public class MembraneModel
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
java.util.Vector<?>[] |
allVectors |
Constructor and Description |
---|
MembraneModel()
Constructs a new Membrane Model.
|
Modifier and Type | Method and Description |
---|---|
void |
addAlgorithmStringRepresentation(java.lang.String algorithmstringrepresentation) |
void |
addExampleLipidExtra(Lipid_3D actLip,
int domainID,
int layerID)
Adds an sample lipid to the membrane
|
void |
addExampleLipidIntra(Lipid_3D actLip,
int domainID,
int layerID)
Adds an sample lipid to the membrane
|
void |
addLayer(Layer layer) |
void |
addLipidExtra(Lipid_3D lip,
int domainID,
int layerID)
adds a Lipid to the Model
|
void |
addLipidIntra(Lipid_3D lip,
int domainID,
int layerID)
adds a Lipid to the Model
|
void |
addMicroDomain(MicroDomain_3D drawingDomain) |
void |
addProtein(Protein_3D pro,
int layerID)
adds a single Protein into the Model
|
boolean |
anyCurrentIntersections(boolean withBorderCheck,
StatusDialog dialog) |
boolean |
areaContainsMolecules(int area,
int layerID) |
boolean |
areLipidAbsoluteValuesOk()
Test, wheter the current absolute value settings have at least one
lipid per side.
|
boolean |
areLipidPercentagesOk()
Test, wheter the current percentage settings of the lipids on both sides
have an overall of 100%
|
long |
calculateTotalFileSize(int domainID,
int layerID)
Returns the maximal FileSize of the current Membrane
|
boolean |
canAddMoreExampleLipidsExtra(int domainID,
int layerID) |
boolean |
canAddMoreExampleLipidsIntra(int domainID,
int layerID) |
void |
clearExampleLipids()
Removes all sample lipids from the model
|
void |
clearLipids()
Removes all lipids from the membrane model (not the sample lipids) Also
clears the info about the last algorithm used
|
void |
clearProteins()
Removes all Proteins from the model
|
void |
clearSampleLipids() |
boolean |
containsExampleLipidExtra(java.lang.String code,
int domainID,
int layerID) |
boolean |
containsExampleLipidIntra(java.lang.String code,
int domainID,
int layerID) |
boolean |
containsMoleculeWithAbsoluteFilepath(java.lang.String key) |
int |
countAtoms(int group,
int domainID,
int layerID,
boolean withOPMAtoms)
Counts the atoms for the specified group of molecules.
|
int |
countChains(int group,
int domainID,
int layerID)
Counts the chains for the specified group of molecules.
|
int |
countMicroDomains() |
int |
countTERs(int group,
int domainID,
int layerID) |
boolean |
createAndAddANewExampleLipid(java.lang.String code,
java.lang.String file,
int modelnumber,
int domainID,
int membraneSide,
int layerID)
Creates and adds a new sample Lipid with the passed parameters
|
Lipid |
createNextLipid(int membraneside,
Lipid_3D[] sampleLipids,
int domainID,
int layerID,
MembranePackingAlgorithm algo) |
void |
deleteExampleLipidAtExtra(int index)
Removes the example lipid at specified index
|
void |
deleteExampleLipidAtIntra(int index)
Removes the example lipid at specified index
|
void |
deleteExampleLipidExtra(Lipid_3D lip) |
void |
deleteExampleLipidIntra(Lipid_3D lip) |
void |
deleteLipidAtExtra(int index)
deletes the Lipid that has the given index
|
void |
deleteLipidAtIntra(int index)
deletes the Lipid that has the given index
|
void |
deleteLipidExtra(Lipid_3D todelete)
deletes the specified lipid
|
void |
deleteLipidIntra(Lipid_3D todelete)
deletes the specified lipid
