molsysmt.form.file_bcif_gz package#

Submodules#

molsysmt.form.file_bcif_gz.add module#

molsysmt.form.file_bcif_gz.add.add(to_item, item, atom_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.append_structures module#

molsysmt.form.file_bcif_gz.append_structures.append_structures(item, structure_id=None, time=None, coordinates=None, box=None, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.attributes module#

molsysmt.form.file_bcif_gz.copy module#

molsysmt.form.file_bcif_gz.copy.copy(item, output_filename=None, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.download module#

molsysmt.form.file_bcif_gz.download.download(pdb_id=None, output_filename=None, tempfile=False, wwPDB_Partner='RCSB PDB', retries=5, timeout=30, backoff_base=2.0)[source]#

Download <pdb_id>.bcif.gz from the specified wwPDB partner, handling rate limiting (HTTP 429) and transient network errors with retries and exponential backoff + jitter.

Parameters:

pdb_id (str) – 4-character PDB ID (case-insensitive).
tempfile (bool, default True) – If True, create a temporary filename via MolSysMT’s temp_filename(). If False and output_filename is None, the output will be “<pdb_id>.bcif.gz” in the current directory.
wwPDB_Partner (str, default 'RCSB PDB') – wwPDB partner source. Currently only ‘RCSB PDB’ is supported.
output_filename (str or None, default None) – If provided, write to this path. Otherwise it is computed from tempfile/pdb_id.
retries (int, default 5) – Maximum number of attempts before failing.
timeout (int or float, default 30) – Per-request timeout (seconds).
backoff_base (float, default 2.0) – Exponential backoff base. Retry wait ~ (backoff_base ** attempt) + jitter.

Returns:

Path to the downloaded file.

Return type:

str

Raises:

NotImplementedError – If the partner is not supported.
RuntimeError – If retries are exhausted or a non-recoverable HTTP error occurs (e.g., 404).

molsysmt.form.file_bcif_gz.extract module#

molsysmt.form.file_bcif_gz.extract.extract(item, atom_indices='all', structure_indices='all', output_filename=None, copy_if_all=True, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get module#

molsysmt.form.file_bcif_gz.get.get_alternate_location_from_system(item, structure_indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_id_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_atom_id_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_id_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_id_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_id_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_id_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_index_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_index_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_index_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_index_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_index_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_index_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_name_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_atom_name_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_name_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_name_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_name_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_name_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_type_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_atom_type_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_type_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_type_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_type_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_atom_type_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_b_factor_from_system(item, structure_indices='all')#

molsysmt.form.file_bcif_gz.get.get_bond_index_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_bond_index_from_bond(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_bond_index_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_bond_order_from_bond(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_bond_type_from_bond(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_bonded_atoms_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_bonded_atoms_from_bond(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_bonded_atoms_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_box_angles_from_system(item, structure_indices='all')#

molsysmt.form.file_bcif_gz.get.get_box_from_system(item, structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_box_lengths_from_system(item, structure_indices='all')#

molsysmt.form.file_bcif_gz.get.get_box_shape_from_system(item, structure_indices='all')#

molsysmt.form.file_bcif_gz.get.get_box_volume_from_system(item, structure_indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_id_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_id_from_chain(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_chain_id_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_id_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_id_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_id_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_index_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_chain_index_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_index_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_index_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_index_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_index_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_name_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_name_from_chain(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_chain_name_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_name_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_name_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_name_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_type_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_type_from_chain(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_chain_type_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_type_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_type_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_chain_type_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_id_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_id_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_id_from_component(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_component_id_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_id_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_id_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_index_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_component_index_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_index_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_index_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_index_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_index_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_name_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_name_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_name_from_component(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_component_name_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_name_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_name_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_type_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_type_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_type_from_component(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_component_type_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_type_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_component_type_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_coordinates_from_atom(item, indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_coordinates_from_system(item, structure_indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_id_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_id_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_id_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_id_from_entity(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_entity_id_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_id_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_index_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_entity_index_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_index_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_index_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_index_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_index_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_name_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_name_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_name_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_name_from_entity(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_entity_name_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_name_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_type_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_type_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_type_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_type_from_entity(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_entity_type_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_entity_type_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_formal_charge_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_formal_charge_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_formal_charge_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_formal_charge_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_formal_charge_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_formal_charge_from_system(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_id_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_id_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_id_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_id_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_id_from_group(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_group_id_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_index_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_group_index_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_index_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_index_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_index_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_index_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_name_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_name_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_name_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_name_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_name_from_group(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_group_name_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_type_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_type_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_type_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_type_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_group_type_from_group(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_group_type_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_inner_bond_index_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_inner_bond_index_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_inner_bonded_atoms_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_inner_bonded_atoms_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_molecule_id_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_id_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_id_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_id_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_id_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_id_from_molecule(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_molecule_index_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_molecule_index_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_index_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_index_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_index_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_index_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_name_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_name_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_name_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_name_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_name_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_name_from_molecule(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_molecule_type_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_type_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_type_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_type_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_type_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_molecule_type_from_molecule(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_n_amino_acids_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_amino_acids_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_amino_acids_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_amino_acids_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_amino_acids_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_amino_acids_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_amino_acids_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_n_atoms_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_atoms_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_atoms_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_atoms_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_atoms_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_atoms_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_atoms_from_system(item, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_n_bonds_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_bonds_from_bond(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_bonds_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_bonds_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_bonds_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_bonds_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_bonds_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_bonds_from_system(item, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_n_chains_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_chains_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_chains_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_chains_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_chains_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_chains_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_chains_from_system(item, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_n_components_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_components_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_components_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_components_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_components_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_components_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_components_from_system(item, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_n_dnas_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_dnas_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_dnas_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_dnas_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_dnas_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_dnas_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_dnas_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_n_entities_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_entities_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_entities_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_entities_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_entities_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_entities_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_entities_from_system(item, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_n_groups_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_groups_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_groups_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_groups_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_groups_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_groups_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_groups_from_system(item, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_n_inner_bonds_from_atom(item, indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_n_inner_bonds_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_inner_bonds_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_inner_bonds_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_inner_bonds_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_inner_bonds_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_ions_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_ions_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_ions_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_ions_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_ions_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_ions_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_ions_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_n_lipids_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_lipids_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_lipids_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_lipids_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_lipids_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_lipids_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_lipids_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_n_molecules_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_molecules_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_molecules_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_molecules_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_molecules_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_molecules_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_molecules_from_system(item, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_n_nucleotides_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_nucleotides_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_nucleotides_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_nucleotides_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_nucleotides_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_nucleotides_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_nucleotides_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_n_peptides_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_peptides_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_peptides_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_peptides_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_peptides_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_peptides_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_peptides_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_n_polysaccharides_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_polysaccharides_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_polysaccharides_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_polysaccharides_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_polysaccharides_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_polysaccharides_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_polysaccharides_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_n_proteins_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_proteins_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_proteins_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_proteins_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_proteins_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_proteins_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_proteins_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_n_rnas_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_rnas_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_rnas_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_rnas_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_rnas_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_rnas_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_rnas_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_n_saccharides_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_saccharides_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_saccharides_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_saccharides_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_saccharides_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_saccharides_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_saccharides_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_n_small_molecules_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_small_molecules_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_small_molecules_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_small_molecules_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_small_molecules_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_small_molecules_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_small_molecules_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_n_structures_from_system(item, structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_n_waters_from_atom(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_waters_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_waters_from_component(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_waters_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_waters_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_waters_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_n_waters_from_system(item)#

