PyCytoplay

A python interface for Cytosim
To use the links, please compile the cytosim documentation. For this run the command :

make doc

List of bound classes and members :

▼▲PyCytoplay
play
setNormalKey sets the callback function for normal keys
setRuntimeCheck sets the callback function for runtime checks
setMouseClick sets the callback function for mouse clicks
▼▲PyCytosim
open loads simulation from object files
start loads simulation from config files
str_to_glos converts string to Glossary
str_to_glos converts string to Glossary
toVector converts numpy array to vector
toTorque converts numpy array to torque
▼▲Object
reference
property
position
Object
__next__
Object
id
writeHeader
points
▼▲Space
thickness
resize
volume
boundaries
inside
project
allInside
allOutside
toSpace
max_extension
projectDeflated
distanceToEdgeSqr
distanceToEdge
signedDistanceToEdge
bounce
normalToEdge
randomPlace
randomPlaceNearEdge
randomPlaceOnEdge
estimateVolume
▼▲Mecable
data
nbPoints
allocated
points Returns read-only point coordinates of the mecable
posPoint
setPoint
setPoint
addPoint
removePoints
clearPoints
shiftPoints
truncateM
truncateP
calculateMomentum
netForce
position
translate
allInside
▼▲Sphere
position
pos
Sphere
resize
reshape
orthogonalize
addSurfacePoint
nbbSurfacePoints
dragCoefficient
Sphere
Sphere
Sphere
▼▲Bead
position
Bead
setPosition
radius
radiusSqr
resize
volume
dragCoefficient
Bead
Bead
Bead
▼▲Chain
nbSegments
lastSegment
setStraight
setStraightLength
placeEnd
setEquilibrated
birthTime
age
Mecapoint
Interpolation
Interpolation
Interpolation
Interpolation
interpolateFromEnd
Interpolation
setEquilibrated
length1
trueLength
betweenMP
outsideMP
belowP
aboveM
FiberEnd
clampedIndexM
setOrigin
abscissaM
abscissaC
abscissaP
abscissaPoint
abscissaEnd
abscissaFrom
someAbscissa
posM
setStraight
posFrom
posMiddle
posEnd
posEndP
posEndM
netForceEndM
netForceEndP
projectedForceEndM
projectedForceEndP
projectedForceEndM
avgDirection
segmentation
flipChainPolarity
curvature
bendingEnergy0
planarIntersect
growM
addSegmentM
cutM
growP
addSegmentP
cutP
grow
adjustLength
truncateM
truncateP
▼▲Mecafil
tension
dragCoefficient
leftoverMobility
▼▲Fiber
points
Fiber
nbPoints
cutM
cutP
sever
severNow
Fiber
join
stateM
stateP
setStateM
setStateP
setDynamicState
freshAssembly
nbHands
addHand
removeHand
updateHands
detachHands
sortHands
Hand
nbHandsInRange
nbHandsNearEnd
__next__
▼▲ClassicFiber
freshAssemblyM
freshAssemblyP
▼▲DynamicFiber
freshAssemblyM
freshAssemblyP
▼▲Solid
position
points
dragCoefficient
addSphere
setRadius
addSphere
centroid
Solid
Solid
tag
property
nbPoints
Solid
▼▲Organizer
nbOrganized
position
positionP
dragCoefficient
Organizer
Organizer
▼▲Aster
Solid
position
nbFibers
Fiber
posLink1
posLink2
posFiber1
posFiber2
getLink1
getLink2
getLink
property
▼▲Couple
position
active
stiffness
force
cosAngle
sidePos
posFree
attachEnd1
attachEnd2
moveToEnd1
moveToEnd2
Fiber
abcissa
toCouple
Hand
Hand
hand
state
__len__
__getitem__
▼▲Single
toSingle
state
__getitem__
__len__
Hand
Single
Fiber
abscissa
posHand
dirFiber
attach
attachEnd
moveToEnd
detach
position
mobile
translate
setPosition
randomizePosition
posFoot
sidePos
Mecable
mobile
force
Single
Single
Space
▼▲Property
name
change
read
change_glos
read_glos
complete
rename
is_named
number
renumber
clear
clone
▼▲SpaceProp
▼▲SolidProp
drag
viscosity
steric
steric_range
Confinement
confine_stiffness
confine_space
display
display_fresh
▼▲HandProp
binding_rate
Hand
binding_key
unbinding_rate
unbinding_force
bind_also_end
bind_end_range
hold_growing_end
hold_shrinking_end
activity
display
▼▲MotorProp
stall_force
unloaded_speed
limit_speed
▼▲FiberProp
segmentation
rigidity
min_length
max_length
total_polymer
persistent
viscosity
drag_radius
drag_length
drag_model
drag_gap
binding_key
lattice
lattice_unit
Confinement
confine_space
confine_stiffness
steric
steric_radius
steric_range
glue
glue_single
activity
display_fresh
display
▼▲ClassicFiberProp
growing_speed
growing_off_speed
growing_force
shrinking_speed
catastrophe_rate
catastrophe_rate_stalled
▼▲DynamicFiberProp