|
void |
deleteMolecule(Molecule_3D mol)
deletes the passed Molecule of any kind
|
void |
deleteProtein(Protein_3D molecule_3D)
deletes the passed Protein
|
void |
deleteProteinAt(int index)
deletes the Protein at specified index
|
java.lang.String |
getAlgorithmDescription() |
java.lang.String |
getAlgorithmName() |
java.lang.String |
getAlgorithmStringRepresentation() |
java.util.Vector<Lipid_3D> |
getAllExampleLipidsExtra() |
Lipid_3D[] |
getAllExampleLipidsExtraInDomain(int domainID,
int layerID) |
java.util.Vector<Lipid_3D> |
getAllExampleLipidsIntra() |
Lipid_3D[] |
getAllExampleLipidsIntraInDomain(int domainID,
int layerID) |
Lipid_3D[] |
getAllExampleLipidsOfTypeExtra(java.lang.String code,
int domainID,
int layerID) |
Lipid_3D[] |
getAllExampleLipidsOfTypeIntra(java.lang.String code,
int domainID,
int layerID) |
java.lang.String[] |
getAllExampleLipidTypesExtra()
returns a list of all types of sample lipids that occur in the membrane
at least once
|
java.lang.String[] |
getAllExampleLipidTypesExtraInDomain(int domainID,
int layerID) |
java.lang.String[] |
getAllExampleLipidTypesIntra()
returns a list of all types of sample lipids that occur in the membrane
at least once
|
java.lang.String[] |
getAllExampleLipidTypesIntraInDomain(int domainID,
int layerID) |
java.util.Vector<Lipid_3D> |
getAllLipidsExtra() |
Lipid_3D[] |
getAllLipidsExtraInDomain(int domainID,
int layerID) |
java.util.Vector<Lipid_3D> |
getAllLipidsIntra() |
Lipid_3D[] |
getAllLipidsIntraInDomain(int domainID,
int layerID) |
Lipid_3D[] |
getAllLipidsOfTypeExtra(java.lang.String code,
int domainID,
int layerID) |
Lipid_3D[] |
getAllLipidsOfTypeIntra(java.lang.String code,
int domainID,
int layerID) |
java.lang.String[] |
getAllLipidTypes()
returns a list of all types of lipids that occur in the membrane at least
once
|
java.lang.String[] |
getAllLipidTypesExtraInDomain(int domainID,
int layerID) |
java.lang.String[] |
getAllLipidTypesInMembraneExtra()
returns a list of all types of proteins that occur in the extracellular membrane at
least once
|
java.lang.String[] |
getAllLipidTypesInMembraneIntra()
returns a list of all types of lipids that occur in the intracellular membrane at least
once
|
java.lang.String[] |
getAllLipidTypesIntraInDomain(int domainID,
int layerID) |
MicroDomain_3D[] |
getAllMicroDomains(int currentLayerID) |
Molecule_3D[] |
getAllMoleculesInMembrane() |
Molecule_3D[] |
getAllMoleculesInMembrane(boolean interimSortByType) |
Molecule_3D[] |
getAllMoleculesInMembrane(int domainID,
int layerID) |
Molecule_3D[] |
getAllMoleculesInMembraneSortedBySide() |
Molecule_3D[] |
getAllMoleculesInMembraneSortedByType() |
java.util.Vector<Protein_3D> |
getAllProteins() |
Protein_3D[] |
getAllProteinsInDomain(int domainID,
int layerID) |
Protein_3D[] |
getAllProteinsOfType(java.lang.String code,
int domainID,
int layerID) |
java.lang.String[] |
getAllProteinTypes()
returns a list of all types of proteins that occur in the membrane at
least once
|
java.lang.String[] |
getAllProteinTypesInDomain(int domainID,
int layerID) |
int |
getArea()
Returns the area of the MembraneModel.
|
java.lang.String |
getAuthor()
Returns the author string
|
java.lang.String |
getCode()
Returns the code string
|
boolean |
getComputeAbsoluteValues()
Check if absolute values are used during the computation process instead of
percental values.
