diff --git a/data/mmcif-popular-field-names.csv b/data/mmcif-popular-field-names.csv
new file mode 100644
index 0000000000000000000000000000000000000000..33dd64ddd21b9137eb9c982925e6c1e1e041a473
--- /dev/null
+++ b/data/mmcif-popular-field-names.csv
@@ -0,0 +1,163 @@
+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
+
+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_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_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
+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_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
+
+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
+
+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
+
+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
\ No newline at end of file
diff --git a/src/mol-io/reader/cif/schema/mmcif.ts b/src/mol-io/reader/cif/schema/mmcif.ts
index 62f3a395ce2a22d971779dd3785b2aa15ba81727..fc886449e2585ae18c72f9bac9cb27a49175b863 100644
--- a/src/mol-io/reader/cif/schema/mmcif.ts
+++ b/src/mol-io/reader/cif/schema/mmcif.ts
@@ -1,7 +1,9 @@
/**
- * 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 David Sehnal <david.sehnal@gmail.com>
+ * Code-generated 'mmCIF' schema file
+ *
+ * @author mol-star package (src/apps/schema-generator/generate)
*/
import { Database, Column } from 'mol-data/db'
@@ -11,241 +13,200 @@ import Schema = Column.Schema
const str = Schema.str;
const int = Schema.int;
const float = Schema.float;
+const coord = Schema.coord;
-const entry = {
- id: str
-}
-
-type EntityType = 'polymer' | 'non-polymer' | 'water' | 'macrolide'
-
-const entity = {
- id: str,
- type: Schema.Aliased<EntityType>(str),
- src_method: str,
- pdbx_description: str,
- formula_weight: float,
- pdbx_number_of_molecules: int,
- details: str,
- pdbx_mutation: str,
- pdbx_fragment: str,
- pdbx_ec: str
-}
-
-const exptl = {
- entry_id: str,
- method: str
-}
-
-const cell = {
- entry_id: str,
- length_a: float,
- length_b: float,
- length_c: float,
- angle_alpha: float,
- angle_beta: float,
- angle_gamma: float,
- Z_PDB: int,
- pdbx_unique_axis: str
-}
-
-const symmetry = {
- entry_id: str,
- 'space_group_name_H-M': str,
- 'pdbx_full_space_group_name_H': str,
- cell_setting: str,
- Int_Tables_number: int,
- space_group_name_Hall: str
-}
-
-const struct_conf = {
- conf_type_id: str,
- id: str,
- pdbx_PDB_helix_id: int,
- beg_label_comp_id: str,
- beg_label_asym_id: str,
- beg_label_seq_id: int,
- pdbx_beg_PDB_ins_code: str,
- end_label_comp_id: str,
- end_label_asym_id: str,
- end_label_seq_id: int,
- pdbx_end_PDB_ins_code: str,
- beg_auth_comp_id: str,
- beg_auth_asym_id: str,
- beg_auth_seq_id: int,
- end_auth_comp_id: str,
- end_auth_asym_id: str,
- end_auth_seq_id: int,
- pdbx_PDB_helix_class: int,
- details: str,
- pdbx_PDB_helix_length: int
-}
-
-const struct_sheet_range = {
- sheet_id: str,
- id: int,
- beg_label_comp_id: str,
- beg_label_asym_id: str,
- beg_label_seq_id: int,
- pdbx_beg_PDB_ins_code: str,
- end_label_comp_id: str,
- end_label_asym_id: str,
- end_label_seq_id: int,
- pdbx_end_PDB_ins_code: str,
- beg_auth_comp_id: str,
