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Commit 3400c8e9 authored by Alexander Rose's avatar Alexander Rose
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update coreCif dictionary

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data/cif-field-names/cif-core-field-names.csv
+ 16
− 23
View file @ 3400c8e9
...@@ -2,11 +2,11 @@ audit.block_doi ...@@ -2,11 +2,11 @@ audit.block_doi
database_code.depnum_ccdc_archive database_code.depnum_ccdc_archive
database_code.depnum_ccdc_fiz database_code.depnum_ccdc_fiz
database_code.ICSD database_code.icsd
database_code.MDF database_code.mdf
database_code.NBS database_code.nbs
database_code.CSD database_code.csd
database_code.COD database_code.cod
chemical.name_systematic chemical.name_systematic
chemical.name_common chemical.name_common
...@@ -24,8 +24,8 @@ atom_type_scat.dispersion_imag ...@@ -24,8 +24,8 @@ atom_type_scat.dispersion_imag
atom_type_scat.source atom_type_scat.source
space_group.crystal_system space_group.crystal_system
space_group.name_H-M_full space_group.name_h-m_full
space_group.IT_number space_group.it_number
space_group_symop.operation_xyz space_group_symop.operation_xyz
cell.length_a cell.length_a
...@@ -35,14 +35,14 @@ cell.angle_alpha ...@@ -35,14 +35,14 @@ cell.angle_alpha
cell.angle_beta cell.angle_beta
cell.angle_gamma cell.angle_gamma
cell.volume cell.volume
cell.formula_units_Z cell.formula_units_z
atom_site.label atom_site.label
atom_site.type_symbol atom_site.type_symbol
atom_site.fract_x atom_site.fract_x
atom_site.fract_y atom_site.fract_y
atom_site.fract_z atom_site.fract_z
atom_site.U_iso_or_equiv atom_site.u_iso_or_equiv
atom_site.adp_type atom_site.adp_type
atom_site.occupancy atom_site.occupancy
atom_site.calc_flag atom_site.calc_flag
...@@ -52,20 +52,13 @@ atom_site.disorder_group ...@@ -52,20 +52,13 @@ atom_site.disorder_group
atom_site.site_symmetry_multiplicity atom_site.site_symmetry_multiplicity
atom_site_aniso.label atom_site_aniso.label
atom_site_aniso.U atom_site_aniso.u
atom_site_aniso.U_11 atom_site_aniso.u_11
atom_site_aniso.U_22 atom_site_aniso.u_22
atom_site_aniso.U_33 atom_site_aniso.u_33
atom_site_aniso.U_23 atom_site_aniso.u_23
atom_site_aniso.U_13 atom_site_aniso.u_13
atom_site_aniso.U_12 atom_site_aniso.u_12
atom_site_aniso.U_su
atom_site_aniso.U_11_su
atom_site_aniso.U_22_su
atom_site_aniso.U_33_su
atom_site_aniso.U_23_su
atom_site_aniso.U_13_su
atom_site_aniso.U_12_su
geom_bond.atom_site_label_1 geom_bond.atom_site_label_1
geom_bond.atom_site_label_2 geom_bond.atom_site_label_2
......
src/cli/cifschema/util/cif-dic.ts
+ 16
− 19
View file @ 3400c8e9
...@@ -81,7 +81,7 @@ export function getFieldType(type: string, description: string, values?: string[ ...@@ -81,7 +81,7 @@ export function getFieldType(type: string, description: string, values?: string[
case 'List(Real,Real)': case 'List(Real,Real)':
case 'List(Real,Real,Real,Real)': case 'List(Real,Real,Real,Real)':
case 'Date': case 'Date':
case 'Datetime': case 'DateTime':
case 'Tag': case 'Tag':
case 'Implied': case 'Implied':
return wrapContainer('str', ',', description, container); return wrapContainer('str', ',', description, container);
...@@ -234,29 +234,26 @@ const FORCE_INT_FIELDS = [ ...@@ -234,29 +234,26 @@ const FORCE_INT_FIELDS = [
'_struct_sheet_range.end_auth_seq_id', '_struct_sheet_range.end_auth_seq_id',
]; ];
/**
* Note that name and mapped name must share a prefix. This is not always the case in
* the cifCore dictionary, but for downstream code to work a container field with the
* same prefix as the member fields must be given here and in the field names filter
* list.
