cif-core.ts 32 KB

123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696697698699700701702703704705706707708709710711712713714715716717718719720721722723724725726727728729730731732733734735736737738739740741742743744745746747748749750751752753754755756757758759760761762763764765766767768769770771772773774775776777778779780781782783784785786787788789790791792793794795
  1. /**
  2. * Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
  3. *
  4. * Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.0.13.
  5. *
  6. * @author molstar/ciftools package
  7. */
  8. import { Database, Column } from '../../../../mol-data/db'
  9. import Schema = Column.Schema
  10. const int = Schema.int;
  11. const float = Schema.float;
  12. const str = Schema.str;
  13. const Matrix = Schema.Matrix;
  14. export const CifCore_Schema = {
  15. /**
  16. * The CATEGORY of data items used to describe the parameters of
  17. * the crystal unit cell and their measurement.
  18. */
  19. cell: {
  20. /**
  21. * The number of the formula units in the unit cell as specified
  22. * by _chemical_formula.structural, _chemical_formula.moiety or
  23. * _chemical_formula.sum.
  24. */
  25. formula_units_Z: int,
  26. /**
  27. * Volume of the crystal unit cell.
  28. */
  29. volume: float,
  30. /**
  31. * The angle between the bounding cell axes.
  32. */
  33. angle_alpha: float,
  34. /**
  35. * The angle between the bounding cell axes.
  36. */
  37. angle_beta: float,
  38. /**
  39. * The angle between the bounding cell axes.
  40. */
  41. angle_gamma: float,
  42. /**
  43. * The length of each cell axis.
  44. */
  45. length_a: float,
  46. /**
  47. * The length of each cell axis.
  48. */
  49. length_b: float,
  50. /**
  51. * The length of each cell axis.
  52. */
  53. length_c: float,
  54. },
  55. /**
  56. * The CATEGORY of data items which describe the composition and
  57. * chemical properties of the compound under study. The formula data
  58. * items must be consistent with the density, unit-cell and Z values.
  59. */
  60. chemical: {
  61. /**
  62. * The temperature at which a crystalline solid changes to a liquid.
  63. */
  64. melting_point: float,
  65. /**
  66. * Trivial name by which the compound is commonly known.
  67. */
  68. name_common: str,
  69. /**
  70. * IUPAC or Chemical Abstracts full name of compound.
  71. */
  72. name_systematic: str,
  73. },
  74. /**
  75. * The CATEGORY of data items which specify the composition and chemical
  76. * properties of the compound. The formula data items must agree
  77. * with those that specify the density, unit-cell and Z values.
  78. *
  79. * The following rules apply to the construction of the data items
  80. * _chemical_formula.analytical, *.structural and *.sum. For the
  81. * data item *.moiety the formula construction is broken up into
  82. * residues or moieties, i.e. groups of atoms that form a molecular
  83. * unit or molecular ion. The rules given below apply within each
  84. * moiety but different requirements apply to the way that moieties
  85. * are connected (see _chemical_formula.moiety).
  86. *
  87. * 1. Only recognized element symbols may be used.
  88. *
  89. * 2. Each element symbol is followed by a 'count' number. A count of
  90. * '1' may be omitted.
  91. *
  92. * 3. A space or parenthesis must separate each cluster of (element
  93. * symbol + count).
  94. *
  95. * 4. Where a group of elements is enclosed in parentheses, the
  96. * multiplier for the group must follow the closing parentheses.
  97. * That is, all element and group multipliers are assumed to be
  98. * printed as subscripted numbers. [An exception to this rule
  99. * exists for *.moiety formulae where pre- and post-multipliers
  100. * are permitted for molecular units].
