Crystallographic Information Framework

[CIF logo]

Index

Protein Data Bank exchange dictionary (pdbx)

Extended data types

The following extended data types are defined in this dictionary:

Code Primitive data type Regular expression construct Description
 
code char [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words ...
ucode uchar [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
line char [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* char item types / multi-word items ...
uline uchar [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* char item types / multi-word items (case insensitive)...
text char [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* text item types / multi-line text ...
int numb [+-]?[0-9]+ int item types are the subset of numbers that are the negative or positive integers.
float numb -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)? float item types are the subset of numbers that are the floating numbers.
name uchar _[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+ name item types take the form...
idname uchar [_A-Za-z0-9]+ idname item types take the form...
any char .* A catch all for items that may take any form...
yyyy-mm-dd char [0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9]-[0-9][0-9] Standard format for CIF dates.
yyyy-mm-dd:hh:mm-flex char [0-9][0-9][0-9][0-9](-[0-9]?[0-9])?(-[0-9][0-9])?(:[0-9]?[0-9]:[0-9][0-9])? Flexible date-time format.
uchar3 uchar [+]?[A-Za-z0-9][A-Za-z0-9]?[A-Za-z0-9]? data item for 3 character codes
uchar1 uchar [+]?[A-Za-z0-9] data item for 1 character codes
symop char ([1-9]|[1-9][0-9]|1[0-8][0-9]|19[0-2])(_[1-9][1-9][1-9])? symop item types take the form n_klm, where n refers to the symmetry operation that is applied to the coordinates in the ATOM_SITE category identified by _atom_site_label. It must match a number given in _symmetry_equiv_pos_site_id. k, l, and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used. These translations (x,y,z) are related to (k,l,m) by k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided.
atcode char [][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* Character data type for atom names ...
yyyy-mm-dd:hh:mm char [0-9]?[0-9]?[0-9][0-9]-[0-9]?[0-9](-[0-9]?[0-9])?(:[0-9]?[0-9]:[0-9][0-9])? Standard format for CIF dates with optional time stamp.
fax uchar [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
phone uchar [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
email uchar [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
int-range numb -?[0-9]+(--?[0-9]+)? int item types are the subset of numbers that are the negative or positive integers with optional range.
float-range numb -?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?(--?(([0-9]+)[.]?|([0-9]*[.][0-9]+))([(][0-9]+[)])?([eE][+-]?[0-9]+)?)? int item types are the subset of numbers that are the floating numbers.
code30 char .?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.?.? A string value, not allowed to exceed 30 characters.
binary char \n--CIF-BINARY-FORMAT-SECTION--\n\ [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]*\ \n--CIF-BINARY-FORMAT-SECTION---- binary items are presented as MIME-like ascii-encoded sections in an imgCIF. In a CBF, raw octet streams are used to convey the same information.
operation_expression char [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* sequence of parenthetical integer ranges and character codes

International Tables for Crystallography

Volume G: Definition and exchange of crystallographic data

First online edition (2006)

Edited by S. R. Hall and B. McMahon

An essential guide and reference to CIF for programmers, data managers handling crystal-structure information and practising crystallographers.