*/
const FORCE_MATRIX_FIELDS_MAP: { [k: string]: string } = { const FORCE_MATRIX_FIELDS_MAP: { [k: string]: string } = {
'atom_site_aniso.U_11': 'U', 'atom_site_aniso.u_11': 'u', // is matrix_u in the the dic
'atom_site_aniso.U_22': 'U', 'atom_site_aniso.u_22': 'u',
'atom_site_aniso.U_33': 'U', 'atom_site_aniso.u_33': 'u',
'atom_site_aniso.U_23': 'U', 'atom_site_aniso.u_23': 'u',
'atom_site_aniso.U_13': 'U', 'atom_site_aniso.u_13': 'u',
'atom_site_aniso.U_12': 'U', 'atom_site_aniso.u_12': 'u',
'atom_site_aniso.U_11_su': 'U_su',
'atom_site_aniso.U_22_su': 'U_su',
'atom_site_aniso.U_33_su': 'U_su',
'atom_site_aniso.U_23_su': 'U_su',
'atom_site_aniso.U_13_su': 'U_su',
'atom_site_aniso.U_12_su': 'U_su',
}; };
const FORCE_MATRIX_FIELDS = Object.keys(FORCE_MATRIX_FIELDS_MAP); const FORCE_MATRIX_FIELDS = Object.keys(FORCE_MATRIX_FIELDS_MAP);
const EXTRA_ALIASES: Database['aliases'] = { const EXTRA_ALIASES: Database['aliases'] = {
'atom_site_aniso.U': [ 'atom_site_aniso.matrix_u': [
'atom_site_anisotrop_U' 'atom_site_anisotrop_U',
], 'atom_site_aniso.U'
'atom_site_aniso.U_su': [
'atom_site_aniso_U_esd',
'atom_site_anisotrop_U_esd',
], ],
}; };
......
src/cli/cifschema/util/helper.ts
+ 2
− 2
View file @ 3400c8e9
...@@ -10,8 +10,8 @@ export function parseImportGet(s: string): Import[] { ...@@ -10,8 +10,8 @@ export function parseImportGet(s: string): Import[] {
// [{'save':hi_ang_Fox_coeffs 'file':templ_attr.cif} {'save':hi_ang_Fox_c0 'file':templ_enum.cif}] // [{'save':hi_ang_Fox_coeffs 'file':templ_attr.cif} {'save':hi_ang_Fox_c0 'file':templ_enum.cif}]
// [{"file":'templ_enum.cif' "save":'H_M_ref'}] // [{"file":'templ_enum.cif' "save":'H_M_ref'}]
return s.trim().substring(2, s.length - 2).split(/}[ \n\t]*{/g).map(s => { return s.trim().substring(2, s.length - 2).split(/}[ \n\t]*{/g).map(s => {
const save = s.match(/('save'|"save"):([^ \t\n]+)/); const save = s.match(/('save'|"save"):([^ \t\n{}]+)/);
const file = s.match(/('file'|"file"):([^ \t\n]+)/); const file = s.match(/('file'|"file"):([^ \t\n{}]+)/);
return { return {
save: save ? save[0].substr(7).replace(/['"]/g, '') : undefined, save: save ? save[0].substr(7).replace(/['"]/g, '') : undefined,
file: file ? file[0].substr(7).replace(/['"]/g, '') : undefined file: file ? file[0].substr(7).replace(/['"]/g, '') : undefined
......
src/mol-io/reader/cif/schema/cif-core.ts
+ 68
− 120
View file @ 3400c8e9
/** /**
* Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info. * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
* *
* Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.0.14. * Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.1.0.