growing_speed
growing_off_speed
growing_force
shrinking_speed
▼▲SimulProp
time
time_step
viscosity
kT
tolerance
acceptable_prop
precondition
steric
steric_stiffness_push
steric_stiffness_pull
steric_max_range
binding_grid_step
verbose
config_file
property_file
trajectory_file
clear_trajectory
skip_free_couple
display_fresh
display
read
read_str
clone
▼▲CoupleProp
hand1
hand2
stiffness
length
diffusion
fast_diffusion
stiff
Specificity
Confinement
confine_space
activity
HandProp
HandProp
▼▲SingleProp
hand
stiffness
length
diffusion
fast_diffusion
Confinement
confine_space
activity
HandProp
▼▲Interface
an interface to cytosim
add adds objects to simulation, see provided examples
execute_new adds objects to simulation, see provided examples
run runs simulation a given number of steps, see provided examples
execute_run runs simulation a given number of steps, see provided examples
set defines objects to simulation, see provided examples
execute_set defines objects to simulation, see provided examples
execute_change changes objects properties in simulation, see provided examples
▼▲Parser
a cytosim parser
▼▲PythonParser
Python interface to a parser
simul
load
frame
next
▼▲Simul
execute_cut performes a cut : sim.cut(filament_name, where), see Parser.execute_cut (C++)
execute_delete deletes objects from simulation, see provided examples
execute_import imports objects from text file, see provided examples
export export objects to text file, see provided examples
save saves current state to trajectory file
frame
SimulProp
Meca
properties
SpaceSet
SpaceSet
FieldSet
FiberSet
SphereSet
BeadSet
SolidSet
CoupleSet
SingleSet
OrganizerSet
remove
erase
nuke
time
time_step
step
computeForces
once
prepared_solve
prepare_meca
prepare
solve
solve_auto
dump
saveSystem
evaluate
Mecable
Mecable
Space
rename
isCategory
findProperty
writePropertiesTo
writeProperties
writePropertiesToNoPrune
▼▲Frame
Python interface to timeframe : behaves as a Python dictionary of Objectsets
fibers
time
simul
index
loaded
update
update
next
__iter__
keys
items
__getitem__
▼▲Group
Behaves as a list of objects with the same properties
__len__
size
prop
__iter__
__getitem__
▼▲Glossary::val_type
value_
defined_
count_
__repr__
▼▲Glossary
terms
__repr__
__iter__
__getitem__
__setitem__
keys
items
▼▲Mecapoint
Mecapoint
set
Mecable
valid
position
pos
overlapping
near
▼▲Interpolation
clear
set
valid
Mecable
Mecapoint
Mecapoint
coef1
coef2
coef
position
pos
pos1
pos2
diff
len
lenSqr
dir
inside
overlapping
overlapPoint
▼▲FiberSite
moveTo
relocateM
relocateP
Fiber
Fiber
update
Interpolation
Fiber
position
posHand
direction
dirFiber
abscissa
abscissaFromM
abscissaFromP
abscissaFrom
FiberEnd
distanceToEnd
▼▲Hand
Hand
Hand
HandProp
HandProp
relocate
relocateTo
moveToEnd
locate
attach
detach
attachEnd
attachTo
Hand
otherPosition
linkStiffness
moveTo
relocateM
relocateP
unattached
attached
update
Interpolation
Fiber
position
posHand
direction
dirFiber
abscissa
abscissaFromM
abscissaFromP
abscissaFrom
FiberEnd
distanceToEnd
▼▲Meca
nb_points
dimension
prepare
base
points
force
addForcePt
addForce
addTorque
addTorqueClamp
addTorqueParrallel
addTorqueAngle
addTorquePoliti
addPointClampPt
addPointClamp
addSphereClamp
addCylinderClampZ
addCylinderClampX
addSidePointClamp
addLineClamp
addLineClampPt
addPlaneClamp
addPlaneClampPt
addLink
addLinkPtI
addLinkIPt
addLinkPt
addLongLink
addLongLinkPt
addLongLinkPtI
addSideLink2D
addSideLink2DIPt
addSideSideLink2D
addSideSlidingLink2D
addSideSlidingLink2DIPt
addSideSlidingLinkS
addSideSlidingLinkSIPt
addSideLink3D
addSideLinkS
addSideLinkSIpt
addSideSlidingLinkS
addSideSlidingLinkSIpt
addSideLink
addSideLinkIpt
addSideSideLink
addSlidingLink
addSlidingLinkIpt
addSideSlidingLink
addSideSlidingLinkIpt
addTriLink
▼▲Vector
▼▲Vector3
▼▲realArray
▼▲ObjectSet
add
remove
link
unlink
erase
erase_all
size
__len__
Object
Object
Object
Object
__getitem__
▼▲SpaceSet
▼▲FiberSet
▼▲FieldSet
▼▲SphereSet
▼▲BeadSet
▼▲SolidSet
▼▲OrganizerSet
▼▲CoupleSet
__getitem__
▼▲SingleSet
__getitem__
▼▲ObjectList
A list-like structure of Cytosim objects
__getitem__
__len__