  101. *
  102. * 5. Unless the elements are ordered in a manner that corresponds to
  103. * their chemical structure, as in _chemical_formula.structural,
  104. * the order of the elements within any group or moiety
  105. * depends on whether or not carbon is present. If carbon is
  106. * present, the order should be: C, then H, then the other
  107. * elements in alphabetical order of their symbol. If carbon is
  108. * not present, the elements are listed purely in alphabetic order
  109. * of their symbol. This is the 'Hill' system used by Chemical
  110. * Abstracts. This ordering is used in _chemical_formula.moiety
  111. * and _chemical_formula.sum.
  112. *
  113. * _chemical_formula.iupac '[Mo (C O)4 (C18 H33 P)2]'
  114. * _chemical_formula.moiety 'C40 H66 Mo O4 P2'
  115. * _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
  116. * _chemical_formula.sum 'C40 H66 Mo O4 P2'
  117. * _chemical_formula.weight 768.81
  118. */
  119. chemical_formula: {
  120. /**
  121. * Formula with each discrete bonded residue or ion shown as a
  122. * separate moiety. See above CHEMICAL_FORMULA for rules
  123. * for writing chemical formulae. In addition to the general
  124. * formulae requirements, the following rules apply:
  125. * 1. Moieties are separated by commas ','.
  126. * 2. The order of elements within a moiety follows general rule
  127. * 5 in CHEMICAL_FORMULA.
  128. * 3. Parentheses are not used within moieties but may surround
  129. * a moiety. Parentheses may not be nested.
  130. * 4. Charges should be placed at the end of the moiety. The
  131. * Singlege '+' or '-' may be preceded by a numerical multiplier
  132. * and should be separated from the last (element symbol +
  133. * count) by a space. Pre- or post-multipliers may be used for
  134. * individual moieties.
  135. */
  136. moiety: str,
  137. /**
  138. * Chemical formulae in which all discrete bonded residues and ions are
  139. * summed over the constituent elements, following the ordering given
  140. * in rule 5 of the CATEGORY description. Parentheses normally not used.
  141. */
  142. sum: str,
  143. /**
  144. * Mass corresponding to the formulae _chemical_formula.structural,
  145. * *_iupac, *_moiety or *_sum and, together with the Z value and cell
  146. * parameters yield the density given as _exptl_crystal.density_diffrn.
  147. */
  148. weight: float,
  149. },
  150. /**
  151. * The CATEGORY of data items used to specify space group
  152. * information about the crystal used in the diffraction measurements.
  153. *
  154. * Space-group types are identified by their number as listed in
  155. * International Tables for Crystallography Volume A, or by their
  156. * Schoenflies symbol. Specific settings of the space groups can
  157. * be identified by their Hall symbol, by specifying their
  158. * symmetry operations or generators, or by giving the
  159. * transformation that relates the specific setting to the
  160. * reference setting based on International Tables Volume A and
  161. * stored in this dictionary.
  162. *
  163. * The commonly used Hermann-Mauguin symbol determines the
  164. * space-group type uniquely but several different Hermann-Mauguin
  165. * symbols may refer to the same space-group type. A
  166. * Hermann-Mauguin symbol contains information on the choice of
  167. * the basis, but not on the choice of origin.
  168. *
  169. * Ref: International Tables for Crystallography (2002). Volume A,
  170. * Space-group symmetry, edited by Th. Hahn, 5th ed.
  171. * Dordrecht: Kluwer Academic Publishers.
  172. */
  173. space_group: {
  174. /**
  175. * The name of the system of geometric crystal classes of space
  176. * groups (crystal system) to which the space group belongs.
  177. * Note that rhombohedral space groups belong to the
  178. * trigonal system.
  179. */
  180. crystal_system: str,
  181. /**
  182. * The number as assigned in International Tables for Crystallography
  183. * Vol A, specifying the proper affine class (i.e. the orientation
  184. * preserving affine class) of space groups (crystallographic space
  185. * group type) to which the space group belongs. This number defines
  186. * the space group type but not the coordinate system expressed.
