From 291701052b484e8720edf0b33ddeddaf7970d5f2 Mon Sep 17 00:00:00 2001
From: Peter Schubert <Peter.Schubert@hhu.de>
Date: Fri, 9 Sep 2022 11:40:13 +0200
Subject: [PATCH] support unit definitions
---
xbanalysis/model/__init__.py | 5 +--
xbanalysis/model/xba_model.py | 3 ++
xbanalysis/model/xba_unit_def.py | 55 ++++++++++++++++++++++++++++++++
3 files changed, 61 insertions(+), 2 deletions(-)
create mode 100644 xbanalysis/model/xba_unit_def.py
diff --git a/xbanalysis/model/__init__.py b/xbanalysis/model/__init__.py
index c050038..3edfe6f 100644
--- a/xbanalysis/model/__init__.py
+++ b/xbanalysis/model/__init__.py
@@ -1,6 +1,7 @@
"""Subpackage with XBA model classes """
from .xba_model import XbaModel
+from .xba_unit_def import XbaUnitDef, XbaUnit
from .xba_compartment import XbaCompartment
from .xba_function import XbaFunction
from .xba_parameter import XbaParameter
@@ -8,5 +9,5 @@ from .xba_reaction import XbaReaction
from .xba_species import XbaSpecies
from .sbo_term import SboTerm
-__all__ = ['XbaModel', 'XbaCompartment', 'XbaFunction', 'XbaParameter',
- 'XbaReaction', 'XbaSpecies', 'SboTerm']
+__all__ = ['XbaModel', 'XbaUnitDef', 'XbaUnit', 'XbaCompartment',
+ 'XbaFunction', 'XbaParameter', 'XbaReaction', 'XbaSpecies', 'SboTerm']
diff --git a/xbanalysis/model/xba_model.py b/xbanalysis/model/xba_model.py
index 495dbcb..f4b3c54 100644
--- a/xbanalysis/model/xba_model.py
+++ b/xbanalysis/model/xba_model.py
@@ -9,6 +9,7 @@ import numpy as np
import sbmlxdf
from scipy.sparse import coo_array
+from .xba_unit_def import XbaUnitDef
from .xba_compartment import XbaCompartment
from .xba_function import XbaFunction
from .xba_parameter import XbaParameter
@@ -32,6 +33,8 @@ class XbaModel:
print(f'{sbml_file} seems not to be a valid SBML model')
return
model_dict = sbml_model.to_df()
+ self.unit_defs = {udid: XbaUnitDef(row)
+ for udid, row in model_dict['unitDefs'].iterrows()}
self.compartments = {cid: XbaCompartment(row)
for cid, row in model_dict['compartments'].iterrows()}
self.parameters = {pid: XbaParameter(row)
diff --git a/xbanalysis/model/xba_unit_def.py b/xbanalysis/model/xba_unit_def.py
new file mode 100644
index 0000000..5cd1326
--- /dev/null
+++ b/xbanalysis/model/xba_unit_def.py
@@ -0,0 +1,55 @@
+"""Implementation of XbaUnitDef class.
+
+Peter Schubert, HHU Duesseldorf, May 2022
+"""
+
+import numpy as np
+import sbmlxdf
+
+
+class XbaUnitDef:
+
+ def __init__(self, s_unit_def):
+ self.id = s_unit_def.name
+ self.name = s_unit_def.get('name', self.id)
+ self.units = [XbaUnit(sbmlxdf.extract_params(u))
+ for u in sbmlxdf.record_generator(s_unit_def['units'])]
+
+ def is_equivalent(self, qry_units):
+ if len(qry_units) != len(self.units):
+ return False
+ else:
+ equivalent_u = np.zeros(len(qry_units))
+ for i, qry_unit in enumerate(qry_units):
+ for unit in self.units:
+ if unit == qry_unit:
+ equivalent_u[i] = 1
+ break
+ return np.all(equivalent_u)
+
+
+class XbaUnit:
+
+ def __init__(self, params):
+ self.kind = params.get('kind')
+ self.exp = float(params.get('exp', '1.0'))
+ self.scale = int(params.get('scale', '0'))
+ self.mult = float(params.get('mult', '1.0'))
+
+ def __eq__(self, other):
+ if (self.kind == other.kind and
+ self.exp == other.exp and
+ self.scale == other.scale and
+ self.mult == other.mult):
+ return True
+ else:
+ return False
+
+ def __str__(self):
+ factor = self.mult * 10**self.scale
+ factor_str = f'{factor} ' if factor != 1.0 else ''
+ if self.exp != 1.0:
+ unit_str = f'({factor_str}{self.kind})^{self.exp}'
+ else:
+ unit_str = f'{factor_str}{self.kind}'
+ return unit_str
--
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