# Cell Class

## Overview
The `Cell` class simulates the structure and behavior of a biological cell, including its organelles, proteins, DNA, metabolism, division, and response to external signals. It supports both mitosis and meiosis, mutation, repair, visualization, and advanced cellular processes like autophagy, apoptosis, and environmental adaptation.

---

## Class Definition
```python
class Cell:
    def __init__(self, name: str, cell_type: Optional[str] = None, receptors: Optional[List[Protein]] = None,
                 surface_proteins: Optional[List[Protein]] = None, dna: Optional['DNA'] = None, health: Optional[int] = None,
                 age: Optional[int] = 0, metabolism_rate: Optional[float] = 1.0, ph: float = 7.0, osmolarity: float = 300.0,
                 ion_concentrations: Optional[Dict[str, float]] = None, id: Optional[int] = None, chromosomes: Optional[List[Chromosome]] = None,
                 structural_integrity: float = 100.0, mutation_count: Optional[int] = 0, growth_rate: Optional[float] = 1.0,
                 repair_rate: Optional[float] = 1.0, max_divisions: Optional[int] = 50):
        ...
```

---

## Attributes


| Attribute | Type | Description |
|-----------|------|-------------|
| `name` | `str` | Name of the cell. |
| `cell_type` | `Optional[str]` | Type of the cell (e.g., "neuron", "muscle cell"). |
| `receptors` | `List[Protein]` | List of receptor proteins on the cell surface. |
| `surface_proteins` | `List[Protein]` | List of proteins expressed on the cell surface. |
| `internal_proteins` | `List[Protein]` | List of proteins inside the cell. |
| `dna` | `Optional[DNA]` | DNA object representing the cell's DNA. |
| `health` | `int` | Health of the cell (0-100). |
| `age` | `int` | Age of the cell. |
| `metabolism_rate` | `float` | Rate of metabolism. |
| `ph` | `float` | pH level of the cell. |
| `osmolarity` | `float` | Osmolarity of the cell (mOsm/L). |
| `ion_concentrations` | `Dict[str, float]` | Dictionary of ion concentrations (mmol/L). |
| `id` | `Optional[int]` | Unique identifier for the cell. |
| `chromosomes` | `List[Chromosome]` | List of chromosomes in the cell. |
| `organelles` | `Dict[str, List[Organelle]]` | Dictionary of organelles by type. |
| `structural_integrity` | `float` | Structural integrity of the cell (0-100). |
| `mutation_count` | `int` | Number of mutations in the cell. |
| `growth_rate` | `float` | Growth rate of the cell. |
| `repair_rate` | `float` | Repair rate of the cell. |
| `division_count` | `int` | Number of times the cell has divided. |
| `max_divisions` | `int` | Maximum number of divisions allowed. |

---

## Methods

### Initialization
- **`__init__(self, name: str, cell_type: Optional[str] = None, receptors: Optional[List[Protein]] = None, surface_proteins: Optional[List[Protein]] = None, dna: Optional['DNA'] = None, health: Optional[int] = None, age: Optional[int] = 0, metabolism_rate: Optional[float] = 1.0, ph: float = 7.0, osmolarity: float = 300.0, ion_concentrations: Optional[Dict[str, float]] = None, id: Optional[int] = None, chromosomes: Optional[List[Chromosome]] = None, structural_integrity: float = 100.0, mutation_count: Optional[int] = 0, growth_rate: Optional[float] = 1.0, repair_rate: Optional[float] = 1.0, max_divisions: Optional[int] = 50)`**
  Initializes a new `Cell` instance with the specified attributes.

---

### Organelle Management
- **`add_organelle(self, organelle: Organelle, quantity: int = 1) -> None`**
  Adds an organelle to the cell.
- **`remove_organelle(self, organelle_type: str, quantity: int = 1) -> None`**
  Removes an organelle from the cell.
- **`add_mitochondrion(self, efficiency: float = 1.0, health: int = 100, quantity: int = 1) -> None`**
  Adds a mitochondrion to the cell.
- **`remove_mitochondrion(self, quantity: int = 1) -> None`**
  Removes a mitochondrion from the cell.

---

### Protein Management
- **`add_receptor(self, receptor: Protein) -> None`**
  Adds a receptor protein to the cell.
- **`add_surface_protein(self, protein: Protein) -> None`**
  Adds a surface protein to the cell.
- **`remove_surface_protein(self, protein: Protein) -> None`**
  Removes a surface protein from the cell.
- **`add_internal_protein(self, protein: Protein) -> None`**
  Adds an internal protein to the cell.
- **`remove_internal_protein(self, protein: Protein) -> None`**
  Removes an internal protein from the cell.

---

### Chromosome Management
- **`add_chromosome(self, chromosome: Chromosome) -> None`**
  Adds a chromosome to the cell.
- **`remove_chromosome(self, chromosome_name: str) -> None`**
  Removes a chromosome from the cell by name.

---

### Cell Division
- **`mitosis(self) -> 'Cell'`**
  Simulates mitotic division, returning a daughter cell.
- **`meiosis(self) -> List['Cell']`**
  Simulates meiotic division, returning four haploid daughter cells.
- **`divide(self) -> Union['Cell', List['Cell'], None]`**
  General method to divide the cell, choosing between mitosis and meiosis.
- **`can_divide(self) -> bool`**
  Checks if the cell can still divide.

