Package qubx :: Module model :: Class QubModel

Class QubModel

object --+
         |
        QubModel

Hidden Markov model, e.g. of one ion channel.

Instance Methods

[hide private]

__init__(self)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

__str__(self)
str(x)

source code

_gen_connecting(self)

source code

_onEditConstraint(self, need_enforced)

source code

_onInsertRate(self, i, undoing)

source code

_onRemovingRate(self, i, undoing)

source code

_onRemovingState(self, i, undoing)

source code

_onSetRate(self, i, field, val, prev, undoing)

source code

_onSetState(self, i, field, val, prev, undoing)

source code

_onUndoChange(self, undoStack)

source code

acceptStateIndex(self, x)

source code

as_json(self)

source code

as_tree(self)
Returns the model as a QMF tree.

source code

balance_all_loops(self)

source code

clear(self)
Removes all states, rates and constraints.

source code

dispose(self)

source code

enforce_constraints(self)
Modifies rates as necessary to satisfy constraints_kin such as detailed (im)balance.

source code

formatStateAsLbl(self, i)

source code

from_json(self, json)

source code

from_mdl(self, f)

source code

from_tree(self, f)
Reads in the model from f, a {qubx.tree.Node_numpy} formatted as QMF.

source code

get_stimulus(self)

source code

pre_close(self)

source code

revert_to_saved(self)
Re-reads the model from path.

source code

saveAs(self, spath=None, progressf=<__builtin__.function object>)
Saves the model at as_path.

source code

set_IeqFv(self, x)

source code

set_balance_loops(self, x)

source code

set_changed(self, x)

source code

set_channelCount(self, x, seal=True)

source code

set_k0format(self, x)

source code

set_k1format(self, x)

source code

set_path(self, x)

source code

set_vRev(self, x)

source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Instance Variables

[hide private]

IeqFv
whether to use Cond instead of Amp

OnChangeBalanceLoops
WeakEvent(QubModel, balance_loops)

OnChangeChanged
WeakEvent(QubModel, is_changed)

OnChangeField
WeakEvent(QubModel, 'Name' or 'In Folder' or 'Channel Count' or 'vRev' or 'k*format') for ObjectTable

OnChangePath
WeakEvent(QubModel, path or "")

OnChangeVariables
WeakEvent(QubModel, [var_name])

OnSetChannelCount
WeakEvent(QubModel, channelCount)

OnSetIeqFv
WeakEvent(QubModel, IeqFv)

OnSetK0Format
WeakEvent(QubModel, k0format)

OnSetK1Format
WeakEvent(QubModel, k1format)

OnSetVRev
WeakEvent(QubModel, vRev)

balance_loops
True to maintain detailed balance

changed
(bool) if different from on disk

channelCount
number of identical mechanisms

classes
qubx.table.SimpleTable of Amp, Std, Cond, CondStd, vRev

constraints_kin
qubx.table.SimpleTable of Type, States

k0format
format expr for all k0s

k1format
format expr for all k1s and k2s

path
folder/file name

rate_connecting
dict: (a,b) -> index of rate connecting from state a to state b

rates
qubx.table.SimpleTable of From, To, k0, k1, k2, Ligand, Voltage, Pressure

should_enforce_constraints
generally True; temporarily False to set many rates at once

states
qubx.table.SimpleTable of Class, Pr, x, y, Label

undoStack
qubx.undo.UndoStack for all model edits

vRev
reversal potential in millivolts

variables
names of active variables e.g.

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

str(self)
(Informal representation operator)

source code

str(x)

Overrides: object.__str__: (inherited documentation)

as_tree(self)

source code

Returns the model as a QMF tree.

Returns:: qubx.tree.Node_numpy

Instance Variable Details

[hide private]

IeqFv

whether to use Cond instead of Amp

Get Method:: unreachable(self)
Set Method:: unreachable(self, x)

balance_loops

True to maintain detailed balance

Get Method:: unreachable(self)
Set Method:: unreachable(self, x)

changed

(bool) if different from on disk

Get Method:: unreachable(self)
Set Method:: unreachable(self, x)

channelCount

number of identical mechanisms

Get Method:: unreachable(self)
Set Method:: unreachable(self, x)

k0format

format expr for all k0s

Get Method:: unreachable(self)
Set Method:: unreachable(self, x)

k1format

format expr for all k1s and k2s

Get Method:: unreachable(self)
Set Method:: unreachable(self, x)

path

folder/file name

Get Method:: unreachable(self)
Set Method:: unreachable(self, x)

vRev

reversal potential in millivolts

Get Method:: unreachable(self)
Set Method:: unreachable(self, x)

variables

names of active variables e.g. Ligand, Voltage

Get Method:: unreachable(self)

Class QubModel

__init__(self) (Constructor)

__str__(self) (Informal representation operator)

as_tree(self)

IeqFv

balance_loops

changed

channelCount

k0format

k1format

path

vRev

variables

init(self)
(Constructor)

str(self)
(Informal representation operator)