* *
* @author molstar/ciftools package * @author molstar/ciftools package
*/ */
...@@ -10,8 +10,8 @@ import { Database, Column } from '../../../../mol-data/db'; ...@@ -10,8 +10,8 @@ import { Database, Column } from '../../../../mol-data/db';
import Schema = Column.Schema; import Schema = Column.Schema;
const int = Schema.int;
const float = Schema.float; const float = Schema.float;
const int = Schema.int;
const str = Schema.str; const str = Schema.str;
const Matrix = Schema.Matrix; const Matrix = Schema.Matrix;
...@@ -21,16 +21,6 @@ export const CifCore_Schema = { ...@@ -21,16 +21,6 @@ export const CifCore_Schema = {
* the crystal unit cell and their measurement. * the crystal unit cell and their measurement.
*/ */
cell: { cell: {
/**
* The number of the formula units in the unit cell as specified
* by _chemical_formula.structural, _chemical_formula.moiety or
* _chemical_formula.sum.
*/
formula_units_Z: int,
/**
* Volume of the crystal unit cell.
*/
volume: float,
/** /**
* The angle between the bounding cell axes. * The angle between the bounding cell axes.
*/ */
...@@ -43,6 +33,12 @@ export const CifCore_Schema = { ...@@ -43,6 +33,12 @@ export const CifCore_Schema = {
* The angle between the bounding cell axes. * The angle between the bounding cell axes.
*/ */
angle_gamma: float, angle_gamma: float,
/**
* The number of the formula units in the unit cell as specified
* by _chemical_formula.structural, _chemical_formula.moiety or
* _chemical_formula.sum.
*/
formula_units_z: int,
/** /**
* The length of each cell axis. * The length of each cell axis.
*/ */
...@@ -55,6 +51,10 @@ export const CifCore_Schema = { ...@@ -55,6 +51,10 @@ export const CifCore_Schema = {
* The length of each cell axis. * The length of each cell axis.
*/ */
length_c: float, length_c: float,
/**
* Volume of the crystal unit cell.
*/
volume: float,
}, },
/** /**
* The CATEGORY of data items which describe the composition and * The CATEGORY of data items which describe the composition and
...@@ -184,12 +184,12 @@ export const CifCore_Schema = { ...@@ -184,12 +184,12 @@ export const CifCore_Schema = {
crystal_system: str, crystal_system: str,
/** /**
* The number as assigned in International Tables for Crystallography * The number as assigned in International Tables for Crystallography
* Vol A, specifying the proper affine class (i.e. the orientation * Vol. A, specifying the proper affine class (i.e. the orientation
* preserving affine class) of space groups (crystallographic space * preserving affine class) of space groups (crystallographic space
* group type) to which the space group belongs. This number defines * group type) to which the space group belongs. This number defines
* the space group type but not the coordinate system expressed. * the space group type but not the coordinate system expressed.
*/ */
IT_number: int, it_number: int,
/** /**
* The full international Hermann-Mauguin space-group symbol as * The full international Hermann-Mauguin space-group symbol as
* defined in Section 2.2.3 and given as the second item of the * defined in Section 2.2.3 and given as the second item of the
...@@ -220,7 +220,7 @@ export const CifCore_Schema = { ...@@ -220,7 +220,7 @@ export const CifCore_Schema = {
* Space-group symmetry, edited by Th. Hahn, 5th ed. * Space-group symmetry, edited by Th. Hahn, 5th ed.
* Dordrecht: Kluwer Academic Publishers. * Dordrecht: Kluwer Academic Publishers.
