p2smi: Generation and Analysis of Drug-like Peptide SMILES Strings

p2smi is a Python toolkit for peptide design and analysis.

It enables generation of peptide sequences, conversion to SMILES representations—including support for cyclic and noncanonical amino acids—and evaluation of molecular properties. The package also provides utilities for structural modification (e.g., N-methylation, PEGylation), synthesis feasibility assessment, and output in a dedicated .p2smi format that links peptide sequences to their corresponding SMILES.

This was developed in support of PeptideCLM, a SMILES-based language model for modified peptides, p2smi provides an extensible foundation for computational peptide chemistry and machine-learning-driven molecular design.

If you use this tool, please cite our paper at the link below:

Features

• Convert peptide FASTA files into valid SMILES strings
• Support five cyclization types: disulfide, head-to-tail, sidechain-to-sidechain, sidechain-to-N-term, sidechain-to-C-term
• Apply random library modifications or deterministic, site-explicit recipes
• Generate random peptide sequences (with modification rates)
• Evaluate synthetic feasibility based on common failure motifs
• Compute molecular properties (MW, logP, TPSA, Lipinski, etc.)

Updates

• Version 2.0.0 - Added JSON residue registries, NCAA import from SMILES or MOL files, SMARTS/graph peptide assembly, and registry-aware FASTA conversion
• Version 1.1.1 - Added functionality to allow for user-defined cyclizing residue constraints
• Version 1.1.0 - Updated codebase, documentation, fixed bugs -- for JOSS review
• Version 1.0.0 - First release for JOSS submission

Manuscript

• PDF | Markdown

Directory

• Installation
• Command-Line Tools
• Example Usage
• Future Work
• Contributing
• License

Installation

Install from PyPI:

pip install p2smi

For local development:

git clone https://github.com/AaronFeller/p2smi.git
cd p2smi
pip install -e .[dev]

Command-Line Tools

Use --help on any command for options:

fasta2smi --help

Manually encoding cyclizations

Cyclizations can be specified directly in the FASTA header to control how fasta2smi interprets bond formation between residues.

Each cyclization tag begins with a two-letter code identifying the bond type (SS or SC), followed by a constraint mask of equal length to the peptide sequence, where:

• X marks positions left unconstrained
• C marks residues participating in a disulphide bond
• N marks nucleophilic sidechains that cyclize to the peptide C-terminus
• E marks ester sidechains that cyclize to the peptide C-terminus
• Z marks carboxyl sidechains that cyclize to the peptide N-terminus
• if N and Z included, form side-chain to side-chain cyclization

Supported Formats:

Example Usage

Generate random peptides with constraints:

generate-peptides \
  --num 10 \
  --min_length 10 \
  --max_length 20 \
  --noncanonical 0.1 \
  --dextro 0.1 \
  --cyclization_constraints all \
  --outfile peptides.fasta

Add a noncanonical amino acid to a v2 registry:

add-amino-acid \
  --registry-file lab-residues.json \
  --id LAB_001 \
  --name "Example NCAA" \
  --smiles "N[C@@H](CC)C(=O)O"

When only an MDL .mol structure file is available, replace --smiles with --mol-file path/to/residue.mol. The command validates the structure and stores its canonical isomeric SMILES in the JSON registry.

Cyclization uses SMARTS assembly and graph-derived sidechain reaction sites; do not provide separate cyclization SMILES. A constrained v2 peptide must select exactly one compatible site per marked residue. Structures with multiple matching cyclization sites are rejected rather than selected arbitrarily.

Use comma-delimited residue IDs in FASTA and pass the same registry when converting:

cat > custom.fasta <<'EOF'
>custom|SCCT
LAB_001,Ala,Ala,Ala
EOF

fasta2smi -i custom.fasta -o custom.p2smi --registry-file lab-residues.json

Convert FASTA to SMILES:

fasta2smi -i peptides.fasta -o peptides.p2smi

Modify SMILES strings:

Random library generation retains rate-based controls. Random PEGylation creates a defined mPEG acyl conjugate at a free amine:

modify-smiles -i peptides.p2smi -o modified.p2smi --peg_rate 0.2 --nmeth_rate 0.2 --nmeth_residues 0.2

Build explicitly modified peptides

Deterministic recipes select termini, chemical roles, residue positions, atom indices, or SMARTS matches. Residue numbers are one-based. Residue-scoped steps run before peptide assembly; terminal/global steps follow them.

