Mem3DG
0.0.7rc1
API Documentation:
Python API Reference
Mem3DG
Index
Index
_
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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X
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Z
_
__init__() (pymem3dg._core.Adsorption method)
(pymem3dg._core.Aggregation method)
(pymem3dg._core.Bending method)
(pymem3dg._core.Boundary method)
(pymem3dg._core.ConjugateGradient method)
(pymem3dg._core.Dirichlet method)
(pymem3dg._core.DPD method)
(pymem3dg._core.Energy method)
(pymem3dg._core.Entropy method)
(pymem3dg._core.Euler method)
(pymem3dg._core.External method)
(pymem3dg._core.Forces method)
(pymem3dg._core.Geometry method)
(pymem3dg._core.MeshMutator method)
(pymem3dg._core.MeshProcessor method)
(pymem3dg._core.Osmotic method)
(pymem3dg._core.Parameters method)
(pymem3dg._core.Point method)
(pymem3dg._core.Protein method)
(pymem3dg._core.SelfAvoidance method)
(pymem3dg._core.spring method)
(pymem3dg._core.System method)
(pymem3dg._core.Tension method)
(pymem3dg._core.Variation method)
(pymem3dg._core.VelocityVerlet method)
A
addNonconservativeForcing() (pymem3dg._core.System method)
Adsorption (class in pymem3dg._core)
adsorption (pymem3dg._core.Parameters property)
adsorptionEnergy (pymem3dg._core.Energy property)
Aggregation (class in pymem3dg._core)
aggregation (pymem3dg._core.Parameters property)
aggregationEnergy (pymem3dg._core.Energy property)
alpha (pymem3dg._core.Bending property)
ambientSolutionOsmoticPressureModel() (in module pymem3dg.boilerplate)
animate() (in module pymem3dg.visual)
areaDifferenceEnergy (pymem3dg._core.Energy property)
B
Bending (class in pymem3dg._core)
bending (pymem3dg._core.Parameters property)
Boundary (class in pymem3dg._core)
boundary (pymem3dg._core.Parameters property)
C
c1 (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
(pymem3dg._core.VelocityVerlet property)
characteristicTimeStep (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
chi (pymem3dg._core.Aggregation property)
closeMutableNetcdfFile() (pymem3dg._core.Euler method)
collapseFlat (pymem3dg._core.MeshMutator property)
collapseFlatScaleFactor (pymem3dg._core.MeshMutator property)
collapseSkinny (pymem3dg._core.MeshMutator property)
collapseSmall (pymem3dg._core.MeshMutator property)
computeConservativeForcing() (pymem3dg._core.System method)
computeGeodesicDistance() (pymem3dg._core.Geometry method)
computeInPlaneFluxForm() (pymem3dg._core.System method)
computeIntegratedPower() (pymem3dg._core.System method)
computeTotalEnergy() (pymem3dg._core.System method)
ConjugateGradient (class in pymem3dg._core)
constantOsmoticPressureModel() (in module pymem3dg.boilerplate)
constantSurfaceTensionModel() (in module pymem3dg.boilerplate)
constraintTolerance (pymem3dg._core.ConjugateGradient property)
createMutableNetcdfFile() (pymem3dg._core.Euler method)
curvTol (pymem3dg._core.MeshMutator property)
D
D (pymem3dg._core.Bending property)
d (pymem3dg._core.SelfAvoidance property)
dA0 (pymem3dg._core.Bending property)
damping (pymem3dg._core.Parameters property)
deviatoricCurvatureEnergy (pymem3dg._core.Energy property)
Dirichlet (class in pymem3dg._core)
dirichlet (pymem3dg._core.Parameters property)
dirichletEnergy (pymem3dg._core.Energy property)
DPD (class in pymem3dg._core)
dpd (pymem3dg._core.Parameters property)
E
edgeSpringEnergy (pymem3dg._core.Energy property)
Energy (class in pymem3dg._core)
Entropy (class in pymem3dg._core)
entropy (pymem3dg._core.Parameters property)
entropyEnergy (pymem3dg._core.Energy property)
epsilon (pymem3dg._core.Adsorption property)
eta (pymem3dg._core.Dirichlet property)
Euler (class in pymem3dg._core)
EXIT (pymem3dg._core.Euler property)
External (class in pymem3dg._core)
external (pymem3dg._core.Parameters property)
externalWork (pymem3dg._core.Energy property)
F
faceSpringEnergy (pymem3dg._core.Energy property)
femtoJToKBT() (in module pymem3dg.util)
flipNonDelaunay (pymem3dg._core.MeshMutator property)