*/ */
'name_H-M_full': str, 'name_h-m_full': str,
}, },
/** /**
* The CATEGORY of data items used to describe symmetry equivalent sites * The CATEGORY of data items used to describe symmetry equivalent sites
...@@ -354,8 +354,8 @@ export const CifCore_Schema = { ...@@ -354,8 +354,8 @@ export const CifCore_Schema = {
* structured extensible way. A DOI is an implementation * structured extensible way. A DOI is an implementation
* of the Internet concepts of Uniform Resource Name and * of the Internet concepts of Uniform Resource Name and
* Universal Resource Locator managed according to the * Universal Resource Locator managed according to the
* specifications of the International DOI Foundation (see * specifications of the International DOI Foundation
* http://www.doi.org). * (see http://www.doi.org).
*/ */
block_doi: str, block_doi: str,
}, },
...@@ -366,13 +366,13 @@ export const CifCore_Schema = { ...@@ -366,13 +366,13 @@ export const CifCore_Schema = {
*/ */
database_code: { database_code: {
/** /**
* Code assigned by Crystallography Open Database (COD). * Code assigned by the Crystallography Open Database (COD).
*/ */
COD: str, cod: str,
/** /**
* Code assigned by the Cambridge Structural Database. * Code assigned by the Cambridge Structural Database.
*/ */
CSD: str, csd: str,
/** /**
* Deposition numbers assigned by the Cambridge Crystallographic * Deposition numbers assigned by the Cambridge Crystallographic
* Data Centre (CCDC) to files containing structural information * Data Centre (CCDC) to files containing structural information
...@@ -388,15 +388,15 @@ export const CifCore_Schema = { ...@@ -388,15 +388,15 @@ export const CifCore_Schema = {
/** /**
* Code assigned by the Inorganic Crystal Structure Database. * Code assigned by the Inorganic Crystal Structure Database.
*/ */
ICSD: str, icsd: str,
/** /**
* Code assigned in the Metals Data File. * Code assigned in the Metals Data File.
*/ */
MDF: str, mdf: str,
/** /**
* Code assigned by the NBS (NIST) Crystal Data Database. * Code assigned by the NBS (NIST) Crystal Data Database.
*/ */
NBS: str, nbs: str,
}, },
/** /**
* The CATEGORY of data items used to describe atom site information * The CATEGORY of data items used to describe atom site information
...@@ -511,7 +511,7 @@ export const CifCore_Schema = { ...@@ -511,7 +511,7 @@ export const CifCore_Schema = {
* a* = the reciprocal-space cell lengths * a* = the reciprocal-space cell lengths
* Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776. * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
*/ */
U_iso_or_equiv: float, u_iso_or_equiv: float,
}, },
/** /**
* The CATEGORY of data items used to describe the anisotropic * The CATEGORY of data items used to describe the anisotropic
...@@ -537,7 +537,7 @@ export const CifCore_Schema = { ...@@ -537,7 +537,7 @@ export const CifCore_Schema = {
* *
* The unique elements of the real symmetric matrix are entered by row. * The unique elements of the real symmetric matrix are entered by row.
*/ */
U_11: float, u_11: float,
/** /**
* These are the standard anisotropic atomic displacement * These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the * components in angstroms squared which appear in the
...@@ -550,21 +550,7 @@ export const CifCore_Schema = { ...@@ -550,21 +550,7 @@ export const CifCore_Schema = {
* *
* The unique elements of the real symmetric matrix are entered by row. * The unique elements of the real symmetric matrix are entered by row.
*/ */
U: Matrix(3, 3), u: Matrix(3, 3),
/**
* These are the standard uncertainty values (SU) for the standard
* form of the Uij anisotropic atomic displacement components (see
* _aniso_UIJ. Because these values are TYPE measurand, the su values
* may in practice be auto generated as part of the Uij calculation.
*/
U_11_su: float,
/**
* These are the standard uncertainty values (SU) for the standard
* form of the Uij anisotropic atomic displacement components (see
* _aniso_UIJ. Because these values are TYPE measurand, the su values
* may in practice be auto generated as part of the Uij calculation.
