@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

package/bin/skills/cobrapy/references/api_quick_reference.md

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+# COBRApy API Quick Reference
+
+This document provides quick reference for common COBRApy functions, signatures, and usage patterns.
+
+## Model I/O
+
+### Loading Models
+
+```python
+from cobra.io import load_model, read_sbml_model, load_json_model, load_yaml_model, load_matlab_model
+
+# Bundled test models
+model = load_model("textbook")   # E. coli core metabolism
+model = load_model("ecoli")      # Full E. coli iJO1366
+model = load_model("salmonella") # Salmonella LT2
+
+# From files
+model = read_sbml_model(filename, f_replace={}, **kwargs)
+model = load_json_model(filename)
+model = load_yaml_model(filename)
+model = load_matlab_model(filename, variable_name=None)
+```
+
+### Saving Models
+
+```python
+from cobra.io import write_sbml_model, save_json_model, save_yaml_model, save_matlab_model
+
+write_sbml_model(model, filename, f_replace={}, **kwargs)
+save_json_model(model, filename, pretty=False, **kwargs)
+save_yaml_model(model, filename, **kwargs)
+save_matlab_model(model, filename, **kwargs)
+```
+
+## Model Structure
+
+### Core Classes
+
+```python
+from cobra import Model, Reaction, Metabolite, Gene
+
+# Create model
+model = Model(id_or_model=None, name=None)
+
+# Create metabolite
+metabolite = Metabolite(
+    id=None,
+    formula=None,
+    name="",
+    charge=None,
+    compartment=None
+)
+
+# Create reaction
+reaction = Reaction(
+    id=None,
+    name="",
+    subsystem="",
+    lower_bound=0.0,
+    upper_bound=None
+)
+
+# Create gene
+gene = Gene(id=None, name="", functional=True)
+```
+
+### Model Attributes
+
+```python
+# Component access (DictList objects)
+model.reactions       # DictList of Reaction objects
+model.metabolites     # DictList of Metabolite objects
+model.genes          # DictList of Gene objects
+
+# Special reaction lists
+model.exchanges      # Exchange reactions (external transport)
+model.demands        # Demand reactions (metabolite sinks)
+model.sinks          # Sink reactions
+model.boundary       # All boundary reactions
+
+# Model properties
+model.objective      # Current objective (read/write)
+model.objective_direction  # "max" or "min"
+model.medium         # Growth medium (dict of exchange: bound)
+model.solver         # Optimization solver
+```
+
+### DictList Methods
+
+```python
+# Access by index
+item = model.reactions[0]
+
+# Access by ID
+item = model.reactions.get_by_id("PFK")
+
+# Query by string (substring match)
+items = model.reactions.query("atp")      # Case-insensitive search
+items = model.reactions.query(lambda x: x.subsystem == "Glycolysis")
+
+# List comprehension
+items = [r for r in model.reactions if r.lower_bound < 0]
+
+# Check membership
+"PFK" in model.reactions
+```
+
+## Optimization
+
+### Basic Optimization
+
+```python
+# Full optimization (returns Solution object)
+solution = model.optimize()
+
+# Attributes of Solution
+solution.objective_value   # Objective function value
+solution.status           # Optimization status ("optimal", "infeasible", etc.)
+solution.fluxes          # Pandas Series of reaction fluxes
+solution.shadow_prices   # Pandas Series of metabolite shadow prices
+solution.reduced_costs   # Pandas Series of reduced costs
+
+# Fast optimization (returns float only)
+objective_value = model.slim_optimize()
+
+# Change objective
+model.objective = "ATPM"
+model.objective = model.reactions.ATPM
+model.objective = {model.reactions.ATPM: 1.0}
+
+# Change optimization direction
+model.objective_direction = "max"  # or "min"
+```
+
+### Solver Configuration
+
+```python
+# Check available solvers
+from cobra.util.solver import solvers
+print(solvers)
+
+# Change solver
+model.solver = "glpk"  # or "cplex", "gurobi", etc.
