Added complex class

pyenzyme/enzymeml/core/complex.py

@@ -0,0 +1,101 @@
+'''
+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
+'''
+
+from pydantic import PositiveFloat, validator, Field
+from typing import Optional, TYPE_CHECKING
+from dataclasses import dataclass
+
+from pyenzyme.enzymeml.core.enzymemlbase import EnzymeMLBase
+from pyenzyme.enzymeml.core.abstract_classes import AbstractSpecies
+from pyenzyme.enzymeml.core.utils import (
+    type_checking,
+)
+
+if TYPE_CHECKING:  # pragma: no cover
+    static_check_init_args = dataclass
+else:
+    static_check_init_args = type_checking
+
+
+@static_check_init_args
+class Protein(EnzymeMLBase, AbstractSpecies):
+
+    name: Optional[str] = Field(
+        None,
+        description="Name of the complex",
+    )
+
+    reactants: list[str] = Field(
+        None,
+        description="Array of reactant IDs the complex contains",
+        regex=r"s[\d]+"
+    )
+
+    proteins: list[str] = Field(
+        None,
+        description="Array of reactant IDs the complex contains",
+        regex=r"p[\d]+"
+    )
+
+    vessel_id: str = Field(
+        ...,
+        description="Identifier of the vessel in which the protein was stored.",
+        regex=r"v[\d.]+"
+    )
+
+    init_conc: PositiveFloat = Field(
+        ...,
+        description="Initial concentration of the protein.",
+        inclusiveMinimum=0.0
+    )
+
+    unit: str = Field(
+        ...,
+        description="Unit of the proteins intial concentration.",
+    )
+
+    constant: bool = Field(
+        False,
+        description="Whether the proteins concentration remains constant or not.",
+    )
+
+    id: Optional[str] = Field(
+        None,
+        description="Unique identifier of the protein.",
+        regex=r"c[\d]+"
+    )
+
+    meta_id: Optional[str] = Field(
+        None,
+        description="Unique meta identifier of the protein.",
+    )
+
+    uri: Optional[str] = Field(
+        None,
+        description="URI of the protein.",
+    )
+
+    creator_id: Optional[str] = Field(
+        None,
+        description="Unique identifier of the author.",
+    )
+
+    # ! Validators
+    @validator("id")
+    def set_meta_id(cls, id: Optional[str], values: dict):
+        """Sets the meta ID when an ID is provided"""
+
+        if id:
+            # Set Meta ID with ID
+            values["meta_id"] = f"METAID_{id.upper()}"
+
+        return id