molstar
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A comprehensive macromolecular library.
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/**
* Copyright (c) 2017-2020 mol* contributors, licensed under MIT, See LICENSE file for more info.
*
* Code-generated 'CifCore' schema file. Dictionary versions: CifCore 3.1.0.
*
* @author molstar/ciftools package
*/
import { Database, Column } from '../../../../mol-data/db';
import Schema = Column.Schema;
export declare const CifCore_Schema: {
/**
* The CATEGORY of data items used to describe the parameters of
* the crystal unit cell and their measurement.
*/
cell: {
/**
* The angle between the bounding cell axes.
*/
angle_alpha: Schema.Float;
/**
* The angle between the bounding cell axes.
*/
angle_beta: Schema.Float;
/**
* The angle between the bounding cell axes.
*/
angle_gamma: Schema.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: Schema.Int;
/**
* The length of each cell axis.
*/
length_a: Schema.Float;
/**
* The length of each cell axis.
*/
length_b: Schema.Float;
/**
* The length of each cell axis.
*/
length_c: Schema.Float;
/**
* Volume of the crystal unit cell.
*/
volume: Schema.Float;
};
/**
* The CATEGORY of data items which describe the composition and
* chemical properties of the compound under study. The formula data
* items must be consistent with the density, unit-cell and Z values.
*/
chemical: {
/**
* The temperature at which a crystalline solid changes to a liquid.
*/
melting_point: Schema.Float;
/**
* Trivial name by which the compound is commonly known.
*/
name_common: Schema.Str;
/**
* IUPAC or Chemical Abstracts full name of compound.
*/
name_systematic: Schema.Str;
};
/**
* The CATEGORY of data items which specify the composition and chemical
* properties of the compound. The formula data items must agree
* with those that specify the density, unit-cell and Z values.
*
* The following rules apply to the construction of the data items
* _chemical_formula.analytical, *.structural and *.sum. For the
* data item *.moiety the formula construction is broken up into
* residues or moieties, i.e. groups of atoms that form a molecular
* unit or molecular ion. The rules given below apply within each
* moiety but different requirements apply to the way that moieties
* are connected (see _chemical_formula.moiety).
*
* 1. Only recognized element symbols may be used.
*
* 2. Each element symbol is followed by a 'count' number. A count of
* '1' may be omitted.
*
* 3. A space or parenthesis must separate each cluster of (element
* symbol + count).
*
* 4. Where a group of elements is enclosed in parentheses, the
* multiplier for the group must follow the closing parentheses.
* That is, all element and group multipliers are assumed to be
* printed as subscripted numbers. [An exception to this rule
* exists for *.moiety formulae where pre- and post-multipliers
* are permitted for molecular units].
*
* 5. Unless the elements are ordered in a manner that corresponds to
* their chemical structure, as in _chemical_formula.structural,
* the order of the elements within any group or moiety
* depends on whether or not carbon is present. If carbon is
* present, the order should be: C, then H, then the other
* elements in alphabetical order of their symbol. If carbon is
* not present, the elements are listed purely in alphabetic order
* of their symbol. This is the 'Hill' system used by Chemical
* Abstracts. This ordering is used in _chemical_formula.moiety
* and _chemical_formula.sum.
*
* _chemical_formula.iupac '[Mo (C O)4 (C18 H33 P)2]'
* _chemical_formula.moiety 'C40 H66 Mo O4 P2'
* _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo'
* _chemical_formula.sum 'C40 H66 Mo O4 P2'
* _chemical_formula.weight 768.81
*/
chemical_formula: {
/**
* Formula with each discrete bonded residue or ion shown as a
* separate moiety. See above CHEMICAL_FORMULA for rules
* for writing chemical formulae. In addition to the general
* formulae requirements, the following rules apply:
* 1. Moieties are separated by commas ','.
* 2. The order of elements within a moiety follows general rule
* 5 in CHEMICAL_FORMULA.
* 3. Parentheses are not used within moieties but may surround
* a moiety. Parentheses may not be nested.
* 4. Charges should be placed at the end of the moiety. The
* Singlege '+' or '-' may be preceded by a numerical multiplier
* and should be separated from the last (element symbol +
* count) by a space. Pre- or post-multipliers may be used for
* individual moieties.
*/
moiety: Schema.Str;
/**
* Chemical formulae in which all discrete bonded residues and ions are
* summed over the constituent elements, following the ordering given
* in rule 5 of the CATEGORY description. Parentheses normally not used.
