added ihm extension to mmcif schema

data/mmcif-field-names.csv

@@ -0,0 +1,590 @@
+atom_site.group_PDB
+atom_site.id
+atom_site.type_symbol
+atom_site.label_atom_id
+atom_site.label_alt_id
+atom_site.label_comp_id
+atom_site.label_asym_id
+atom_site.label_entity_id
+atom_site.label_seq_id
+atom_site.pdbx_PDB_ins_code
+atom_site.pdbx_formal_charge
+atom_site.Cartn_x
+atom_site.Cartn_y
+atom_site.Cartn_z
+atom_site.occupancy
+atom_site.B_iso_or_equiv
+atom_site.auth_atom_id
+atom_site.auth_comp_id
+atom_site.auth_asym_id
+atom_site.auth_seq_id
+atom_site.pdbx_PDB_model_num
+atom_site.ihm_model_id
+
+chem_comp.id
+chem_comp.type
+chem_comp.mon_nstd_flag
+chem_comp.name
+chem_comp.pdbx_synonyms
+chem_comp.formula
+chem_comp.formula_weight
+
+chem_comp_bond.comp_id
+chem_comp_bond.pdbx_stereo_config
+chem_comp_bond.pdbx_ordinal
+chem_comp_bond.pdbx_aromatic_flag
+chem_comp_bond.atom_id_1
+chem_comp_bond.atom_id_2
+chem_comp_bond.value_order
+
+cell.entry_id
+cell.length_a
+cell.length_b
+cell.length_c
+cell.angle_alpha
+cell.angle_beta
+cell.angle_gamma
+cell.Z_PDB
+cell.pdbx_unique_axis
+
+entity.id
+entity.type
+entity.src_method
+entity.pdbx_description
+entity.formula_weight
+entity.pdbx_number_of_molecules
+entity.details
+entity.pdbx_mutation
+entity.pdbx_fragment
+entity.pdbx_ec
+
+entry.id
+
+exptl.entry_id
+exptl.method
+
+struct.entry_id
+struct.title
+
+struct_asym.id
+struct_asym.pdbx_blank_PDB_chainid_flag
+struct_asym.pdbx_modified
+struct_asym.entity_id
+struct_asym.details
+
+struct_conf.conf_type_id
+struct_conf.id
+struct_conf.pdbx_PDB_helix_id
+struct_conf.beg_label_comp_id
+struct_conf.beg_label_asym_id
+struct_conf.beg_label_seq_id
+struct_conf.pdbx_beg_PDB_ins_code
+struct_conf.end_label_comp_id
+struct_conf.end_label_asym_id
+struct_conf.end_label_seq_id
+struct_conf.pdbx_end_PDB_ins_code
+struct_conf.beg_auth_comp_id
+struct_conf.beg_auth_asym_id
+struct_conf.beg_auth_seq_id
+struct_conf.end_auth_comp_id
+struct_conf.end_auth_asym_id
+struct_conf.end_auth_seq_id
+struct_conf.pdbx_PDB_helix_class
+struct_conf.details
+struct_conf.pdbx_PDB_helix_length
+
+struct_conn.id
+struct_conn.conn_type_id
+struct_conn.pdbx_PDB_id
+struct_conn.ptnr1_label_asym_id
+struct_conn.ptnr1_label_comp_id
+struct_conn.ptnr1_label_seq_id
+struct_conn.ptnr1_label_atom_id
+struct_conn.pdbx_ptnr1_label_alt_id
+struct_conn.pdbx_ptnr1_PDB_ins_code
+struct_conn.pdbx_ptnr1_standard_comp_id
+struct_conn.ptnr1_symmetry
+struct_conn.ptnr2_label_asym_id
+struct_conn.ptnr2_label_comp_id
+struct_conn.ptnr2_label_seq_id
+struct_conn.ptnr2_label_atom_id
+struct_conn.pdbx_ptnr2_label_alt_id
+struct_conn.pdbx_ptnr2_PDB_ins_code
+struct_conn.ptnr1_auth_asym_id
+struct_conn.ptnr1_auth_comp_id
+struct_conn.ptnr1_auth_seq_id
+struct_conn.ptnr2_auth_asym_id
+struct_conn.ptnr2_auth_comp_id
+struct_conn.ptnr2_auth_seq_id
+struct_conn.ptnr2_symmetry
+struct_conn.pdbx_ptnr3_label_atom_id
+struct_conn.pdbx_ptnr3_label_seq_id
+struct_conn.pdbx_ptnr3_label_comp_id
+struct_conn.pdbx_ptnr3_label_asym_id
+struct_conn.pdbx_ptnr3_label_alt_id
+struct_conn.pdbx_ptnr3_PDB_ins_code
+struct_conn.details
+struct_conn.pdbx_dist_value
+struct_conn.pdbx_value_order
+
+struct_conn_type.id
+struct_conn_type.criteria
+struct_conn_type.reference
+
+struct_keywords.entry_id
+struct_keywords.pdbx_keywords
+struct_keywords.text
+
+struct_sheet_range.sheet_id
+struct_sheet_range.id
+struct_sheet_range.beg_label_comp_id
+struct_sheet_range.beg_label_asym_id
+struct_sheet_range.beg_label_seq_id
+struct_sheet_range.pdbx_beg_PDB_ins_code
+struct_sheet_range.end_label_comp_id
+struct_sheet_range.end_label_asym_id
+struct_sheet_range.end_label_seq_id
+struct_sheet_range.pdbx_end_PDB_ins_code
+struct_sheet_range.beg_auth_comp_id
+struct_sheet_range.beg_auth_asym_id
+struct_sheet_range.beg_auth_seq_id
+struct_sheet_range.end_auth_comp_id
+struct_sheet_range.end_auth_asym_id
+struct_sheet_range.end_auth_seq_id
+
+struct_site.id
+struct_site.pdbx_evidence_code
+struct_site.pdbx_auth_asym_id
+struct_site.pdbx_auth_comp_id
+struct_site.pdbx_auth_seq_id
+struct_site.pdbx_auth_ins_code
+struct_site.pdbx_num_residues
+struct_site.details
+
+struct_site_gen.id
+struct_site_gen.site_id
+struct_site_gen.pdbx_num_res
+struct_site_gen.label_comp_id
+struct_site_gen.label_asym_id
+struct_site_gen.label_seq_id
+struct_site_gen.pdbx_auth_ins_code
+struct_site_gen.auth_comp_id
+struct_site_gen.auth_asym_id
+struct_site_gen.auth_seq_id
+struct_site_gen.label_atom_id
+struct_site_gen.label_alt_id
+struct_site_gen.symmetry
+struct_site_gen.details
+
+symmetry.entry_id
+symmetry.space_group_name_H-M
+symmetry.pdbx_full_space_group_name_H
+symmetry.cell_setting
+symmetry.Int_Tables_number
+symmetry.space_group_name_Hall
+
+pdbx_molecule.instance_id
+pdbx_molecule.prd_id
+pdbx_molecule.asym_id
+
+pdbx_molecule_features.prd_id
+pdbx_molecule_features.name
+pdbx_molecule_features.type
+pdbx_molecule_features.class
+pdbx_molecule_features.details
+
+pdbx_reference_entity_link.prd_id
+pdbx_reference_entity_link.link_id
+pdbx_reference_entity_link.link_class
+pdbx_reference_entity_link.ref_entity_id_1
+pdbx_reference_entity_link.entity_seq_num_1
+pdbx_reference_entity_link.comp_id_1
+pdbx_reference_entity_link.atom_id_1
+pdbx_reference_entity_link.ref_entity_id_2
+pdbx_reference_entity_link.entity_seq_num_2
+pdbx_reference_entity_link.comp_id_2
+pdbx_reference_entity_link.atom_id_2
+pdbx_reference_entity_link.value_order
+pdbx_reference_entity_link.component_1
+pdbx_reference_entity_link.component_2
+pdbx_reference_entity_link.details
+
+pdbx_reference_entity_list.prd_id
+pdbx_reference_entity_list.ref_entity_id
+pdbx_reference_entity_list.component_id
+pdbx_reference_entity_list.type
+pdbx_reference_entity_list.details
+
+pdbx_reference_entity_poly_link.prd_id
+pdbx_reference_entity_poly_link.ref_entity_id
+pdbx_reference_entity_poly_link.link_id
+pdbx_reference_entity_poly_link.atom_id_1
+pdbx_reference_entity_poly_link.comp_id_1
+pdbx_reference_entity_poly_link.entity_seq_num_1
+pdbx_reference_entity_poly_link.atom_id_2
+pdbx_reference_entity_poly_link.comp_id_2
+pdbx_reference_entity_poly_link.entity_seq_num_2
+pdbx_reference_entity_poly_link.value_order
+pdbx_reference_entity_poly_link.component_id
+
+pdbx_struct_assembly.id
+pdbx_struct_assembly.details
