prefect<4,>=3.8.4
PyYAML<7,>=6.0

[chemistry]
rdkit==2026.3.1

[coding-design]
dnachisel==3.2.16
biopython==1.88

[construct]
pydna==5.5.16
biopython==1.88

[dossier]
gemmi==0.7.5

[embedding-analysis]
scikit-learn<2,>=1.6
umap-learn==0.5.12

[openmm]
openmm==8.6.0

[protein-repair]
openmm==8.6.0
pdbfixer==1.12.0

[quantitative]
numpy<3,>=1.26
scipy<2,>=1.14
scikit-learn<2,>=1.6

[routes]
doranet==0.5.7a1
rdkit==2026.3.1

[thermodynamics]
equilibrator-api==0.8.0
equilibrator-cache==0.8.1
component-contribution==0.8.0
equilibrator-cache-data==0.1.0
rdkit==2026.3.1

[trajectory]
mdtraj==1.11.1.post2
