices in the vector of {x_min,y_min,z_min,x_max, y_max, z_max} of the protein

getLength

public double getLength()

Returns:

Returns the maximal length of the protein

setLength

public void setLength()

Sets the maximal length of the protein

getSubcomponent

public java.lang.String getSubcomponent()

Returns:

Returns the subcomponent.

setSubcomponent

public void setSubcomponent(java.lang.String subcomponent)

Parameters:

subcomponent - The subcomponent to set.

getComponent

public java.lang.String getComponent()

Returns:

Returns the component.

setComponent

public void setComponent(java.lang.String component)

Parameters:

component - The component to set.

lipidFillingInCube

public java.util.Vector lipidFillingInCube()

Returns:

Returns a Vector containing the positions in the proteincube lipids can be inserted. Finetuning of Membrane Generating

getCOMPD

public java.lang.String getCOMPD()

Returns:

Returns the cOMPD.

setCOMPD

public void setCOMPD(java.lang.String compd)

Parameters:

compd - The cOMPD to set.

getSOURCE

public java.lang.String getSOURCE()

Returns:

Returns the sOURCE.

getRotationMatrix

public void getRotationMatrix(javax.vecmath.Matrix3f givenRotation)

Returns the rotationMatrix of the protein and writes it to the given Matrix3f.

Parameters:

givenRotation - Matrix3f

getRotationMatrix

public javax.vecmath.Matrix3f getRotationMatrix()

Return an instance of the rotationMatrix.

Returns:

rotationMatrix

setRotationMatrix

public void setRotationMatrix(javax.vecmath.Matrix3f givenRotation)

Sets the rotationMatrix of the protein.

Parameters:

givenRotation - Matrix3f

setSOURCE

public void setSOURCE(java.lang.String source)

Parameters:

source - The SOURCE to set.

getDBREF

public java.lang.String getDBREF()

Returns:

Returns the dBREF.

setDBREF

public void setDBREF(java.lang.String dbref)

Parameters:

dbref - The dBREF to set.

getHET

public java.lang.String getHET()

Returns:

Returns the hET.

getYTranslation

public float getYTranslation()

Returns the yTranslation of the protein.

Returns:

yTranslation

getYTranslation4Jmol

public float getYTranslation4Jmol()

Returns the yTranslation of the protein for Jmol, multiplicated by 2.8.

setYTranslation

public void setYTranslation(float translation)

Sets the yTranslation of the protein. This method is used by PDBPreview, when the user changes the yTranslation by mouse. The yTranslation of the Jmol-application is not the same like the one of the protein, because of another scalefactor.

Parameters:

translation - float

setYTranslationLoad

public void setYTranslationLoad(float translation)

Sets the yTranslation of the protein which ist used when loading the protein for the first time into the program. It's the standard value which does not mind the scalefactor of the Jmol-application.

Parameters:

translation - float

setHET

public void setHET(java.lang.String het)

Parameters:

het - The hET to set.

getMODRES

public java.lang.String getMODRES()

Returns:

Returns the mODRES.

setMODRES

public void setMODRES(java.lang.String modres)

Parameters:

modres - The mODRES to set.

getSEQRES

public java.lang.String getSEQRES()

Returns:

Returns the sEQRES.

setSEQRES

public void setSEQRES(java.lang.String seqres)

Parameters:

seqres - The sEQRES to set.

getHETNAM

public java.lang.String getHETNAM()

Returns:

Returns the hETNAM.

setHETNAM

public void setHETNAM(java.lang.String hetnam)

Parameters:

hetnam - The hETNAM to set.

getFORMUL

public java.lang.String getFORMUL()

Returns:

Returns the fORMUL.

setFORMUL

public void setFORMUL(java.lang.String formul)

Parameters:

formul - The fORMUL to set.

getHELIX

public java.lang.String getHELIX()

Returns:

Returns the hELIX.

setHELIX

public void setHELIX(java.lang.String helix)

Parameters:

helix - The hELIX to set.

getSHEET

public java.lang.String getSHEET()

Returns:

Returns the sHEET.

setSHEET

public void setSHEET(java.lang.String sheet)

Parameters:

sheet - The sHEET to set.

getTURN

public java.lang.String getTURN()

Returns:

Returns the tURN.

setTURN

public void setTURN(java.lang.String turn)

Parameters:

turn - The tURN to set.