  187. */
  188. IT_number: int,
  189. /**
  190. * The full international Hermann-Mauguin space-group symbol as
  191. * defined in Section 2.2.3 and given as the second item of the
  192. * second line of each of the space-group tables of Part 7 of
  193. * International Tables for Crystallography Volume A (2002).
  194. *
  195. * Each component of the space-group name is separated by a
  196. * space or an underscore character. The use of a space is
  197. * strongly recommended. The underscore is only retained
  198. * because it was used in old CIFs. It should not be used in
  199. * new CIFs.
  200. *
  201. * Subscripts should appear without special symbols. Bars should
  202. * be given as negative signs before the numbers to which they
  203. * apply. The commonly used Hermann-Mauguin symbol determines the
  204. * space-group type uniquely but a given space-group type may
  205. * be described by more than one Hermann-Mauguin symbol. The
  206. * space-group type is best described using
  207. * _space_group.IT_number or _space_group.name_Schoenflies. The
  208. * full international Hermann-Mauguin symbol contains information
  209. * about the choice of basis for monoclinic and orthorhombic
  210. * space groups but does not give information about the choice
  211. * of origin. To define the setting uniquely use
  212. * _space_group.name_Hall, or list the symmetry operations
  213. * or generators.
  214. *
  215. * Ref: International Tables for Crystallography (2002). Volume A,
  216. * Space-group symmetry, edited by Th. Hahn, 5th ed.
  217. * Dordrecht: Kluwer Academic Publishers.
  218. */
  219. 'name_H-M_full': str,
  220. },
  221. /**
  222. * The CATEGORY of data items used to describe symmetry equivalent sites
  223. * in the crystal unit cell.
  224. */
  225. space_group_symop: {
  226. /**
  227. * A parsable string giving one of the symmetry operations of the
  228. * space group in algebraic form. If W is a matrix representation
  229. * of the rotational part of the symmetry operation defined by the
  230. * positions and signs of x, y and z, and w is a column of
  231. * translations defined by fractions, an equivalent position
  232. * X' is generated from a given position X by the equation
  233. *
  234. * X' = WX + w
  235. *
  236. * (Note: X is used to represent bold_italics_x in International
  237. * Tables for Crystallography Vol. A, Part 5)
  238. *
  239. * When a list of symmetry operations is given, it must contain
  240. * a complete set of coordinate representatives which generates
  241. * all the operations of the space group by the addition of
  242. * all primitive translations of the space group. Such
  243. * representatives are to be found as the coordinates of
  244. * the general-equivalent position in International Tables for
  245. * Crystallography Vol. A (2002), to which it is necessary to
  246. * add any centring translations shown above the
  247. * general-equivalent position.
  248. *
  249. * That is to say, it is necessary to list explicitly all the
  250. * symmetry operations required to generate all the atoms in
  251. * the unit cell defined by the setting used.
  252. */
  253. operation_xyz: str,
  254. },
  255. /**
  256. * The CATEGORY of data items used to specify the geometry bonds in the
  257. * structural model as derived from the atomic sites.
  258. */
  259. geom_bond: {
  260. /**
  261. * This label is a unique identifier for a particular site in the
  262. * asymmetric unit of the crystal unit cell.
  263. */
  264. atom_site_label_1: str,
  265. /**
  266. * This label is a unique identifier for a particular site in the
  267. * asymmetric unit of the crystal unit cell.
  268. */
  269. atom_site_label_2: str,
  270. /**
  271. * Intramolecular bond distance between the sites identified
  272. * by _geom_bond.id
  273. */
  274. distance: float,
  275. /**
  276. * This code signals whether the angle is referred to in a
  277. * publication or should be placed in a table of significant angles.
  278. */
  279. publ_flag: str,
  280. /**
  281. * The set of data items which specify the symmetry operation codes
  282. * which must be applied to the atom sites involved in the geometry angle.
  283. *
  284. * The symmetry code of each atom site as the symmetry-equivalent position
  285. * number 'n' and the cell translation number 'pqr'. These numbers are
  286. * combined to form the code 'n pqr' or n_pqr.