flipNonDelaunayRequireFlat (pymem3dg._core.MeshMutator property)
Forces (class in pymem3dg._core)
form (pymem3dg._core.External property)
(pymem3dg._core.Osmotic property)
(pymem3dg._core.Tension property)
G
gamma (pymem3dg._core.DPD property)
gaussianDistribution() (in module pymem3dg.util)
geodesicMask (pymem3dg._core.Variation property)
Geometry (class in pymem3dg._core)
getAdsorptionForceVec() (pymem3dg._core.Forces method)
getAdsorptionPotential() (pymem3dg._core.Forces method)
getAggregationForceVec() (pymem3dg._core.Forces method)
getAggregationPotential() (pymem3dg._core.Forces method)
getAreaDifferenceForceVec() (pymem3dg._core.Forces method)
getCapillaryForceVec() (pymem3dg._core.Forces method)
getChemicalPotential() (pymem3dg._core.Forces method)
getColorbar() (in module pymem3dg.visual)
getCotanLaplacian() (pymem3dg._core.Geometry method)
getCylinder() (in module pymem3dg._core)
getData() (in module pymem3dg._core)
getDataElementName() (in module pymem3dg._core)
getDataPropertyName() (in module pymem3dg._core)
getDeviatoricCurvatureForceVec() (pymem3dg._core.Forces method)
getDeviatoricCurvaturePotential() (pymem3dg._core.Forces method)
getDiamond() (in module pymem3dg._core)
getDirichletPotential() (pymem3dg._core.Forces method)
getEdgeAdjacencyMatrix() (pymem3dg._core.Geometry method)
getEdgeLengths() (pymem3dg._core.Geometry method)
getEnergy() (pymem3dg._core.System method)
getEntropyForceVec() (pymem3dg._core.Forces method)
getEntropyPotential() (pymem3dg._core.Forces method)
getExternalForceVec() (pymem3dg._core.Forces method)
getFaceAndVertexMatrix() (in module pymem3dg._core)
getFaceAreas() (pymem3dg._core.Geometry method)
getFaceMatrix() (pymem3dg._core.Geometry method)
getFaceSurfacePointClosestToEmbeddedCoordinate() (in module pymem3dg._core)
getForces() (pymem3dg._core.System method)
getGeodesicDistance() (pymem3dg._core.Geometry method)
getGeometry() (pymem3dg._core.System method)
getHexagon() (in module pymem3dg._core)
getIcosphere() (in module pymem3dg._core)
getInteriorPenaltyPotential() (pymem3dg._core.Forces method)
getLineCapillaryForceVec() (pymem3dg._core.Forces method)
getLumpedMassMatrix() (pymem3dg._core.Geometry method)
getMechanicalForceVec() (pymem3dg._core.Forces method)
getNotableVertex() (pymem3dg._core.Geometry method)
getOsmoticForceVec() (pymem3dg._core.Forces method)
getOsmoticPressure() (pymem3dg._core.Forces method)
getPolyscopeEdgeOrientations() (pymem3dg._core.Geometry method)
getPolyscopePermutations() (pymem3dg._core.Geometry method)
getProteinDensity() (pymem3dg._core.System method)
getProteinRateOfChange() (pymem3dg._core.System method)
getSpontaneousCurvature() (pymem3dg._core.System method)
getSpontaneousCurvatureForceVec() (pymem3dg._core.Forces method)
getSpontaneousCurvatureForceVec_areaGrad() (pymem3dg._core.Forces method)
getSpontaneousCurvatureForceVec_gaussVec() (pymem3dg._core.Forces method)
getSpontaneousCurvatureForceVec_schlafliVec() (pymem3dg._core.Forces method)
getSpontaneousCurvaturePotential() (pymem3dg._core.Forces method)
getSpringForceVec() (pymem3dg._core.Forces method)
getSurfaceArea() (pymem3dg._core.Geometry method)
getSurfaceTension() (pymem3dg._core.Forces method)
getTetrahedron() (in module pymem3dg._core)
getVelocity() (pymem3dg._core.System method)
getVertexAdjacencyMatrix() (pymem3dg._core.Geometry method)
getVertexClosestToEmbeddedCoordinate() (in module pymem3dg._core)
getVertexDualAreas() (pymem3dg._core.Geometry method)
getVertexFurthestFromBoundary() (in module pymem3dg._core)
getVertexGaussianCurvatures() (pymem3dg._core.Geometry method)
getVertexGaussianCurvatureVectors() (pymem3dg._core.Geometry method)
getVertexMatrix() (pymem3dg._core.Geometry method)
getVertexMeanCurvatures() (pymem3dg._core.Geometry method)
getVertexMeanCurvatureVectors() (pymem3dg._core.Geometry method)
getVertexNormals() (pymem3dg._core.Geometry method)
getVertexSchlafliLaplacianMeanCurvatureVectors() (pymem3dg._core.Geometry method)
getVertexVolumeVariationVectors() (pymem3dg._core.Geometry method)