|
java.util.Vector<Molecule_3D> |
getCurrentIntersections(boolean withBorderCheck) |
java.lang.String |
getDate()
returns the date String
|
int |
getDecimalPlaces() |
Lipid_3D |
getExampleLipidAtExtra(int index)
Returns the sample lipid at the specified index
|
Lipid_3D |
getExampleLipidAtIntra(int index)
Returns the sample lipid at the specified index
|
Lipid_3D[] |
getExampleLipidsByPDBCodeExtra(java.lang.String PDBCode)
returns all Sample Lipid individues which are of the specified type.
|
Lipid_3D[] |
getExampleLipidsByPDBCodeIntra(java.lang.String PDBCode)
returns all Sample Lipid individues which are of the specified type.
|
int |
getExampleLipidsCountExtra()
Returns the count of example lipids
|
int |
getExampleLipidsCountIntra()
Returns the count of example lipids
|
boolean |
getExampleLipidTypeAlreadyInside(java.lang.String PDBCode)
Tests if a ExampleLipid with the passed PdbCode is already added
|
java.lang.String |
getEXPDTA() |
Molecule_3D |
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
|
java.lang.String |
getHeader()
Returns the header string
|
Lipid_3D |
getHighestExampleLipid(int mode)
Returns the lipid with the higest percentage in the specified group
|
java.lang.String |
getJRNL() |
java.lang.String |
getKEYWDS() |
java.io.File |
getLastGeneratedMembraneFile() |
Layer |
getLayer(int index) |
Layer |
getLayerByID(int layerID) |
int |
getLayerCount() |
Lipid_3D |
getLipidAtExtra(int index)
returns the lipid at the specified index
|
Lipid_3D |
getLipidAtIntra(int index)
returns the lipid at the specified index
|
int |
getLipidCountExtra()
returns the current number of lipids in the model
|
int |
getLipidCountIntra()
returns the current number of lipids in the model
|
Lipid_3D[] |
getLipidsByPDBCodeExtra(java.lang.String PDBCode)
returns all Lipid individues which are of the specified type.
|
Lipid_3D[] |
getLipidsByPDBCodeIntra(java.lang.String PDBCode)
returns all Lipid individues which are of the specified type.
|
boolean |
getLipidTypeAlreadyInside(java.lang.String PDBCode)
Tests if a Lipid with the passed PdbCode is already inside the Membrane
|
boolean |
getMembraneHasBeenEditedAgain()
Indicates wether or not the current MembraneModel has been edited again
since last load or save
|
MicroDomain_3D |
getMicroDomain(int index) |
int |
getMicroDomainAtPoint(java.awt.Point point,
int layerID) |
Protein_3D |
getProteinAt(int index)
gets the protein at the specifed index
|
int |
getProteinCount()
returns the current number of Proteins in the model
|
Protein_3D[] |
getProteinsByPDBCode(java.lang.String PDBCode)
returns all Protein individues which are of the specified type.
|
boolean |
getProteinTypeAlreadyInside(java.lang.String PDBCode)
Tests if a Protein with the passed PdbCode is already inside the Membrane
|
java.lang.String |
getRemark()
returns the comment String
|
java.awt.Dimension |
getSize()
Returns the size of the membrane
|
java.lang.String |
getSOURCE()
returns a list of entered species
|
java.lang.String |
getTitle()
Returns the title String
|
int |
getTotalMoleculeCount(int group)
Returns the total molecule count.
|
boolean |
hasMultipleLayers() |
boolean |
hasProteinWithId(java.lang.String id)
Tests, wheter a Protein with the passed ID is currently present in the
model
|
boolean |
isEmpty()
Tests, wether the Membrane is completely Empty or not
|
boolean |
isMoleculeStillIn(Molecule_3D mol)
Tests, if the passed protein is currently in the model
|
void |
organizeDomains() |
void |
prepare(MembranePackingAlgorithm memb) |
void |
removeLayer(Layer currentLayer) |
void |
removeMicroDomain(MicroDomain_3D toremove) |
void |
reshapeDomains() |
void |
setAlgorithmdescription(java.lang.String algorithmdescription) |
void |
setAlgorithmname(java.lang.String algorithmname) |
void |
setAlgorithmStringRepresentation(java.lang.String algorithmstringrepresentation) |
void |
setAuthor(java.lang.String author)
Sets the author string
|
void |
setCode(java.lang.String code)
Sets the code string
|
void |
setComputeAbsoluteValues(boolean computeAbsoluteValues)
Set if absolute values are used during the computation process instead of
percental values.
