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CifCore CIF dictionary

Version 3.2.0 (2023-04-04)

The CIF_CORE dictionary records all the CORE data items defined and used with in the Crystallographic Information Framework (CIF).

Category tree view of data-item definitions

FUNCTION

CIF

The crystallographic functions the invoked in the definition
methods of CORE STRUCTURE data items defined and used with in
the Crystallographic Information Framework (CIF).

save_FUNCTION

    _definition.id                FUNCTION
    _definition.scope             Category
    _definition.class             Functions
    _definition.update            2012-12-18
    _description.text
;
    The crystallographic functions the invoked in the definition
    methods of CORE STRUCTURE data items defined and used with in
    the Crystallographic Information Framework (CIF).
;
    _name.category_id             CIF_CORE
    _name.object_id               FUNCTION

save_

_function.AtomType

CIF

The function

r  =  AtomType( s )

returns an atom type symbol (element name) from the atom site label.

save_function.atomtype

    _definition.id                '_function.AtomType'
    _definition.update            2021-10-27
    _description.text
;
    The function
                  r  =  AtomType( s )

    returns an atom type symbol (element name) from the atom site label.
;
    _name.category_id             function
    _name.object_id               AtomType
    _type.purpose                 Encode
    _type.source                  Assigned
    _type.container               Single
    _type.contents                Word
    _method.purpose               Evaluation
    _method.expression
;
    Function AtomType( s :[Single, Word])  {  # atom label

       m = Len(s)
       n = 1
       If (m > 1 and s[1] not in '0123456789') n = 2
       If (m > 2 and s[2]     in '+-'        ) n = 3
       If (m > 3 and s[3]     in '+-'        ) n = 4

                AtomType =  s[0:n]
    }
;

save_

_function.Closest

CIF

The function

d  =  Closest( v, w )

returns the cell translation vector required to obtain the

closest cell-translated occurrence of the vector V to the vector

W.

save_function.closest

    _definition.id                '_function.Closest'
    _definition.update            2021-03-03
    _description.text
;
    The function
                  d  =  Closest( v, w )

    returns the cell translation vector required to obtain the
    closest cell-translated occurrence of the vector V to the vector
    W.
;
    _name.category_id             function
    _name.object_id               Closest
    _type.purpose                 Number
    _type.source                  Derived
    _type.container               Matrix
    _type.dimension               '[3]'
    _type.contents                Real
    _units.code                   none
    _method.purpose               Evaluation
    _method.expression
;
    Function Closest( v :[Matrix, Real],   # coord vector to be cell translated
                      w :[Matrix, Real]) { # target vector

           d  =  v - w
           Closest  =  Int( Mod( 99.5 + d, 1.0 ) - d )
    }
;

save_

_function.SeitzFromJones

CIF

The function

s  =  SeitzFromJones( j )

returns a 4x4 Seitz matrix from the Jones faithful representation of

the equivalent position which is a character string e.g. 1/2+x,-x,z.

save_function.seitzfromjones

    _definition.id                '_function.SeitzFromJones'
    _definition.update            2021-03-01
    _description.text
;
    The function
                  s  =  SeitzFromJones( j )

    returns a 4x4 Seitz matrix from the Jones faithful representation of
    the equivalent position which is a character string e.g. 1/2+x,-x,z.
;
    _name.category_id             function
    _name.object_id               SeitzFromJones
    _type.purpose                 Number
    _type.source                  Derived
    _type.container               Matrix
    _type.dimension               '[4,4]'
    _type.contents                Real
    _units.code                   none
    _method.purpose               Evaluation
    _method.expression
;
     Function SeitzFromJones( j :[Single, Text])  { # Jones symmetry notation

      joneschrs = "123456xyz/,+- "
      s         = Matrix([[0,0,0,0],[0,0,0,0],[0,0,0,0],[0,0,0,1]])
      axis      = 0
      sign      = 1
      inum      = 0

      do i=0,Len(j)-1    {
          c = j[i]
          If (c not in joneschrs) dummy = print('illegal char in symmetry xyz')

          If      (c == ' ') Next
          If      (c == ',') {
                             axis     += 1
                             inum      = 0
                             sign      = 1
          }
          Else If (c == '+') sign      = +1
          Else If (c == '-') sign      = -1
          Else If (c == 'x') s[axis,0] = sign
          Else If (c == 'y') s[axis,1] = sign
          Else If (c == 'z') s[axis,2] = sign
          Else   {
               If (inum == 0)   m  = AtoI(c)
               If (inum == 1 and c != '/') dummy = print('illegal num in
    symmetry xyz')            If (inum == 2)   {
                                n  = AtoI(c)
                     If(n == 5) dummy = print('illegal translation in symmetry
    xyz')                  s[axis,3] = Mod(10.+ Float(sign*m)/Float(n), 1.)
                     sign      = 1
               }
               inum += 1
       }  }
                          SeitzFromJones = s
    }
;

save_

_function.SymEquiv

CIF

The function

xyz' =  SymEquiv( symop, xyz )

returns a fractional coordinate vector xyz' which is input vector

xyz transformed by the input symop 'n_pqr' applied to the symmetry

equivalent matrix extracted from the category space_group_symop.