molsysmt.form.file_bcif_gz.get.get_occupancy_from_system(item, structure_indices='all')#

molsysmt.form.file_bcif_gz.get.get_partial_charge_from_chain(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_partial_charge_from_entity(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_partial_charge_from_group(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_partial_charge_from_molecule(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_partial_charge_from_system(item, indices='all')#

molsysmt.form.file_bcif_gz.get.get_structure_id_from_system(item, structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_time_from_system(item, structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.get.get_velocities_from_system(item, structure_indices='all')#

molsysmt.form.file_bcif_gz.has_attribute module#

molsysmt.form.file_bcif_gz.has_attribute.has_attribute(molecular_system, attribute, include_none=False, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.is_form module#

molsysmt.form.file_bcif_gz.is_form.is_form(item)[source]#

molsysmt.form.file_bcif_gz.iterators module#

class molsysmt.form.file_bcif_gz.iterators.StructuresIterator(molecular_system, atom_indices='all', start=0, step=1, stop=None, chunk=1, structure_indices=None, output_type='values', skip_digestion=False, **kwargs)[source]#: Bases: StructuresIterator

class molsysmt.form.file_bcif_gz.iterators.TopologyIterator(molecular_system, element='atom', indices='all', start=0, step=1, stop=None, chunk=1, output_type='values', skip_digestion=False, **kwargs)[source]#: Bases: TopologyIterator

molsysmt.form.file_bcif_gz.merge module#

molsysmt.form.file_bcif_gz.merge.merge(items, atom_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.set module#

molsysmt.form.file_bcif_gz.to_bcifreader_PdbxContainers_DataContainer module#

molsysmt.form.file_bcif_gz.to_bcifreader_PdbxContainers_DataContainer.to_bcifreader_PdbxContainers_DataContainer(item, atom_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.to_file_bcif_gz module#

molsysmt.form.file_bcif_gz.to_file_bcif_gz.to_file_bcif_gz(item, atom_indices='all', structure_indices='all', output_name=None, copy_if_all=True, skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.to_file_h5msm module#

molsysmt.form.file_bcif_gz.to_file_h5msm.to_file_h5msm(item, atom_indices='all', structure_indices='all', output_filename=None, compression='gzip', compression_opts=4, int_precision='single', float_precision='single', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.to_mmcif_PdbxContainers_DataContainer module#

molsysmt.form.file_bcif_gz.to_mmcif_PdbxContainers_DataContainer.to_mmcif_PdbxContainers_DataContainer(item, atom_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.to_molsysmt_MolSys module#

molsysmt.form.file_bcif_gz.to_molsysmt_MolSys.to_molsysmt_MolSys(item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.to_molsysmt_Structures module#

molsysmt.form.file_bcif_gz.to_molsysmt_Structures.to_molsysmt_Structures(item, atom_indices='all', structure_indices='all', skip_digestion=False)[source]#

molsysmt.form.file_bcif_gz.to_molsysmt_Topology module#

molsysmt.form.file_bcif_gz.to_molsysmt_Topology.to_molsysmt_Topology(item, atom_indices='all', skip_digestion=False)[source]#