+pdbx_struct_assembly.method_details
+pdbx_struct_assembly.oligomeric_details
+pdbx_struct_assembly.oligomeric_count
+
+pdbx_struct_assembly_gen.assembly_id
+pdbx_struct_assembly_gen.oper_expression
+pdbx_struct_assembly_gen.asym_id_list
+
+pdbx_struct_oper_list.id
+pdbx_struct_oper_list.type
+pdbx_struct_oper_list.name
+pdbx_struct_oper_list.symmetry_operation
+pdbx_struct_oper_list.matrix
+pdbx_struct_oper_list.vector
+
+pdbx_struct_mod_residue.id
+pdbx_struct_mod_residue.label_asym_id
+pdbx_struct_mod_residue.label_seq_id
+pdbx_struct_mod_residue.label_comp_id
+pdbx_struct_mod_residue.auth_asym_id
+pdbx_struct_mod_residue.auth_seq_id
+pdbx_struct_mod_residue.auth_comp_id
+pdbx_struct_mod_residue.PDB_ins_code
+pdbx_struct_mod_residue.parent_comp_id
+pdbx_struct_mod_residue.details
+
+ihm_struct_assembly.ordinal_id
+ihm_struct_assembly.assembly_id
+ihm_struct_assembly.parent_assembly_id
+ihm_struct_assembly.entity_description
+ihm_struct_assembly.entity_id
+ihm_struct_assembly.asym_id
+ihm_struct_assembly.seq_id_begin
+ihm_struct_assembly.seq_id_end
+
+ihm_struct_assembly_details.assembly_id
+ihm_struct_assembly_details.assembly_name
+ihm_struct_assembly_details.assembly_description
+
+ihm_model_representation.ordinal_id
+ihm_model_representation.representation_id
+ihm_model_representation.segment_id
+ihm_model_representation.entity_id
+ihm_model_representation.entity_description
+ihm_model_representation.entity_asym_id
+ihm_model_representation.seq_id_begin
+ihm_model_representation.seq_id_end
+ihm_model_representation.model_object_primitive
+ihm_model_representation.starting_model_id
+ihm_model_representation.model_mode
+ihm_model_representation.model_granularity
+ihm_model_representation.model_object_count
+
+ihm_external_reference_info.reference_id
+ihm_external_reference_info.reference_provider
+ihm_external_reference_info.reference_type
+ihm_external_reference_info.reference
+ihm_external_reference_info.refers_to
+ihm_external_reference_info.associated_url
+
+ihm_external_files.id
+ihm_external_files.reference_id
+ihm_external_files.file_path
+ihm_external_files.content_type
+ihm_external_files.file_size_bytes
+ihm_external_files.details
+
+ihm_dataset_list.id
+ihm_dataset_list.data_type
+ihm_dataset_list.database_hosted
+
+ihm_dataset_group.ordinal_id
+ihm_dataset_group.group_id
+ihm_dataset_group.dataset_list_id
+
+ihm_dataset_external_reference.id
+ihm_dataset_external_reference.dataset_list_id
+ihm_dataset_external_reference.file_id
+
+ihm_dataset_related_db_reference.id
+ihm_dataset_related_db_reference.dataset_list_id
+ihm_dataset_related_db_reference.db_name
+ihm_dataset_related_db_reference.accession_code
+ihm_dataset_related_db_reference.version
+ihm_dataset_related_db_reference.details
+
+ihm_related_datasets.ordinal_id
+ihm_related_datasets.dataset_list_id_derived
+ihm_related_datasets.dataset_list_id_primary
+
+ihm_poly_residue_feature.ordinal_id
+ihm_poly_residue_feature.feature_id
+ihm_poly_residue_feature.entity_id
+ihm_poly_residue_feature.asym_id
+ihm_poly_residue_feature.seq_id_begin
+ihm_poly_residue_feature.comp_id_begin
+ihm_poly_residue_feature.seq_id_end
+ihm_poly_residue_feature.comp_id_end
+
+ihm_feature_list.feature_id
+ihm_feature_list.feature_type
+ihm_feature_list.entity_type
+
+ihm_cross_link_list.id
+ihm_cross_link_list.group_id
+ihm_cross_link_list.entity_description_1
+ihm_cross_link_list.entity_id_1
+ihm_cross_link_list.seq_id_1
+ihm_cross_link_list.comp_id_1
+ihm_cross_link_list.entity_description_2
+ihm_cross_link_list.entity_id_2
+ihm_cross_link_list.seq_id_2
+ihm_cross_link_list.comp_id_2
+ihm_cross_link_list.linker_type
+ihm_cross_link_list.dataset_list_id
+
+ihm_cross_link_restraint.id
+ihm_cross_link_restraint.group_id
+ihm_cross_link_restraint.entity_id_1
+ihm_cross_link_restraint.asym_id_1
+ihm_cross_link_restraint.seq_id_1
+ihm_cross_link_restraint.comp_id_1
+ihm_cross_link_restraint.entity_id_2
+ihm_cross_link_restraint.asym_id_2
+ihm_cross_link_restraint.seq_id_2
+ihm_cross_link_restraint.comp_id_2
+ihm_cross_link_restraint.restraint_type
+ihm_cross_link_restraint.conditional_crosslink_flag
+ihm_cross_link_restraint.model_granularity
+ihm_cross_link_restraint.distance_threshold
+ihm_cross_link_restraint.psi
+ihm_cross_link_restraint.sigma_1
+ihm_cross_link_restraint.sigma_2
+
+ihm_cross_link_result_parameters.ordinal_id
+ihm_cross_link_result_parameters.restraint_id
+ihm_cross_link_result_parameters.model_id
+ihm_cross_link_result_parameters.psi
+ihm_cross_link_result_parameters.sigma_1
+ihm_cross_link_result_parameters.sigma_2
+
+ihm_sas_restraint.ordinal_id
+ihm_sas_restraint.dataset_list_id
+ihm_sas_restraint.model_id
+ihm_sas_restraint.struct_assembly_id
+ihm_sas_restraint.profile_segment_flag
+ihm_sas_restraint.fitting_atom_type
+ihm_sas_restraint.fitting_method
+ihm_sas_restraint.fitting_state
+ihm_sas_restraint.radius_of_gyration
+ihm_sas_restraint.chi_value
+ihm_sas_restraint.details
+
+ihm_derived_distance_restraint.id
+ihm_derived_distance_restraint.group_id
+ihm_derived_distance_restraint.feature_id_1
+ihm_derived_distance_restraint.feature_id_2
+ihm_derived_distance_restraint.group_conditionality
+ihm_derived_distance_restraint.restraint_type
+ihm_derived_distance_restraint.distance_upper_limit
+ihm_derived_distance_restraint.random_exclusion_fraction
+ihm_derived_distance_restraint.dataset_list_id
+
+ihm_2dem_class_average_restraint.id
+ihm_2dem_class_average_restraint.dataset_list_id
+ihm_2dem_class_average_restraint.number_raw_micrographs
+ihm_2dem_class_average_restraint.pixel_size_width
+ihm_2dem_class_average_restraint.pixel_size_height
+ihm_2dem_class_average_restraint.image_resolution
+ihm_2dem_class_average_restraint.image_segment_flag
+ihm_2dem_class_average_restraint.number_of_projections
+ihm_2dem_class_average_restraint.struct_assembly_id
+ihm_2dem_class_average_restraint.details
+
+ihm_2dem_class_average_fitting.ordinal_id
+ihm_2dem_class_average_fitting.restraint_id
+ihm_2dem_class_average_fitting.model_id
+ihm_2dem_class_average_fitting.cross_correlation_coefficient
+ihm_2dem_class_average_fitting.rot_matrix
+ihm_2dem_class_average_fitting.tr_vector
+
+ihm_3dem_restraint.ordinal_id
+ihm_3dem_restraint.dataset_list_id
+ihm_3dem_restraint.fitting_method
+ihm_3dem_restraint.struct_assembly_id
