updated mmcif: reordered, added chem_comp, entry, struct, struct_keywords

data/mmcif-popular-field-names.csv

@@ -1,3 +1,51 @@
+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
@@ -9,25 +57,13 @@ entity.pdbx_mutation
 entity.pdbx_fragment
 entity.pdbx_ec
 
+entry.id
+
 exptl.entry_id
 exptl.method
 
-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
-
-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
+struct.entry_id
+struct.title
 
 struct_conf.conf_type_id
 struct_conf.id
@@ -50,23 +86,6 @@ struct_conf.pdbx_PDB_helix_class
 struct_conf.details
 struct_conf.pdbx_PDB_helix_length
 
-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_conn.id
 struct_conn.conn_type_id
 struct_conn.pdbx_PDB_id
@@ -104,13 +123,33 @@ struct_conn_type.id
 struct_conn_type.criteria
 struct_conn_type.reference
 
-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
+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
+
+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_struct_assembly.id
 pdbx_struct_assembly.details
@@ -138,26 +177,4 @@ 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
-
-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
+pdbx_struct_mod_residue.details

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

@@ -55,6 +55,15 @@ export const mmCIF_Schema = {
         Z_PDB: int,
         pdbx_unique_axis: str,
     },
+    chem_comp: {
+        formula: str,
+        formula_weight: float,
+        id: str,
+        mon_nstd_flag: Aliased<'no' | 'n' | 'yes' | 'y'>(str),
+        name: str,
+        type: Aliased<'D-peptide linking' | 'L-peptide linking' | 'D-peptide NH3 amino terminus' | 'L-peptide NH3 amino terminus' | 'D-peptide COOH carboxy terminus' | 'L-peptide COOH carboxy terminus' | 'DNA linking' | 'RNA linking' | 'L-RNA linking' | 'L-DNA linking' | 'DNA OH 5 prime terminus' | 'RNA OH 5 prime terminus' | 'DNA OH 3 prime terminus' | 'RNA OH 3 prime terminus' | 'D-saccharide 1,4 and 1,4 linking' | 'L-saccharide 1,4 and 1,4 linking' | 'D-saccharide 1,4 and 1,6 linking' | 'L-saccharide 1,4 and 1,6 linking' | 'L-saccharide' | 'D-saccharide' | 'saccharide' | 'non-polymer' | 'peptide linking' | 'peptide-like' | 'L-gamma-peptide, C-delta linking' | 'D-gamma-peptide, C-delta linking' | 'L-beta-peptide, C-gamma linking' | 'D-beta-peptide, C-gamma linking' | 'other'>(str),
+        pdbx_synonyms: str,
+    },
     chem_comp_bond: {
         atom_id_1: str,
         atom_id_2: str,
@@ -76,10 +85,17 @@ export const mmCIF_Schema = {
         pdbx_fragment: str,
         pdbx_ec: List(',', x => x),
     },
+    entry: {
+        id: str,
+    },
     exptl: {
         entry_id: str,
         method: Aliased<'X-RAY DIFFRACTION' | 'NEUTRON DIFFRACTION' | 'FIBER DIFFRACTION' | 'ELECTRON CRYSTALLOGRAPHY' | 'ELECTRON MICROSCOPY' | 'SOLUTION NMR' | 'SOLID-STATE NMR' | 'SOLUTION SCATTERING' | 'POWDER DIFFRACTION' | 'INFRARED SPECTROSCOPY' | 'EPR' | 'FLUORESCENCE TRANSFER' | 'THEORETICAL MODEL'>(str),
     },
+    struct: {
+        entry_id: str,
+        title: str,
+    },
     struct_conf: {
         beg_label_asym_id: str,
         beg_label_comp_id: str,
@@ -141,6 +157,11 @@ export const mmCIF_Schema = {
         id: Aliased<'covale' | 'disulf' | 'hydrog' | 'metalc' | 'mismat' | 'saltbr' | 'modres' | 'covale_base' | 'covale_sugar' | 'covale_phosphate'>(str),
         reference: str,
     },
+    struct_keywords: {
+        entry_id: str,
+        text: List(',', x => x),
+        pdbx_keywords: str,
+    },
     struct_sheet_range: {
         beg_label_asym_id: str,
         beg_label_comp_id: str,