save_function.symequiv

    _definition.id                '_function.SymEquiv'
    _definition.update            2021-03-01
    _description.text
;
    The function
                    xyz' =  SymEquiv( symop, xyz )

    returns a fractional coordinate vector xyz' which is input vector
    xyz transformed by the input symop 'n_pqr' applied to the symmetry
    equivalent matrix extracted from the category space_group_symop.
;
    _name.category_id             function
    _name.object_id               SymEquiv
    _type.purpose                 Number
    _type.source                  Derived
    _type.container               Matrix
    _type.dimension               '[3]'
    _type.contents                Real
    _units.code                   none
    _method.purpose               Evaluation
    _method.expression
;
    Function SymEquiv( c :[Single, Symop],    # symop string n_pqr
                       x :[Matrix, Real]   ){  # fract coordinate vector

            s = space_group_symop [ SymKey( c ) ]
            SymEquiv = s.R * x + s.T + SymLat( c )
    }
;

save_

_function.SymKey

CIF

The function

m  =  SymKey( s )

returns an integer index to the Seitz matrices from the character

string of the form 'n_pqr'.

save_function.symkey

    _definition.id                '_function.SymKey'
    _definition.update            2021-03-01
    _description.text
;
    The function
                  m  =  SymKey( s )

    returns an integer index to the Seitz matrices from the character
    string of the form 'n_pqr'.
;
    _name.category_id             function
    _name.object_id               SymKey
    _type.purpose                 Number
    _type.source                  Derived
    _type.container               Single
    _type.contents                Integer
    _enumeration.range            1:192
    _units.code                   none
    _method.purpose               Evaluation
    _method.expression
;
    Function SymKey( s :[Single, Symop])  {  # symop string

           If (s == '.')   n = 1
           Else            n = AtoI(s[0])

                SymKey =  n       # index from 1
    }
;

save_

_function.SymLat

CIF

The function

v  =  SymLat( s )

returns a vector of the cell translations applied to the coordinates

from the character string of the form 'n_pqr'. i.e. p-5, q-5, r-5.

save_function.symlat

    _definition.id                '_function.SymLat'
    _definition.update            2021-03-01
    _description.text
;
    The function
                  v  =  SymLat( s )

    returns a vector of the cell translations applied to the coordinates
    from the character string of the form 'n_pqr'. i.e. p-5, q-5, r-5.
;
    _name.category_id             function
    _name.object_id               SymLat
    _type.purpose                 Number
    _type.source                  Derived
    _type.container               Matrix
    _type.dimension               '[3]'
    _type.contents                Integer
    _units.code                   none
    _method.purpose               Evaluation
    _method.expression
;
    Function SymLat( s :[Single, Symop])  {  # symop string

           If (s[0] == ' ')  v = [ 5, 5, 5 ]
           Else              v = [ AtoI(s[2]), AtoI(s[3]), AtoI(s[4]) ]

                 SymLat  =  v - 5
    }
;

save_

_function.Symop

CIF

The function

s  =  Symop( n, t )

returns a character string of the form 'n_pqr' where n is the

symmetry equivalent site number and [p,q,r] is the cell translation

vector PLUS [5,5,5].

save_function.symop

    _definition.id                '_function.Symop'
    _definition.update            2006-06-30
    _description.text
;
    The function
                  s  =  Symop( n, t )

    returns a character string of the form 'n_pqr' where n is the
    symmetry equivalent site number and [p,q,r] is the cell translation
    vector PLUS [5,5,5].
;
    _name.category_id             function
    _name.object_id               Symop
    _type.purpose                 Composite
    _type.source                  Derived
    _type.container               Single
    _type.contents                Symop
    _method.purpose               Evaluation
    _method.expression
;
    Function Symop( n  :[Single, Integer],   # symmetry equivalent site number
                    t  :[List  , Integer]) { # cell translation vector

           d  =  t + 5
        Symop =  repr(n) + '_' + repr(d[0]) + repr(d[1]) + repr(d[2])
    }
;

save_

Revision history

Version 3.0.5 (2016-05-13) Merged in most symmetry dictionary definitions (James Hester)

Version 3.0.6 (2016-09-13) Adjusted and removed keys for changes in dREL operation.
       _citation_id added to key list of citation_author (James Hester).
       _diffrn.crystal_id removed as diffrn is Set category. Changed
       EXPTL_CRYSTAL to Set type in keeping with current use patterns.
       Removed all child keys of exptl_crystal_id.