  287. *
  288. * The character string n_pqr is composed as follows:
  289. *
  290. * n refers to the symmetry operation that is applied to the
  291. * coordinates stored in _atom_site.fract_xyz. It must match a
  292. * number given in _symmetry_equiv.pos_site_id.
  293. *
  294. * p, q and r refer to the translations that are subsequently
  295. * applied to the symmetry transformed coordinates to generate
  296. * the atom used in calculating the angle. These translations
  297. * (x,y,z) are related to (p,q,r) by the relations
  298. * p = 5 + x
  299. * q = 5 + y
  300. * r = 5 + z
  301. */
  302. site_symmetry_1: str,
  303. /**
  304. * The set of data items which specify the symmetry operation codes
  305. * which must be applied to the atom sites involved in the geometry angle.
  306. *
  307. * The symmetry code of each atom site as the symmetry-equivalent position
  308. * number 'n' and the cell translation number 'pqr'. These numbers are
  309. * combined to form the code 'n pqr' or n_pqr.
  310. *
  311. * The character string n_pqr is composed as follows:
  312. *
  313. * n refers to the symmetry operation that is applied to the
  314. * coordinates stored in _atom_site.fract_xyz. It must match a
  315. * number given in _symmetry_equiv.pos_site_id.
  316. *
  317. * p, q and r refer to the translations that are subsequently
  318. * applied to the symmetry transformed coordinates to generate
  319. * the atom used in calculating the angle. These translations
  320. * (x,y,z) are related to (p,q,r) by the relations
  321. * p = 5 + x
  322. * q = 5 + y
  323. * r = 5 + z
  324. */
  325. site_symmetry_2: str,
  326. /**
  327. * Bond valence calculated from the bond distance.
  328. */
  329. valence: float,
  330. },
  331. /**
  332. * The CATEGORY of data items used to record details about the
  333. * creation and subsequent updating of the data block.
  334. */
  335. audit: {
  336. /**
  337. * The digital object identifier (DOI) registered to identify
  338. * the data set publication represented by the current
  339. * datablock. This can be used as a unique identifier for
  340. * the datablock so long as the code used is a valid DOI
  341. * (i.e. begins with a valid publisher prefix assigned by a
  342. * Registration Agency and a suffix guaranteed to be unique
  343. * by the publisher) and has had its metadata deposited
  344. * with a DOI Registration Agency.
  345. *
  346. * A DOI is a unique character string identifying any
  347. * object of intellectual property. It provides a
  348. * persistent identifier for an object on a digital network
  349. * and permits the association of related current data in a
  350. * structured extensible way. A DOI is an implementation
  351. * of the Internet concepts of Uniform Resource Name and
  352. * Universal Resource Locator managed according to the
  353. * specifications of the International DOI Foundation (see
  354. * http://www.doi.org).
  355. */
  356. block_doi: str,
  357. },
  358. /**
  359. * The CATEGORY of data items recording database deposition. These data items
  360. * are assigned by database managers and should only appear in a CIF if they
  361. * originate from that source.
  362. */
  363. database_code: {
  364. /**
  365. * Code assigned by Crystallography Open Database (COD).
  366. */
  367. COD: str,
  368. /**
  369. * Code assigned by the Cambridge Structural Database.
  370. */
  371. CSD: str,
  372. /**
  373. * Deposition numbers assigned by the Cambridge Crystallographic
  374. * Data Centre (CCDC) to files containing structural information
  375. * archived by the CCDC.
  376. */
  377. depnum_ccdc_archive: str,
  378. /**
  379. * Deposition numbers assigned by the Fachinformationszentrum
  380. * Karlsruhe (FIZ) to files containing structural information
  381. * archived by the Cambridge Crystallographic Data Centre (CCDC).
  382. */
  383. depnum_ccdc_fiz: str,
  384. /**
  385. * Code assigned by the Inorganic Crystal Structure Database.
