public class Distributor extends MembranePackingAlgorithm
Modifier and Type | Field and Description |
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javax.swing.JCheckBox |
cbAlgoAddLipids |
javax.swing.JCheckBox |
cbAlgoApproach |
javax.swing.JCheckBox |
cbAlgoShake |
javax.swing.JCheckBox |
cbAlgoTwist |
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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Distributor() |
Modifier and Type | Method and Description |
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boolean |
buildAndShowGui() |
void |
fillWithLipids()
The runtime of this algorithm is:
r*((n*M || RP) + n*D), where
r = repetitions until the user stopped the algorithm or the defined values are reached
n = number of actual lipids in the membrane
M = mix up attempt (repositioning of already placed lipid)
D = distribute procedure
The runtime of RandomPlacing (RP) is:
RP = (l*A+n*P+l*S), where
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 cbAlgoAddLipids
public javax.swing.JCheckBox cbAlgoApproach
public javax.swing.JCheckBox cbAlgoShake
public javax.swing.JCheckBox cbAlgoTwist
public boolean buildAndShowGui()
public java.lang.String getFullInformation()
public java.lang.String getShortInformation()
public java.lang.String getName()
public java.awt.Component getRuntimeControlPanel()
public java.lang.String getStringRepresentationOfSetupParameters()
public boolean overrideExistingLipids()
public void stopAlgorithm()
public boolean supportsAbsoluteValues()
public boolean supportsMicrodomains()
public void fillWithLipids() throws java.lang.Exception
java.lang.Exception