fluxpyt package¶
Submodules¶
fluxpyt.build_model module¶
Created on Sat Feb 6 21:09:50 2016
@author: Trunil
Reads and build model from csv. Note 2Jul2016: this program reads csv model into stoichiometric matrix with list of rxns and metabolites
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fluxpyt.build_model.
get_linenumber
()[source]¶ Get line number in the code. Usefull to find which line of the code this function occurrs.
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fluxpyt.build_model.
make_stoich_matrix
(reactions, reaction_formulae, excludedMetabolites=[])[source]¶ - Stoichiometric matrix (S) from reaction formulae
- Reactions must be written in form:
A -> 2 B
A + B <-> C
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fluxpyt.build_model.
metabolite_list
(reaction_formulae, excludedMetabolites=[])[source]¶ - Make list of metabolites from reaction formula.
- Reactions must be written in form:
- A -> 2 B C <- A + B A + B <-> C
fluxpyt.create_atm_transition_equations module¶
Created on Mon Jul 4 12:46:38 2016
Generates elementary reaction list.
@author: Trunil
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fluxpyt.create_atm_transition_equations.
create_atm_transition_equations
(rxnIDs, rxnList, atm_transition_rxns, moleculeList)[source]¶ - Input:
- rxnList = reaction formulae in form of list atm_transition_rxns = respective atom transition reaction list moleculeList = list of molecules observed (emu types e.g. A:0111)
- Output:
- reaction list with atom transitions, new metabolite (emu types) list
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fluxpyt.create_atm_transition_equations.
findMolRxns
(rxnIDs, molecule, rxnList, atm_transition_rxns)[source]¶
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fluxpyt.create_atm_transition_equations.
get_new_molecule
(rxn, moleculeList, current_molecule)[source]¶
fluxpyt.input_substrate_emu module¶
Created on Tue Aug 2 15:44:59 2016
@author: Trunil
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fluxpyt.input_substrate_emu.
cal_substrate_mid
(fileName, elementary_rxn_list)[source]¶ Calculates substrate mids.
Note: Only 13C carbon mids can be calculated for now.
- Input:
- fileName: substrate input file name. (csv format file)
- elementary_rxn_list: list of elementary reactions.
- assumption:
- nat = [0.9893, 0.0107] ... naturnal carbon isotope abundance
- lab = [0.01,0.99]... labeled carbon abundance
fluxpyt.main module¶
Created on Mon Jul 4 12:23:46 2016
Main module of FluxPyt.
Collects user inputs.
All the modules are run through this.
@author: Trunil
fluxpyt.make_emu_model module¶
fluxpyt.mid_corr module¶
Created on Wed Mar 8 12:03:26 2017
Adapted from function corrMatGen in Openflux
@author: Trunil
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fluxpyt.mid_corr.
corrMatGen
(output_size, input_size=0, molecularFormula='')[source]¶ function CM = corrMatGen(output_size, input_size, molform)
Returns correction matrix.
example: outputMDV = CM * inputMDV
- Inputs:
- output_size: int. length of output MDV (truncated length) (number of values in measured MID
- e.g. pyruvate has 3 carbons (ideally 4 mids) but only three are measured or detected.)
input_size: int. lenght of input MDV (carbon backbone + 1)
molform: molecular formula without carbon backbone.
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fluxpyt.mid_corr.
corrMatGen1
(output_row, input_size=0, molecularFormula='')[source]¶ function CM = corrMatGen(output_size, input_size, molform)
Generates correction matrix.
example: outputMDV = CM * inputMDV
Inputs:
- output_row: list of output rows i.e. masses to be calculated
- e.g. [0,1,2] will give corrected mids of M+0 , M+1 and M+2 .
input_size: int. lenght of input MDV (carbon backbone + 1)
molform: molecular formula without carbon backbone.
fluxpyt.mid_vec_gen module¶
- Generate correction vector for a given natural isotope distribution vector and number of atomic elements
- iDist = isotope_dist = isotopomer distribution vector of the atom ele = num_atom = number of elements of the same atom
Similar to corr_vect = cVectGen(iDist, ele) in openFLux by Lake-Ee Quek, AIBN Created on Mon Jul 18 16:44:48 2016
@author: Trunil
fluxpyt.monte_carlo module¶
Created on Sun Jun 25 12:36:28 2017
Monte Carlo for confidence interval estimation
@author: Trunil
fluxpyt.priliminary_fba module¶
Created on Thu Jul 14 11:50:41 2016
@author: Trunil
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fluxpyt.priliminary_fba.
create_objective
(stoich_matrix, model_metabolite, rxnInd='minTotal', maximize=False, boundTag=True)[source]¶
fluxpyt.solve_mfa_lm module¶
Created on Thu Jun 8 10:55:41 2017
Function to solve MFA problem using lmfit package
@author: Trunil
fluxpyt.solve_mid_networks module¶
Solves the elementory metabolite unit networks.
Solves mids for only one set of flux_distribution
Created on Fri Jul 15 10:57:23 2016
@author: Trunil
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fluxpyt.solve_mid_networks.
append_mids
(mids1, mids2)[source]¶ used when we have two lists of mids. Joins these two
fluxpyt.utility module¶
Created on Tue Jul 19 10:44:54 2016
@author: Trunil
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fluxpyt.utility.
nCr
(n, r)[source]¶ http://stackoverflow.com/questions/4941753/is-there-a-math-ncr-function-in-python