Fixes #33

EnzymeML · Mar 16, 2022 · 2629df0 · 2629df0
1 parent 0441f29
commit 2629df0
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Showing 35 changed files with 211 additions and 322 deletions.
diff --git a/pyenzyme/__init__.py b/pyenzyme/__init__.py
@@ -1,14 +1,8 @@
-"""
-File: __init__.py
-Project: pyenzyme
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 22nd 2021 10:16:57 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: __init__.py
+# Project: pyenzyme
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 from pyenzyme.enzymeml.core import EnzymeMLDocument
 from pyenzyme.enzymeml.core import Vessel

diff --git a/pyenzyme/enzymeml/__init__.py b/pyenzyme/enzymeml/__init__.py
@@ -1,14 +1,8 @@
-'''
-File: __init__.py
-Project: enzymeml
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 22nd 2021 10:15:34 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-'''
+# File: __init__.py
+# Project: enzymeml
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 from pyenzyme.enzymeml.core import EnzymeMLDocument
 from pyenzyme.enzymeml.core import Creator

diff --git a/pyenzyme/enzymeml/core/__init__.py b/pyenzyme/enzymeml/core/__init__.py
@@ -1,14 +1,8 @@
-"""
-File: __init__.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 15th 2021 7:32:36 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: __init__.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 from pyenzyme.enzymeml.core.creator import Creator
 from pyenzyme.enzymeml.core.enzymemldocument import EnzymeMLDocument

diff --git a/pyenzyme/enzymeml/core/abstract_classes.py b/pyenzyme/enzymeml/core/abstract_classes.py
@@ -1,18 +1,11 @@
-"""
-File: creator.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 15th 2021 6:28:16 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: creator.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 from pydantic import BaseModel, PrivateAttr, validator
 from typing import Optional
-from enum import Enum
 from abc import ABC, abstractmethod
 
 from pyenzyme.enzymeml.core.ontology import SBOTerm

diff --git a/pyenzyme/enzymeml/core/complex.py b/pyenzyme/enzymeml/core/complex.py
@@ -1,14 +1,8 @@
-"""
-File: complex.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 22nd 2021 9:53:42 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: complex.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 import re
 

diff --git a/pyenzyme/enzymeml/core/creator.py b/pyenzyme/enzymeml/core/creator.py
@@ -1,14 +1,8 @@
-"""
-File: creator.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 15th 2021 6:28:16 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: creator.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 from pydantic import Field, validator, ValidationError
 from typing import TYPE_CHECKING, Optional

diff --git a/pyenzyme/enzymeml/core/enzymemlbase.py b/pyenzyme/enzymeml/core/enzymemlbase.py
@@ -1,14 +1,8 @@
-"""
-File: baseclass.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 15th 2021 7:48:31 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: baseclass.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 import json
 import logging

diff --git a/pyenzyme/enzymeml/core/enzymemldocument.py b/pyenzyme/enzymeml/core/enzymemldocument.py
@@ -1,20 +1,13 @@
-"""
-File: enzymemldocument.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Thursday July 15th 2021 1:00:05 am
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: enzymemldocument.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 import os
 import re
 import ast
 import json
-from tkinter import TRUE
 import yaml
 import logging
 import pandas as pd

diff --git a/pyenzyme/enzymeml/core/enzymereaction.py b/pyenzyme/enzymeml/core/enzymereaction.py
@@ -1,20 +1,14 @@
-"""
-File: enzymereaction.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Wednesday June 23rd 2021 9:06:54 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: enzymereaction.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 import logging
 import re
 import ast
 
-from typing import List, Dict, Optional, TYPE_CHECKING
+from typing import List, Dict, Union, Optional, TYPE_CHECKING
 from dataclasses import dataclass
 from pydantic import (
     BaseModel,
@@ -574,6 +568,7 @@ def fromEquation(
         equation: str,
         name: str,
         enzmldoc,
+        modifiers: Union[List[str], str] = [],
         temperature: Optional[float] = None,
         temperature_unit: Optional[str] = None,
         ph: Optional[float] = None,
@@ -595,6 +590,10 @@ def fromEquation(
             enzmldoc ([type]): Used to validate species IDs.
         """
 