- beg_auth_asym_id: str,
- beg_auth_seq_id: int,
- end_auth_comp_id: str,
- end_auth_asym_id: str,
- end_auth_seq_id: int
-}
-
-type StructConnTypeId =
- | 'covale'
- | 'covale_base'
- | 'covale_phosphate'
- | 'covale_sugar'
- | 'disulf'
- | 'hydrog'
- | 'metalc'
- | 'mismat'
- | 'modres'
- | 'saltbr'
-
-type BondValueOrder =
- | 'SING'
- | 'DOUB'
- | 'TRIP'
- | 'QUAD'
-
-const struct_conn = {
- id: str,
- conn_type_id: Schema.Aliased<StructConnTypeId>(str),
- pdbx_PDB_id: str,
- ptnr1_label_asym_id: str,
- ptnr1_label_comp_id: str,
- ptnr1_label_seq_id: int,
- ptnr1_label_atom_id: str,
- pdbx_ptnr1_label_alt_id: str,
- pdbx_ptnr1_PDB_ins_code: str,
- pdbx_ptnr1_standard_comp_id: str,
- ptnr1_symmetry: str,
- ptnr2_label_asym_id: str,
- ptnr2_label_comp_id: str,
- ptnr2_label_seq_id: int,
- ptnr2_label_atom_id: str,
- pdbx_ptnr2_label_alt_id: str,
- pdbx_ptnr2_PDB_ins_code: str,
- ptnr1_auth_asym_id: str,
- ptnr1_auth_comp_id: str,
- ptnr1_auth_seq_id: int,
- ptnr2_auth_asym_id: str,
- ptnr2_auth_comp_id: str,
- ptnr2_auth_seq_id: int,
- ptnr2_symmetry: str,
- pdbx_ptnr3_label_atom_id: str,
- pdbx_ptnr3_label_seq_id: int,
- pdbx_ptnr3_label_comp_id: str,
- pdbx_ptnr3_label_asym_id: str,
- pdbx_ptnr3_label_alt_id: str,
- pdbx_ptnr3_PDB_ins_code: str,
- details: str,
- pdbx_dist_value: float,
- pdbx_value_order: Schema.Aliased<BondValueOrder>(str)
-}
-
-const struct_conn_type = {
- id: Schema.Aliased<StructConnTypeId>(str),
- criteria: str,
- reference: str
-}
-
-const chem_comp_bond = {
- comp_id: str,
- pdbx_stereo_config: str,
- pdbx_ordinal: int,
- pdbx_aromatic_flag: Schema.Aliased<'Y' | 'N'>(str),
- atom_id_1: str,
- atom_id_2: str,
- value_order: Schema.Aliased<BondValueOrder>(str)
-}
-
-const pdbx_struct_assembly = {
- id: str,
- details: str,
- method_details: str,
- oligomeric_details: str,
- oligomeric_count: int
-}
-
-const pdbx_struct_assembly_gen = {
- assembly_id: str,
- oper_expression: str,
- asym_id_list: str
-}
-
-const pdbx_struct_oper_list = {
- id: str,
- type: str,
- name: str,
- symmetry_operation: str,
- matrix: Schema.Matrix(3, 3),
- vector: Schema.Vector(3)
-}
-
-const pdbx_struct_mod_residue = {
- id: int,
- label_asym_id: str,
- label_seq_id: int,
- label_comp_id: str,
- auth_asym_id: str,
- auth_seq_id: int,
- auth_comp_id: str,
- PDB_ins_code: str,
- parent_comp_id: str,
- details: str
-}
-
-const atom_site = {
- group_PDB: str,
- id: int,
- type_symbol: str,
- label_atom_id: str,
- label_alt_id: str,
- label_comp_id: str,
- label_asym_id: str,
- label_entity_id: str,
- label_seq_id: int,
- pdbx_PDB_ins_code: str,
- pdbx_formal_charge: str,
- Cartn_x: Schema.coord,
- Cartn_y: Schema.coord,
- Cartn_z: Schema.coord,
- occupancy: float,
- B_iso_or_equiv: float,
- auth_atom_id: str,
- auth_comp_id: str,
- auth_asym_id: str,
- auth_seq_id: int,
- pdbx_PDB_model_num: int
-}
+const Aliased = Schema.Aliased;
+const Matrix = Schema.Matrix;
+const Vector = Schema.Vector;
export const mmCIF_Schema = {
- entry,
- entity,
- exptl,
- cell,
- symmetry,
- struct_conf,
- struct_sheet_range,
- struct_conn,
- struct_conn_type,
- chem_comp_bond,