+
+# Solver-specific configuration
+model.solver.configuration.timeout = 60  # seconds
+model.solver.configuration.verbosity = 1
+model.solver.configuration.tolerances.feasibility = 1e-9
+```
+
+## Flux Analysis
+
+### Flux Balance Analysis (FBA)
+
+```python
+from cobra.flux_analysis import pfba, geometric_fba
+
+# Parsimonious FBA
+solution = pfba(model, fraction_of_optimum=1.0, **kwargs)
+
+# Geometric FBA
+solution = geometric_fba(model, epsilon=1e-06, max_tries=200)
+```
+
+### Flux Variability Analysis (FVA)
+
+```python
+from cobra.flux_analysis import flux_variability_analysis
+
+fva_result = flux_variability_analysis(
+    model,
+    reaction_list=None,        # List of reaction IDs or None for all
+    loopless=False,            # Eliminate thermodynamically infeasible loops
+    fraction_of_optimum=1.0,   # Optimality fraction (0.0-1.0)
+    pfba_factor=None,          # Optional pFBA constraint
+    processes=1                # Number of parallel processes
+)
+
+# Returns DataFrame with columns: minimum, maximum
+```
+
+### Gene and Reaction Deletions
+
+```python
+from cobra.flux_analysis import (
+    single_gene_deletion,
+    single_reaction_deletion,
+    double_gene_deletion,
+    double_reaction_deletion
+)
+
+# Single deletions
+results = single_gene_deletion(
+    model,
+    gene_list=None,     # None for all genes
+    processes=1,
+    **kwargs
+)
+
+results = single_reaction_deletion(
+    model,
+    reaction_list=None,  # None for all reactions
+    processes=1,
+    **kwargs
+)
+
+# Double deletions
+results = double_gene_deletion(
+    model,
+    gene_list1=None,
+    gene_list2=None,
+    processes=1,
+    **kwargs
+)
+
+results = double_reaction_deletion(
+    model,
+    reaction_list1=None,
+    reaction_list2=None,
+    processes=1,
+    **kwargs
+)
+
+# Returns DataFrame with columns: ids, growth, status
+# For double deletions, index is MultiIndex of gene/reaction pairs
+```
+
+### Flux Sampling
+
+```python
+from cobra.sampling import sample, OptGPSampler, ACHRSampler
+
+# Simple interface
+samples = sample(
+    model,
+    n,                  # Number of samples
+    method="optgp",     # or "achr"
+    thinning=100,       # Thinning factor (sample every n iterations)
+    processes=1,        # Parallel processes (OptGP only)
+    seed=None          # Random seed
+)
+
+# Advanced interface with sampler objects
+sampler = OptGPSampler(model, processes=4, thinning=100)
+sampler = ACHRSampler(model, thinning=100)
+
+# Generate samples
+samples = sampler.sample(n)
+
+# Validate samples
+validation = sampler.validate(sampler.samples)
+# Returns array of 'v' (valid), 'l' (lower bound violation),
+# 'u' (upper bound violation), 'e' (equality violation)
+
+# Batch sampling
+sampler.batch(n_samples, n_batches)
+```
+
+### Production Envelopes
+
+```python
+from cobra.flux_analysis import production_envelope
+
+envelope = production_envelope(
+    model,
+    reactions,              # List of 1-2 reaction IDs
+    objective=None,         # Objective reaction ID (None uses model objective)
+    carbon_sources=None,    # Carbon source for yield calculation
+    points=20,              # Number of points to calculate
+    threshold=0.01          # Minimum objective value threshold
+)
+
+# Returns DataFrame with columns:
+# - First reaction flux
+# - Second reaction flux (if provided)
+# - objective_minimum, objective_maximum
+# - carbon_yield_minimum, carbon_yield_maximum (if carbon source specified)
+# - mass_yield_minimum, mass_yield_maximum
+```
+
+### Gapfilling
+
+```python
+from cobra.flux_analysis import gapfill
+
+# Basic gapfilling
+solution = gapfill(
+    model,
+    universal=None,         # Universal model with candidate reactions
+    lower_bound=0.05,       # Minimum objective flux
+    penalties=None,         # Dict of reaction: penalty
+    demand_reactions=True,  # Add demand reactions if needed
+    exchange_reactions=False,
+    iterations=1
+)
+
+# Returns list of Reaction objects to add
+
+# Multiple solutions
+solutions = []
+for i in range(5):
+    sol = gapfill(model, universal, iterations=1)
+    solutions.append(sol)
+    # Prevent finding same solution by increasing penalties
+```
+
+### Other Analysis Methods
+
+```python
+from cobra.flux_analysis import (
+    find_blocked_reactions,
