Supporting Data mmcif_nef.dic
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Dictionary Revision History
| Version | Revision Date | Revision Description | |
|---|---|---|---|
| 1.1 | 2020-11-25 | Eliza Ploskon - Updated to reflect suggestions from WWPDB - Updated _item_description.description in restraints origin for consistency - Updated to reflect Commented_Example_v1_1.nef |
mmcif_nef.dic |
| 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 missing 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 Gntert, 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 |
| 1.1 | 2020-11-25 | Eliza Ploskon - Updated to reflect suggestions from WWPDB - Updated _item_description.description in restraints origin for consistency - Updated to reflect Commented_Example_v1_1.nef |
mmcif_nef.dic |
| 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 missing 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 Gntert, 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 List
| 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 ... |
| 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 (including 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 | [][ ()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* | All printable ascii characters (including space). Equivalent to atcode, but renamed to avoid confusion |
| text | char | [][ \n\t()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* | text item types / multi-line text ... |
| timestamp | char | [][()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* | ISO 8601 time stamp, without time zone information. E.g. '2013-02-29T13:12:03.521773' |
| uchar1 | uchar | [+]?[A-Za-z0-9] | data item for 1 character codes |
| uchar3 | uchar | [+]?[A-Za-z0-9][A-Za-z0-9]?[A-Za-z0-9]? | data item for 3 character codes |
| ucode | uchar | [][_,.;:"&<>()/\{}'`~!@#$%A-Za-z0-9*|+-]* | code item types/single words (case insensitive) ... |
| uline | uchar | [][ \t_(),.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* | char item types / multi-word items (case insensitive)... |
| uuid | char | [][()_,.;:"&<>/\{}'`~!@#$%?+=*A-Za-z0-9|^-]* | 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 List
| 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 List
| Units Identifier | Description |
|---|
Units Conversion List
| From Units&Identifier | To Units&Identifier | Operator | Conversion Factor |
|---|