ljmartin

import pandas as pd
from rdkit import Chem

from rdkit.Chem import AllChem
from rdkit.Chem import rdMolDescriptors
from rdkit.Chem import AllChem, rdMolDescriptors, rdMolAlign, rdMolTransforms

import numpy as np
from tqdm.notebook import tqdm

ljmartin

import modal

image = (
    modal.Image.micromamba(python_version="3.10")
    .apt_install('gcc')
    .apt_install('git', 'wget')
    .micromamba_install('openmm==8.0.0', 'pdbfixer','kalign2=2.04', 'hhsuite=3.3.0',
                        'mmseqs2', channels=['conda-forge', 'bioconda'])
    .run_commands('pip install "colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold"')
    .run_commands('pip install "colabfold[alphafold]"')

ljmartin

ljmartin

ljmartin

import modal

image = (
    modal.Image.debian_slim()
    .pip_install("uv")
    .run_commands("uv pip install --system --compile-bytecode chai_lab==0.4.2")
    .run_commands('mkdir -p /usr/local/lib/python3.11/site-packages/downloads/models_v2')
    .apt_install("wget")
    .run_commands('wget -O /usr/local/lib/python3.11/site-packages/downloads/conformers_v1.apkl https://chaiassets.com/chai1-inference-depencencies/conformers_v1.apkl')
    .run_commands('wget -O  /usr/local/lib/python3.11/site-packages/downloads/models_v2/trunk.pt https://chaiassets.com/chai1-inference-depencencies/models_v2/trunk.pt')

ljmartin

ljmartin

sequences:
  - protein:
      id: [A, B]
      sequence: MVTPEGNVSLVDESLLVGVTDEDRAVRSAHQFYERLIGLWAPAVMEAAHELGVFAALAEAPADSGELARRLDCDARAMRVLLDALYAYDVIDRIHDTNGFRYLLSAEARECLLPGTLFSLVGKFMHDINVAWPAWRNLAEVVRHGARDTSGAESPNGIAQEDYESLVGGINFWAPPIVTTLSRKLRASGRSGDATASVLDVGCGTGLYSQLLLREFPRWTATGLDVERIATLANAQALRLGVEERFATRAGDFWRGGWGTGYDLVLFANIFHLQTPASAVRLMRHAAACLAPDGLVAVVDQIVDADREPKTPQDRFALLFAASMTNTGGGDAYTFQEYEEWFTAAGLQRIETLDTPMHRILLARRATEPSAVPEGQASENLYFQ
      msa: ./seq1.a3m
  - ligand:
      id: [C, D]
      ccd: SAH
  - ligand:
      id: [E, F]

ljmartin

ljmartin

ljmartin

#https://github.com/rdkit/rdkit/discussions/6135

from rdkit import Chem
from rdkit.Chem import AllChem

def mol_to_bits(mol, radius=0):
    bi = {}
    fp = AllChem.GetMorganFingerprint(mol, radius, bitInfo=bi,useFeatures=False)
    bits = np.zeros(mol.GetNumAtoms(),dtype=int)
    for key, value in bi.items():