1 """Hold MetaTool data in a straightforward format.
2 """
3
4
5 import numpy.oldnumeric.matrix as Matrix
6
7
8 import Bio.MetaTool
9
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66
68
69 """Hold MetaTool output information.
70 """
71
86
88 out = ''
89 out = out + 'Input file name: %s\n' % self.input_file_name
90 out = out + 'Number of internal metabolites: %d\n' % self.num_int_metabolites
91 out = out + 'Number of reactions: %d\n' % self.num_reactions
92 out = out + '\n\nExternal Metabolites\n\ncount name\n\n'
93 for metabolite in self.external_metabolites:
94 out = out + str( metabolite )
95 out = out + '\n\nInternal Metabolites\n\ncount name\n\n'
96 for metabolite in self.internal_metabolites:
97 out = out + str( metabolite )
98 out = out + '\n\nBranch Metabolites\n\n'
99 for metabolite in self.branch_metabolites:
100 out = out + str( metabolite )
101 out = out + '\n\nNon Branch Metabolites\n\n'
102 for metabolite in self.non_branch_metabolites:
103 out = out + str( metabolite )
104 out = out + '\n\nStochiometric\n\n'
105 out = out + str( self.stochiometric )
106 if( len( self.unbalanced_metabolites ) > 0 ):
107 out = out + '\n\nUnbalanced Metabolites\n\n'
108 for metabolite in self.unbalanced_metabolites:
109 out = out + '%s\n' % metabolite
110 out = out + '\n\nKernel\n\n'
111 out = out + str( self.kernel )
112 out = out + '\n\nSubsets\n\n'
113 out = out + str( self.subsets )
114 out = out + '\n\nReduced System\n\n'
115 out = out + str( self.reduced_system )
116 out = out + '\n\nConvex Basis\n\n'
117 out = out + str( self.convex_basis )
118 out = out + '\n\nConservation Relations\n\n'
119 out = out + str( self.conservation_relations )
120 out = out + '\n'
121 for line in self.sum_is_constant_lines:
122 out = out + '%s\n' % line
123 out = out + '\n\nElementary Modes\n\n'
124 out = out + str( self.elementary_modes )
125 return out
126