*/
sum: Schema.Str;
/**
* Mass corresponding to the formulae _chemical_formula.structural,
* *_iupac, *_moiety or *_sum and, together with the Z value and cell
* parameters yield the density given as _exptl_crystal.density_diffrn.
*/
weight: Schema.Float;
};
/**
* The CATEGORY of data items used to specify space group
* information about the crystal used in the diffraction measurements.
*
* Space-group types are identified by their number as listed in
* International Tables for Crystallography Volume A, or by their
* Schoenflies symbol. Specific settings of the space groups can
* be identified by their Hall symbol, by specifying their
* symmetry operations or generators, or by giving the
* transformation that relates the specific setting to the
* reference setting based on International Tables Volume A and
* stored in this dictionary.
*
* The commonly used Hermann-Mauguin symbol determines the
* space-group type uniquely but several different Hermann-Mauguin
* symbols may refer to the same space-group type. A
* Hermann-Mauguin symbol contains information on the choice of
* the basis, but not on the choice of origin.
*
* Ref: International Tables for Crystallography (2002). Volume A,
* Space-group symmetry, edited by Th. Hahn, 5th ed.
* Dordrecht: Kluwer Academic Publishers.
*/
space_group: {
/**
* The name of the system of geometric crystal classes of space
* groups (crystal system) to which the space group belongs.
* Note that rhombohedral space groups belong to the
* trigonal system.
*/
crystal_system: Schema.Str;
/**
* The number as assigned in International Tables for Crystallography
* Vol. A, specifying the proper affine class (i.e. the orientation
* preserving affine class) of space groups (crystallographic space
* group type) to which the space group belongs. This number defines
* the space group type but not the coordinate system expressed.
*/
it_number: Schema.Int;
/**
* The full international Hermann-Mauguin space-group symbol as
* defined in Section 2.2.3 and given as the second item of the
* second line of each of the space-group tables of Part 7 of
* International Tables for Crystallography Volume A (2002).
*
* Each component of the space-group name is separated by a
* space or an underscore character. The use of a space is
* strongly recommended. The underscore is only retained
* because it was used in old CIFs. It should not be used in
* new CIFs.
*
* Subscripts should appear without special symbols. Bars should
* be given as negative signs before the numbers to which they
* apply. The commonly used Hermann-Mauguin symbol determines the
* space-group type uniquely but a given space-group type may
* be described by more than one Hermann-Mauguin symbol. The
* space-group type is best described using
* _space_group.IT_number or _space_group.name_Schoenflies. The
* full international Hermann-Mauguin symbol contains information
* about the choice of basis for monoclinic and orthorhombic
* space groups but does not give information about the choice
* of origin. To define the setting uniquely use
* _space_group.name_Hall, or list the symmetry operations
* or generators.
*
* Ref: International Tables for Crystallography (2002). Volume A,
* Space-group symmetry, edited by Th. Hahn, 5th ed.
* Dordrecht: Kluwer Academic Publishers.
*/
'name_h-m_full': Schema.Str;
};
/**
* The CATEGORY of data items used to describe symmetry equivalent sites
* in the crystal unit cell.
*/
space_group_symop: {
/**
* A parsable string giving one of the symmetry operations of the
* space group in algebraic form. If W is a matrix representation
* of the rotational part of the symmetry operation defined by the
* positions and signs of x, y and z, and w is a column of
* translations defined by fractions, an equivalent position
* X' is generated from a given position X by the equation
*
* X' = WX + w
*
* (Note: X is used to represent bold_italics_x in International
* Tables for Crystallography Vol. A, Part 5)
*
* When a list of symmetry operations is given, it must contain
* a complete set of coordinate representatives which generates
* all the operations of the space group by the addition of
* all primitive translations of the space group. Such
* representatives are to be found as the coordinates of
* the general-equivalent position in International Tables for
* Crystallography Vol. A (2002), to which it is necessary to
* add any centring translations shown above the
* general-equivalent position.
*
* That is to say, it is necessary to list explicitly all the
* symmetry operations required to generate all the atoms in
* the unit cell defined by the setting used.
*/
operation_xyz: Schema.Str;
};
/**
* The CATEGORY of data items used to specify the geometry bonds in the
* structural model as derived from the atomic sites.
*/
geom_bond: {
/**
* This label is a unique identifier for a particular site in the
* asymmetric unit of the crystal unit cell.
