Supporting Data mmcif_nef.dic

Dictionary Revision History

Version Revision Date Revision Description
1.0 2016-11-06 Rasmus Fogh
- Updated to reflect discussion and participant survey
- changed ordinal and index_id to index
- changed run_ordinal to run_number
- removed _nef_chemical_shift_list.atom_chemical_shift_units
- renamed residue_type to residue_name
- Added _nef_sequence.cis_peptide tag
- Added _nef_chemical_shift.element
- Added _nef_chemical_shift.isotope_number
- Changed examples to reflect new semantics
-
mmcif_nef.dic
.101 2016-02-23 Rasmus Fogh
- Entered mising data
- Reordered to match display ordered
- Added new tag _category.parent_category_id to show saveframe location of loops
- Added new data types
mmcif_nef.dic
.100 2015-01-09 Changes (NEF Working Group): Preliminary version release

NMR Exchange Format Working: Geerten Vuister (chair), Rasmus Fogh, Peter G√ľntert,
Charles Schwieters, Michael Nilges,T.J. Ragan,Torsten Herrmann, David A Case
Gaetano Montelione, David Wishart, Wim F. Vranken, Paul Adams, Roberto Tejero, Eldon Ulrich,
Naohiro Kobayashi, John Markley, Sameer Velankar, Aleksandras Gutmanas, John Westbrook
mmcif_nef.dic
Data Type Code Primitive Type Code Regular Expression Description
any char .* A catch all for items that may take any form...
atcode char [][ _(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* Character data type for atom names ...
boolean char true|false enumeration for Boolean true/false values ...
code char [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words ...
email uchar [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
fax uchar [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
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.
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.
framecode char [.;:"&<>(){}'`~!$%A-Za-z0-9*|+-][_.;:"&<>(){}'`~!$%A-Za-z0-9*|+-]* A value that points to a saveframe.
idname uchar [_A-Za-z0-9]+ idname item types take the form...
int numb [+-]?[0-9]+ int item types are the subset of numbers that are the negative or positive integers.
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.
line char [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* char item types / multi-word items ...
multiline char [][ \n()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* All printable ascii characters (includind space) plus linebreak
name uchar _[_A-Za-z0-9]+\.[][_A-Za-z0-9%-]+ name item types take the form...
nef_framecode char [][()_,.;:&<>/\{}`~!@$%?+=*A-Za-z0-9|^-]* Printable ascii characters (except for space, single or double quotes, or pound sign).
Values may also not start with reserved strings 'data_', 'save_', 'loop_', or 'stop_'.
phone uchar [_,.;:"&<>/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
potential_type char undefined|log-harmonic|parabolic|square-well-parabolic|square-well-parabolic-linear|upper-bound-parabolic|lower-bound-parabolic|upper-bound-parabolic-linear|lower-bound-parabolic-linear enumeration for Restraint list potential types
Potential types are defined aS follows::

- log-harmonic:
Parameters: target_value, target_value_error

- parabolic:
Parameters: target_value, target_value_error
Formula: E = k(r-target_value)**2

- square-well-parabolic:
Parameters: upper_limit, lower_limit (optionally: target_value, target_value_error)
Formula:
E = k(r-upper_limit)**\2 for r > upper_limit
E = k(r-lower_limit)**2 for r < lower_limit

- 'square-well-parabolic-linear:
Parameters: upper_limit, lower_limit, upper_linear_limit, lower_linear_limit, (optional: target_value, target_value_error)
Formula:
If upper_limit = u, upper_linear_limit = u2, lower_limit = l, lower_linear_limit = l2:
E = 2k(u2-u)(r - (u2+u)/2) for r > u2
E = k(r-u)**2 for u < r < u2
E = k(r-l)**2 for l > r > l2
E = 2k(l2-l)(r - (l2+l)/2) for r < l2

Additional potential types
('upper-bound-parabolic', 'lower-bound-parabolic', 'upper-bound-parabolic-linear', 'lower-bound-parabolic-linear')
can be derived from the two-sided versions given above.
singleline char [][ ()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* All printable ascii characters (includind space). Equivalent to atcode, but renamed to avoid confusion
text char [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* text item types / multi-line text ...
timestamp char . ISO 8601 time stamp, without time zone information. E.g. '2013-02-29T13:12:03.521773'
uchar1 uchar [+]?[A-Za-z0-9]
data item for 1 character codes
uchar3 uchar [+]?[A-Za-z0-9][A-Za-z0-9]?[A-Za-z0-9]?
data item for 3 character codes
ucode uchar [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* code item types/single words (case insensitive) ...
uline uchar [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* char item types / multi-word items (case insensitive)...
uuid char . Unique data set identifier, combined from a program name string, a timestamp, and a random integer.
E.g. 'CYANA-2013-02-29T13:12:04.521773-1172436'
word char [][()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* All printable ascii characters (NOT including space).
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 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.
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.
SubCategory Identifier Description
cartesian_coordinate The collection of x, y, and z components of a position specified
with reference to a Cartesian (orthogonal angstrom) coordinate
system.
matrix The collection of elements of a matrix.
Units Identifier Description

Units Conversion List

From Units&Identifier To Units&Identifier Operator Conversion Factor