bhallalab / hilltau Goto Github PK

Json File : eqn_with_constants.json
{ "FileType": "HillTau",
"Constants": { "molBase": 100, "KA": 1, "tau": 1.0, "eqBase":0.0002, "eqScale": 2.0},
"Groups": {
"output_g": {
"Species": {"mol": "molBase" },
"Reacs": {
"output": {"subs": ["mol", "input"],
"KA": "KA", "tau": "tau" }
},
"Eqns": { "eq": "eqBase + eqScale * input + mol + output" }
}
}
}
pytho-vs-cpp.txt
To get equation from json file, we query via e,t = modelpath.eqnInfo.items()

CppCode: returns
name = eq
mol = ['input', 'mol', 'output']
eqnstr = 0.0002 + 2.0 * input + mol + output

In cppCode the constants are replace with values in the 'eqnstr' and consts are not populated

PythonCode: returns
name = eq
mol = ['input', 'mol', 'output']
eqnstr = eqBase + eqScale * input + mol + output
consts = ['eqBase', 'eqScale']
eqnstr = returns exact equation which is written in json file and consts list is populated

Difference behaviour is observed with using PythonCode v/s CppCode
E.g aut6.json
"S6K_g": {
"Species": { "S6K": 0.2733 },
"Reacs": {
"gS6K": {
"tau": 203.0, "KA": 0.01, "baseline": 0.01997,
"subs": [ "S6K", "glu", "glu" ]
},
}
},
"glu_g": {
"Species": { "glu": 0.0 }
},

Species glu is placed under glu_g when we use PythonCode/hillTau.py
But when we use CppCode/hillTau.py species glu is placed under S6K_g group which is wrong
One can check this
for molname, mol in ( modelpath.molInfo.items() ):
print ("species ",molname,mol.grp)

species glu S6K_g (when path is CppCode)
species glu glu_g (when path is PythonCode)

"Groups": {
"input_g": {
"Species": {"mol1": 0.0 }
},
"output_g": {
"Species": {"mol": 1.0,"mol1":1.0}
}
mol1 is duplicate name which exist in different groups while reading HillTau script over writes the first group species name and stores only second one.
We need to restrict this by warning error, else user is unaware as this happens silently