+ihm_3dem_restraint.number_of_gaussians
+ihm_3dem_restraint.model_id
+ihm_3dem_restraint.cross_correlation_coefficient
+
+ihm_predicted_contact_restraint.id
+ihm_predicted_contact_restraint.entity_id_1
+ihm_predicted_contact_restraint.asym_id_1
+ihm_predicted_contact_restraint.seq_id_1
+ihm_predicted_contact_restraint.comp_id_1
+ihm_predicted_contact_restraint.atom_id_1
+ihm_predicted_contact_restraint.entity_id_2
+ihm_predicted_contact_restraint.asym_id_2
+ihm_predicted_contact_restraint.seq_id_2
+ihm_predicted_contact_restraint.comp_id_2
+ihm_predicted_contact_restraint.atom_id_2
+ihm_predicted_contact_restraint.restraint_type
+ihm_predicted_contact_restraint.distance_upper_limit
+ihm_predicted_contact_restraint.probability
+ihm_predicted_contact_restraint.model_granularity
+ihm_predicted_contact_restraint.dataset_list_id
+ihm_predicted_contact_restraint.software_id
+
+ihm_starting_model_details.starting_model_id
+ihm_starting_model_details.entity_id
+ihm_starting_model_details.entity_description
+ihm_starting_model_details.asym_id
+ihm_starting_model_details.seq_id_begin
+ihm_starting_model_details.seq_id_end
+ihm_starting_model_details.starting_model_source
+ihm_starting_model_details.starting_model_auth_asym_id
+ihm_starting_model_details.starting_model_sequence_offset
+ihm_starting_model_details.dataset_list_id
+
+ihm_starting_comparative_models.ordinal_id
+ihm_starting_comparative_models.starting_model_id
+ihm_starting_comparative_models.starting_model_auth_asym_id
+ihm_starting_comparative_models.starting_model_seq_id_begin
+ihm_starting_comparative_models.starting_model_seq_id_end
+ihm_starting_comparative_models.template_auth_asym_id
+ihm_starting_comparative_models.template_seq_id_begin
+ihm_starting_comparative_models.template_seq_id_end
+ihm_starting_comparative_models.template_sequence_identity
+ihm_starting_comparative_models.template_sequence_identity_denominator
+ihm_starting_comparative_models.template_dataset_list_id
+ihm_starting_comparative_models.alignment_file_id
+
+ihm_starting_model_coord.starting_model_id
+ihm_starting_model_coord.group_PDB
+ihm_starting_model_coord.id
+ihm_starting_model_coord.type_symbol
+ihm_starting_model_coord.atom_id
+ihm_starting_model_coord.comp_id
+ihm_starting_model_coord.entity_id
+ihm_starting_model_coord.asym_id
+ihm_starting_model_coord.seq_id
+ihm_starting_model_coord.Cartn_x
+ihm_starting_model_coord.Cartn_y
+ihm_starting_model_coord.Cartn_z
+ihm_starting_model_coord.B_iso_or_equiv
+ihm_starting_model_coord.ordinal_id
+
+ihm_starting_model_seq_dif.ordinal_id
+ihm_starting_model_seq_dif.entity_id
+ihm_starting_model_seq_dif.asym_id
+ihm_starting_model_seq_dif.seq_id
+ihm_starting_model_seq_dif.comp_id
+ihm_starting_model_seq_dif.starting_model_id
+ihm_starting_model_seq_dif.db_asym_id
+ihm_starting_model_seq_dif.db_seq_id
+ihm_starting_model_seq_dif.db_comp_id
+ihm_starting_model_seq_dif.details
+
+ihm_modeling_protocol.ordinal_id
+ihm_modeling_protocol.protocol_id
+ihm_modeling_protocol.step_id
+ihm_modeling_protocol.struct_assembly_id
+ihm_modeling_protocol.dataset_group_id
+ihm_modeling_protocol.struct_assembly_description
+ihm_modeling_protocol.protocol_name
+ihm_modeling_protocol.step_name
+ihm_modeling_protocol.step_method
+ihm_modeling_protocol.num_models_begin
+ihm_modeling_protocol.num_models_end
+ihm_modeling_protocol.multi_scale_flag
+ihm_modeling_protocol.multi_state_flag
+ihm_modeling_protocol.ordered_flag
+
+ihm_modeling_post_process.id
+ihm_modeling_post_process.protocol_id
+ihm_modeling_post_process.analysis_id
+ihm_modeling_post_process.step_id
+ihm_modeling_post_process.type
+ihm_modeling_post_process.feature
+ihm_modeling_post_process.num_models_begin
+ihm_modeling_post_process.num_models_end
+
+ihm_ensemble_info.ensemble_id
+ihm_ensemble_info.ensemble_name
+ihm_ensemble_info.post_process_id
+ihm_ensemble_info.model_group_id
+ihm_ensemble_info.ensemble_clustering_method
+ihm_ensemble_info.ensemble_clustering_feature
+ihm_ensemble_info.num_ensemble_models
+ihm_ensemble_info.num_ensemble_models_deposited
+ihm_ensemble_info.ensemble_precision_value
+ihm_ensemble_info.ensemble_file_id
+
+ihm_localization_density_files.id
+ihm_localization_density_files.file_id
+ihm_localization_density_files.ensemble_id
+ihm_localization_density_files.entity_id
+ihm_localization_density_files.asym_id
+ihm_localization_density_files.seq_id_begin
+ihm_localization_density_files.seq_id_end
+
+ihm_model_list.ordinal_id
+ihm_model_list.model_id
+ihm_model_list.model_group_id
+ihm_model_list.model_name
+ihm_model_list.model_group_name
+ihm_model_list.assembly_id
+ihm_model_list.protocol_id
+ihm_model_list.representation_id
+
+ihm_model_representative.id
+ihm_model_representative.model_group_id
+ihm_model_representative.model_id
+ihm_model_representative.selection_criteria
+
+ihm_sphere_obj_site.ordinal_id
+ihm_sphere_obj_site.entity_id
+ihm_sphere_obj_site.seq_id_begin
+ihm_sphere_obj_site.seq_id_end
+ihm_sphere_obj_site.asym_id
+ihm_sphere_obj_site.Cartn_x
+ihm_sphere_obj_site.Cartn_y
+ihm_sphere_obj_site.Cartn_z
+ihm_sphere_obj_site.object_radius
+ihm_sphere_obj_site.rmsf
+ihm_sphere_obj_site.model_id
+
+ihm_gaussian_obj_site.ordinal_id
+ihm_gaussian_obj_site.entity_id
+ihm_gaussian_obj_site.seq_id_begin
+ihm_gaussian_obj_site.seq_id_end
+ihm_gaussian_obj_site.asym_id
+ihm_gaussian_obj_site.mean_Cartn_x
+ihm_gaussian_obj_site.mean_Cartn_y
+ihm_gaussian_obj_site.mean_Cartn_z
+ihm_gaussian_obj_site.weight
+ihm_gaussian_obj_site.covariance_matrix
+ihm_gaussian_obj_site.model_id
+
+ihm_gaussian_obj_ensemble.ordinal_id
+ihm_gaussian_obj_ensemble.entity_id
+ihm_gaussian_obj_ensemble.seq_id_begin
+ihm_gaussian_obj_ensemble.seq_id_end
+ihm_gaussian_obj_ensemble.asym_id
+ihm_gaussian_obj_ensemble.mean_Cartn_x
+ihm_gaussian_obj_ensemble.mean_Cartn_y
+ihm_gaussian_obj_ensemble.mean_Cartn_z
+ihm_gaussian_obj_ensemble.weight
+ihm_gaussian_obj_ensemble.covariance_matrix
+ihm_gaussian_obj_ensemble.ensemble_id
+
+ihm_multi_state_modeling.ordinal_id
+ihm_multi_state_modeling.state_id
+ihm_multi_state_modeling.state_group_id
+ihm_multi_state_modeling.population_fraction
+ihm_multi_state_modeling.state_type
+ihm_multi_state_modeling.state_name
+ihm_multi_state_modeling.model_group_id
+ihm_multi_state_modeling.experiment_type
+ihm_multi_state_modeling.details