  386. */
  387. ICSD: str,
  388. /**
  389. * Code assigned in the Metals Data File.
  390. */
  391. MDF: str,
  392. /**
  393. * Code assigned by the NBS (NIST) Crystal Data Database.
  394. */
  395. NBS: str,
  396. },
  397. /**
  398. * The CATEGORY of data items used to describe atom site information
  399. * used in crystallographic structure studies.
  400. */
  401. atom_site: {
  402. /**
  403. * Code for type of atomic displacement parameters used for the site.
  404. */
  405. adp_type: str,
  406. /**
  407. * A standard code to signal if the site coordinates have been
  408. * determined from the intensities or calculated from the geometry
  409. * of surrounding sites, or have been assigned dummy coordinates.
  410. */
  411. calc_flag: str,
  412. /**
  413. * A code which identifies a cluster of atoms that show long range
  414. * positional disorder but are locally ordered. Within each such
  415. * cluster of atoms, _atom_site.disorder_group is used to identify
  416. * the sites that are simultaneously occupied. This field is only
  417. * needed if there is more than one cluster of disordered atoms
  418. * showing independent local order.
  419. */
  420. disorder_assembly: str,
  421. /**
  422. * A code that identifies a group of positionally disordered atom
  423. * sites that are locally simultaneously occupied. Atoms that are
  424. * positionally disordered over two or more sites (e.g. the H
  425. * atoms of a methyl group that exists in two orientations) can
  426. * be assigned to two or more groups. Sites belonging to the same
  427. * group are simultaneously occupied, but those belonging to
  428. * different groups are not. A minus prefix (e.g. "-1") is used to
  429. * indicate sites disordered about a special position.
  430. */
  431. disorder_group: str,
  432. /**
  433. * Atom site coordinates as fractions of the cell length values.
  434. */
  435. fract_x: float,
  436. /**
  437. * Atom site coordinates as fractions of the cell length values.
  438. */
  439. fract_y: float,
  440. /**
  441. * Atom site coordinates as fractions of the cell length values.
  442. */
  443. fract_z: float,
  444. /**
  445. * This label is a unique identifier for a particular site in the
  446. * asymmetric unit of the crystal unit cell. It is made up of
  447. * components, _atom_site.label_component_0 to *_6, which may be
  448. * specified as separate data items. Component 0 usually matches one
  449. * of the specified _atom_type.symbol codes. This is not mandatory
  450. * if an _atom_site.type_symbol item is included in the atom site
  451. * list. The _atom_site.type_symbol always takes precedence over
  452. * an _atom_site.label in the identification of the atom type. The
  453. * label components 1 to 6 are optional, and normally only
  454. * components 0 and 1 are used. Note that components 0 and 1 are
  455. * concatenated, while all other components, if specified, are
  456. * separated by an underline character. Underline separators are
  457. * only used if higher-order components exist. If an intermediate
  458. * component is not used it may be omitted provided the underline
  459. * separators are inserted. For example the label 'C233__ggg' is
  460. * acceptable and represents the components C, 233, '', and ggg.
  461. * Each label may have a different number of components.
  462. */
  463. label: str,
  464. /**
  465. * The fraction of the atom type present at this site.
  466. * The sum of the occupancies of all the atom types at this site
  467. * may not significantly exceed 1.0 unless it is a dummy site. The
  468. * value must lie in the 99.97% Gaussian confidence interval
  469. * -3u =< x =< 1 + 3u. The _enumeration.range of 0.0:1.0 is thus
  470. * correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
  471. */
  472. occupancy: float,
  473. /**
  474. * A concatenated series of single-letter codes which indicate the
  475. * refinement restraints or constraints applied to this site. This
  476. * item should not be used. It has been replaced by
  477. * _atom_site.refinement_flags_posn, _adp and _occupancy. It is
  478. * retained in this dictionary only to provide compatibility with
  479. * legacy CIFs.
