{"library":"pyocse","title":"Python Organic Crystal Simulation Environment (pyocse)","description":"Python Organic Crystal Simulation Environment (pyocse) is a library designed for simulating organic crystals. It facilitates tasks like automated force field generation for CHARMM and handling crystal structures and molecules. The current stable version is 0.1.3, with releases being infrequent, primarily tied to significant feature additions and core updates.","language":"python","status":"active","last_verified":"Thu Apr 16","install":{"commands":["pip install pyocse"],"cli":null},"imports":["from pyocse.data import Molecule","from pyocse.crystal import Crystal","from pyocse.builder import Builder","from pyocse.force_field import ForceField"],"auth":{"required":false,"env_vars":[]},"quickstart":{"code":"from pyocse.data import Molecule\nfrom ase.build import molecule as ase_build_molecule\n\n# Create an ASE Atoms object for water\nh2o_ase = ase_build_molecule(\"H2O\")\n\n# Initialize a pyocse Molecule from the ASE object\nmol_h2o = Molecule(ase_atom=h2o_ase, name=\"Water\")\n\nprint(f\"Molecule Name: {mol_h2o.name}\")\nprint(f\"Number of Atoms in pyocse Molecule: {len(mol_h2o.atoms)}\")\nprint(f\"Atom symbols: {[atom.symbol for atom in mol_h2o.atoms]}\")\n\n# Access the underlying ASE Atoms object for ASE-specific methods\nif mol_h2o.ase_atom:\n    print(f\"Positions of first atom (via ASE): {mol_h2o.ase_atom.get_positions()[0]}\")\nelse:\n    print(\"Underlying ASE Atoms object not available.\")","lang":"python","description":"This quickstart demonstrates how to initialize a `pyocse.data.Molecule` object, specifically by converting an `ase.Atoms` object. It then shows how to access basic molecular properties and interact with the underlying `ase` object for more detailed atomic manipulation, highlighting the interoperability.","tag":null,"tag_description":null,"last_tested":null,"results":[]},"compatibility":null}