Package qubx :: Package fast :: Module model

Module model

Compiled routines for graph theory and linear constraints.

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QUB Express is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

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Classes

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ModelStruct

PModel

Model

MultiModelStruct

PMultiModel

MultiModel

ConstrainedStruct

PConstrained

ConstrainedBase

Constrained

StimAmpsStruct

PStimAmps

StimAmps

StimRatesStruct

PStimRates

StimRates

Functions

[hide private]

find_loops(edges)
Returns a list of the fundamental cycles in a bidirectional graph.

source code

EliminateFixedParams(K, Ain, Bin)
Returns K, Ain, Bin, kR_indices with all fixed rates (and corresponding constraint rows) removed.

source code

Kr_to_K(Kr, K, Kr_indices)

source code

ReduceConstraints(Ain, Bin)

source code

SetupLinearConstraints(Ain, Bin, K)

source code

ef_from_param(cls, obj)

source code

Eigen_Scipy(n, a_, wr_, wi_, v_, v_inv_)

source code

Variables

[hide private]

Eigen_Scipy_Ptr = Eigen_Scipy_Ptr

__package__ = 'qubx.fast'

Function Details

[hide private]

find_loops(edges)

source code

Returns a list of the fundamental cycles in a bidirectional graph.

Parameters:

edges - a list of pairs (From, To) of connected state indices; should have both (From, To) and (To, From).

Returns:

a list of cycles; each cycle is a list of state indices

See David Colquhoun, Kathryn Dowsland, Marco Beato and Andrew Plested. (2004). How to impose microscopic reversibility in complex reaction mechanisms. (with appendix by Kathryn. A. Dowsland and Frank G. Ball) Biophysical Journal, 86, 3510-3518.Available here.