  480. */
  481. refinement_flags: str,
  482. /**
  483. * The number of different sites that are generated by the
  484. * application of the space-group symmetry to the coordinates
  485. * given for this site. It is equal to the multiplicity given
  486. * for this Wyckoff site in International Tables for Cryst.
  487. * Vol. A (2002). It is equal to the multiplicity of the general
  488. * position divided by the order of the site symmetry given in
  489. * _atom_site.site_symmetry_order.
  490. */
  491. site_symmetry_multiplicity: int,
  492. /**
  493. * A code to identify the atom specie(s) occupying this site.
  494. * This code must match a corresponding _atom_type.symbol. The
  495. * specification of this code is optional if component_0 of the
  496. * _atom_site.label is used for this purpose. See _atom_type.symbol.
  497. */
  498. type_symbol: str,
  499. /**
  500. * Isotropic atomic displacement parameter, or equivalent isotropic
  501. * atomic displacement parameter, U(equiv), in angstroms squared,
  502. * calculated from anisotropic atomic displacement parameters.
  503. *
  504. * U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
  505. *
  506. * a = the real-space cell lengths
  507. * a* = the reciprocal-space cell lengths
  508. * Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
  509. */
  510. U_iso_or_equiv: float,
  511. },
  512. /**
  513. * The CATEGORY of data items used to describe the anisotropic
  514. * thermal parameters of the atomic sites in a crystal structure.
  515. */
  516. atom_site_aniso: {
  517. /**
  518. * Anisotropic atomic displacement parameters are usually looped in
  519. * a separate list. If this is the case, this code must match the
  520. * _atom_site.label of the associated atom in the atom coordinate
  521. * list and conform with the same rules described in _atom_site.label.
  522. */
  523. label: str,
  524. /**
  525. * These are the standard anisotropic atomic displacement
  526. * components in angstroms squared which appear in the
  527. * structure factor term:
  528. *
  529. * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
  530. *
  531. * h = the Miller indices
  532. * a* = the reciprocal-space cell lengths
  533. *
  534. * The unique elements of the real symmetric matrix are entered by row.
  535. */
  536. U_11: float,
  537. /**
  538. * These are the standard anisotropic atomic displacement
  539. * components in angstroms squared which appear in the
  540. * structure factor term:
  541. *
  542. * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
  543. *
  544. * h = the Miller indices
  545. * a* = the reciprocal-space cell lengths
  546. *
  547. * The unique elements of the real symmetric matrix are entered by row.
  548. */
  549. U: Matrix(3, 3),
  550. /**
  551. * These are the standard uncertainty values (SU) for the standard
  552. * form of the Uij anisotropic atomic displacement components (see
  553. * _aniso_UIJ. Because these values are TYPE measurand, the su values
  554. * may in practice be auto generated as part of the Uij calculation.
  555. */
  556. U_11_su: float,
  557. /**
  558. * These are the standard uncertainty values (SU) for the standard
  559. * form of the Uij anisotropic atomic displacement components (see
  560. * _aniso_UIJ. Because these values are TYPE measurand, the su values
  561. * may in practice be auto generated as part of the Uij calculation.
  562. */
  563. U_su: Matrix(3, 3),
  564. /**
  565. * These are the standard anisotropic atomic displacement
  566. * components in angstroms squared which appear in the
  567. * structure factor term:
  568. *
  569. * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
  570. *
  571. * h = the Miller indices
  572. * a* = the reciprocal-space cell lengths
  573. *
  574. * The unique elements of the real symmetric matrix are entered by row.
  575. */
  576. U_12: float,
  577. /**
  578. * These are the standard uncertainty values (SU) for the standard
  579. * form of the Uij anisotropic atomic displacement components (see
  580. * _aniso_UIJ. Because these values are TYPE measurand, the su values
  581. * may in practice be auto generated as part of the Uij calculation.
