straindesign.efmtool_cmp_interface
EFMtool compression interface for straindesign.
This module provides compression utilities for metabolic networks. By default, the pure Python ‘sparse_rref’ compression backend is used. The Java EFMTool backend is available via compression_backend=’efmtool_rref’ (requires jpype1).
For the documentation of the compression API provided by StrainDesign, refer to straindesign.compression.compress_model.
Module Contents
- straindesign.efmtool_cmp_interface.basic_columns_rat(mx, tolerance=0)[source]
Find basic columns using exact rational arithmetic (FLINT or sympy).
- straindesign.efmtool_cmp_interface.basic_columns_rat_java(mx, tolerance=0)[source]
Find basic columns using Java Gaussian elimination.
Legacy implementation using jpype and Java efmtool. Requires jpype1 and sympy to be installed.
- Parameters:
mx – Matrix (numpy array or Java matrix)
tolerance – Tolerance (unused in exact arithmetic)
- Returns:
Array of indices of basic columns
- straindesign.efmtool_cmp_interface.compress_model_java(model)[source]
Legacy Java compression using jpype (requires jpype and sympy).
- Parameters:
model – COBRA model (will be modified in place)
- Returns:
Reaction map from compressed to original reactions with scaling factors
- Return type:
- straindesign.efmtool_cmp_interface.jBigFraction2sympyRat(val)[source]
Convert Java BigFraction to sympy Rational (requires Java init).
- straindesign.efmtool_cmp_interface.jBigIntegerPair2sympyRat(numer, denom)[source]
Convert Java BigInteger pair to sympy Rational (requires sympy).
- straindesign.efmtool_cmp_interface.jpypeArrayOfArrays2numpy_mat(jmat)[source]
Convert jpype array of arrays to numpy matrix.