{
  "schema_version": 1,
  "kind": "p2smi_modifier_registry",
  "modifiers": [],
  "recipes": [
    {
      "id": "lipidated_candidate",
      "steps": [
        {
          "modifier": "octadecanedioyl",
          "site": {"residue": 2, "role": "sidechain_amine"},
          "params": {"linker": "gamma_glu_aeea2"}
        },
        {
          "modifier": "n_methyl",
          "site": {"residue": 3, "role": "backbone_n"}
        },
        {
          "modifier": "c_amide",
          "site": {"terminus": "C"}
        }
      ]
    }
  ]
}

Apply residue-addressed recipes during sequence assembly:

fasta2smi \
  -i candidate.fasta \
  -o candidate.p2smi \
  --modifier-registry modifiers.json \
  --recipe lipidated_candidate

Apply recipes using terminal, role, atom-index, or SMARTS selectors to existing SMILES:

modify-smiles \
  -i peptides.p2smi \
  -o modified.p2smi \
  --modifier-registry modifiers.json \
  --recipe terminal_caps

Supported semantic roles are n_terminal_amine, c_terminal_carboxyl, backbone_n, backbone_amide_n, sidechain_amine, sidechain_hydroxyl, and sidechain_thiol. Selector examples:

{"terminus": "N"}
{"residue": 4, "role": "sidechain_amine"}
{"residue": 3, "smarts": "[O;H1]", "match_index": 1}
{"atom_index": 12}
{"smarts": "[S;H1]"}

An atom_index refers to the original input graph and fails if an earlier step removes that atom. SMARTS selectors must match exactly once unless match_index is provided. Explicit selectors must still satisfy the modifier's allowed chemistry.

Built-in modifiers are:

Lipid linkers

Any acyl modifier whose fragment ends in C(=O)*, including imported LMSD monoacids, can be applied through a linker:

{
  "modifier": "octadecanedioyl",
  "site": {"residue": 26, "role": "sidechain_amine"},
  "params": {"linker": "gamma_glu_aeea2"}
}

Available linker IDs are:

These building blocks cover several literature-studied architectures. A C16 acyl cargo with gamma_glu gives a liraglutide-like side chain. The C18 or C20 diacid cargos with gamma_glu_aeea2 give semaglutide-type or tirzepatide-type hydrophilic lipid side chains, respectively. These labels describe the side chain architecture only; complete drug identity also depends on peptide sequence, attachment residue, stereochemistry, and all other substitutions.

Direct attachment remains the default when params.linker is omitted. Linkers are accepted only for amine-targeted acyl fragments, preventing accidental use with phosphorylation or other non-acyl grafts.

Custom graft modifiers contain one terminal * attachment atom:

{
  "id": "fluoroacetyl",
  "name": "Fluoroacetylation",
  "operation": "graft",
  "allowed_roles": ["n_terminal_amine", "sidechain_amine"],
  "fragment_smiles": "FCC(=O)*"
}

For an amine-targeted lipid, write the desired side chain as R-C(=O)*. The * marks the carbonyl that bonds to the selected peptide nitrogen. This supports structures outside the curated panel, including branched lipids:

{
  "id": "branched_c8",
  "name": "Branched C8 acyl group",
  "operation": "graft",
  "allowed_roles": ["n_terminal_amine", "sidechain_amine"],
  "fragment_smiles": "CCCCC(CC)C(=O)*"
}

Unsaturation, isotopes, heteroatoms, and protecting groups can likewise be encoded in fragment_smiles. For an asymmetric diacid, explicitly protect or choose one terminus and place * at the carbonyl intended for peptide attachment. The registry validates the graph and attachment point, while the user controls the exact chemistry.