---

### Metabolism and Health
- **`metabolize(self) -> int`**
  Simulates the cell's metabolism, returning total ATP produced.
- **`repair(self, amount: float) -> None`**
  Repairs the cell, increasing its health and structural integrity.
- **`mutate(self) -> None`**
  Simulates a random mutation in the cell.
- **`calculate_structural_integrity(self) -> float`**
  Calculates the cell's structural integrity.
- **`update_structural_integrity(self) -> None`**
  Updates the cell's structural integrity based on current conditions.
- **`maintain_homeostasis(self) -> Dict[str, str]`**
  Maintains cellular homeostasis by regulating internal conditions.
- **`autophagy(self) -> Dict[str, int]`**
  Simulates autophagy: cellular cleanup and recycling process.
- **`apoptosis_check(self) -> bool`**
  Checks if the cell should undergo programmed cell death (apoptosis).
- **`stress_response(self, stressor: str, intensity: float = 1.0) -> str`**
  Responds to cellular stress conditions.

---

### Chemical Properties
- **`adjust_ph(self, delta: float) -> None`**
  Adjusts the pH of the cell.
- **`adjust_osmolarity(self, delta: float) -> None`**
  Adjusts the osmolarity of the cell.
- **`adjust_ion_concentration(self, ion: str, delta: float) -> None`**
  Adjusts the concentration of a specific ion.

---

### Interaction and Signaling
- **`interact_with_protein(self, protein: Protein) -> None`**
  Simulates interaction between the cell and a protein.
- **`receive_signal(self, signal: str, intensity: float = 1.0) -> str`**
  Processes an external signal and returns the cell's response.
- **`quorum_sensing(self, cell_density: float, signal_molecule: str = "AHL") -> str`**
  Simulates quorum sensing: density-dependent gene regulation.

---

### Protein Synthesis and Cellular Processes
- **`protein_synthesis(self, amino_acids: List[str] = None) -> Protein`**
  Simulates protein synthesis based on DNA/mRNA template.
- **`cellular_respiration(self, glucose: float = 1.0, oxygen: float = 1.0) -> Dict[str, float]`**
  Simulates cellular respiration process.
- **`endocytosis(self, material: str, size: float = 1.0) -> str`**
  Simulates endocytosis: uptake of external materials.
- **`exocytosis(self, material: str, quantity: float = 1.0) -> str`**
  Simulates exocytosis: secretion of materials from the cell.
- **`dna_repair(self) -> Dict[str, int]`**
  Simulates DNA repair mechanisms.
- **`cell_cycle_checkpoint(self, phase: str) -> bool`**
  Checks if the cell can proceed through cell cycle checkpoints.

---

### Differentiation and Adaptation
- **`differentiate(self, target_type: str, growth_factors: List[str] = None) -> str`**
  Simulates cellular differentiation into specialized cell types.
- **`environmental_adaptation(self, environment: Dict[str, float]) -> str`**
  Adapts to environmental conditions.

---

### Molecular Weight Calculation
- **`calculate_molecular_weight(self, custom_weights: Optional[Dict[str, float]] = None) -> float`**
  Calculates the total molecular weight of the cell.
- **`get_molecular_weight_breakdown(self, custom_weights: Optional[Dict[str, float]] = None) -> Dict[str, float]`**
  Returns a breakdown of the molecular weight of cell components.

---

### Visualization and Serialization
- **`visualize_cell(self) -> None`**
  Creates a 2D visual representation of the cell.
- **`to_json(self) -> str`**
  Returns a JSON representation of the cell.
- **`from_json(cls, json_str: str) -> 'Cell'`**
  Creates a `Cell` object from a JSON string.
- **`to_dict(self) -> dict`**
  Returns a dictionary representation of the cell.
- **`from_dict(cls, cell_dict: dict) -> 'Cell'`**
  Creates a `Cell` object from a dictionary.

---

### Utility Methods
- **`describe(self) -> str`**
  Provides a detailed description of the cell.
- **`reset(self) -> None`**
  Resets the cell to its initial state.
- **`__str__(self) -> str`**
  Returns a string representation of the cell.
- **`__len__(self) -> int`**
  Returns the total number of proteins, chromosomes, and organelles.
- **`__getitem__(self, item)`**
  Returns a new `Cell` instance from the dictionary representation.
- **`__iter__(self)`**
  Iterates over the cell's proteins, chromosomes, and organelles.
- **`calculate_fitness(self) -> float`**
  Calculates the overall cellular fitness score.

---

## Example Usage
```python
# Create a cell
cell = Cell(name="Cell_0001", cell_type="epithelial")
# Add a mitochondrion
cell.add_mitochondrion(efficiency=1.2, health=95)
# Add a receptor
receptor = Protein(name="Receptor_1", sequence="ABCDEF")
cell.add_receptor(receptor)
# Simulate metabolism
cell.metabolize()
# Visualize the cell
cell.visualize_cell()
# Print cell description
print(cell.describe())
```