data/mmcif-popular-field-names.csv

@@ -1,255 +0,0 @@
-atom_site.group_PDB
-atom_site.id
-atom_site.type_symbol
-atom_site.label_atom_id
-atom_site.label_alt_id
-atom_site.label_comp_id
-atom_site.label_asym_id
-atom_site.label_entity_id
-atom_site.label_seq_id
-atom_site.pdbx_PDB_ins_code
-atom_site.pdbx_formal_charge
-atom_site.Cartn_x
-atom_site.Cartn_y
-atom_site.Cartn_z
-atom_site.occupancy
-atom_site.B_iso_or_equiv
-atom_site.auth_atom_id
-atom_site.auth_comp_id
-atom_site.auth_asym_id
-atom_site.auth_seq_id
-atom_site.pdbx_PDB_model_num
-
-chem_comp.id
-chem_comp.type
-chem_comp.mon_nstd_flag
-chem_comp.name
-chem_comp.pdbx_synonyms
-chem_comp.formula
-chem_comp.formula_weight
-
-chem_comp_bond.comp_id
-chem_comp_bond.pdbx_stereo_config
-chem_comp_bond.pdbx_ordinal
-chem_comp_bond.pdbx_aromatic_flag
-chem_comp_bond.atom_id_1
-chem_comp_bond.atom_id_2
-chem_comp_bond.value_order
-
-cell.entry_id
-cell.length_a
-cell.length_b
-cell.length_c
-cell.angle_alpha
-cell.angle_beta
-cell.angle_gamma
-cell.Z_PDB
-cell.pdbx_unique_axis
-
-entity.id
-entity.type
-entity.src_method
-entity.pdbx_description
-entity.formula_weight
-entity.pdbx_number_of_molecules
-entity.details
-entity.pdbx_mutation
-entity.pdbx_fragment
-entity.pdbx_ec
-
-entry.id
-
-exptl.entry_id
-exptl.method
-
-struct.entry_id
-struct.title
-
-struct_asym.id
-struct_asym.pdbx_blank_PDB_chainid_flag
-struct_asym.pdbx_modified
-struct_asym.entity_id
-struct_asym.details
-
-struct_conf.conf_type_id
-struct_conf.id
-struct_conf.pdbx_PDB_helix_id
-struct_conf.beg_label_comp_id
-struct_conf.beg_label_asym_id
-struct_conf.beg_label_seq_id
-struct_conf.pdbx_beg_PDB_ins_code
-struct_conf.end_label_comp_id
-struct_conf.end_label_asym_id
-struct_conf.end_label_seq_id
-struct_conf.pdbx_end_PDB_ins_code
-struct_conf.beg_auth_comp_id
-struct_conf.beg_auth_asym_id
-struct_conf.beg_auth_seq_id
-struct_conf.end_auth_comp_id
-struct_conf.end_auth_asym_id
-struct_conf.end_auth_seq_id
-struct_conf.pdbx_PDB_helix_class
-struct_conf.details
-struct_conf.pdbx_PDB_helix_length
-
-struct_conn.id
-struct_conn.conn_type_id
-struct_conn.pdbx_PDB_id
-struct_conn.ptnr1_label_asym_id
-struct_conn.ptnr1_label_comp_id
-struct_conn.ptnr1_label_seq_id
-struct_conn.ptnr1_label_atom_id
-struct_conn.pdbx_ptnr1_label_alt_id
-struct_conn.pdbx_ptnr1_PDB_ins_code
-struct_conn.pdbx_ptnr1_standard_comp_id
-struct_conn.ptnr1_symmetry
-struct_conn.ptnr2_label_asym_id
-struct_conn.ptnr2_label_comp_id
-struct_conn.ptnr2_label_seq_id
-struct_conn.ptnr2_label_atom_id
-struct_conn.pdbx_ptnr2_label_alt_id
-struct_conn.pdbx_ptnr2_PDB_ins_code
-struct_conn.ptnr1_auth_asym_id
-struct_conn.ptnr1_auth_comp_id
-struct_conn.ptnr1_auth_seq_id
-struct_conn.ptnr2_auth_asym_id
-struct_conn.ptnr2_auth_comp_id
-struct_conn.ptnr2_auth_seq_id
-struct_conn.ptnr2_symmetry
-struct_conn.pdbx_ptnr3_label_atom_id
-struct_conn.pdbx_ptnr3_label_seq_id
-struct_conn.pdbx_ptnr3_label_comp_id
-struct_conn.pdbx_ptnr3_label_asym_id
-struct_conn.pdbx_ptnr3_label_alt_id
-struct_conn.pdbx_ptnr3_PDB_ins_code
-struct_conn.details
-struct_conn.pdbx_dist_value
-struct_conn.pdbx_value_order
-
-struct_conn_type.id
-struct_conn_type.criteria
-struct_conn_type.reference
-
-struct_keywords.entry_id
-struct_keywords.pdbx_keywords
-struct_keywords.text
-
-struct_sheet_range.sheet_id
-struct_sheet_range.id
-struct_sheet_range.beg_label_comp_id
-struct_sheet_range.beg_label_asym_id
-struct_sheet_range.beg_label_seq_id
-struct_sheet_range.pdbx_beg_PDB_ins_code
-struct_sheet_range.end_label_comp_id
-struct_sheet_range.end_label_asym_id
-struct_sheet_range.end_label_seq_id
-struct_sheet_range.pdbx_end_PDB_ins_code
-struct_sheet_range.beg_auth_comp_id
-struct_sheet_range.beg_auth_asym_id
-struct_sheet_range.beg_auth_seq_id
-struct_sheet_range.end_auth_comp_id
-struct_sheet_range.end_auth_asym_id
-struct_sheet_range.end_auth_seq_id
-
-struct_site.id
-struct_site.pdbx_evidence_code
-struct_site.pdbx_auth_asym_id
-struct_site.pdbx_auth_comp_id
-struct_site.pdbx_auth_seq_id
-struct_site.pdbx_auth_ins_code
-struct_site.pdbx_num_residues
-struct_site.details
-
-struct_site_gen.id
-struct_site_gen.site_id
-struct_site_gen.pdbx_num_res
-struct_site_gen.label_comp_id
-struct_site_gen.label_asym_id
-struct_site_gen.label_seq_id
-struct_site_gen.pdbx_auth_ins_code
-struct_site_gen.auth_comp_id
-struct_site_gen.auth_asym_id
-struct_site_gen.auth_seq_id
-struct_site_gen.label_atom_id
-struct_site_gen.label_alt_id
-struct_site_gen.symmetry
-struct_site_gen.details
-
-symmetry.entry_id
-symmetry.space_group_name_H-M
-symmetry.pdbx_full_space_group_name_H
-symmetry.cell_setting
-symmetry.Int_Tables_number
-symmetry.space_group_name_Hall
-
-pdbx_molecule.instance_id
-pdbx_molecule.prd_id
-pdbx_molecule.asym_id
-
-pdbx_molecule_features.prd_id
-pdbx_molecule_features.name
-pdbx_molecule_features.type
-pdbx_molecule_features.class
-pdbx_molecule_features.details
-
-pdbx_reference_entity_link.prd_id
-pdbx_reference_entity_link.link_id
-pdbx_reference_entity_link.link_class
-pdbx_reference_entity_link.ref_entity_id_1
-pdbx_reference_entity_link.entity_seq_num_1
-pdbx_reference_entity_link.comp_id_1
-pdbx_reference_entity_link.atom_id_1
-pdbx_reference_entity_link.ref_entity_id_2
-pdbx_reference_entity_link.entity_seq_num_2
-pdbx_reference_entity_link.comp_id_2
-pdbx_reference_entity_link.atom_id_2
-pdbx_reference_entity_link.value_order
-pdbx_reference_entity_link.component_1
-pdbx_reference_entity_link.component_2
-pdbx_reference_entity_link.details
-
-pdbx_reference_entity_list.prd_id
-pdbx_reference_entity_list.ref_entity_id
-pdbx_reference_entity_list.component_id
-pdbx_reference_entity_list.type
-pdbx_reference_entity_list.details
-
-pdbx_reference_entity_poly_link.prd_id
-pdbx_reference_entity_poly_link.ref_entity_id
-pdbx_reference_entity_poly_link.link_id
-pdbx_reference_entity_poly_link.atom_id_1
-pdbx_reference_entity_poly_link.comp_id_1
-pdbx_reference_entity_poly_link.entity_seq_num_1
-pdbx_reference_entity_poly_link.atom_id_2
-pdbx_reference_entity_poly_link.comp_id_2
-pdbx_reference_entity_poly_link.entity_seq_num_2
-pdbx_reference_entity_poly_link.value_order
-pdbx_reference_entity_poly_link.component_id
-
-pdbx_struct_assembly.id
-pdbx_struct_assembly.details
-pdbx_struct_assembly.method_details
-pdbx_struct_assembly.oligomeric_details
-pdbx_struct_assembly.oligomeric_count
-
-pdbx_struct_assembly_gen.assembly_id
-pdbx_struct_assembly_gen.oper_expression
-pdbx_struct_assembly_gen.asym_id_list
-
-pdbx_struct_oper_list.id
-pdbx_struct_oper_list.type
-pdbx_struct_oper_list.name
-pdbx_struct_oper_list.symmetry_operation
-pdbx_struct_oper_list.matrix
-pdbx_struct_oper_list.vector
-
-pdbx_struct_mod_residue.id
-pdbx_struct_mod_residue.label_asym_id
-pdbx_struct_mod_residue.label_seq_id
-pdbx_struct_mod_residue.label_comp_id
-pdbx_struct_mod_residue.auth_asym_id
-pdbx_struct_mod_residue.auth_seq_id
-pdbx_struct_mod_residue.auth_comp_id
-pdbx_struct_mod_residue.PDB_ins_code
-pdbx_struct_mod_residue.parent_comp_id
-pdbx_struct_mod_residue.details