- pdbx_struct_assembly,
- pdbx_struct_assembly_gen,
- pdbx_struct_oper_list,
- pdbx_struct_mod_residue,
- atom_site
-};
+ atom_site: {
+ auth_asym_id: str,
+ auth_atom_id: str,
+ auth_comp_id: str,
+ // auth_seq_id: str,
+ auth_seq_id: int,
+ B_iso_or_equiv: float,
+ Cartn_x: coord,
+ Cartn_y: coord,
+ Cartn_z: coord,
+ group_PDB: str,
+ // id: str,
+ id: int,
+ label_alt_id: str,
+ label_asym_id: str,
+ label_atom_id: str,
+ label_comp_id: str,
+ label_entity_id: str,
+ label_seq_id: int,
+ occupancy: float,
+ type_symbol: str,
+ pdbx_PDB_ins_code: str,
+ pdbx_PDB_model_num: int,
+ pdbx_formal_charge: int,
+ },
+ cell: {
+ angle_alpha: float,
+ angle_beta: float,
+ angle_gamma: float,
+ entry_id: str,
+ length_a: float,
+ length_b: float,
+ length_c: float,
+ Z_PDB: int,
+ pdbx_unique_axis: str,
+ },
+ chem_comp_bond: {
+ atom_id_1: str,
+ atom_id_2: str,
+ comp_id: str,
+ value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad' | 'arom' | 'poly' | 'delo' | 'pi'>(str),
+ pdbx_ordinal: int,
+ pdbx_stereo_config: Aliased<'E' | 'Z' | 'N'>(str),
+ pdbx_aromatic_flag: Aliased<'Y' | 'N'>(str),
+ },
+ entity: {
+ details: str,
+ formula_weight: float,
+ id: str,
+ src_method: Aliased<'nat' | 'man' | 'syn'>(str),
+ type: Aliased<'polymer' | 'non-polymer' | 'macrolide' | 'water'>(str),
+ pdbx_description: str,
+ pdbx_number_of_molecules: float,
+ pdbx_mutation: str,
+ pdbx_fragment: str,
+ pdbx_ec: str,
+ },
+ exptl: {
+ entry_id: str,
+ method: str,
+ },
+ struct_conf: {
+ beg_label_asym_id: str,
+ beg_label_comp_id: str,
+ beg_label_seq_id: int,
+ beg_auth_asym_id: str,
+ beg_auth_comp_id: str,
+ // beg_auth_seq_id: str,
+ beg_auth_seq_id: int,
+ conf_type_id: Aliased<'HELX_P' | 'HELX_OT_P' | 'HELX_RH_P' | 'HELX_RH_OT_P' | 'HELX_RH_AL_P' | 'HELX_RH_GA_P' | 'HELX_RH_OM_P' | 'HELX_RH_PI_P' | 'HELX_RH_27_P' | 'HELX_RH_3T_P' | 'HELX_RH_PP_P' | 'HELX_LH_P' | 'HELX_LH_OT_P' | 'HELX_LH_AL_P' | 'HELX_LH_GA_P' | 'HELX_LH_OM_P' | 'HELX_LH_PI_P' | 'HELX_LH_27_P' | 'HELX_LH_3T_P' | 'HELX_LH_PP_P' | 'HELX_N' | 'HELX_OT_N' | 'HELX_RH_N' | 'HELX_RH_OT_N' | 'HELX_RH_A_N' | 'HELX_RH_B_N' | 'HELX_RH_Z_N' | 'HELX_LH_N' | 'HELX_LH_OT_N' | 'HELX_LH_A_N' | 'HELX_LH_B_N' | 'HELX_LH_Z_N' | 'TURN_P' | 'TURN_OT_P' | 'TURN_TY1_P' | 'TURN_TY1P_P' | 'TURN_TY2_P' | 'TURN_TY2P_P' | 'TURN_TY3_P' | 'TURN_TY3P_P' | 'STRN'>(str),
+ details: str,
+ end_label_asym_id: str,
+ end_label_comp_id: str,
+ end_label_seq_id: int,
+ end_auth_asym_id: str,
+ end_auth_comp_id: str,
+ // end_auth_seq_id: str,
+ end_auth_seq_id: int,
+ id: str,
+ pdbx_beg_PDB_ins_code: str,
+ pdbx_end_PDB_ins_code: str,
+ pdbx_PDB_helix_class: str,
+ pdbx_PDB_helix_length: int,
+ pdbx_PDB_helix_id: str,
+ },
+ struct_conn: {
+ conn_type_id: Aliased<'covale' | 'disulf' | 'hydrog' | 'metalc' | 'mismat' | 'saltbr' | 'modres' | 'covale_base' | 'covale_sugar' | 'covale_phosphate'>(str),
+ details: str,
+ id: str,
+ ptnr1_label_asym_id: str,
+ ptnr1_label_atom_id: str,
+ ptnr1_label_comp_id: str,
+ ptnr1_label_seq_id: int,
+ ptnr1_auth_asym_id: str,
+ ptnr1_auth_comp_id: str,
+ // ptnr1_auth_seq_id: str,
+ ptnr1_auth_seq_id: int,