*/
atom_site_label_1: Schema.Str;
/**
* This label is a unique identifier for a particular site in the
* asymmetric unit of the crystal unit cell.
*/
atom_site_label_2: Schema.Str;
/**
* Intramolecular bond distance between the sites identified
* by _geom_bond.id
*/
distance: Schema.Float;
/**
* This code signals whether the angle is referred to in a
* publication or should be placed in a table of significant angles.
*/
publ_flag: Schema.Str;
/**
* The set of data items which specify the symmetry operation codes
* which must be applied to the atom sites involved in the geometry angle.
*
* The symmetry code of each atom site as the symmetry-equivalent position
* number 'n' and the cell translation number 'pqr'. These numbers are
* combined to form the code 'n pqr' or n_pqr.
*
* The character string n_pqr is composed as follows:
*
* n refers to the symmetry operation that is applied to the
* coordinates stored in _atom_site.fract_xyz. It must match a
* number given in _symmetry_equiv.pos_site_id.
*
* p, q and r refer to the translations that are subsequently
* applied to the symmetry transformed coordinates to generate
* the atom used in calculating the angle. These translations
* (x,y,z) are related to (p,q,r) by the relations
* p = 5 + x
* q = 5 + y
* r = 5 + z
*/
site_symmetry_1: Schema.Str;
/**
* The set of data items which specify the symmetry operation codes
* which must be applied to the atom sites involved in the geometry angle.
*
* The symmetry code of each atom site as the symmetry-equivalent position
* number 'n' and the cell translation number 'pqr'. These numbers are
* combined to form the code 'n pqr' or n_pqr.
*
* The character string n_pqr is composed as follows:
*
* n refers to the symmetry operation that is applied to the
* coordinates stored in _atom_site.fract_xyz. It must match a
* number given in _symmetry_equiv.pos_site_id.
*
* p, q and r refer to the translations that are subsequently
* applied to the symmetry transformed coordinates to generate
* the atom used in calculating the angle. These translations
* (x,y,z) are related to (p,q,r) by the relations
* p = 5 + x
* q = 5 + y
* r = 5 + z
*/
site_symmetry_2: Schema.Str;
/**
* Bond valence calculated from the bond distance.
*/
valence: Schema.Float;
};
/**
* The CATEGORY of data items used to record details about the
* creation and subsequent updating of the data block.
*/
audit: {
/**
* The digital object identifier (DOI) registered to identify
* the data set publication represented by the current
* data block. This can be used as a unique identifier for
* the data block so long as the code used is a valid DOI
* (i.e. begins with a valid publisher prefix assigned by a
* Registration Agency and a suffix guaranteed to be unique
* by the publisher) and has had its metadata deposited
* with a DOI Registration Agency.
*
* A DOI is a unique character string identifying any
* object of intellectual property. It provides a
* persistent identifier for an object on a digital network
* and permits the association of related current data in a
* structured extensible way. A DOI is an implementation
* of the Internet concepts of Uniform Resource Name and
* Universal Resource Locator managed according to the
* specifications of the International DOI Foundation
* (see http://www.doi.org).
*/
block_doi: Schema.Str;
};
/**
* The CATEGORY of data items recording database deposition. These data items
* are assigned by database managers and should only appear in a CIF if they
* originate from that source.
*/
database_code: {
/**
* Code assigned by the Crystallography Open Database (COD).
*/
cod: Schema.Str;
/**
* Code assigned by the Cambridge Structural Database.
*/
csd: Schema.Str;
/**
* Deposition numbers assigned by the Cambridge Crystallographic
* Data Centre (CCDC) to files containing structural information
* archived by the CCDC.
*/
depnum_ccdc_archive: Schema.Str;
/**
* Deposition numbers assigned by the Fachinformationszentrum
* Karlsruhe (FIZ) to files containing structural information
* archived by the Cambridge Crystallographic Data Centre (CCDC).
*/
depnum_ccdc_fiz: Schema.Str;
/**
* Code assigned by the Inorganic Crystal Structure Database.
*/
icsd: Schema.Str;
/**
* Code assigned in the Metals Data File.
*/
mdf: Schema.Str;
/**
* Code assigned by the NBS (NIST) Crystal Data Database.
*/
nbs: Schema.Str;
};
/**
* The CATEGORY of data items used to describe atom site information
* used in crystallographic structure studies.