*/
U_su: Matrix(3, 3),
/** /**
* These are the standard anisotropic atomic displacement * These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the * components in angstroms squared which appear in the
...@@ -577,14 +563,7 @@ export const CifCore_Schema = { ...@@ -577,14 +563,7 @@ export const CifCore_Schema = {
* *
* The unique elements of the real symmetric matrix are entered by row. * The unique elements of the real symmetric matrix are entered by row.
*/ */
U_12: float, u_12: float,
/**
* These are the standard uncertainty values (SU) for the standard
* form of the Uij anisotropic atomic displacement components (see
* _aniso_UIJ. Because these values are TYPE measurand, the su values
* may in practice be auto generated as part of the Uij calculation.
*/
U_12_su: float,
/** /**
* These are the standard anisotropic atomic displacement * These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the * components in angstroms squared which appear in the
...@@ -597,14 +576,7 @@ export const CifCore_Schema = { ...@@ -597,14 +576,7 @@ export const CifCore_Schema = {
* *
* The unique elements of the real symmetric matrix are entered by row. * The unique elements of the real symmetric matrix are entered by row.
*/ */
U_13: float, u_13: float,
/**
* These are the standard uncertainty values (SU) for the standard
* form of the Uij anisotropic atomic displacement components (see
* _aniso_UIJ. Because these values are TYPE measurand, the su values
* may in practice be auto generated as part of the Uij calculation.
*/
U_13_su: float,
/** /**
* These are the standard anisotropic atomic displacement * These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the * components in angstroms squared which appear in the
...@@ -617,14 +589,7 @@ export const CifCore_Schema = { ...@@ -617,14 +589,7 @@ export const CifCore_Schema = {
* *
* The unique elements of the real symmetric matrix are entered by row. * The unique elements of the real symmetric matrix are entered by row.
*/ */
U_22: float, u_22: float,
/**
* These are the standard uncertainty values (SU) for the standard
* form of the Uij anisotropic atomic displacement components (see
* _aniso_UIJ. Because these values are TYPE measurand, the su values
* may in practice be auto generated as part of the Uij calculation.
*/
U_22_su: float,
/** /**
* These are the standard anisotropic atomic displacement * These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the * components in angstroms squared which appear in the
...@@ -637,14 +602,7 @@ export const CifCore_Schema = { ...@@ -637,14 +602,7 @@ export const CifCore_Schema = {
* *
* The unique elements of the real symmetric matrix are entered by row. * The unique elements of the real symmetric matrix are entered by row.
*/ */
U_23: float, u_23: float,
/**
* These are the standard uncertainty values (SU) for the standard
* form of the Uij anisotropic atomic displacement components (see
* _aniso_UIJ. Because these values are TYPE measurand, the su values
* may in practice be auto generated as part of the Uij calculation.
*/
U_23_su: float,
/** /**
* These are the standard anisotropic atomic displacement * These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the * components in angstroms squared which appear in the
...@@ -657,14 +615,7 @@ export const CifCore_Schema = { ...@@ -657,14 +615,7 @@ export const CifCore_Schema = {
* *
* The unique elements of the real symmetric matrix are entered by row. * The unique elements of the real symmetric matrix are entered by row.
*/ */
U_33: float, u_33: float,
/**
* These are the standard uncertainty values (SU) for the standard
* form of the Uij anisotropic atomic displacement components (see
* _aniso_UIJ. Because these values are TYPE measurand, the su values
* may in practice be auto generated as part of the Uij calculation.