Version 3.0.7 (2017-06-10) Added and deprecated symmetry.cell_setting. Removed rhombohedral
       option from dREL method for space_group.crystal_system. (James Hester)

Version 3.0.8 (2017-09-23) Added missing items from DDL1 version: _citation.doi, _audit.block_doi
       _citation.publisher, _database.dataset_doi,
       _publ_contact_author.id_orcid, _publ_author.id_orcid (James Hester)

Version 3.0.9 (2018-04-10) Rewrote CITATION category description to cover all relevant uses rather
       than only publication-related uses (James Hester).

Version 3.0.10 (2019-01-08) Added DATABASE_RELATED category (James Hester).

Version 3.0.11 (2019-09-25) Removed the _chemical_conn_bond.distance_su data item.
       Changed the purpose of the diffrn_radiation_wavelength.value data item
       from 'Number' to 'Measurand'. Added the
       diffrn_radiation_wavelength.value_su data item.

       Replaced all instances of the _definition.replaced_by data item with
       data items from the DEFINITION_REPLACED category.

       Marked the _atom_site.refinement_flags data item as deprecated and
       replaced by the _atom_site.refinement_flags_posn,
       _atom_site.refinement_flags_adp and _atom_site.refinement_flags_occupancy
       data items.

       Changed the _type.purpose from 'Encode' to 'Link' in the definitions of
       the _geom_angle.atom_site_label_2, _valence_param_atom_1,
       _valence_param_atom_2, _valence_param_ref_id, _atom_site_aniso.label
       and _atom_type_scat.symbol data items. Removed the _name.linked_item_id
       data item from the definitions of the _diffrn_scale_group.code and
       diffrn_standard_refln.code data items.

       Updated the definitions of the _geom_hbond.angle_DHA and
       _geom_hbond.angle_DHA_su data items.

       Corrected the definitions of the _cell_measurement.temperature_su and
       _cell_measurement.pressure_su data items.

       Corrected a typo in the definitions of the _geom_contact.distance and
       _geom_torsion.angle and data items.

       Changed the content type of multiple data items from 'Index' or 'Count'
       to 'Integer' and assigned the appropriate enumeration range if needed.

Version 3.0.12 (2020-03-13) Adjusted the ranges of _geom_bond.angle and _geom_hbond.angle_DHA to
       be 0:180 degrees.

       Changed dREL methods for Cartesian transformation matrix elements
       to calculate default values rather than required values.

Version 3.0.13 (2020-03-16) Changed all synthetic identifiers ('id') to be Text, and removed dREL.
       Validation method for _space_group.crystal_system removed as it contained
       undefined dREL functions "throw" and "alert".

Version 3.0.14 (2021-06-29) Added opaque author identifiers to AUDIT_AUTHOR and PUBL_AUTHOR as well
       as relevant linking identifiers to AUDIT_CONTACT_AUTHOR and
       PUBL_CONTACT_AUTHOR.

       Added _diffrn_measurement.specimen_attachment_type.

       Changed to DDL version 4.

       Removed all instances of the _category.key_id attribute since it is no
       longer defined in the DDLm reference dictionary.

       Miscellaneous corrections to dREL and fixing typos.

Version 3.1.0 (2021-12-01) Replaced _model_site.adp_eigen_system with _model_site.adp_eigenvectors
       and _model_site.adp_eigenvalues.

       Added additional enumeration values to the _journal_index.type data item
       definition.

       Numerous corrections to measurement units.

       Numerous improvements to types and harmonisation of spelling.

Version 3.2.0 (2023-04-04) Added data names to allow multi-data-block expression of data sets.

       Deprecated and replaced _diffrn_radiation.type and
       _diffrn_radiation.xray_symbol.

       Added _diffrn_refln.intensity* data items.

       Added the _exptl_absorpt.special_details data item.

       Added categories and data names to allow for the elemental composition
       of specimens to be recorded.

       Corrections and additions for conformance with DDL1.

       Explicitly added _diffrn_source.details to the list items that replaced
       _diffrn_source.description.

       Added the _citation.URL and _journal.paper_URL data items.

       Added the _journal.paper_number and _journal.paper_pages data items.

       Reparented CELL to DIFFRN category and added key data names to allow
       multiple cells for different diffraction conditions. Deprecated
       _cell_measurement.temperature,pressure data names.

       Changed the purpose of the _diffrn_radiation_wavelength.id data item
       from 'Encode' to 'Key'.

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Revision history

International Tables for Crystallography

Volume G: Definition and exchange of crystallographic data

Edited by S. R. Hall and B. McMahon

IUCrData