proteinpulse 0.1.0

Analyze protein sequences from the CLI — MW, pI, GRAVY, instability, domains, secondary structure, and PDB lookup.

🧬 ProteinPulse

Analyze protein sequences from the command line.

ProteinPulse is a fast, dependency-light CLI tool for protein sequence analysis. No internet connection required for core analysis — just paste a sequence and go.

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Features

Command	What it does
analyze	MW, pI, GRAVY, instability index, charge, extinction coefficient
domains	Scan for zinc fingers, RGD, NLS, TM regions, glycosylation sites, and 20+ more motifs
structure	Chou-Fasman secondary structure prediction (α-helix / β-sheet / coil)
pdb	Fetch structure metadata from RCSB PDB
full	All of the above in one shot

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Installation

pip install proteinpulse

Requires Python 3.9+. No conda, no virtualenv required.

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Quick Start

# Physicochemical properties
proteinpulse analyze MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

# From a FASTA file
proteinpulse analyze my_protein.fasta

# Domain scan
proteinpulse domains MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

# Secondary structure prediction
proteinpulse structure MQIFVKTLTGKTITLEVEPSDTIENVKAK

# Fetch PDB metadata
proteinpulse pdb 1UBQ

# Full report in one command
proteinpulse full MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG --pdb 1UBQ

# Save output as JSON
proteinpulse full my_protein.fasta --output json --save report.json

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Output Formats

All commands support --output with three options:

• table — rich, coloured terminal table (default)
• json — machine-readable JSON
• csv — flat CSV (for analyze and domains)

Use --save <file> to write output to disk.

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Commands Reference

analyze

proteinpulse analyze SEQUENCE [--output table|json|csv] [--save FILE]

Computes:

• Molecular weight (Da and kDa)
• Isoelectric point (pI)
• GRAVY hydrophobicity index (Kyte-Doolittle)
• Instability index (Guruprasad et al.)
• Net charge at pH 7
• Extinction coefficient
• Aromaticity and aliphatic index
• Full amino acid composition

domains

proteinpulse domains SEQUENCE [--output table|json] [--save FILE]

Scans for 20+ motifs including: zinc fingers, RGD, KDEL/HDEL ER retention, nuclear localisation signals, transmembrane regions, N/O-glycosylation, phosphorylation sites (CK2, PKC, PKA), leucine zippers, EF-hands, SH2/SH3 binding, 14-3-3 binding, and more.

structure

proteinpulse structure SEQUENCE

Predicts α-helix, β-sheet, turn, and coil percentages using Chou-Fasman propensity scores.

pdb

proteinpulse pdb PDB_ID [--output table|json] [--save FILE]

Fetches title, experimental method, resolution, chain count, residue count, and deposition dates from RCSB PDB.

full

proteinpulse full SEQUENCE [--pdb PDB_ID] [--output table|json] [--save FILE]

Runs all analyses and optionally fetches a PDB entry.

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Programmatic Use

from proteinpulse.sequence import load_sequence
from proteinpulse.properties import compute_properties
from proteinpulse.domains import scan_domains
from proteinpulse.structure import predict_secondary_structure

seq   = load_sequence("MQIFVKTLTGKTITLEVEPSDTIENVKAK")
props = compute_properties(seq)
hits  = scan_domains(seq)
struct = predict_secondary_structure(seq)

print(props.molecular_weight_kda)   # e.g. 3.24
print(props.isoelectric_point)      # e.g. 6.73
print([h.name for h in hits])       # e.g. ['SH3 binding (PXXP)']
print(struct.dominant)              # e.g. 'Alpha-Helix'

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Development

git clone https://github.com/Eswar-mse/proteinpulse
cd proteinpulse
pip install -e ".[dev]"
pytest tests/ -v

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License

MIT © ProteinPulse Contributors