*/
U_33_su: float,
}, },
/** /**
* The CATEGORY of data items used to describe atomic type information * The CATEGORY of data items used to describe atomic type information
...@@ -710,17 +661,14 @@ export const CifCore_Schema = { ...@@ -710,17 +661,14 @@ export const CifCore_Schema = {
}; };
export const CifCore_Aliases = { export const CifCore_Aliases = {
'atom_site_aniso.U': [ 'cell.formula_units_z': [
'atom_site_anisotrop_U', 'cell_formula_units_Z',
],
'atom_site_aniso.U_su': [
'atom_site_aniso_U_esd',
'atom_site_anisotrop_U_esd',
], ],
'space_group.IT_number': [ 'space_group.it_number': [
'space_group_IT_number',
'symmetry_Int_Tables_number', 'symmetry_Int_Tables_number',
], ],
'space_group.name_H-M_full': [ 'space_group.name_h-m_full': [
'symmetry_space_group_name_H-M', 'symmetry_space_group_name_H-M',
], ],
'space_group_symop.operation_xyz': [ 'space_group_symop.operation_xyz': [
...@@ -735,6 +683,21 @@ export const CifCore_Aliases = { ...@@ -735,6 +683,21 @@ export const CifCore_Aliases = {
'geom_bond.distance': [ 'geom_bond.distance': [
'geom_bond_dist', 'geom_bond_dist',
], ],
'database_code.cod': [
'database_code_COD',
],
'database_code.csd': [
'database_code_CSD',
],
'database_code.icsd': [
'database_code_ICSD',
],
'database_code.mdf': [
'database_code_MDF',
],
'database_code.nbs': [
'database_code_NBS',
],
'atom_site.adp_type': [ 'atom_site.adp_type': [
'atom_site_thermal_displace_type', 'atom_site_thermal_displace_type',
], ],
...@@ -744,51 +707,36 @@ export const CifCore_Aliases = { ...@@ -744,51 +707,36 @@ export const CifCore_Aliases = {
'atom_site.site_symmetry_multiplicity': [ 'atom_site.site_symmetry_multiplicity': [
'atom_site_symmetry_multiplicity', 'atom_site_symmetry_multiplicity',
], ],
'atom_site.u_iso_or_equiv': [
'atom_site_U_iso_or_equiv',
],
'atom_site_aniso.label': [ 'atom_site_aniso.label': [
'atom_site_anisotrop_id', 'atom_site_anisotrop_id',
], ],
'atom_site_aniso.U_11': [ 'atom_site_aniso.u_11': [
'atom_site_aniso_U_11',
'atom_site_anisotrop_U_11', 'atom_site_anisotrop_U_11',
], ],
'atom_site_aniso.U_11_su': [ 'atom_site_aniso.u_12': [
'atom_site_aniso_U_11_esd', 'atom_site_aniso_U_12',
'atom_site_anisotrop_U_11_esd',
],
'atom_site_aniso.U_12': [
'atom_site_anisotrop_U_12', 'atom_site_anisotrop_U_12',
], ],
'atom_site_aniso.U_12_su': [ 'atom_site_aniso.u_13': [
'atom_site_aniso_U_12_esd', 'atom_site_aniso_U_13',
'atom_site_anisotrop_U_12_esd',
],
'atom_site_aniso.U_13': [
'atom_site_anisotrop_U_13', 'atom_site_anisotrop_U_13',
], ],
'atom_site_aniso.U_13_su': [ 'atom_site_aniso.u_22': [
'atom_site_aniso_U_13_esd', 'atom_site_aniso_U_22',
'atom_site_anisotrop_U_13_esd',
],
'atom_site_aniso.U_22': [
'atom_site_anisotrop_U_22', 'atom_site_anisotrop_U_22',
], ],
'atom_site_aniso.U_22_su': [ 'atom_site_aniso.u_23': [
'atom_site_aniso_U_22_esd', 'atom_site_aniso_U_23',
'atom_site_anisotrop_U_22_esd',
],
'atom_site_aniso.U_23': [
'atom_site_anisotrop_U_23', 'atom_site_anisotrop_U_23',
], ],
'atom_site_aniso.U_23_su': [ 'atom_site_aniso.u_33': [
'atom_site_aniso_U_23_esd', 'atom_site_aniso_U_33',
'atom_site_anisotrop_U_23_esd',
],
'atom_site_aniso.U_33': [
'atom_site_anisotrop_U_33', 'atom_site_anisotrop_U_33',
], ],
'atom_site_aniso.U_33_su': [
'atom_site_aniso_U_33_esd',
'atom_site_anisotrop_U_33_esd',
],
}; };
export type CifCore_Schema = typeof CifCore_Schema; export type CifCore_Schema = typeof CifCore_Schema;
......