src/apps/schema-generator/generate-typescript.ts

@@ -11,7 +11,7 @@ import { generate } from './util/generate'
 
 function generateSchema (name: string, path: string) {
     const str = fs.readFileSync(path, 'utf8')
-    return generate(name, JSON.parse(str))
+    return generate(name, '', JSON.parse(str))
 }
 
 const parser = new argparse.ArgumentParser({

src/apps/schema-generator/schema-from-mmcif-dic.ts

@@ -10,34 +10,30 @@ import * as fs from 'fs'
 import fetch from 'node-fetch'
 
 import Csv from 'mol-io/reader/csv/parser'
-import CIF from 'mol-io/reader/cif'
+import CIF, { Frame } from 'mol-io/reader/cif'
 import { generateSchema } from './util/cif-dic'
 import { generate } from './util/generate'
-import { Filter, mergeFilters } from './util/json-schema'
-import { Run } from 'mol-task';
+import { Filter } from './util/json-schema'
+import { Run } from 'mol-task'
 
-async function runGenerateSchema(name: string, fieldNamesPath?: string, minCount = 0, typescript = false, out?: string) {
+async function runGenerateSchema(name: string, fieldNamesPath?: string, typescript = false, out?: string) {
     await ensureMmcifDicAvailable()
-    const comp = CIF.parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8'))
-    const parsed = await Run(comp);
-    if (parsed.isError) throw parsed
+    const mmcifDic = await Run(CIF.parseText(fs.readFileSync(MMCIF_DIC_PATH, 'utf8')));
+    if (mmcifDic.isError) throw mmcifDic
 
-    // console.log(fieldNamesPath, minCount)
+    await ensureIhmDicAvailable()
+    const ihmDic = await Run(CIF.parseText(fs.readFileSync(IHM_DIC_PATH, 'utf8')));
+    if (ihmDic.isError) throw ihmDic
 
-    let filter: Filter | undefined
-    if (minCount && fieldNamesPath) {
-        filter = mergeFilters(
-            await getUsageCountsFilter(minCount),
-            await getFieldNamesFilter(fieldNamesPath)
-        )
-    } else if (minCount) {
-        filter = await getUsageCountsFilter(minCount)
-    } else if (fieldNamesPath) {
-        filter = await getFieldNamesFilter(fieldNamesPath)
-    }
+    const mmcifDicVersion = CIF.schema.dic(mmcifDic.result.blocks[0]).dictionary.version.value(0)
+    const ihmDicVersion = CIF.schema.dic(ihmDic.result.blocks[0]).dictionary.version.value(0)
+    const version = `Dictionary versions: mmCIF ${mmcifDicVersion}, IHM ${ihmDicVersion}.`
 
-    const schema = generateSchema(parsed.result.blocks[0])
-    const output = typescript ? generate(name, schema, filter) : JSON.stringify(schema, undefined, 4)
+    const frames: Frame[] = [...mmcifDic.result.blocks[0].saveFrames, ...ihmDic.result.blocks[0].saveFrames]
+    const schema = generateSchema(frames)
+
+    const filter = fieldNamesPath ? await getFieldNamesFilter(fieldNamesPath) : undefined
+    const output = typescript ? generate(name, version, schema, filter) : JSON.stringify(schema, undefined, 4)
 
     if (out) {
         fs.writeFileSync(out, output)
@@ -67,44 +63,31 @@ async function getFieldNamesFilter(fieldNamesPath: string): Promise<Filter> {
     return filter
 }
 
-async function getUsageCountsFilter(minCount: number): Promise<Filter> {
-    const usageCountsStr = fs.readFileSync(MMCIF_USAGE_COUNTS_PATH, 'utf8')
-    const parsed = await Run(Csv(usageCountsStr, { delimiter: ' ' }));
-    if (parsed.isError) throw parser.error
-    const csvFile = parsed.result;
-
-    const fieldNamesCol = csvFile.table.getColumn('field_name')
-    const usageCountsCol = csvFile.table.getColumn('usage_count')
-    if (!fieldNamesCol || !usageCountsCol) throw 'error getting usage columns'
-    const fieldNames = fieldNamesCol.toStringArray()
-    const usageCounts = usageCountsCol.toIntArray()
-
-    const filter: Filter = {}
-    fieldNames.forEach((name, i) => {
-        if (usageCounts[i] < minCount) return
-        const [ category, field ] = name.substr(1).split('.')
-        if (!filter[ category ]) filter[ category ] = {}
-        filter[ category ][ field ] = true
-    })
-    return filter
+async function ensureMmcifDicAvailable() {
+    await ensureDicAvailable(MMCIF_DIC_PATH, MMCIF_DIC_URL)
 }
 
