Reactor - Buffer Calculator

A CLI tool for calculating reaction buffer recipes that account for buffer components contributed by protein stocks.

Tool Location

scripts/reactor_cli.py

Usage

# List available presets
python3 scripts/reactor_cli.py --list-presets

# List predefined stock concentrations
python3 scripts/reactor_cli.py --list-stocks

# Calculate using presets
python3 scripts/reactor_cli.py \
    --protein-preset kinase_panel \
    --buffer-preset kinase_assay \
    --volume 100

# Calculate with direct specifications (concentration)
python3 scripts/reactor_cli.py \
    --protein "CDK2:50nM:stock=10uM:buffer=HEPES/20mM,NaCl/150mM" \
    --buffer "HEPES:1M->25mM" \
    --buffer "NaCl:5M->100mM" \
    --volume 100

# Calculate using pmol amounts (auto-converted to concentration)
python3 scripts/reactor_cli.py \
    --protein "PolII:70pmol:stock=5.17uM:buffer=HEPES/20mM,NaCl/150mM" \
    --buffer "HEPES:1M->20mM" \
    --volume 100

# Calculate using molar ratios with reference
python3 scripts/reactor_cli.py \
    --reference 70pmol \
    --protein "PolII:1x:stock=5.17uM:buffer=HEPES/20mM" \
    --protein "DSIF:1.5x:stock=50.8uM:buffer=HEPES/20mM" \
    --buffer "HEPES:1M->20mM" \
    --volume 100

# Use compensation buffer mode (creates concentrated buffer)
python3 scripts/reactor_cli.py \
    --protein "MyProtein:100nM:stock=5uM:buffer=HEPES/20mM,NaCl/300mM" \
    --buffer "HEPES:1M->25mM" \
    --buffer "NaCl:5M->150mM" \
    --volume 50 \
    --mode compensation \
    --fold 10

# Output as JSON
python3 scripts/reactor_cli.py \
    --protein-preset kinase_panel \
    --buffer-preset storage \
    --volume 100 \
    --json

Key Concepts

Calculation Modes

1. •

   Direct Mode (default): Calculates exact volumes of each buffer component to add, accounting for contributions from protein stocks.

2. •

   Compensation Mode: Creates a concentrated buffer (e.g., 10X) that compensates for buffer components in protein stocks. Useful for preparing batch buffers.

Protein Specification Format

"Name:Amount:stock=StockConc[:buffer=Component/Conc,Component/Conc,...]"

Amount can be specified as:

• •Concentration: 50nM, 1uM, 100mM
• •Absolute amount: 70pmol, 100fmol, 1nmol (auto-converted to concentration based on volume)
• •Molar ratio: 1.5x, 2x (requires --reference flag)

Examples:

• •"CDK2:50nM:stock=10uM" - Simple protein without buffer info
• •"CDK2:50nM:stock=10uM:buffer=HEPES/20mM,NaCl/150mM" - Protein with storage buffer components
• •"PolII:70pmol:stock=5.17uM:buffer=HEPES/20mM" - Using absolute pmol amount
• •"DSIF:1.5x:stock=50.8uM:buffer=HEPES/20mM" - Using molar ratio (with --reference 70pmol)

Buffer Component Format

"Name:StockConc->FinalConc"

Examples:

• •"HEPES:1M->25mM" - HEPES from 1M stock to 25mM final
• •"NaCl:5M->150mM" - NaCl from 5M stock to 150mM final
• •"Glycerol:100%->10%" - Glycerol from 100% to 10% final

Available Presets

Protein Presets (built-in):

• •kinase_panel - CDK2 and MEK1 for kinase assays
• •purification_stocks - His-tagged protein and TEV protease
• •reconstitution - Nucleosome reconstitution
• •polii_elongation_complex - Pol II elongation complex (PolII, DSIF, IWS1, ELOF1, SPT6, PAF1c, P-TEFb, CSB, DNA-RNA, ntDNA)

Buffer Presets (built-in):

• •lysis - Cell lysis buffer (50mM HEPES, 300mM NaCl, 1mM TCEP, 5% glycerol)
• •gel_filtration - SEC buffer (25mM Tris, 150mM NaCl, 1mM EDTA, 10% glycerol)
• •storage - Protein storage buffer (20mM HEPES, 150mM NaCl, 0.5mM TCEP, 10% glycerol)
• •kinase_assay - Kinase reaction buffer (25mM HEPES, 100mM NaCl, 10mM MgCl2, 1mM DTT, 1mM ATP)
• •cryo_em - Cryo-EM buffer (20mM HEPES, 150mM NaCl, 1mM TCEP)
• •elongation_buffer - Elongation assay buffer (20mM HEPES, 75mM NaCl, 10% glycerol, 1mM TCEP, 1mM ATP, 3mM MgCl2)

External Preset Files

Presets can be loaded from external YAML or JSON files using --presets-file. Default locations searched:

• •~/.config/reactor/presets.yaml

Predefined Stocks

Common laboratory stock concentrations are predefined:

• •HEPES: 1M
• •NaCl: 5M
• •TCEP: 200mM
• •Glycerol: 100%
• •MgCl2: 1M
• •DTT: 1M
• •ATP/GTP: 100mM
• •And more (use --list-stocks to see all)

Units Supported

• •Concentration: M, mM, uM, nM, %, mg/ml
• •Absolute amount: pmol, fmol, nmol (converted to concentration based on volume)
• •Ratio: x (e.g., 1.5x, 2x - requires --reference)
• •Volume: uL (microliters)