Custom reaction SMARTS

For transformations that do not fit a graft or built-in operation, a modifier can define an RDKit reaction SMARTS template. Atom map :1 identifies the atom chosen by the recipe's site selector:

{
  "id": "custom_o_methyl",
  "name": "Custom hydroxyl methylation",
  "operation": "reaction",
  "allowed_roles": ["sidechain_hydroxyl"],
  "reaction_smarts": "[O;H1:1]>>[O:1]C"
}

The same modifier can then be applied through a semantic or explicit selector:

{
  "modifier": "custom_o_methyl",
  "site": {"residue": 4, "role": "sidechain_hydroxyl"}
}

Custom reactions intentionally use a constrained contract:

• Exactly one reactant template and one product template are required.
• Atom map :1 must occur exactly once on both sides and survive the reaction.
• Other product atom maps must exist in the reactant; newly created atoms are left unmapped.
• The selected atom must match :1, even when the reaction SMARTS matches other atoms in the molecule.
• Products must be unique, connected, sanitizable, and chemically changed.
• Reactions generating more than 256 candidate products are rejected.

Reaction SMARTS is an expert escape hatch: p2smi validates graph integrity and site selection, but the author remains responsible for whether the encoded transformation is chemically meaningful.

Recipes fail on missing, ambiguous, chemically incompatible, or consumed sites. Use --on-error skip only when batch processing should continue.

Import fatty-acid modifiers

The default installation uses only the curated C8-C20 panel above. It does not bundle the full LMSD catalog. Create a focused registry from an LMSD-style or laboratory SDF with:

import-lipid-modifiers \
  --input structures.sdf \
  --output lipid-modifiers.json \
  --max-carbons 20 \
  --acid-mode both

Import controls:

• --acid-mode monoacid imports records with one free acid.
• --acid-mode diacid imports unprotected diacids only when both termini are symmetry-equivalent.
• --acid-mode both accepts either case and is the default.
• --max-carbons 20 is the default; increase it explicitly for longer lipids.
• --strict stops at the first rejected structure instead of skipping it.

A diacid with one protected terminus has one free acid and can be imported as a monoacid. An unprotected asymmetric diacid is rejected because choosing an end would silently select a regioisomer. Define that structure directly in JSON after deciding which carbonyl is used for peptide attachment.

The importer uses LM_ID as the default ID and NAME as the display name. Use --id-property and --name-property for other SDF annotations. Output JSON contains only fields needed by p2smi; molfiles, formulas, synonyms, and external cross-references are not copied.

Add a recipe to lipid-modifiers.json that references an imported ID, then use the registry during peptide assembly:

{
  "id": "custom_lipid_candidate",
  "steps": [
    {
      "modifier": "LMFA01010001",
      "site": {"residue": 8, "role": "sidechain_amine"},
      "params": {"linker": "gamma_glu"}
    }
  ]
}

fasta2smi \
  --input candidate.fasta \
  --output candidate.p2smi \
  --modifier-registry lipid-modifiers.json \
  --recipe custom_lipid_candidate

Use the same --modifier-registry and --recipe options with modify-smiles to modify existing SMILES instead of assembling a peptide sequence.

Compute molecular properties:

smiles-props -i modified.p2smi

To preserve input labels in batch JSON output and fail fast on invalid SMILES:

smiles-props -i modified.p2smi -o props.jsonl --include_id --strict

Check synthesis feasibility (natural AAs only):

generate-peptides -o nat_peptides.fasta
synthesis-check -i nat_peptides.fasta

To tune synthesis heuristics for a different campaign:

synthesis-check -i nat_peptides.fasta --max_length 40 --max_logp 1.5 --charge_window 6

Future Work

• Extend synthesis rules to NCAAs and modified peptides
• Support alternative encodings (HELM, SELFIES)
• Batch processing and multiprocessing support
• Integration with predictive models
• Explicit atom selectors for ambiguous cyclization sites
• Curated import adapters for additional modification databases

For Contributors

You’re welcome to contribute! Suggestions, bugs, and pull requests are appreciated.

• 📂 Open an Issue
• 🛠 Submit a pull request
• 📝 Improve the docs

License

MIT License