+ ptnr1_symmetry: str,
+ ptnr2_label_asym_id: str,
+ ptnr2_label_atom_id: str,
+ ptnr2_label_seq_id: int,
+ ptnr2_auth_asym_id: str,
+ ptnr2_auth_comp_id: str,
+ // ptnr2_auth_seq_id: str,
+ ptnr2_auth_seq_id: int,
+ ptnr2_symmetry: str,
+ pdbx_ptnr1_PDB_ins_code: str,
+ pdbx_ptnr1_label_alt_id: str,
+ pdbx_ptnr1_standard_comp_id: str,
+ pdbx_ptnr2_PDB_ins_code: str,
+ pdbx_ptnr2_label_alt_id: str,
+ pdbx_ptnr3_PDB_ins_code: str,
+ pdbx_ptnr3_label_alt_id: str,
+ pdbx_ptnr3_label_asym_id: str,
+ pdbx_ptnr3_label_atom_id: str,
+ pdbx_ptnr3_label_comp_id: str,
+ pdbx_ptnr3_label_seq_id: int,
+ pdbx_PDB_id: str,
+ pdbx_dist_value: float,
+ pdbx_value_order: Aliased<'sing' | 'doub' | 'trip' | 'quad'>(str),
+ },
+ struct_conn_type: {
+ criteria: str,
+ id: Aliased<'covale' | 'disulf' | 'hydrog' | 'metalc' | 'mismat' | 'saltbr' | 'modres' | 'covale_base' | 'covale_sugar' | 'covale_phosphate'>(str),
+ reference: str,
+ },
+ struct_sheet_range: {
+ beg_label_asym_id: str,
+ beg_label_comp_id: str,
+ beg_label_seq_id: int,
+ end_label_asym_id: str,
+ end_label_comp_id: str,
+ end_label_seq_id: int,
+ beg_auth_asym_id: str,
+ beg_auth_comp_id: str,
+ // beg_auth_seq_id: str,
+ beg_auth_seq_id: int,
+ end_auth_asym_id: str,
+ end_auth_comp_id: str,
+ // end_auth_seq_id: str,
+ end_auth_seq_id: int,
+ id: str,
+ sheet_id: str,
+ pdbx_beg_PDB_ins_code: str,
+ pdbx_end_PDB_ins_code: str,
+ },
+ symmetry: {
+ entry_id: str,
+ cell_setting: Aliased<'triclinic' | 'monoclinic' | 'orthorhombic' | 'tetragonal' | 'rhombohedral' | 'trigonal' | 'hexagonal' | 'cubic'>(str),
+ Int_Tables_number: int,
+ space_group_name_Hall: str,
+ 'space_group_name_H-M': str,
+ },
+ pdbx_struct_assembly: {
+ method_details: str,
+ oligomeric_details: str,
+ oligomeric_count: int,
+ details: str,
+ id: str,
+ },
+ pdbx_struct_mod_residue: {
+ id: int,
+ auth_asym_id: str,
+ auth_comp_id: str,
+ // auth_seq_id: str,
+ auth_seq_id: int,
+ PDB_ins_code: str,
+ label_asym_id: str,
+ label_comp_id: str,
+ label_seq_id: int,
+ parent_comp_id: str,
+ details: str,
+ },
+ pdbx_struct_oper_list: {
+ id: str,
+ type: str,
+ name: str,
+ symmetry_operation: str,
+ matrix: Matrix(3, 3),
+ vector: Vector(3),
+ },
+ pdbx_struct_assembly_gen: {
+ asym_id_list: str,
+ assembly_id: str,
+ oper_expression: str,
+ },
+}
export type mmCIF_Schema = typeof mmCIF_Schema;
export interface mmCIF_Database extends Database<mmCIF_Schema> { }
\ No newline at end of file
diff --git a/src/mol-model/structure/export/mmcif.ts b/src/mol-model/structure/export/mmcif.ts
index 09d54ab04d10396846bd09b69d6393aba03c30c5..6af666d843779c1b55ca99f83e903775e228a5a7 100644
--- a/src/mol-model/structure/export/mmcif.ts
+++ b/src/mol-model/structure/export/mmcif.ts
@@ -111,7 +111,7 @@ const atom_site: Encoder.CategoryDefinition<Atom.Location> = {
float('Cartn_y', P.atom.y),
float('Cartn_z', P.atom.z),
float('occupancy', P.atom.occupancy),
- str('pdbx_formal_charge', P.atom.pdbx_formal_charge),
+ int('pdbx_formal_charge', P.atom.pdbx_formal_charge),
str('auth_atom_id', P.atom.auth_atom_id),
str('auth_comp_id', P.residue.auth_comp_id),