-async function ensureMmcifDicAvailable() {
-    if (FORCE_MMCIF_DOWNLOAD || !fs.existsSync(MMCIF_DIC_PATH)) {
+async function ensureIhmDicAvailable() {
+    await ensureDicAvailable(IHM_DIC_PATH, IHM_DIC_URL)
+}
+
+async function ensureDicAvailable(dicPath: string, dicUrl: string) {
+    if (FORCE_DIC_DOWNLOAD || !fs.existsSync(dicPath)) {
         console.log('downloading mmcif dic...')
-        const data = await fetch(MMCIF_DIC_URL)
-        if (!fs.existsSync(MMCIF_DIC_DIR)) {
-            fs.mkdirSync(MMCIF_DIC_DIR);
+        const data = await fetch(dicUrl)
+        if (!fs.existsSync(DIC_DIR)) {
+            fs.mkdirSync(DIC_DIR);
         }
-        fs.writeFileSync(MMCIF_DIC_PATH, await data.text())
+        fs.writeFileSync(dicPath, await data.text())
         console.log('done downloading mmcif dic')
     }
 }
 
-const MMCIF_USAGE_COUNTS_PATH = './data/mmcif-usage-counts.txt'
-const MMCIF_DIC_DIR = './build/dics'
-const MMCIF_DIC_PATH = `${MMCIF_DIC_DIR}/mmcif_pdbx_v50.dic`
+const DIC_DIR = './build/dics'
+const MMCIF_DIC_PATH = `${DIC_DIR}/mmcif_pdbx_v50.dic`
 const MMCIF_DIC_URL = 'http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic'
+const IHM_DIC_PATH = `${DIC_DIR}/ihm-extension.dic`
+const IHM_DIC_URL = 'https://raw.githubusercontent.com/ihmwg/IHM-dictionary/master/ihm-extension.dic'
 
 const parser = new argparse.ArgumentParser({
   addHelp: true,
@@ -121,31 +104,25 @@ parser.addArgument([ '--typescript', '-ts' ], {
     action: 'storeTrue',
     help: 'Output schema as TypeScript instead of as JSON'
 });
-parser.addArgument([ '--minFieldUsageCount', '-mc' ], {
-    defaultValue: 0,
-    type: parseInt,
-    help: 'Minimum mmcif field usage counts'
-});
 parser.addArgument([ '--fieldNamesPath', '-fn' ], {
     defaultValue: '',
     help: 'Field names to include'
 });
-parser.addArgument([ '--forceMmcifDicDownload', '-f' ], {
+parser.addArgument([ '--forceDicDownload', '-f' ], {
     action: 'storeTrue',
-    help: 'Force download of mmcif dictionary'
+    help: 'Force download of dictionaries'
 });
 interface Args {
     name: string
-    forceMmcifDicDownload: boolean
+    forceDicDownload: boolean
     fieldNamesPath: string
-    minFieldUsageCount: number
     typescript: boolean
     out: string
 }
 const args: Args = parser.parseArgs();
 
-const FORCE_MMCIF_DOWNLOAD = args.forceMmcifDicDownload
+const FORCE_DIC_DOWNLOAD = args.forceDicDownload
 
 if (args.name) {
-    runGenerateSchema(args.name, args.fieldNamesPath, args.minFieldUsageCount, args.typescript, args.out)
+    runGenerateSchema(args.name, args.fieldNamesPath, args.typescript, args.out)
 }

src/apps/schema-generator/util/cif-dic.ts

@@ -6,6 +6,7 @@
 
 import { Database, ValueColumn, ListColumn } from './json-schema'
 import * as Data from 'mol-io/reader/cif/data-model'
+import { Frame } from 'mol-io/reader/cif/data-model';
 
 export function getFieldType (type: string, values?: string[]): ValueColumn|ListColumn {
     switch (type) {
@@ -92,7 +93,12 @@ function getField ( category: string, field: string, d: Data.Frame, ctx: FrameDa
         return cat.getField(field)
     } else {
         if (d.header in links) {
-            return getField(category, field, categories[links[d.header]], ctx)
+            const linkName = links[d.header]
+            if (linkName in categories) {
+                return getField(category, field, categories[linkName], ctx)
+            } else {
+                console.log(`link '${linkName}' not found`)
+            }
         } else {
             // console.log(`no links found for '${d.header}'`)
         }
@@ -172,14 +178,14 @@ const SPACE_SEPARATED_LIST_FIELDS = [
     '_pdbx_soln_scatter.data_analysis_software_list', // SCTPL5 GNOM
 ];
 
-export function generateSchema (dic: Data.Block) {
+export function generateSchema (frames: Frame[]) {
     const schema: Database = {}
 
     const categories: FrameCategories = {}
     const links: FrameLinks = {}
     const ctx = { categories, links }
 
-    dic.saveFrames.forEach(d => {
+    frames.forEach(d => {
         if (d.header[0] !== '_') return
         categories[d.header] = d
         const item_linked = d.categories['item_linked']
@@ -201,6 +207,10 @@ export function generateSchema (dic: Data.Block) {
 
     Object.keys(categories).forEach(fullName => {
         const d = categories[fullName]
+        if (!d) {
+            console.log('foo', fullName)
+            return
+        }
         const categoryName = d.header.substring(1, d.header.indexOf('.'))
         const itemName = d.header.substring(d.header.indexOf('.') + 1)
         let fields

src/apps/schema-generator/util/generate.ts

@@ -7,11 +7,11 @@
 import { validate } from './validate'
 import { Database, getTypeAndArgs, Filter } from './json-schema'
 
-function header (name: string, importDatabasePath = 'mol-data/db') {
+function header (name: string, info: string, importDatabasePath = 'mol-data/db') {
     return `/**
  * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated '${name}' schema file
+ * Code-generated '${name}' schema file. ${info}
  *
  * @author mol-star package (src/apps/schema-generator/generate)
  */
@@ -39,7 +39,7 @@ export interface ${name}_Database extends Database<${name}_Schema> {}`
 
 const value: { [k: string]: (...args: any[]) => string } = {
     enum: function (type: string, values: string[]) {
-        return `Aliased<'${values.join(`' | '`)}'>(${type})`
+        return `Aliased<'${values.map(v => v.replace(/'/g, '\\\'')).join(`' | '`)}'>(${type})`
     },
     matrix: function (rows: number, cols: number) {
         return `Matrix(${rows}, ${cols})`
@@ -63,7 +63,7 @@ function safePropertyString(name: string) {
     return name.match(reSafePropertyName) ? name : `'${name}'`
 }
 
-export function generate (name: string, schema: Database, fields?: Filter, importDatabasePath?: string) {
+export function generate (name: string, info: string, schema: Database, fields?: Filter, importDatabasePath?: string) {
     const validationResult = validate(schema)
     if (validationResult !== true) {
         throw validationResult
@@ -92,5 +92,5 @@ export function generate (name: string, schema: Database, fields?: Filter, impor
     })
     codeLines.push('}')
 