|
void |
setDate(java.lang.String date)
sets the date string
|
void |
setDecimalPlaces(int decimalplaces) |
void |
setExpdta(java.lang.String expdta) |
void |
setHeader(java.lang.String header)
Sets the header string
|
void |
setJrnl(java.lang.String jrnl) |
void |
setKeywds(java.lang.String keywds) |
void |
setLastGeneratedMembraneFile(java.io.File lastGeneratedMembraneFile) |
void |
setMembraneHasBeenEditedAgain(boolean membraneHasBeenEditedAgain)
sets the state of membraneHasBeenEditedAgain
|
void |
setPolygonMode(int polygon_mode)
Changes the PolygonMode for all Molecules during 3d runtime
|
void |
setRemark(java.lang.String comment)
sets the comment string
|
void |
setShininess(int value,
int mode)
Changes the shininess for all Molecules during 3d runtime
|
void |
setSize(java.awt.Dimension size)
Sets the size of the membrane
|
void |
setSortByType(boolean sortByType)
Set if the lipids in the membrane PDB file are sorted by type during export.
|
void |
setSOURCE(java.lang.String species)
sets a list of species
|
void |
setTitle(java.lang.String title)
Sets the title String
|
void |
showAllMultilayers(boolean show) |
boolean |
sortByType()
Check if the lipids in the membrane PDB file is sorted by type during export.
|
void |
sortMolecules() |
void |
translateAllMolecules(float factor,
boolean move,
boolean updatePresentation) |
public MembraneModel()
public Molecule_3D[] getAllMoleculesInMembrane(boolean interimSortByType)
public Molecule_3D[] getAllMoleculesInMembrane()
public Molecule_3D[] getAllMoleculesInMembraneSortedBySide()
public Molecule_3D[] getAllMoleculesInMembraneSortedByType()
public boolean getMembraneHasBeenEditedAgain()
public void setMembraneHasBeenEditedAgain(boolean membraneHasBeenEditedAgain)
membraneHasBeenEditedAgain
- public java.lang.String getCode()
public void setCode(java.lang.String code)
code
- public java.lang.String getHeader()
public void setHeader(java.lang.String header)
header
- public java.lang.String getDate()
public void setDate(java.lang.String date)
date
- public int getArea()
public java.lang.String getAuthor()
public void setAuthor(java.lang.String author)
author
- public void setSOURCE(java.lang.String species)
species
- public java.lang.String getSOURCE()
public java.lang.String getTitle()
public void setTitle(java.lang.String title)
title
- public java.lang.String getRemark()
public void setRemark(java.lang.String comment)
comment
- public java.lang.String getKEYWDS()
public void setKeywds(java.lang.String keywds)
public java.lang.String getEXPDTA()
public void setExpdta(java.lang.String expdta)
public java.lang.String getJRNL()
public void setJrnl(java.lang.String jrnl)
public java.util.Vector<Protein_3D> getAllProteins()
public java.util.Vector<Lipid_3D> getAllLipidsExtra()
public java.util.Vector<Lipid_3D> getAllLipidsIntra()
public java.util.Vector<Lipid_3D> getAllExampleLipidsExtra()
public java.util.Vector<Lipid_3D> getAllExampleLipidsIntra()
public void addProtein(Protein_3D pro, int layerID)
pro
- layerID
- public Protein_3D getProteinAt(int index)
index
- public void deleteProtein(Protein_3D molecule_3D)
molecule_3D
- public void deleteProteinAt(int index)
index
- public int getProteinCount()
public void addLipidExtra(Lipid_3D lip, int domainID, int layerID)
lip
- domainID
- public void addLipidIntra(Lipid_3D lip, int domainID, int layerID)
lip
- public Lipid_3D getLipidAtExtra(int index)
index
- public Lipid_3D getLipidAtIntra(int index)
index
- public void deleteLipidExtra(Lipid_3D todelete)
todelete
- public void deleteLipidIntra(Lipid_3D todelete)