  582. */
  583. U_12_su: float,
  584. /**
  585. * These are the standard anisotropic atomic displacement
  586. * components in angstroms squared which appear in the
  587. * structure factor term:
  588. *
  589. * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
  590. *
  591. * h = the Miller indices
  592. * a* = the reciprocal-space cell lengths
  593. *
  594. * The unique elements of the real symmetric matrix are entered by row.
  595. */
  596. U_13: float,
  597. /**
  598. * These are the standard uncertainty values (SU) for the standard
  599. * form of the Uij anisotropic atomic displacement components (see
  600. * _aniso_UIJ. Because these values are TYPE measurand, the su values
  601. * may in practice be auto generated as part of the Uij calculation.
  602. */
  603. U_13_su: float,
  604. /**
  605. * These are the standard anisotropic atomic displacement
  606. * components in angstroms squared which appear in the
  607. * structure factor term:
  608. *
  609. * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
  610. *
  611. * h = the Miller indices
  612. * a* = the reciprocal-space cell lengths
  613. *
  614. * The unique elements of the real symmetric matrix are entered by row.
  615. */
  616. U_22: float,
  617. /**
  618. * These are the standard uncertainty values (SU) for the standard
  619. * form of the Uij anisotropic atomic displacement components (see
  620. * _aniso_UIJ. Because these values are TYPE measurand, the su values
  621. * may in practice be auto generated as part of the Uij calculation.
  622. */
  623. U_22_su: float,
  624. /**
  625. * These are the standard anisotropic atomic displacement
  626. * components in angstroms squared which appear in the
  627. * structure factor term:
  628. *
  629. * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
  630. *
  631. * h = the Miller indices
  632. * a* = the reciprocal-space cell lengths
  633. *
  634. * The unique elements of the real symmetric matrix are entered by row.
  635. */
  636. U_23: float,
  637. /**
  638. * These are the standard uncertainty values (SU) for the standard
  639. * form of the Uij anisotropic atomic displacement components (see
  640. * _aniso_UIJ. Because these values are TYPE measurand, the su values
  641. * may in practice be auto generated as part of the Uij calculation.
  642. */
  643. U_23_su: float,
  644. /**
  645. * These are the standard anisotropic atomic displacement
  646. * components in angstroms squared which appear in the
  647. * structure factor term:
  648. *
  649. * T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
  650. *
  651. * h = the Miller indices
  652. * a* = the reciprocal-space cell lengths
  653. *
  654. * The unique elements of the real symmetric matrix are entered by row.
  655. */
  656. U_33: float,
  657. /**
  658. * These are the standard uncertainty values (SU) for the standard
  659. * form of the Uij anisotropic atomic displacement components (see
  660. * _aniso_UIJ. Because these values are TYPE measurand, the su values
  661. * may in practice be auto generated as part of the Uij calculation.
  662. */
  663. U_33_su: float,
  664. },
  665. /**
  666. * The CATEGORY of data items used to describe atomic type information
  667. * used in crystallographic structure studies.
  668. */
  669. atom_type: {
  670. /**
  671. * A description of the atom(s) designated by this atom type. In
  672. * most cases this will be the element name and oxidation state of
  673. * a single atom species. For disordered or nonstoichiometric
  674. * structures it will describe a combination of atom species.
  675. */
  676. description: str,
  677. /**
  678. * The identity of the atom specie(s) representing this atom type.
  679. * Normally this code is the element symbol followed by the charge
  680. * if there is one. The symbol may be composed of any character except
  681. * an underline or a blank, with the proviso that digits designate an
  682. * oxidation state and must be followed by a + or - character.
  683. */
  684. symbol: str,
  685. },
  686. /**
  687. * The CATEGORY of data items used to describe atomic scattering
  688. * information used in crystallographic structure studies.