+        if isinstance(modifiers, str):
+            # Catch single modifiers
+            modifiers = [modifiers]
+
         if "=" in equation:
             reversible = True
         elif "->" in equation:
@@ -613,6 +612,15 @@ def fromEquation(
             ph=ph,
         )
 
+        for modifier in modifiers:
+            # Add modifiers
+            reaction.addModifier(
+                species_id=enzmldoc.getAny(modifier).id,
+                constant=True,
+                stoichiometry=1.0,
+                enzmldoc=enzmldoc,
+            )
+
         # Parse the reaction equation
         reaction._addFromEquation(equation, enzmldoc)
 

diff --git a/pyenzyme/enzymeml/core/exceptions.py b/pyenzyme/enzymeml/core/exceptions.py
@@ -1,14 +1,8 @@
-"""
-File: functionalities.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 15th 2021 6:43:34 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: functionalities.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 import yaml
 

diff --git a/pyenzyme/enzymeml/core/measurement.py b/pyenzyme/enzymeml/core/measurement.py
@@ -1,14 +1,8 @@
-"""
-File: measurement.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Thursday July 15th 2021 1:19:51 am
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: measurement.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 import copy
 import logging

diff --git a/pyenzyme/enzymeml/core/measurementData.py b/pyenzyme/enzymeml/core/measurementData.py
@@ -1,14 +1,8 @@
-"""
-File: measurementData.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Thursday July 15th 2021 1:19:51 am
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: measurementData.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 from pydantic import PositiveFloat, validate_arguments, validator, Field, PrivateAttr
 from dataclasses import dataclass

diff --git a/pyenzyme/enzymeml/core/ontology.py b/pyenzyme/enzymeml/core/ontology.py
@@ -1,3 +1,10 @@
+# File: ontology.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
+
+
 from enum import Enum
 
 

diff --git a/pyenzyme/enzymeml/core/protein.py b/pyenzyme/enzymeml/core/protein.py
@@ -1,14 +1,8 @@
-"""
-File: protein.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 22nd 2021 9:53:42 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: protein.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 import re
 

diff --git a/pyenzyme/enzymeml/core/reactant.py b/pyenzyme/enzymeml/core/reactant.py
@@ -1,14 +1,8 @@
-"""
-File: reactant.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 15th 2021 8:40:52 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: reactant.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 from pydantic import Field
 from typing import Dict, TYPE_CHECKING, Optional, Union, Any

diff --git a/pyenzyme/enzymeml/core/replicate.py b/pyenzyme/enzymeml/core/replicate.py
@@ -1,14 +1,8 @@
-"""
-File: replicate.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Thursday July 15th 2021 1:00:51 am
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: replicate.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 from pydantic import Field, validator, PrivateAttr
 from typing import List, TYPE_CHECKING, Optional

diff --git a/pyenzyme/enzymeml/core/unitdef.py b/pyenzyme/enzymeml/core/unitdef.py
@@ -1,14 +1,8 @@
-"""
-File: unitdef.py
-Project: core
-Author: Jan Range
-License: BSD-2 clause
------
-Last Modified: Tuesday June 15th 2021 7:48:57 pm
-Modified By: Jan Range (<jan.range@simtech.uni-stuttgart.de>)
------
-Copyright (c) 2021 Institute of Biochemistry and Technical Biochemistry Stuttgart
-"""
+# File: unitdef.py
+# Project: core
+# Author: Jan Range
+# License: BSD-2 clause
+# Copyright (c) 2022 Institute of Biochemistry and Technical Biochemistry Stuttgart
 
 from pydantic import Field, validator, validate_arguments
 from typing import List, TYPE_CHECKING, Optional