-    return `${header(name, importDatabasePath)}\n\n${codeLines.join('\n')}\n${footer(name)}`
+    return `${header(name, info, importDatabasePath)}\n\n${codeLines.join('\n')}\n${footer(name)}`
 }

src/mol-io/reader/cif.ts

@@ -12,6 +12,7 @@ import { toDatabaseCollection, toDatabase } from './cif/schema'
 import { mmCIF_Schema, mmCIF_Database } from './cif/schema/mmcif'
 import { CCD_Schema, CCD_Database } from './cif/schema/ccd'
 import { BIRD_Schema, BIRD_Database } from './cif/schema/bird'
+import { dic_Schema, dic_Database } from './cif/schema/dic';
 
 export default {
     parse: (data: string|Uint8Array) => typeof data === 'string' ? parseText(data) : parseBinary(data),
@@ -22,7 +23,8 @@ export default {
     schema: {
         mmCIF: (frame: Frame) => toDatabase<mmCIF_Schema, mmCIF_Database>(mmCIF_Schema, frame),
         CCD: (frame: Frame) => toDatabase<CCD_Schema, CCD_Database>(CCD_Schema, frame),
-        BIRD: (frame: Frame) => toDatabase<BIRD_Schema, BIRD_Database>(BIRD_Schema, frame)
+        BIRD: (frame: Frame) => toDatabase<BIRD_Schema, BIRD_Database>(BIRD_Schema, frame),
+        dic: (frame: Frame) => toDatabase<dic_Schema, dic_Database>(dic_Schema, frame)
     }
 }
 

src/mol-io/reader/cif/schema/dic.ts

@@ -1,5 +1,5 @@
 /**
- * Copyright (c) 2017 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
  */
@@ -60,7 +60,7 @@ const item_units_conversion = {
 
 // TODO save frame dic schema
 
-export const CIFDictionary_Schema = {
+export const dic_Schema = {
     datablock,
     dictionary,
     dictionary_history,
@@ -71,5 +71,5 @@ export const CIFDictionary_Schema = {
     item_units_conversion
 }
 
-export type CIFDictionary_Schema = typeof CIFDictionary_Schema;
-export type CIFDictionary_Database = Database.Tables<CIFDictionary_Schema>
+export type dic_Schema = typeof dic_Schema;
+export interface dic_Database extends Database<dic_Schema> {}