getVolume() (pymem3dg._core.Geometry method)
H
H0c (pymem3dg._core.Bending property)
I
ifAdaptiveStep (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
(pymem3dg._core.VelocityVerlet property)
ifJustGeometryPly (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
ifOutputMeshFile (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
(pymem3dg._core.VelocityVerlet property)
ifOutputTrajFile (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
(pymem3dg._core.VelocityVerlet property)
ifPrintToConsole (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
(pymem3dg._core.VelocityVerlet property)
initialize() (pymem3dg._core.System method)
integrate() (pymem3dg._core.ConjugateGradient method)
(pymem3dg._core.Euler method)
(pymem3dg._core.VelocityVerlet method)
interlaceImages() (in module pymem3dg.visual)
isAugementedLagrangian (pymem3dg._core.ConjugateGradient property)
isBacktrack (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
(pymem3dg._core.VelocityVerlet property)
isCapEnergy (pymem3dg._core.VelocityVerlet property)
isChangeTopology (pymem3dg._core.MeshMutator property)
isCollapseEdge (pymem3dg._core.MeshMutator property)
isFlipEdge (pymem3dg._core.MeshMutator property)
isMeshMutate (pymem3dg._core.MeshProcessor property)
isProteinConservation (pymem3dg._core.Variation property)
isProteinVariation (pymem3dg._core.Variation property)
isShapeVariation (pymem3dg._core.Variation property)
isShiftVertex (pymem3dg._core.MeshMutator property)
isSmoothenMesh (pymem3dg._core.MeshMutator property)
isSplitEdge (pymem3dg._core.MeshMutator property)
K
Kb (pymem3dg._core.Bending property)
Kbc (pymem3dg._core.Bending property)
Kd (pymem3dg._core.Bending property)
Kdc (pymem3dg._core.Bending property)
Kg (pymem3dg._core.Bending property)
Kgc (pymem3dg._core.Bending property)
kineticEnergy (pymem3dg._core.Energy property)
Kse (pymem3dg._core.spring property)
Ksl (pymem3dg._core.spring property)
Kst (pymem3dg._core.spring property)
L
lcrSpringEnergy (pymem3dg._core.Energy property)
linearSampling() (in module pymem3dg.util)
linearSubdivide() (in module pymem3dg._core)
loopSubdivide() (in module pymem3dg._core)
M
march() (pymem3dg._core.ConjugateGradient method)
(pymem3dg._core.Euler method)
(pymem3dg._core.VelocityVerlet method)
matplotlibStyle() (in module pymem3dg.visual)
maximumEdgeLength (pymem3dg._core.MeshMutator property)
maximumFaceArea (pymem3dg._core.MeshMutator property)
MeshMutator (class in pymem3dg._core)
meshMutator (pymem3dg._core.MeshProcessor property)
MeshProcessor (class in pymem3dg._core)
meshProcessor (pymem3dg._core.System property)
minimumEdgeLength (pymem3dg._core.MeshMutator property)
minimumFaceArea (pymem3dg._core.MeshMutator property)
module
pymem3dg._core
pymem3dg.boilerplate
pymem3dg.util
pymem3dg.visual
mu (pymem3dg._core.SelfAvoidance property)
mutateMesh() (pymem3dg._core.System method)
mutateMeshPeriod (pymem3dg._core.MeshMutator property)
N
n (pymem3dg._core.SelfAvoidance property)
O
Osmotic (class in pymem3dg._core)
osmotic (pymem3dg._core.Parameters property)
outputDirectory (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
(pymem3dg._core.VelocityVerlet property)
overlayColorbar() (in module pymem3dg.visual)
P
p (pymem3dg._core.SelfAvoidance property)
Parameters (class in pymem3dg._core)
parameters (pymem3dg._core.System property)
plotChemicalPotentials() (in module pymem3dg.visual)
plotEnergy() (in module pymem3dg.visual)
plotMechanicalForces() (in module pymem3dg.visual)
plotProteinDensity() (in module pymem3dg.visual)
plotScreenshot() (in module pymem3dg.visual)
Point (class in pymem3dg._core)
point (pymem3dg._core.Parameters property)
polyscopeStyle() (in module pymem3dg.visual)
potentialEnergy (pymem3dg._core.Energy property)
preferredAreaSurfaceTensionModel() (in module pymem3dg.boilerplate)
preferredVolumeOsmoticPressureModel() (in module pymem3dg.boilerplate)
prescribeExternalForce() (pymem3dg._core.System method)
prescribeGaussianPointForce() (in module pymem3dg.boilerplate)
