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af3cli

Skill4 starsChanged 6 months agoMITView on GitHub

CLI and Python library for generating AlphaFold3 input JSON files. Use when the user wants to: create or modify AlphaFold3 input files, prepare protein/DNA/RNA sequences for AlphaFold3, add ligands/ions/bonds to AlphaFold3 jobs, convert FASTA/SDF to AlphaFold3 input format, or build complex multi-chain AlphaFold3 structures with modifications, templates, and MSA data. Triggers on mentions of AlphaFold3, af3cli, AlphaFold input, AF3 JSON.

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The file

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  1. Very specific:

    All commands are chainable with -.

    line 21
  2. Very specific:

    Merge files: Use merge to combine base system with new ligands/sequences

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SKILL.md

af3cli

CLI and Python library for generating AlphaFold3 input JSON files. Repo: https://github.com/SLx64/af3cli

Quick Start (Install)

git clone https://github.com/SLx64/af3cli.git
cd af3cli
uv sync --locked
# or: pip install af3cli[biopython,rdkit]

CLI Usage

All commands are chainable with -. Show help: af3cli -- --help

Basic Workflow

# 1. Config
af3cli config -f "output.json" -j "my_job" -v 2

# 2. Random seeds
af3cli seeds -n 5 - \
  # 3. Add sequences
  - protein add "MVKLAGST..." \
  - dna add --sequence "AATTTTCC" \
  - rna add --sequence "UUUGGCCGG" \
  # 4. Add ligands
  - ligand add --smiles "CCC" \
  - ligand add --ccd "MG" \
  # 5. Add bonds
  - bond --add "A:1:C-B:1:O" \
  # 6. Write file
  - debug --show

Key Commands

CommandPurpose
config -f <file> -j <name> -v <version>Set output file, job name, AF version
seeds -n <count> / seeds -v "1,2,3"Generate random seeds or specify list
protein add --sequence <seq>Add protein sequence
dna add --sequence <seq>Add DNA sequence
rna add --sequence <seq>Add RNA sequence
protein add --sequence <fasta> --fastaRead sequence from FASTA file
protein [...] - modification <CCD> <pos>Add residue modification
protein [...] - template <mmcif> --readAdd structural template
protein [...] - msa --paired ... --unpaired ...Add MSA data
ligand add --smiles <SMILES>Add ligand by SMILES
ligand add --ccd <CCD>Add ligand by CCD ID
ligand add --sdf <file>Read ligands from SDF (needs RDKit)
bond --add "A:1:C-B:1:O"Add bonded atom pair (E:R:N-E:R:N)
ccd <filename>Add custom CCD mmCIF
protein add -i "A,B"Specify chain IDs manually
protein add -n 2Specify copy number for homomultimers
merge <file> - protein add ...Merge with existing file, add new entries
debug --showPreview JSON without writing

Sequence descriptions (optional JSON-only comments)

af3cli protein description "kinase domain of protein X" - add --sequence "MVKLAGST"

The description field is auto-excluded for AF version <= 3 (compatibility).

Python API

from af3cli import InputBuilder
from af3cli import ProteinSequence, DNASequence, RNASequence
from af3cli import SMILigand, CCDLigand
from af3cli import ResidueModification, Template, TemplateType, Bond

builder = InputBuilder()
builder.set_name("my_job")
builder.set_version(2)

# Sequences
prot = ProteinSequence("MVKLAGST...", description="kinase domain")
prot.modifications.append(ResidueModification("SEP", 5))
builder.add_sequence(prot)

dna = DNASequence("AATTTTCC")
rc = dna.reverse_complement()
builder.add_sequence(dna)
builder.add_sequence(rc)

# Ligands
builder.add_ligand(SMILigand("CCC", description="propane"))
builder.add_ligand(CCDLigand(["MG"], description="magnesium"))

# Bonds
builder.add_bonded_atom_pair(Bond.from_string("A:1:C-B:1:O"))

# Seeds
builder.set_seeds([1, 2, 3])

# Write
input_file = builder.build()
input_file.write("output.json")

See references/api-reference.md for full API docs and references/cli-reference.md for detailed CLI reference.

Common Patterns

  • FASTA import: af3cli protein add --sequence <file> --fasta or fasta top-level command for bulk
  • SDF import: af3cli ligand add --sdf ligands.sdf (requires RDKit)
  • DNA reverse complement: dna add --sequence "AATTTTCC" --complement
  • Merge files: Use merge to combine base system with new ligands/sequences
  • User CCD: af3cli ccd my_ligand.cif for custom CCD mmCIF data

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