  689. */
  690. atom_type_scat: {
  691. /**
  692. * The imaginary component of the anomalous dispersion scattering factors
  693. * for this atom type and radiation by _diffrn_radiation_wavelength.value
  694. */
  695. dispersion_imag: float,
  696. /**
  697. * The real component of the anomalous dispersion scattering factors
  698. * for this atom type and radiation by _diffrn_radiation_wavelength.value
  699. */
  700. dispersion_real: float,
  701. /**
  702. * Reference to source of scattering factors used for this atom type.
  703. */
  704. source: str,
  705. },
  706. }
  707. export const CifCore_Aliases = {
  708. 'atom_site_aniso.U': [
  709. 'atom_site_anisotrop_U',
  710. ],
  711. 'atom_site_aniso.U_su': [
  712. 'atom_site_aniso_U_esd',
  713. 'atom_site_anisotrop_U_esd',
  714. ],
  715. 'space_group.IT_number': [
  716. 'symmetry_Int_Tables_number',
  717. ],
  718. 'space_group.name_H-M_full': [
  719. 'symmetry_space_group_name_H-M',
  720. ],
  721. 'space_group_symop.operation_xyz': [
  722. 'symmetry_equiv_pos_as_xyz',
  723. ],
  724. 'geom_bond.atom_site_label_1': [
  725. 'geom_bond_atom_site_id_1',
  726. ],
  727. 'geom_bond.atom_site_label_2': [
  728. 'geom_bond_atom_site_id_2',
  729. ],
  730. 'geom_bond.distance': [
  731. 'geom_bond_dist',
  732. ],
  733. 'atom_site.adp_type': [
  734. 'atom_site_thermal_displace_type',
  735. ],
  736. 'atom_site.label': [
  737. 'atom_site_id',
  738. ],
  739. 'atom_site.site_symmetry_multiplicity': [
  740. 'atom_site_symmetry_multiplicity',
  741. ],
  742. 'atom_site_aniso.label': [
  743. 'atom_site_anisotrop_id',
  744. ],
  745. 'atom_site_aniso.U_11': [
  746. 'atom_site_anisotrop_U_11',
  747. ],
  748. 'atom_site_aniso.U_11_su': [
  749. 'atom_site_aniso_U_11_esd',
  750. 'atom_site_anisotrop_U_11_esd',
  751. ],
  752. 'atom_site_aniso.U_12': [
  753. 'atom_site_anisotrop_U_12',
  754. ],
  755. 'atom_site_aniso.U_12_su': [
  756. 'atom_site_aniso_U_12_esd',
  757. 'atom_site_anisotrop_U_12_esd',
  758. ],
  759. 'atom_site_aniso.U_13': [
  760. 'atom_site_anisotrop_U_13',
  761. ],
  762. 'atom_site_aniso.U_13_su': [
  763. 'atom_site_aniso_U_13_esd',
  764. 'atom_site_anisotrop_U_13_esd',
  765. ],
  766. 'atom_site_aniso.U_22': [
  767. 'atom_site_anisotrop_U_22',
  768. ],
  769. 'atom_site_aniso.U_22_su': [
  770. 'atom_site_aniso_U_22_esd',
  771. 'atom_site_anisotrop_U_22_esd',
  772. ],
  773. 'atom_site_aniso.U_23': [
  774. 'atom_site_anisotrop_U_23',
  775. ],
  776. 'atom_site_aniso.U_23_su': [
  777. 'atom_site_aniso_U_23_esd',
  778. 'atom_site_anisotrop_U_23_esd',
  779. ],
  780. 'atom_site_aniso.U_33': [
  781. 'atom_site_anisotrop_U_33',
  782. ],
  783. 'atom_site_aniso.U_33_su': [
  784. 'atom_site_aniso_U_33_esd',
  785. 'atom_site_anisotrop_U_33_esd',
  786. ],
  787. }
  788. export type CifCore_Schema = typeof CifCore_Schema;
  789. export interface CifCore_Database extends Database<CifCore_Schema> {}