Index

A | C | D | E | F | G | H | I | K | L | M | O | P | Q | R | S | T | U | Y

A

addAttractionToTheCore() (openmmlib.SimulationWithCrosslinks method)
addBond() (openmmlib.Simulation method)
addCylindricalConfinement() (openmmlib.Simulation method)
addGravity() (openmmlib.Simulation method)
addGrosbergPolymerBonds() (openmmlib.Simulation method)
addGrosbergRepulsiveForce() (openmmlib.Simulation method)
addGrosbergStiffness() (openmmlib.Simulation method)
addHarmonicPolymerBonds() (openmmlib.Simulation method)
addInteraction() (openmmlib.Simulation method)
addLaminaAttraction() (openmmlib.Simulation method)
addLennardJonesForce() (openmmlib.Simulation method)
addMinimizingRepulsiveForce() (openmmlib.Simulation method)
addMutualException() (openmmlib.Simulation method)
addNucleolus() (openmmlib.YeastSimulation method)
addPolynomialRepulsiveForce() (openmmlib.Simulation method)
addPullForce() (openmmlib.Simulation method)
addSmoothSquareWellForce() (openmmlib.Simulation method)
addSmoothSquareWellTailedForce() (openmmlib.Simulation method)
addSoftLennardJonesForce() (openmmlib.Simulation method)
addSphericalConfinement() (openmmlib.Simulation method)
addSphericalWell() (openmmlib.ExperimentalSimulation method)
addStiffness() (openmmlib.Simulation method)
analyzeKnot() (in module knotAnalysis)
averageBinnedContactMap() (in module contactmaps)
averagePureContactMap() (in module contactmaps)

C

Cload() (in module polymerutils)
contactmaps (module)
cool_trunk() (in module contactmaps)
create_spiral() (in module polymerutils)
createSpiralRing() (in module polymerutils)
createWalls() (openmmlib.ExperimentalSimulation method)

D

dist() (openmmlib.Simulation method)
distance_matrix() (in module polymerutils)
doBlock() (openmmlib.Simulation method)

E

endtoend() (in module polymerutils)
energyMinimization() (openmmlib.Simulation method)
excludeSphere() (openmmlib.Simulation method)
expandPolymerRing() (in module knotAnalysis)
ExperimentalSimulation (class in openmmlib)

F

findSimplifiedPolymer() (in module polymerutils)
fixParticlesZCoordinate() (openmmlib.SimulationWithCrosslinks method)

G

getChains() (openmmlib.Simulation method)
getCloudGeometry() (in module polymerutils)
getData() (openmmlib.Simulation method)
getKnotNumber() (in module knotAnalysis)
getLayout() (openmmlib.Simulation method)
getScaledData() (openmmlib.Simulation method)
give_distance() (in module polymerScalings)
give_radius_scaling() (in module polymerScalings)
giveContacts() (in module contactmaps)
giveContactsAny() (in module contactmaps)
giveContactsOpenMM() (in module contactmaps)
giveCpScaling() (in module polymerScalings)
giveDistanceMap() (in module contactmaps)
giveIntContacts() (in module contactmaps)
grow_rw() (in module polymerutils)

H

h5dictLoad (class in contactmaps)

I

initPositions() (openmmlib.Simulation method)
initStorage() (openmmlib.Simulation method)
initVelocities() (openmmlib.Simulation method)
intload() (in module contactmaps)

K

knotAnalysis (module)

L

load() (in module polymerutils)
(openmmlib.Simulation method)
localEnergyMinimization() (openmmlib.Simulation method)

M

msd() (in module polymerutils)

O

openmmlib (module)

P

polymerScalings (module)
polymerutils (module)
printStats() (openmmlib.Simulation method)
pureMap() (in module contactmaps)

Q

quickLoad() (openmmlib.ExperimentalSimulation method)

R

rad2() (in module contactmaps)
randomizeData() (openmmlib.Simulation method)
reinitialize() (openmmlib.Simulation method)
rescaledMap() (in module contactmaps)
rescalePoints() (in module contactmaps)
RG() (openmmlib.Simulation method)
RMAX() (openmmlib.Simulation method)
rotation_matrix() (in module polymerutils)

S

save() (openmmlib.Simulation method)
saveFolder() (openmmlib.Simulation method)
setChains() (openmmlib.Simulation method)
setData() (openmmlib.Simulation method)
setLayout() (openmmlib.Simulation method)
setup() (openmmlib.Simulation method)
show() (openmmlib.Simulation method)
Simulation (class in openmmlib)
SimulationWithCrosslinks (class in openmmlib)
smooth_conformation() (in module polymerutils)
subchainDensityFunction() (in module polymerScalings)

T

tetherParticles() (openmmlib.Simulation method)

U

useDomains() (openmmlib.Simulation method)

Y

YeastSimulation (class in openmmlib)