+    find_essential_genes,
+    find_essential_reactions
+)
+
+# Blocked reactions (cannot carry flux)
+blocked = find_blocked_reactions(
+    model,
+    reaction_list=None,
+    zero_cutoff=1e-9,
+    open_exchanges=False
+)
+
+# Essential genes/reactions
+essential_genes = find_essential_genes(model, threshold=0.01)
+essential_reactions = find_essential_reactions(model, threshold=0.01)
+```
+
+## Media and Boundary Conditions
+
+### Medium Management
+
+```python
+# Get current medium (returns dict)
+medium = model.medium
+
+# Set medium (must reassign entire dict)
+medium = model.medium
+medium["EX_glc__D_e"] = 10.0
+medium["EX_o2_e"] = 20.0
+model.medium = medium
+
+# Alternative: individual modification
+with model:
+    model.reactions.EX_glc__D_e.lower_bound = -10.0
+```
+
+### Minimal Media
+
+```python
+from cobra.medium import minimal_medium
+
+min_medium = minimal_medium(
+    model,
+    min_objective_value=0.1,  # Minimum growth rate
+    minimize_components=False, # If True, uses MILP (slower)
+    open_exchanges=False,      # Open all exchanges before optimization
+    exports=False,             # Allow metabolite export
+    penalties=None             # Dict of exchange: penalty
+)
+
+# Returns Series of exchange reactions with fluxes
+```
+
+### Boundary Reactions
+
+```python
+# Add boundary reaction
+model.add_boundary(
+    metabolite,
+    type="exchange",    # or "demand", "sink"
+    reaction_id=None,   # Auto-generated if None
+    lb=None,
+    ub=None,
+    sbo_term=None
+)
+
+# Access boundary reactions
+exchanges = model.exchanges     # System boundary
+demands = model.demands         # Intracellular removal
+sinks = model.sinks            # Intracellular exchange
+boundaries = model.boundary    # All boundary reactions
+```
+
+## Model Manipulation
+
+### Adding Components
+
+```python
+# Add reactions
+model.add_reactions([reaction1, reaction2, ...])
+model.add_reaction(reaction)
+
+# Add metabolites
+reaction.add_metabolites({
+    metabolite1: -1.0,  # Consumed (negative stoichiometry)
+    metabolite2: 1.0    # Produced (positive stoichiometry)
+})
+
+# Add metabolites to model
+model.add_metabolites([metabolite1, metabolite2, ...])
+
+# Add genes (usually automatic via gene_reaction_rule)
+model.genes += [gene1, gene2, ...]
+```
+
+### Removing Components
+
+```python
+# Remove reactions
+model.remove_reactions([reaction1, reaction2, ...])
+model.remove_reactions(["PFK", "FBA"])
+
+# Remove metabolites (removes from reactions too)
+model.remove_metabolites([metabolite1, metabolite2, ...])
+
+# Remove genes (usually via gene_reaction_rule)
+model.genes.remove(gene)
+```
+
+### Modifying Reactions
+
+```python
+# Set bounds
+reaction.bounds = (lower, upper)
+reaction.lower_bound = 0.0
+reaction.upper_bound = 1000.0
+
+# Modify stoichiometry
+reaction.add_metabolites({metabolite: 1.0})
+reaction.subtract_metabolites({metabolite: 1.0})
+
+# Change gene-reaction rule
+reaction.gene_reaction_rule = "(gene1 and gene2) or gene3"
+
+# Knock out
+reaction.knock_out()
+gene.knock_out()
+```
+
+### Model Copying
+
+```python
+# Deep copy (independent model)
+model_copy = model.copy()
+
+# Copy specific reactions
+new_model = Model("subset")
+reactions_to_copy = [model.reactions.PFK, model.reactions.FBA]
+new_model.add_reactions(reactions_to_copy)
+```
+
+## Context Management
+
+Use context managers for temporary modifications:
+
+```python
+# Changes automatically revert after with block
+with model:
+    model.objective = "ATPM"
+    model.reactions.EX_glc__D_e.lower_bound = -5.0
+    model.genes.b0008.knock_out()
+    solution = model.optimize()
+
+# Model state restored here
+
+# Multiple nested contexts
+with model:
+    model.objective = "ATPM"
+    with model:
+        model.genes.b0008.knock_out()
+        # Both modifications active
+    # Only objective change active
+
+# Context management with reactions
+with model:
+    model.reactions.PFK.knock_out()
+    # Equivalent to: reaction.lower_bound = reaction.upper_bound = 0
+```
+
+## Reaction and Metabolite Properties
+
+### Reaction Attributes
+
+```python
+reaction.id                      # Unique identifier
+reaction.name                    # Human-readable name
+reaction.subsystem               # Pathway/subsystem
+reaction.bounds                  # (lower_bound, upper_bound)
