B b@s@dZddlmZmZddlmZddlmZGdddeZ dS)zE This package contains classes responsible for loading rdkit objects )print_functionabsolute_import)PDBFile)StringIOc@s4eZdZeddZed ddZed ddZd S) RDKitcCs$ddlm}t||}t|S)a Load a :class:`Mol` object and return a populated :class:`Structure` instance Parameters ---------- rmol: :class:`Mol` RDKit :class:`Mol` object to convert Examples -------- >>> from rdkit import Chem >>> import parmed as pmd >>> mol = Chem.MolFromSmiles('Cc1ccccc1') >>> struct = pmd.load_rdkit(mol) r)Chem)rdkitrrZ MolToPDBBlockrparse)ZrmolrZfhr 1lib/python3.7/site-packages/parmed/rdkit/rdkit.pyload s z RDKit.loadTcCsTddlm}ddlm}||}|r6|j|dddt|}|sPd|_d|_ |S)a@ Load smiles string to :class:`Structure` Parameters ---------- smiles : str, smiles coordinates : bool, default True if True, use `rdkit.Chem.AllChem.EmbedMultipleConfs to assign coordinates Returns ------- parm : :class:`Structure` r)r)AllChemT)ZuseExpTorsionAnglePrefsZuseBasicKnowledgeN) rrZ rdkit.Chemr Z MolFromSmilesZEmbedMultipleConfsrr coordinatesZ _coordinates)Zsmilesrrr molZparmr r r from_smiles"s    zRDKit.from_smilesFcCsBddlm}|j|dd}|r0t|}t|Sdd|DSdS)a Load SDF file to :class:`Structure` Parameters ---------- filename: str structure : bool, default False if True, return a :class:`Structure` if False, return a list of :class:`Structure` r)rF)ZremoveHscSsg|]}t|qSr )rr ).0rr r r Qsz"RDKit.from_sdf..N)rrZ SDMolSuppliernextrr )filenameZ structurerZsdf_collectionrr r r from_sdf?s  zRDKit.from_sdfN)T)F)__name__ __module__ __qualname__ staticmethodr rrr r r r r s   rN) __doc__Z __future__rrZparmed.formatsrZparmed.utils.six.movesrobjectrr r r r s