iphasimulator.export

Export helpers for RDKit PHA molecules.

Functions

prepare_molecule_3d(→ rdkit.Chem.Mol)	Return a copy with explicit hydrogens and an optimized 3D conformer.
to_sdf(→ None)	Embed an RDKit molecule with ETKDG and write it to SDF.
to_pdb(→ None)	Embed an RDKit molecule with ETKDG and write it to PDB.

Module Contents

iphasimulator.export.prepare_molecule_3d(mol: rdkit.Chem.Mol) → rdkit.Chem.Mol

Return a copy with explicit hydrogens and an optimized 3D conformer.

iphasimulator.export.to_sdf(mol: rdkit.Chem.Mol, path: str | pathlib.Path) → None

Embed an RDKit molecule with ETKDG and write it to SDF.

iphasimulator.export.to_pdb(mol: rdkit.Chem.Mol, path: str | pathlib.Path) → None

Embed an RDKit molecule with ETKDG and write it to PDB.