src/mol-model-formats/structure/_spec/cif-core.spec.ts
+ 9
− 4
View file @ 3400c8e9
/** /**
* Copyright (c) 2019 mol* contributors, licensed under MIT, See LICENSE file for more info. * Copyright (c) 2019-2021 mol* contributors, licensed under MIT, See LICENSE file for more info.
* *
* @author Alexander Rose <alexander.rose@weirdbyte.de> * @author Alexander Rose <alexander.rose@weirdbyte.de>
*/ */
...@@ -32,6 +32,9 @@ N N 0.0311 0.0180 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' ...@@ -32,6 +32,9 @@ N N 0.0311 0.0180 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
O O 0.0492 0.0322 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' O O 0.0492 0.0322 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
F F 0.0727 0.0534 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' F F 0.0727 0.0534 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
_symmetry_cell_setting Triclinic
_symmetry_space_group_name_H-M P-1
_cell_length_a 11.0829(8) _cell_length_a 11.0829(8)
_cell_length_b 14.6829(10) _cell_length_b 14.6829(10)
_cell_length_c 16.8532(17) _cell_length_c 16.8532(17)
...@@ -82,7 +85,8 @@ describe('cif-core read', () => { ...@@ -82,7 +85,8 @@ describe('cif-core read', () => {
const block = cifFile.blocks[0]; const block = cifFile.blocks[0];
expect(block.getField('cell_length_a')!.float(0)).toBe(11.0829); expect(block.getField('cell_length_a')!.float(0)).toBe(11.0829);
expect.assertions(1); expect(block.getField('symmetry_space_group_name_H-M')!.str(0)).toBe('P-1');
expect.assertions(2);
}); });
it('schema', async () => { it('schema', async () => {
...@@ -93,7 +97,8 @@ describe('cif-core read', () => { ...@@ -93,7 +97,8 @@ describe('cif-core read', () => {
const cifCore = CIF.schema.cifCore(block); const cifCore = CIF.schema.cifCore(block);
expect(cifCore.cell.length_a.value(0)).toBe(11.0829); expect(cifCore.cell.length_a.value(0)).toBe(11.0829);
expect(cifCore.atom_site_aniso.U.value(0)).toEqual(new Float64Array([ 0.0425, 0, 0, 0.00089, 0.0423, 0, 0.01515, 0.00066, 0.0375 ])); expect(cifCore.space_group['name_h-m_full'].value(0)).toBe('P-1');
expect.assertions(2); expect(cifCore.atom_site_aniso.u.value(0)).toEqual(new Float64Array([ 0.0425, 0, 0, 0.00089, 0.0423, 0, 0.01515, 0.00066, 0.0375 ]));
expect.assertions(3);
}); });
}); });
\ No newline at end of file
src/mol-model-formats/structure/cif-core.ts
+ 12
− 13
View file @ 3400c8e9
...@@ -25,10 +25,10 @@ import { Trajectory } from '../../mol-model/structure'; ...@@ -25,10 +25,10 @@ import { Trajectory } from '../../mol-model/structure';
import { cantorPairing } from '../../mol-data/util'; import { cantorPairing } from '../../mol-data/util';
function getSpacegroupNameOrNumber(space_group: CifCore_Database['space_group']) { function getSpacegroupNameOrNumber(space_group: CifCore_Database['space_group']) {
const groupNumber = space_group.IT_number.value(0); const groupNumber = space_group.it_number.value(0);
const groupName = space_group['name_H-M_full'].value(0); const groupName = space_group['name_h-m_full'].value(0).replace('-', ' ');