todelete
- public void deleteLipidAtExtra(int index)
index
- public void deleteExampleLipidExtra(Lipid_3D lip)
public void deleteLipidAtIntra(int index)
index
- public void deleteExampleLipidIntra(Lipid_3D lip)
public void deleteMolecule(Molecule_3D mol)
molecule_3D
- public int getLipidCountExtra()
public int getLipidCountIntra()
public Protein_3D[] getProteinsByPDBCode(java.lang.String PDBCode)
PDBCode
- the pdb code of all proteins that should be returnedpublic Lipid_3D[] getLipidsByPDBCodeExtra(java.lang.String PDBCode)
PDBCode
- the pdb code of all lipids that should be returnedpublic Lipid_3D[] getLipidsByPDBCodeIntra(java.lang.String PDBCode)
PDBCode
- the pdb code of all lipids that should be returnedpublic Lipid_3D[] getExampleLipidsByPDBCodeIntra(java.lang.String PDBCode)
PDBCode
- the pdb code of all lipids that should be returnedpublic Lipid_3D[] getExampleLipidsByPDBCodeExtra(java.lang.String PDBCode)
PDBCode
- the pdb code of all lipids that should be returnedpublic java.lang.String[] getAllProteinTypes()
public java.lang.String[] getAllExampleLipidTypesExtra()
public java.lang.String[] getAllExampleLipidTypesIntra()
public java.lang.String[] getAllLipidTypesInMembraneExtra()
public java.lang.String[] getAllLipidTypesInMembraneIntra()
public java.lang.String[] getAllLipidTypes()
public boolean getProteinTypeAlreadyInside(java.lang.String PDBCode)
public boolean getLipidTypeAlreadyInside(java.lang.String PDBCode)
public boolean getExampleLipidTypeAlreadyInside(java.lang.String PDBCode)
public java.awt.Dimension getSize()
public void setSize(java.awt.Dimension size)
size
- public int getTotalMoleculeCount(int group)
group
- public void clearLipids()
public void clearSampleLipids()
public void clearProteins()
public void clearExampleLipids()
public void addExampleLipidExtra(Lipid_3D actLip, int domainID, int layerID)
lip
- domainID
- public void addExampleLipidIntra(Lipid_3D actLip, int domainID, int layerID)
lip
- domainID
- public Lipid_3D getExampleLipidAtExtra(int index)
index
- public Lipid_3D getExampleLipidAtIntra(int index)
index
- public int getExampleLipidsCountExtra()
public int getExampleLipidsCountIntra()
public void deleteExampleLipidAtExtra(int index)
public void deleteExampleLipidAtIntra(int index)
public Molecule_3D getFirstMoleculeThatHasFile(java.io.File file, int group, int modelnumber)
file
- group
- modelnumber
- public Lipid_3D getHighestExampleLipid(int mode)
mode
- 0 extra, 1 intrapublic long calculateTotalFileSize(int domainID, int layerID)
public boolean isMoleculeStillIn(Molecule_3D mol)
mol
- public boolean areLipidPercentagesOk()
public boolean areLipidAbsoluteValuesOk()
public boolean hasProteinWithId(java.lang.String id)
id
- public void setShininess(int value, int mode)
value
- mode
- 0 PROTEINS, 1 LIPIDSpublic void setPolygonMode(int polygon_mode)
polygon_mode
- public boolean createAndAddANewExampleLipid(java.lang.String code, java.lang.String file, int modelnumber, int domainID, int membraneSide, int layerID)
code
- file
- domainID
- membraneSide
- public int countAtoms(int group, int domainID, int layerID, boolean withOPMAtoms)
group
- public int countChains(int group, int domainID, int layerID)
group
- public boolean isEmpty()
public java.lang.String getAlgorithmName()
public java.lang.String getAlgorithmDescription()
public java.lang.String getAlgorithmStringRepresentation()
public void setAlgorithmdescription(java.lang.String algorithmdescription)
public void setAlgorithmname(java.lang.String algorithmname)
