hydride

library1.2.3pypypi✓ verified 79d ago

A Python library for adding hydrogen atoms to molecular models (protein structures, ligands, etc.). Version 1.2.3, with regular releases. Recommended for computational chemistry workflows.

ai-ml

pip install hydride

INSTALL

IMPORT

SIG · HYDRIDE

hydride

ai-mlpythonv1.2.3

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

add_hydrogen

✓ from hydride import add_hydrogen

✗ from hydride import add_hydrogens

AtomNameLibrary

✓ from hydride import AtomNameLibrary

FragmentLibrary

✓ from hydride import FragmentLibrary

Add hydrogens to a simple ethanol molecule.

from hydride import add_hydrogens from rdkit import Chem mol = Chem.MolFromSmiles('CCO') try: mol_with_h = add_hydrogens(mol) print(Chem.MolToSmiles(mol_with_h)) except Exception as e: print(f'Error: {e}')

Debug

Known issues

breakingIn version 1.2.0, the add_hydrogens function moved from hydride.core to hydride. Import via 'from hydride import add_hydrogens'. The old path 'from hydride.core import add_hydrogens' will raise ImportError in 1.2.x.

fix

Update import to 'from hydride import add_hydrogens'.

affects: >=1.2.0

deprecatedThe function 'hydride.add_all_hydrogens' is deprecated since 1.1.0 and will be removed in 2.0.0. Use 'add_hydrogens' with appropriate options instead.

fix

Replace with 'add_hydrogens(mol, add_all=True)'.

affects: >=1.1.0, <2.0.0

gotchaInput molecules must have explicit hydrogens removed before processing. Passing a molecule with existing hydrogens will cause incorrect geometry or failure.

fix

Use Chem.RemoveHs(mol) before calling add_hydrogens, or ensure the molecule has no explicit hydrogens.

affects: all

Upgrade

Version history

1.2.3latest on PyPI · released Nov 4, 2024

Audit

Dependencies

rdkitoptionalMolecular representation and operations

Agent activity

12 hits · last 30 days

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Resources

No resource links recorded.