prescribeGeodesicProteinDensityDistribution() (in module pymem3dg.boilerplate)
prescribeNotableVertex (pymem3dg._core.Point property)
prescribePeriodicForceOnCylinder() (in module pymem3dg.boilerplate)
prescribeProteinDensityDistribution (pymem3dg._core.Protein property)
pressureEnergy (pymem3dg._core.Energy property)
processSoup() (in module pymem3dg._core)
Protein (class in pymem3dg._core)
protein (pymem3dg._core.Parameters property)
proteinBoundaryCondition (pymem3dg._core.Boundary property)
proteinInteriorPenalty (pymem3dg._core.Energy property)
(pymem3dg._core.Protein property)
proteinMobility (pymem3dg._core.Parameters property)
pymem3dg._core
module
pymem3dg.boilerplate
module
pymem3dg.util
module
pymem3dg.visual
module
R
relation (pymem3dg._core.Bending property)
restartPeriod (pymem3dg._core.ConjugateGradient property)
rho (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
(pymem3dg._core.VelocityVerlet property)
rowwiseDotProduct() (in module pymem3dg.util)
rowwiseNorm() (in module pymem3dg.util)
rowwiseNormalize() (in module pymem3dg.util)
rowwiseScaling() (in module pymem3dg.util)
S
saveData() (pymem3dg._core.ConjugateGradient method)
(pymem3dg._core.Euler method)
(pymem3dg._core.VelocityVerlet method)
saveMutableNetcdfData() (pymem3dg._core.Euler method)
savePeriod (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
saveRichData() (pymem3dg._core.System method)
SelfAvoidance (class in pymem3dg._core)
selfAvoidance (pymem3dg._core.Parameters property)
setDefaultMeshProcessor() (in module pymem3dg.boilerplate)
setInputVertexPositions() (pymem3dg._core.Geometry method)
setPolyscopePermutations() (in module pymem3dg.visual)
shapeBoundaryCondition (pymem3dg._core.Boundary property)
smooth() (in module pymem3dg.util)
smoothenMesh() (pymem3dg._core.System method)
sphericalHarmonicsPerturbation() (in module pymem3dg.util)
splitCurved (pymem3dg._core.MeshMutator property)
splitCurvedScaleFactor (pymem3dg._core.MeshMutator property)
splitFat (pymem3dg._core.MeshMutator property)
splitLarge (pymem3dg._core.MeshMutator property)
splitLong (pymem3dg._core.MeshMutator property)
splitSharp (pymem3dg._core.MeshMutator property)
splitSkinnyDelaunay (pymem3dg._core.MeshMutator property)
spontaneousCurvatureEnergy (pymem3dg._core.Energy property)
spring (class in pymem3dg._core)
(pymem3dg._core.Parameters property)
startProfiler() (in module pymem3dg._core)
status() (pymem3dg._core.ConjugateGradient method)
(pymem3dg._core.Euler method)
(pymem3dg._core.VelocityVerlet method)
step() (pymem3dg._core.ConjugateGradient method)
(pymem3dg._core.Euler method)
(pymem3dg._core.VelocityVerlet method)
stopProfiler() (in module pymem3dg._core)
surfaceEnergy (pymem3dg._core.Energy property)
System (class in pymem3dg._core)
T
tanhDistribution() (in module pymem3dg.util)
temperature (pymem3dg._core.Parameters property)
Tension (class in pymem3dg._core)
tension (pymem3dg._core.Parameters property)
testConservativeForcing() (pymem3dg._core.System method)
time (pymem3dg._core.System property)
timeStep (pymem3dg._core.Euler property)
tolerance (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
totalEnergy (pymem3dg._core.Energy property)
totalTime (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
trajFileName (pymem3dg._core.ConjugateGradient property)
(pymem3dg._core.Euler property)
(pymem3dg._core.VelocityVerlet property)
U
updateConfigurations() (pymem3dg._core.System method)
updateGeodesicsPeriod (pymem3dg._core.Point property)
updateMaskPeriod (pymem3dg._core.Variation property)
updateNotableVertexPeriod (pymem3dg._core.Point property)
updateProteinDensityDistributionPeriod (pymem3dg._core.Protein property)
V
Variation (class in pymem3dg._core)
variation (pymem3dg._core.Parameters property)
VelocityVerlet (class in pymem3dg._core)
visualizeGeometry() (in module pymem3dg.visual)
visualizePly() (in module pymem3dg.visual)
X
xi (pymem3dg._core.Entropy property)
Z
zeroPadding() (in module pymem3dg.util)