if (!space_group.IT_number.isDefined) return groupName; if (!space_group.it_number.isDefined) return groupName;
if (!space_group['name_H-M_full'].isDefined) return groupNumber; if (!space_group['name_h-m_full'].isDefined) return groupNumber;
return groupNumber; return groupNumber;
} }
...@@ -129,7 +129,7 @@ async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: Runti ...@@ -129,7 +129,7 @@ async function getModels(db: CifCore_Database, format: CifCoreFormat, ctx: Runti
pdbx_formal_charge: formalCharge, pdbx_formal_charge: formalCharge,
pdbx_PDB_model_num: Column.ofConst(1, atomCount, Column.Schema.int), pdbx_PDB_model_num: Column.ofConst(1, atomCount, Column.Schema.int),
B_iso_or_equiv: db.atom_site.U_iso_or_equiv, B_iso_or_equiv: db.atom_site.u_iso_or_equiv,
}, atomCount); }, atomCount);
const name = ( const name = (
...@@ -231,15 +231,14 @@ function atomSiteAnisotropFromCifCore(model: Model) { ...@@ -231,15 +231,14 @@ function atomSiteAnisotropFromCifCore(model: Model) {
if (!CifCoreFormat.is(model.sourceData)) return; if (!CifCoreFormat.is(model.sourceData)) return;
const { atom_site, atom_site_aniso } = model.sourceData.data.db; const { atom_site, atom_site_aniso } = model.sourceData.data.db;
const data = Table.ofPartialColumns(AtomSiteAnisotrop.Schema, { const data = Table.ofPartialColumns(AtomSiteAnisotrop.Schema, {
U: atom_site_aniso.U, U: atom_site_aniso.u,
U_esd: atom_site_aniso.U_su
}, atom_site_aniso._rowCount); }, atom_site_aniso._rowCount);
const elementToAnsiotrop = AtomSiteAnisotrop.getElementToAnsiotropFromLabel(atom_site.label, atom_site_aniso.label); const elementToAnsiotrop = AtomSiteAnisotrop.getElementToAnsiotropFromLabel(atom_site.label, atom_site_aniso.label);
return { data, elementToAnsiotrop }; return { data, elementToAnsiotrop };
} }
function atomSiteAnisotropApplicableCifCore(model: Model) { function atomSiteAnisotropApplicableCifCore(model: Model) {
if (!CifCoreFormat.is(model.sourceData)) return false; if (!CifCoreFormat.is(model.sourceData)) return false;
return model.sourceData.data.db.atom_site_aniso.U.isDefined; return model.sourceData.data.db.atom_site_aniso.u.isDefined;
} }
AtomSiteAnisotrop.Provider.formatRegistry.add('cifCore', atomSiteAnisotropFromCifCore, atomSiteAnisotropApplicableCifCore); AtomSiteAnisotrop.Provider.formatRegistry.add('cifCore', atomSiteAnisotropFromCifCore, atomSiteAnisotropApplicableCifCore);
...@@ -261,11 +260,11 @@ namespace CifCoreFormat { ...@@ -261,11 +260,11 @@ namespace CifCoreFormat {
const name = ( const name = (
db.database_code.depnum_ccdc_archive.value(0) || db.database_code.depnum_ccdc_archive.value(0) ||
db.database_code.depnum_ccdc_fiz.value(0) || db.database_code.depnum_ccdc_fiz.value(0) ||
db.database_code.ICSD.value(0) || db.database_code.icsd.value(0) ||
db.database_code.MDF.value(0) || db.database_code.mdf.value(0) ||
db.database_code.NBS.value(0) || db.database_code.nbs.value(0) ||
db.database_code.CSD.value(0) || db.database_code.csd.value(0) ||
db.database_code.COD.value(0) || db.database_code.cod.value(0) ||
db._name db._name
); );
......
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