src/mol-io/reader/cif/schema/mmcif.ts

@@ -1,7 +1,7 @@
 /**
  * Copyright (c) 2017-2018 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
- * Code-generated 'mmCIF' schema file
+ * Code-generated 'mmCIF' schema file. Dictionary versions: mmCIF 5.293, IHM 0.130.
  *
  * @author mol-star package (src/apps/schema-generator/generate)
  */
@@ -43,6 +43,7 @@ export const mmCIF_Schema = {
         pdbx_PDB_ins_code: str,
         pdbx_PDB_model_num: int,
         pdbx_formal_charge: int,
+        ihm_model_id: int,
     },
     cell: {
         angle_alpha: float,
@@ -302,6 +303,375 @@ export const mmCIF_Schema = {
         name: str,
         details: str,
     },
+    ihm_starting_model_details: {
+        starting_model_id: str,
+        entity_id: str,
+        entity_description: str,
+        asym_id: str,
+        seq_id_begin: int,
+        seq_id_end: int,
+        starting_model_source: Aliased<'comparative model' | 'experimental model' | 'integrative model' | 'other ab initio models'>(str),
+        starting_model_auth_asym_id: str,
+        starting_model_sequence_offset: int,
+        dataset_list_id: int,
+    },
+    ihm_starting_comparative_models: {
+        ordinal_id: int,
+        starting_model_id: str,
+        starting_model_auth_asym_id: str,
+        starting_model_seq_id_begin: int,
+        starting_model_seq_id_end: int,
+        template_auth_asym_id: str,
+        template_seq_id_begin: int,
+        template_seq_id_end: int,
+        template_sequence_identity: float,
+        template_sequence_identity_denominator: Aliased<'1' | '2' | '3' | '4' | '5'>(int),
+        template_dataset_list_id: int,
+        alignment_file_id: int,
+    },
+    ihm_starting_model_seq_dif: {
+        ordinal_id: int,
+        entity_id: str,
+        asym_id: str,
+        seq_id: int,
+        comp_id: str,
+        starting_model_id: str,
+        db_asym_id: str,
+        db_seq_id: int,
+        db_comp_id: str,
+        details: str,
+    },
+    ihm_model_representation: {
+        ordinal_id: int,
+        representation_id: int,
+        segment_id: int,
+        entity_id: str,
+        entity_description: str,
+        entity_asym_id: str,
+        seq_id_begin: int,
+        seq_id_end: int,
+        model_object_primitive: Aliased<'atomistic' | 'sphere' | 'gaussian' | 'other'>(str),
+        starting_model_id: str,
+        model_mode: Aliased<'rigid' | 'flexible'>(str),
+        model_granularity: Aliased<'by-atom' | 'by-residue' | 'multi-residue' | 'by-feature'>(str),
+        model_object_count: int,
+    },
+    ihm_struct_assembly: {
+        ordinal_id: int,
+        assembly_id: int,
+        parent_assembly_id: int,
+        entity_description: str,
+        entity_id: str,
+        asym_id: str,
+        seq_id_begin: int,
+        seq_id_end: int,
+    },
+    ihm_struct_assembly_details: {
+        assembly_id: int,
+        assembly_name: str,
+        assembly_description: str,
+    },
+    ihm_modeling_protocol: {
+        ordinal_id: int,
+        protocol_id: int,
+        step_id: int,
+        struct_assembly_id: int,
+        dataset_group_id: int,
+        struct_assembly_description: str,
+        protocol_name: str,
+        step_name: str,
+        step_method: str,
+        num_models_begin: int,
+        num_models_end: int,
+        multi_scale_flag: Aliased<'YES' | 'NO'>(str),
+        multi_state_flag: Aliased<'YES' | 'NO'>(str),
+        ordered_flag: Aliased<'YES' | 'NO'>(str),
+    },
+    ihm_multi_state_modeling: {
+        ordinal_id: int,
+        state_id: int,
+        state_group_id: int,
+        population_fraction: float,
+        state_type: str,
+        state_name: str,
+        model_group_id: int,
+        experiment_type: Aliased<'Fraction of bulk' | 'Single molecule'>(str),
+        details: str,
+    },
+    ihm_modeling_post_process: {
+        id: int,
+        protocol_id: int,
+        analysis_id: int,
+        step_id: int,
+        type: Aliased<'filter' | 'cluster' | 'rescore' | 'validation' | 'other' | 'none'>(str),
+        feature: Aliased<'energy/score' | 'RMSD' | 'dRMSD' | 'other' | 'none'>(str),
+        num_models_begin: int,
+        num_models_end: int,
+    },
+    ihm_ensemble_info: {
+        ensemble_id: int,
+        ensemble_name: str,
+        post_process_id: int,
+        model_group_id: int,
+        ensemble_clustering_method: Aliased<'Hierarchical' | 'Partitioning (k-means)' | 'Other'>(str),
+        ensemble_clustering_feature: Aliased<'RMSD' | 'dRMSD' | 'other'>(str),
+        num_ensemble_models: int,
+        num_ensemble_models_deposited: int,
+        ensemble_precision_value: float,
+        ensemble_file_id: int,
+    },
+    ihm_model_list: {
+        ordinal_id: int,
+        model_id: int,
+        model_group_id: int,
+        model_name: str,
+        model_group_name: str,
+        assembly_id: int,
+        protocol_id: int,
+        representation_id: int,
+    },
+    ihm_model_representative: {
+        id: int,
+        model_group_id: int,
+        model_id: int,
+        selection_criteria: Aliased<'medoid' | 'closest to the average' | 'lowest energy' | 'target function' | 'fewest violations' | 'minimized average structure' | 'best scoring model' | 'centroid' | 'other selction criteria'>(str),
+    },
+    ihm_dataset_list: {
+        id: int,
+        data_type: Aliased<'NMR data' | '3DEM volume' | '2DEM class average' | 'EM raw micrographs' | 'SAS data' | 'CX-MS data' | 'Mass Spectrometry data' | 'EPR data' | 'H/D exchange data' | 'Single molecule FRET data' | 'Experimental model' | 'Comparative model' | 'Integrative model' | 'De Novo model' | 'Predicted contacts' | 'Mutagenesis data' | 'DNA footprinting data' | 'Yeast two-hybrid screening data' | 'Other'>(str),
+        database_hosted: Aliased<'YES' | 'NO'>(str),
+    },
+    ihm_dataset_group: {
+        ordinal_id: int,
+        group_id: int,
+        dataset_list_id: int,
+    },
+    ihm_related_datasets: {
+        ordinal_id: int,
+        dataset_list_id_derived: int,
+        dataset_list_id_primary: int,
+    },
+    ihm_dataset_related_db_reference: {
+        id: int,
+        dataset_list_id: int,
+        db_name: Aliased<'PDB' | 'BMRB' | 'EMDB' | 'EMPIAR' | 'SASBDB' | 'PRIDE' | 'MODEL ARCHIVE' | 'MASSIVE' | 'BioGRID' | 'Other'>(str),
+        accession_code: str,
+        version: str,
+        details: str,
+    },
+    ihm_external_reference_info: {
+        reference_id: int,
+        reference_provider: str,
+        reference_type: Aliased<'DOI' | 'Supplementary Files'>(str),
+        reference: str,
+        refers_to: Aliased<'File' | 'Archive' | 'Publication' | 'Other'>(str),
+        associated_url: str,
+    },
+    ihm_external_files: {
+        id: int,
+        reference_id: int,
+        file_path: str,
+        content_type: Aliased<'Input data or restraints' | 'Modeling or post-processing output' | 'Modeling workflow or script' | 'Visualization script' | 'Other'>(str),
+        file_size_bytes: float,
+        details: str,
+    },
+    ihm_dataset_external_reference: {
+        id: int,
+        dataset_list_id: int,
+        file_id: int,
+    },
+    ihm_localization_density_files: {
+        id: int,
+        file_id: int,
+        ensemble_id: int,
+        entity_id: str,
+        seq_id_begin: int,
+        seq_id_end: int,
+        asym_id: str,
+    },
+    ihm_predicted_contact_restraint: {
+        id: int,
+        entity_id_1: str,
+        entity_id_2: str,
+        asym_id_1: str,
+        asym_id_2: str,
+        comp_id_1: str,
+        comp_id_2: str,
+        seq_id_1: int,
+        seq_id_2: int,
+        atom_id_1: str,
+        atom_id_2: str,
+        distance_upper_limit: float,
+        probability: float,
+        restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound'>(str),
+        model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
+        dataset_list_id: int,
+        software_id: int,
+    },
+    ihm_cross_link_list: {
+        id: int,
+        group_id: int,
+        entity_description_1: str,
+        entity_description_2: str,
+        entity_id_1: str,
+        entity_id_2: str,
+        comp_id_1: str,
+        comp_id_2: str,
+        seq_id_1: int,
+        seq_id_2: int,
+        linker_type: Aliased<'EDC' | 'DSS' | 'EGS' | 'BS3' | 'BS2G' | 'DST' | 'sulfo-SDA' | 'sulfo-SMCC' | 'Other'>(str),
+        dataset_list_id: int,
+    },
+    ihm_cross_link_restraint: {
+        id: int,
+        group_id: int,
+        entity_id_1: str,
+        entity_id_2: str,
+        asym_id_1: str,
+        asym_id_2: str,
+        comp_id_1: str,
+        comp_id_2: str,
+        seq_id_1: int,
+        seq_id_2: int,
+        restraint_type: Aliased<'harmonic' | 'upper bound' | 'lower bound'>(str),
+        conditional_crosslink_flag: Aliased<'ALL' | 'ANY'>(str),
+        model_granularity: Aliased<'by-residue' | 'by-feature' | 'by-atom'>(str),
+        distance_threshold: float,
+        psi: float,
+        sigma_1: float,
+        sigma_2: float,
+    },
+    ihm_cross_link_result_parameters: {
+        ordinal_id: int,
+        restraint_id: int,
+        model_id: int,
+        psi: float,
+        sigma_1: float,
+        sigma_2: float,
+    },
+    ihm_2dem_class_average_restraint: {
+        id: int,
+        dataset_list_id: int,
+        number_raw_micrographs: int,
+        pixel_size_width: float,
+        pixel_size_height: float,
+        image_resolution: float,
+        image_segment_flag: Aliased<'YES' | 'NO'>(str),
+        number_of_projections: int,
+        struct_assembly_id: int,
+        details: str,
+    },
+    ihm_2dem_class_average_fitting: {
+        ordinal_id: int,
+        restraint_id: int,
+        model_id: int,
+        cross_correlation_coefficient: float,
+        rot_matrix: Matrix(3, 3),
+        tr_vector: Vector(3),
+    },
+    ihm_3dem_restraint: {
+        ordinal_id: int,
+        dataset_list_id: int,
+        model_id: int,
+        struct_assembly_id: int,
+        fitting_method: str,
+        number_of_gaussians: int,
+        cross_correlation_coefficient: float,
+    },
+    ihm_sas_restraint: {
+        ordinal_id: int,
+        dataset_list_id: int,
+        model_id: int,
+        struct_assembly_id: int,
+        profile_segment_flag: Aliased<'YES' | 'NO'>(str),
+        fitting_atom_type: str,
+        fitting_method: str,
+        fitting_state: Aliased<'Single' | 'Multiple'>(str),
+        radius_of_gyration: float,
+        chi_value: float,
+        details: str,
+    },
+    ihm_starting_model_coord: {
+        ordinal_id: int,
+        starting_model_id: str,
+        group_PDB: Aliased<'ATOM' | 'HETATM'>(str),
+        id: int,
+        type_symbol: str,
+        entity_id: str,
+        atom_id: str,
+        comp_id: str,
+        seq_id: int,
+        asym_id: str,
+        Cartn_x: float,
+        Cartn_y: float,
+        Cartn_z: float,
+        B_iso_or_equiv: float,
+    },
+    ihm_sphere_obj_site: {
+        ordinal_id: int,
+        entity_id: str,
+        seq_id_begin: int,
+        seq_id_end: int,
+        asym_id: str,
+        Cartn_x: float,
+        Cartn_y: float,
+        Cartn_z: float,
+        object_radius: float,
+        rmsf: float,
+        model_id: int,
+    },
+    ihm_gaussian_obj_site: {
+        ordinal_id: int,
+        entity_id: str,
+        seq_id_begin: int,
+        seq_id_end: int,
+        asym_id: str,
+        mean_Cartn_x: float,
+        mean_Cartn_y: float,
+        mean_Cartn_z: float,
+        weight: float,
+        covariance_matrix: Matrix(3, 3),
+        model_id: int,
+    },
+    ihm_gaussian_obj_ensemble: {
+        ordinal_id: int,
+        entity_id: str,
+        seq_id_begin: int,
+        seq_id_end: int,
+        asym_id: str,
+        mean_Cartn_x: float,
+        mean_Cartn_y: float,
+        mean_Cartn_z: float,
+        weight: float,
+        covariance_matrix: Matrix(3, 3),
+        ensemble_id: int,
+    },
+    ihm_feature_list: {
+        feature_id: int,
+        feature_type: Aliased<'atom' | 'residue' | 'residue range'>(str),
+        entity_type: Aliased<'polymer' | 'non-polymer' | 'macrolide' | 'water'>(str),
+    },
+    ihm_poly_residue_feature: {
+        ordinal_id: int,
+        feature_id: int,
+        entity_id: str,
+        asym_id: str,
+        comp_id_begin: str,
+        comp_id_end: str,
+        seq_id_begin: int,
+        seq_id_end: int,
+    },
+    ihm_derived_distance_restraint: {
+        id: int,
+        group_id: int,
+        feature_id_1: int,
+        feature_id_2: int,
+        group_conditionality: Aliased<'ALL' | 'ANY'>(str),
+        random_exclusion_fraction: float,
+        distance_upper_limit: float,
+        restraint_type: Aliased<'lower bound' | 'upper bound' | 'lower and upper bound'>(str),
+        dataset_list_id: int,
+    },
 }
 
 export type mmCIF_Schema = typeof mmCIF_Schema;