*/
atom_site: {
/**
* Code for type of atomic displacement parameters used for the site.
*/
adp_type: Schema.Str;
/**
* A standard code to signal if the site coordinates have been
* determined from the intensities or calculated from the geometry
* of surrounding sites, or have been assigned dummy coordinates.
*/
calc_flag: Schema.Str;
/**
* A code which identifies a cluster of atoms that show long range
* positional disorder but are locally ordered. Within each such
* cluster of atoms, _atom_site.disorder_group is used to identify
* the sites that are simultaneously occupied. This field is only
* needed if there is more than one cluster of disordered atoms
* showing independent local order.
*/
disorder_assembly: Schema.Str;
/**
* A code that identifies a group of positionally disordered atom
* sites that are locally simultaneously occupied. Atoms that are
* positionally disordered over two or more sites (e.g. the H
* atoms of a methyl group that exists in two orientations) can
* be assigned to two or more groups. Sites belonging to the same
* group are simultaneously occupied, but those belonging to
* different groups are not. A minus prefix (e.g. "-1") is used to
* indicate sites disordered about a special position.
*/
disorder_group: Schema.Str;
/**
* Atom site coordinates as fractions of the cell length values.
*/
fract_x: Schema.Float;
/**
* Atom site coordinates as fractions of the cell length values.
*/
fract_y: Schema.Float;
/**
* Atom site coordinates as fractions of the cell length values.
*/
fract_z: Schema.Float;
/**
* This label is a unique identifier for a particular site in the
* asymmetric unit of the crystal unit cell. It is made up of
* components, _atom_site.label_component_0 to *_6, which may be
* specified as separate data items. Component 0 usually matches one
* of the specified _atom_type.symbol codes. This is not mandatory
* if an _atom_site.type_symbol item is included in the atom site
* list. The _atom_site.type_symbol always takes precedence over
* an _atom_site.label in the identification of the atom type. The
* label components 1 to 6 are optional, and normally only
* components 0 and 1 are used. Note that components 0 and 1 are
* concatenated, while all other components, if specified, are
* separated by an underline character. Underline separators are
* only used if higher-order components exist. If an intermediate
* component is not used it may be omitted provided the underline
* separators are inserted. For example the label 'C233__ggg' is
* acceptable and represents the components C, 233, '', and ggg.
* Each label may have a different number of components.
*/
label: Schema.Str;
/**
* The fraction of the atom type present at this site.
* The sum of the occupancies of all the atom types at this site
* may not significantly exceed 1.0 unless it is a dummy site. The
* value must lie in the 99.97% Gaussian confidence interval
* -3u =< x =< 1 + 3u. The _enumeration.range of 0.0:1.0 is thus
* correctly interpreted as meaning (0.0 - 3u) =< x =< (1.0 + 3u).
*/
occupancy: Schema.Float;
/**
* A concatenated series of single-letter codes which indicate the
* refinement restraints or constraints applied to this site. This
* item should not be used. It has been replaced by
* _atom_site.refinement_flags_posn, _adp and _occupancy. It is
* retained in this dictionary only to provide compatibility with
* legacy CIFs.
*/
refinement_flags: Schema.Str;
/**
* The number of different sites that are generated by the
* application of the space-group symmetry to the coordinates
* given for this site. It is equal to the multiplicity given
* for this Wyckoff site in International Tables for Cryst.
* Vol. A (2002). It is equal to the multiplicity of the general
* position divided by the order of the site symmetry given in
* _atom_site.site_symmetry_order.
*/
site_symmetry_multiplicity: Schema.Int;
/**
* A code to identify the atom specie(s) occupying this site.
* This code must match a corresponding _atom_type.symbol. The
* specification of this code is optional if component_0 of the
* _atom_site.label is used for this purpose. See _atom_type.symbol.
*/
type_symbol: Schema.Str;
/**
* Isotropic atomic displacement parameter, or equivalent isotropic
* atomic displacement parameter, U(equiv), in angstroms squared,
* calculated from anisotropic atomic displacement parameters.
*
* U(equiv) = (1/3) sum~i~[sum~j~(U^ij^ a*~i~ a*~j~ a~i~ a~j~)]
*
* a = the real-space cell lengths
* a* = the reciprocal-space cell lengths
* Ref: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.
*/
u_iso_or_equiv: Schema.Float;
};
/**
* The CATEGORY of data items used to describe the anisotropic
* thermal parameters of the atomic sites in a crystal structure.
