Index A | C | D | F | G | I | L | M | N | P | R | S | T | X A anchor_constrained_optimization() (mofa.model.LigandDescription method) anchor_type (mofa.model.LigandDescription attribute) (mofa.model.LigandTemplate attribute) assemble_COO_pcuMOF() (in module mofa.assembly.assemble) assemble_many() (in module mofa.assembly.assemble) assemble_mof() (in module mofa.assembly.assemble) assemble_pillaredPaddleWheel_pcuMOF() (in module mofa.assembly.assemble) atoms (mofa.model.LigandDescription property) (mofa.model.MOFRecord property) C catenation (mofa.model.MOFRecord attribute) compute_partial_charges() (in module mofa.simulation.dft) create_description() (mofa.model.LigandTemplate method) D dummy_element (mofa.model.LigandDescription attribute) (mofa.model.LigandTemplate attribute) F from_file() (mofa.model.MOFRecord class method) from_yaml() (mofa.model.LigandDescription class method) (mofa.model.LigandTemplate class method) full_ligand_optimization() (mofa.model.LigandDescription method) G gas_storage (mofa.model.MOFRecord attribute) I identifiers (mofa.model.MOFRecord attribute) in_progress (mofa.model.MOFRecord attribute) L LigandDescription (class in mofa.model) ligands (mofa.model.MOFRecord attribute) LigandTemplate (class in mofa.model) load_atoms_with_charges() (in module mofa.simulation.dft) M md_trajectory (mofa.model.MOFRecord attribute) metadata (mofa.model.LigandDescription attribute) module mofa.assembly mofa.assembly.assemble mofa.model mofa.simulation mofa.simulation.dft mofa.assembly module mofa.assembly.assemble module mofa.model module mofa.simulation module mofa.simulation.dft module MOFRecord (class in mofa.model) N name (mofa.model.LigandDescription attribute) (mofa.model.MOFRecord attribute) NodeDescription (class in mofa.model) nodes (mofa.model.MOFRecord attribute) P pandas2xyzfile() (in module mofa.assembly.assemble) prepare_inputs() (mofa.model.LigandTemplate method) prompt_atoms (mofa.model.LigandDescription attribute) prompts (mofa.model.LigandTemplate property) R readCOOLinkerXYZ() (in module mofa.assembly.assemble) readNbasedLinkerXYZ() (in module mofa.assembly.assemble) readPillaredPaddleWheelXYZ() (in module mofa.assembly.assemble) readTetramerXYZ() (in module mofa.assembly.assemble) replace_with_dummy_atoms() (mofa.model.LigandDescription method) rotmat2align() (in module mofa.assembly.assemble) S smiles (mofa.model.LigandDescription attribute) (mofa.model.NodeDescription attribute) structure (mofa.model.MOFRecord attribute) structure_stability (mofa.model.MOFRecord attribute) T times (mofa.model.MOFRecord attribute) to_json() (mofa.model.MOFRecord method) to_training_example() (mofa.model.LigandDescription method) topology (mofa.model.MOFRecord attribute) X xyz (mofa.model.LigandDescription attribute) (mofa.model.NodeDescription attribute) xyzs (mofa.model.LigandTemplate attribute)