public class RandomPlacing extends MembranePackingAlgorithm
Modifier and Type | Field and Description |
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javax.swing.JCheckBox |
cbAddLipids |
javax.swing.JCheckBox |
cbAlgoAddLipids |
javax.swing.JCheckBox |
cbAlgoApproach |
javax.swing.JCheckBox |
cbAlgoShake |
javax.swing.JCheckBox |
cbAlgoTwist |
javax.swing.JCheckBox |
cbApproach |
javax.swing.JCheckBox |
cbShake |
javax.swing.JCheckBox |
cbTwist |
javax.swing.JRadioButton |
rb1 |
javax.swing.JRadioButton |
rb2 |
basicOperations, BORDER_EAST, BORDER_MAX_Y, BORDER_MIN_Y, BORDER_NORTH, BORDER_SOUTH, BORDER_WEST, calculationManager, CurrentMicroDomain, databaseOperations, EXTRA, INTRA, lipidsEC, lipidsIC, LIPIDTYPE, membraneViewListener, microDomains, PROTEINTYPE, random
Constructor and Description |
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RandomPlacing() |
Modifier and Type | Method and Description |
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void |
addLipids(int userSelectedDomain,
boolean toggleSide)
Tries to add new lipids to the membrane.
|
boolean |
buildAndShowGui() |
void |
fillWithLipids()
The runtime of this algorithm is:
r*(l*A+n*P+l*S), where
r = repetitions until the user stopped the algorithm
l = limit = membrane width + membrane depth
A = lipid random placing attempt
n = number of actual lipids in the membrane
P = protein or membrane center approaching
S = shaking and/or twisting
|
java.lang.String |
getFullInformation() |
java.lang.String |
getName() |
java.awt.Component |
getRuntimeControlPanel() |
java.lang.String |
getShortInformation() |
java.lang.String |
getStringRepresentationOfSetupParameters() |
boolean |
overrideExistingLipids() |
void |
stopAlgorithm() |
boolean |
supportsAbsoluteValues() |
boolean |
supportsMicrodomains() |
addEntryToDB, addExtracellularLipid, addIntracellularLipid, clearAllLipids, copyMatrix, countSampleLipids_Extracellular, countSampleLipids_Intracellular, countTotalLipidsThatAreAdded, createAUnitMatrix, createNextExtracellularLipid, createNextExtracellularLipid, createNextIntracellularLipid, createNextIntracellularLipid, createRandomLayerID, createRandomXZPosition, displayInformation, distance, distance, dock, getAlgorithm_Directory_In_Workspace, getAllLipids, getAllLipidsInDomain, getAllMoleculesInCurrentModel, getAllProteins, getAllProteinsInDomain, getAllSampleLipids_ExtraCellular, getAllSampleLipids_ExtraCellular, getAllSampleLipids_IntraCellular, getAllSampleLipids_IntraCellular, getAllSampleLipidsInModel, getCurrentLayerID, getCurrentRenderMode, getDecimalPlaces, getDesiredAtomDistance, getExtracellularLipidByPDBCode, getIntersectedBorders, getIntersectedMolecules, getIntracellularLipidByPDBCode, getJ3DBranchGroup, getLayerAtIndex, getLayerByLayerID, getLayerCount, getLipidInMembraneHeight, getLipidsInRadiusExcept, getMembraneArea, getMembraneBounds2D, getMembraneSize, getMicroDomain, getMicroDomainAt, getMicroDomainAtPoint, getMicroDomainAtPoint, getMicroDomainCount, getMinAtomDistance, getMoleculesInRadius, getMoleculesInRadiusExcept, getMoleculesInRadiusOnMySide, getMoleculesInRadiusOnMySide, getMoleculesInRadiusOnMySideExcept, getNearestLipidOnMySide, getNearestMolecule, getNearestMoleculeExcept, getNearestMoleculeExceptDetailed, getNearestMoleculeExceptOnMySide, getNearestMoleculeExceptOnMySideDetailed, getNearestMoleculeOnMySide, getNearestMoleculeOnMySideDetailed, getNearestProtein, getNearestProteinDetailed, getNearestProteinExcept, getNearestProteinExceptDetailed, getOriginalConstraintLenghts, getOriginalConstraintLengths, getPercentages_ExtraCellular, getPercentages_IntraCellular, getSampleLipid_Extracellular, getSampleLipid_Intracellular, getSelectedArea, getStartingTime, getSystemCovalentRadius, getSystemVanDerWaalsRadius, getTerminationTime, getTotalHeight, getTotalHeight, hasMembraneAnyExtracellularLipids, hasMembraneAnyIntracellularLipids, hasMembraneAnyProteins, hasMultipleLayers, intersects, intersectsAnyMicroDomain, intersectsBorderEast, intersectsBorderNorth, intersectsBorders, intersectsBorderSouth, intersectsBorderWest, intersectsEarth, intersectsEarthOrSky, intersectsMoleculeWithMolecule, intersectsMoleculeWithMolecules, intersectsSky, intersectsWithLipid, intersectsWithProteins, isAtomCollisionOn, isAtomDistanceAbsolute, isComputeAbsoluteValuesSelected, isInSystemTray, isOnAir, isStartInBackgroundAllowed, isStartInBackgroundSelected, manuallyUpdateStatistics, MembraneHasAnyExtracellularLipids, MembraneHasAnyIntracellularLipids, nearestAtomPoints, nearestTrianglePoints, refreshViews, removeExtracellularLipid, removeIntracellularLipid, removeLipidsFromMembrane, requestChangeOfRenderMode, restoreMembraneFromPDB, returnFromSystemTray, sendToSystemTray, setComputeAbsoluteValues, setDisplayedProgress, setListenerAndPrepare, setListenerAndPrepare, setListenerAndPrepare, setPercentages, setSimpleRandom, setStartInBackgroundAllowed, setStartInBackgroundSelected, setStartingTime, setTerminationTime, setUniqueRandom
public javax.swing.JCheckBox cbAddLipids
public javax.swing.JCheckBox cbApproach
public javax.swing.JCheckBox cbShake
public javax.swing.JCheckBox cbTwist
public javax.swing.JCheckBox cbAlgoAddLipids
public javax.swing.JCheckBox cbAlgoApproach
public javax.swing.JCheckBox cbAlgoShake
public javax.swing.JCheckBox cbAlgoTwist
public javax.swing.JRadioButton rb1
public javax.swing.JRadioButton rb2
public boolean buildAndShowGui()
public void fillWithLipids() throws IllegalOperationException
IllegalOperationException
public void addLipids(int userSelectedDomain, boolean toggleSide) throws IllegalOperationException
userSelectedDomain
- toggleSide
- IllegalOperationException
public java.lang.String getFullInformation()
public java.lang.String getName()
public java.lang.String getShortInformation()
public java.lang.String getStringRepresentationOfSetupParameters()
public void stopAlgorithm()
public boolean supportsAbsoluteValues()
public boolean supportsMicrodomains()
public boolean overrideExistingLipids()
public java.awt.Component getRuntimeControlPanel()