getCISPEP

public java.lang.String getCISPEP()

Returns:

Returns the cISPEP.

setCISPEP

public void setCISPEP(java.lang.String cispep)

Parameters:

cispep - The cISPEP to set.

getHYDBND

public java.lang.String getHYDBND()

Returns:

Returns the hYDBND.

setHYDBND

public void setHYDBND(java.lang.String hydbnd)

Parameters:

hydbnd - The hYDBND to set.

getLINK

public java.lang.String getLINK()

Returns:

Returns the lINK.

setLINK

public void setLINK(java.lang.String link)

Parameters:

link - The lINK to set.

getSLTBRG

public java.lang.String getSLTBRG()

Returns:

Returns the sLTBRG.

setSLTBRG

public void setSLTBRG(java.lang.String sltbrg)

Parameters:

sltbrg - The sLTBRG to set.

getSSBOND

public java.lang.String getSSBOND()

Returns:

Returns the sSBOND.

setSSBOND

public void setSSBOND(java.lang.String ssbond)

Parameters:

ssbond - The sSBOND to set.

getModel_count

public int getModel_count()

Returns:

Returns the model_count.

setModel_count

public void setModel_count(int model_count)

Parameters:

model_count - The model_count to set.

getSuperAtom

public java.lang.String getSuperAtom()

Returns:

Returns the superAtom.

setSuperAtom

public void setSuperAtom(java.lang.String superAtom)

Parameters:

superAtom - The superAtom to set.

getFilepath

public java.lang.String getFilepath()

Returns:

Returns the filepath.

setFilepath

public void setFilepath(java.lang.String filepath)

Parameters:

filepath - The filepath to set.

scaleProteintoNull

public void scaleProteintoNull()

Scaling of the Coordinates. The lowest coordinates in x,y, and z dimension are scaled to null and the other valuesa are adjusted

getResidueSequenceCount

public int getResidueSequenceCount()

Returns:

Returns the residueSequenceCount.

setResidueSequenceCount

public void setResidueSequenceCount(int residueSequenceCount)

Parameters:

residueSequenceCount - The residueSequenceCount to set.

getProteinColor

public java.awt.Color getProteinColor()

Returns:

Returns the proteinColor.

setProteinColor

public void setProteinColor(java.awt.Color proteinColor)

Parameters:

proteinColor - The proteinColor to set.

lipidScaling

public void lipidScaling(javax.vecmath.Matrix3f matrix)

Parameters:

matrix - the matrix containing the rotation of the lipid The matrix is applied to the Coordinates of the lipid. This method is only for bilayerType usage and not for ordinary proteins

completeScaling

public void completeScaling()

Scales the protein by applying the matrix to the original Coordinates.

getOriginalCoordinates

public java.util.Vector[] getOriginalCoordinates()

Returns:

Returns the originalCoordinates.

setOriginalCoordinates

public void setOriginalCoordinates(java.util.Vector[] givenCoordinates)

The originalCoordinates to set.

Parameters:

givenCoordinates -

getNodeName

public java.lang.String getNodeName()

Returns:

Returns the nodeName.

setNodeName

public void setNodeName(java.lang.String nodeName)

Sets the name of a node.

Parameters:

nodeName -

getAtom_count

public int getAtom_count()

returns the amount of the atom_coordinates

Returns:

int

setAtom_count

public void setAtom_count(int atom_count)

sets the amount of the atom coordinates

Parameters:

atom_count -

get_Line_quantity

public int get_Line_quantity()

Returns:

Returns the rest.

set_Line_quantity

public void set_Line_quantity(int rest)

Parameters:

rest - The rest to set.

getxz_area

public double getxz_area()

Returns:

Returns the xz_area.

setxz_area

public void setxz_area(double xz_area)

Parameters:

xz_area - The xz_area to set.

setxz_area

public void setxz_area()

The xz_area to set. Calculates the area by the x,z-size of the protein

get_xz_percentage

public int get_xz_percentage()

Returns:

Returns in percent how many space one instance of the protein needs of the whole membrane in x,z-view (perspective from above, membrane preview)

getrotatedCoordinatesforWriter

public java.util.Vector[] getrotatedCoordinatesforWriter(int degree)

Parameters:

degree - The degree gives information in which way a single protein instance is rotated

Returns:

Returns Coordinates after rotation around the y-axis with the given degree