+reaction.lower_bound
+reaction.upper_bound
+reaction.reversibility          # Boolean (lower_bound < 0)
+reaction.gene_reaction_rule     # GPR string
+reaction.genes                  # Set of associated Gene objects
+reaction.metabolites            # Dict of {metabolite: stoichiometry}
+
+# Methods
+reaction.reaction               # Stoichiometric equation string
+reaction.build_reaction_string() # Same as above
+reaction.check_mass_balance()   # Returns imbalances or empty dict
+reaction.get_coefficient(metabolite_id)
+reaction.add_metabolites({metabolite: coeff})
+reaction.subtract_metabolites({metabolite: coeff})
+reaction.knock_out()
+```
+
+### Metabolite Attributes
+
+```python
+metabolite.id                   # Unique identifier
+metabolite.name                 # Human-readable name
+metabolite.formula              # Chemical formula
+metabolite.charge               # Charge
+metabolite.compartment          # Compartment ID
+metabolite.reactions            # FrozenSet of associated reactions
+
+# Methods
+metabolite.summary()            # Print production/consumption
+metabolite.copy()
+```
+
+### Gene Attributes
+
+```python
+gene.id                         # Unique identifier
+gene.name                       # Human-readable name
+gene.functional                 # Boolean activity status
+gene.reactions                  # FrozenSet of associated reactions
+
+# Methods
+gene.knock_out()
+```
+
+## Model Validation
+
+### Consistency Checking
+
+```python
+from cobra.manipulation import check_mass_balance, check_metabolite_compartment_formula
+
+# Check all reactions for mass balance
+unbalanced = {}
+for reaction in model.reactions:
+    balance = reaction.check_mass_balance()
+    if balance:
+        unbalanced[reaction.id] = balance
+
+# Check metabolite formulas are valid
+check_metabolite_compartment_formula(model)
+```
+
+### Model Statistics
+
+```python
+# Basic stats
+print(f"Reactions: {len(model.reactions)}")
+print(f"Metabolites: {len(model.metabolites)}")
+print(f"Genes: {len(model.genes)}")
+
+# Advanced stats
+print(f"Exchanges: {len(model.exchanges)}")
+print(f"Demands: {len(model.demands)}")
+
+# Blocked reactions
+from cobra.flux_analysis import find_blocked_reactions
+blocked = find_blocked_reactions(model)
+print(f"Blocked reactions: {len(blocked)}")
+
+# Essential genes
+from cobra.flux_analysis import find_essential_genes
+essential = find_essential_genes(model)
+print(f"Essential genes: {len(essential)}")
+```
+
+## Summary Methods
+
+```python
+# Model summary
+model.summary()                  # Overall model info
+
+# Metabolite summary
+model.metabolites.atp_c.summary()
+
+# Reaction summary
+model.reactions.PFK.summary()
+
+# Summary with FVA
+model.summary(fva=0.95)         # Include FVA at 95% optimality
+```
+
+## Common Patterns
+
+### Batch Analysis Pattern
+
+```python
+results = []
+for condition in conditions:
+    with model:
+        # Apply condition
+        setup_condition(model, condition)
+
+        # Analyze
+        solution = model.optimize()
+
+        # Store result
+        results.append({
+            "condition": condition,
+            "growth": solution.objective_value,
+            "status": solution.status
+        })
+
+df = pd.DataFrame(results)
+```
+
+### Systematic Knockout Pattern
+
+```python
+knockout_results = []
+for gene in model.genes:
+    with model:
+        gene.knock_out()
+
+        solution = model.optimize()
+
+        knockout_results.append({
+            "gene": gene.id,
+            "growth": solution.objective_value if solution.status == "optimal" else 0,
+            "status": solution.status
+        })
+
+df = pd.DataFrame(knockout_results)
+```
+
+### Parameter Scan Pattern
+
+```python
+parameter_values = np.linspace(0, 20, 21)
+results = []
+
+for value in parameter_values:
+    with model:
+        model.reactions.EX_glc__D_e.lower_bound = -value
+
+        solution = model.optimize()
+
+        results.append({
+            "glucose_uptake": value,
+            "growth": solution.objective_value,
+            "acetate_secretion": solution.fluxes["EX_ac_e"]
+        })
+
+df = pd.DataFrame(results)
+```
+
+This quick reference covers the most commonly used COBRApy functions and patterns. For complete API documentation, see https://cobrapy.readthedocs.io/