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Package qubx :: Module model :: Class QubModel
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Class QubModel

source code

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)

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