*/
atom_site_aniso: {
/**
* Anisotropic atomic displacement parameters are usually looped in
* a separate list. If this is the case, this code must match the
* _atom_site.label of the associated atom in the atom coordinate
* list and conform with the same rules described in _atom_site.label.
*/
label: Schema.Str;
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
* structure factor term:
*
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
*
* h = the Miller indices
* a* = the reciprocal-space cell lengths
*
* The unique elements of the real symmetric matrix are entered by row.
*/
u_11: Schema.Float;
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
* structure factor term:
*
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
*
* h = the Miller indices
* a* = the reciprocal-space cell lengths
*
* The unique elements of the real symmetric matrix are entered by row.
*/
u: Schema.Tensor;
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
* structure factor term:
*
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
*
* h = the Miller indices
* a* = the reciprocal-space cell lengths
*
* The unique elements of the real symmetric matrix are entered by row.
*/
u_12: Schema.Float;
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
* structure factor term:
*
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
*
* h = the Miller indices
* a* = the reciprocal-space cell lengths
*
* The unique elements of the real symmetric matrix are entered by row.
*/
u_13: Schema.Float;
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
* structure factor term:
*
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
*
* h = the Miller indices
* a* = the reciprocal-space cell lengths
*
* The unique elements of the real symmetric matrix are entered by row.
*/
u_22: Schema.Float;
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
* structure factor term:
*
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
*
* h = the Miller indices
* a* = the reciprocal-space cell lengths
*
* The unique elements of the real symmetric matrix are entered by row.
*/
u_23: Schema.Float;
/**
* These are the standard anisotropic atomic displacement
* components in angstroms squared which appear in the
* structure factor term:
*
* T = exp{-2pi^2^ sum~i~ [sum~j~ (U^ij^ h~i~ h~j~ a*~i~ a*~j~) ] }
*
* h = the Miller indices
* a* = the reciprocal-space cell lengths
*
* The unique elements of the real symmetric matrix are entered by row.
*/
u_33: Schema.Float;
};
/**
* The CATEGORY of data items used to describe atomic type information
* used in crystallographic structure studies.
*/
atom_type: {
/**
* A description of the atom(s) designated by this atom type. In
* most cases this will be the element name and oxidation state of
* a single atom species. For disordered or nonstoichiometric
* structures it will describe a combination of atom species.
*/
description: Schema.Str;
/**
* The identity of the atom specie(s) representing this atom type.
* Normally this code is the element symbol followed by the charge
* if there is one. The symbol may be composed of any character except
* an underline or a blank, with the proviso that digits designate an
* oxidation state and must be followed by a + or - character.
*/
symbol: Schema.Str;
};
/**
* The CATEGORY of data items used to describe atomic scattering
* information used in crystallographic structure studies.
*/
atom_type_scat: {
/**
* The imaginary component of the anomalous dispersion scattering factors
* for this atom type and radiation by _diffrn_radiation_wavelength.value
*/
dispersion_imag: Schema.Float;
/**
* The real component of the anomalous dispersion scattering factors
* for this atom type and radiation by _diffrn_radiation_wavelength.value
*/
dispersion_real: Schema.Float;
/**
* Reference to source of scattering factors used for this atom type.
*/
source: Schema.Str;
};
};
export declare const CifCore_Aliases: {
'cell.formula_units_z': string[];
'space_group.it_number': string[];
'space_group.name_h-m_full': string[];
'space_group_symop.operation_xyz': string[];
'geom_bond.atom_site_label_1': string[];
'geom_bond.atom_site_label_2': string[];
'geom_bond.distance': string[];
'database_code.cod': string[];
'database_code.csd': string[];
'database_code.icsd': string[];
'database_code.mdf': string[];
'database_code.nbs': string[];
'atom_site.adp_type': string[];
'atom_site.label': string[];
'atom_site.site_symmetry_multiplicity': string[];
'atom_site.u_iso_or_equiv': string[];
'atom_site_aniso.label': string[];
'atom_site_aniso.u_11': string[];
'atom_site_aniso.u_12': string[];
'atom_site_aniso.u_13': string[];
'atom_site_aniso.u_22': string[];
'atom_site_aniso.u_23': string[];
'atom_site_aniso.u_33': string[];
};
export declare type CifCore_Schema = typeof CifCore_Schema;
export interface CifCore_Database extends Database<CifCore_Schema> {
}