public void setAlgorithmStringRepresentation(java.lang.String algorithmstringrepresentation)
public void addAlgorithmStringRepresentation(java.lang.String algorithmstringrepresentation)
public java.io.File getLastGeneratedMembraneFile()
public void setLastGeneratedMembraneFile(java.io.File lastGeneratedMembraneFile)
public void addMicroDomain(MicroDomain_3D drawingDomain)
public MicroDomain_3D getMicroDomain(int index)
public void removeMicroDomain(MicroDomain_3D toremove)
public int countMicroDomains()
public void organizeDomains()
public boolean containsExampleLipidExtra(java.lang.String code, int domainID, int layerID)
public boolean containsExampleLipidIntra(java.lang.String code, int domainID, int layerID)
public boolean canAddMoreExampleLipidsExtra(int domainID, int layerID)
public boolean canAddMoreExampleLipidsIntra(int domainID, int layerID)
public int getMicroDomainAtPoint(java.awt.Point point, int layerID)
public void reshapeDomains()
public Molecule_3D[] getAllMoleculesInMembrane(int domainID, int layerID)
public Protein_3D[] getAllProteinsInDomain(int domainID, int layerID)
public Lipid_3D[] getAllExampleLipidsExtraInDomain(int domainID, int layerID)
public Lipid_3D[] getAllExampleLipidsIntraInDomain(int domainID, int layerID)
public Lipid_3D[] getAllLipidsExtraInDomain(int domainID, int layerID)
public Lipid_3D[] getAllLipidsIntraInDomain(int domainID, int layerID)
public java.lang.String[] getAllProteinTypesInDomain(int domainID, int layerID)
public java.lang.String[] getAllExampleLipidTypesExtraInDomain(int domainID, int layerID)
public java.lang.String[] getAllExampleLipidTypesIntraInDomain(int domainID, int layerID)
public java.lang.String[] getAllLipidTypesExtraInDomain(int domainID, int layerID)
public java.lang.String[] getAllLipidTypesIntraInDomain(int domainID, int layerID)
public Protein_3D[] getAllProteinsOfType(java.lang.String code, int domainID, int layerID)
public Lipid_3D[] getAllExampleLipidsOfTypeExtra(java.lang.String code, int domainID, int layerID)
public Lipid_3D[] getAllExampleLipidsOfTypeIntra(java.lang.String code, int domainID, int layerID)
public Lipid_3D[] getAllLipidsOfTypeExtra(java.lang.String code, int domainID, int layerID)
public Lipid_3D[] getAllLipidsOfTypeIntra(java.lang.String code, int domainID, int layerID)
public void prepare(MembranePackingAlgorithm memb)
public void setDecimalPlaces(int decimalplaces)
public int getDecimalPlaces()
public Lipid createNextLipid(int membraneside, Lipid_3D[] sampleLipids, int domainID, int layerID, MembranePackingAlgorithm algo)
public boolean areaContainsMolecules(int area, int layerID)
public void sortMolecules()
public boolean anyCurrentIntersections(boolean withBorderCheck, StatusDialog dialog)
public java.util.Vector<Molecule_3D> getCurrentIntersections(boolean withBorderCheck)
public boolean containsMoleculeWithAbsoluteFilepath(java.lang.String key)
public int getLayerCount()
public Layer getLayer(int index)
public boolean hasMultipleLayers()
public Layer getLayerByID(int layerID)
public void addLayer(Layer layer)
public void removeLayer(Layer currentLayer)
public void showAllMultilayers(boolean show)
public void translateAllMolecules(float factor, boolean move, boolean updatePresentation)
public MicroDomain_3D[] getAllMicroDomains(int currentLayerID)
public int countTERs(int group, int domainID, int layerID)
public boolean sortByType()
public void setSortByType(boolean sortByType)
boolean
- sortByTypepublic boolean getComputeAbsoluteValues()
public void setComputeAbsoluteValues(boolean computeAbsoluteValues)
boolean
- computeAbsoluteValues