Syntactic utilities for CIF

McMahon, B.

doi:10.1107/97809553602060000753

International Tables for Crystallography (2006). Vol. G. ch. 5.3, pp. 499-525
https://doi.org/10.1107/97809553602060000753

Chapter 5.3. Syntactic utilities for CIF

5.3. Syntactic utilities for CIF (pp. 499-525) | html | pdf | chapter contents |
B. McMahon
- 5.3.1. Introduction (p. 499) | html | pdf |
- 5.3.2. Syntax checker (pp. 499-501) | html | pdf |
  - 5.3.2.1. vcif (pp. 499-501) | html | pdf |
    - 5.3.2.1.1. How to use vcif (pp. 499-500) | html | pdf |
    - 5.3.2.1.2. Options to vcif (p. 500) | html | pdf |
    - 5.3.2.1.3. Limitations of vcif (p. 501) | html | pdf |
- 5.3.3. Editors with graphical user interfaces (pp. 501-507) | html | pdf |
  - 5.3.3.1. enCIFer (pp. 501-504) | html | pdf |
    - 5.3.3.1.1. The main graphical window (p. 501) | html | pdf |
    - 5.3.3.1.2. The interface toolbar (pp. 501-502) | html | pdf |
    - 5.3.3.1.3. The task bar (p. 502) | html | pdf |
    - 5.3.3.1.4. The main edit pane (p. 502) | html | pdf |
    - 5.3.3.1.5. The dictionary browse pane (p. 502) | html | pdf |
    - 5.3.3.1.6. The error notification pane and logging area (pp. 502-503) | html | pdf |
    - 5.3.3.1.7. The loop editor (p. 503) | html | pdf |
    - 5.3.3.1.8. The publication and chemical and crystal data wizards (p. 503) | html | pdf |
    - 5.3.3.1.9. The visualization window (pp. 503-504) | html | pdf |
  - 5.3.3.2. CIFEDIT (p. 504) | html | pdf |
  - 5.3.3.3. HICCuP (pp. 504-506) | html | pdf |
    - 5.3.3.3.1. Interactive use of the program (pp. 505-506) | html | pdf |
      - 5.3.3.3.1.1. The control window (p. 505) | html | pdf |
      - 5.3.3.3.1.2. The report frame and edit window (p. 505) | html | pdf |
      - 5.3.3.3.1.3. Dictionary browsing (pp. 505-506) | html | pdf |
    - 5.3.3.3.2. Options (p. 506) | html | pdf |
  - 5.3.3.4. Platform-specific editors (pp. 506-507) | html | pdf |
    - 5.3.3.4.1. beCIF (p. 506) | html | pdf |
    - 5.3.3.4.2. printCIF for Word (pp. 506-507) | html | pdf |
- 5.3.4. Data-name validation (pp. 507-509) | html | pdf |
  - 5.3.4.1. CYCLOPS (pp. 508-509) | html | pdf |
    - 5.3.4.1.1. Operation (p. 508) | html | pdf |
    - 5.3.4.1.2. Invocation of the program (pp. 508-509) | html | pdf |
- 5.3.5. File transformation software (pp. 509-515) | html | pdf |
  - 5.3.5.1. QUASAR: a data extractor (pp. 509-511) | html | pdf |
    - 5.3.5.1.1. Purpose (p. 509) | html | pdf |
    - 5.3.5.1.2. Mode of operation (p. 509) | html | pdf |
    - 5.3.5.1.3. The request list (pp. 509-510) | html | pdf |
    - 5.3.5.1.4. Output from QUASAR (p. 511) | html | pdf |
      - 5.3.5.1.4.1. Treatment of missing data (p. 511) | html | pdf |
      - 5.3.5.1.4.2. Matching data names (p. 511) | html | pdf |
      - 5.3.5.1.4.3. Case sensitivity (p. 511) | html | pdf |
  - 5.3.5.2. cif2cif (pp. 511-512) | html | pdf |
    - 5.3.5.2.1. Operation (pp. 511-512) | html | pdf |
      - 5.3.5.2.1.1. Copying (p. 511) | html | pdf |
      - 5.3.5.2.1.2. Constraining standard uncertainties to specified ranges (p. 511) | html | pdf |
      - 5.3.5.2.1.3. Dictionary validation (p. 511) | html | pdf |
      - 5.3.5.2.1.4. Serving a request list (pp. 511-512) | html | pdf |
      - 5.3.5.2.1.5. Other features (p. 512) | html | pdf |
    - 5.3.5.2.2. Invocation of the program (p. 512) | html | pdf |
  - 5.3.5.3. ciftex: translating to a typesetting language (pp. 512-515) | html | pdf |
    - 5.3.5.3.1. Basic operation of ciftex (pp. 512-514) | html | pdf |
      - 5.3.5.3.1.1. Non-looped data (p. 513) | html | pdf |
      - 5.3.5.3.1.2. Looped data (p. 513) | html | pdf |
      - 5.3.5.3.1.3. The ancillary map file (pp. 513-514) | html | pdf |
      - 5.3.5.3.1.4. The ancillary format file (p. 514) | html | pdf |
    - 5.3.5.3.2. Invocation of the program (p. 514) | html | pdf |
    - 5.3.5.3.3. Some general comments (pp. 514-515) | html | pdf |
- 5.3.6. Libraries for scripting languages (pp. 515-517) | html | pdf |
  - 5.3.6.1. STAR::Parser and related Perl modules (pp. 515-517) | html | pdf |
    - 5.3.6.1.1. STAR::Parser (p. 515) | html | pdf |
    - 5.3.6.1.2. STAR::Dictionary (p. 515) | html | pdf |
    - 5.3.6.1.3. STAR::DataBlock (pp. 515-516) | html | pdf |
    - 5.3.6.1.4. STAR::Checker (p. 516) | html | pdf |
    - 5.3.6.1.5. STAR::Writer and STAR::Filter (p. 517) | html | pdf |
  - 5.3.6.2. PyCifRW: CIF reading and writing in Python (p. 517) | html | pdf |
- 5.3.7. Rapid development tools (pp. 517-522) | html | pdf |
  - 5.3.7.1. ZINC: an interface to CIF for standard Unix tools (pp. 518-519) | html | pdf |
    - 5.3.7.1.1. Description of the ZINC format (p. 518) | html | pdf |
    - 5.3.7.1.2. ZINC-based utilities (pp. 518-519) | html | pdf |
      - 5.3.7.1.2.1. cifZinc (p. 518) | html | pdf |
      - 5.3.7.1.2.2. zincCif (p. 519) | html | pdf |
      - 5.3.7.1.2.3. zincGrep (p. 519) | html | pdf |
      - 5.3.7.1.2.4. cifdiff (p. 519) | html | pdf |
      - 5.3.7.1.2.5. zb (p. 519) | html | pdf |
      - 5.3.7.1.2.6. zincNl (p. 519) | html | pdf |
      - 5.3.7.1.2.7. zincSubset (p. 519) | html | pdf |
  - 5.3.7.2. CifSieve: automatic construction of CIF input functions (pp. 520-522) | html | pdf |
    - 5.3.7.2.1. Overview of the process (p. 520) | html | pdf |
    - 5.3.7.2.2. The augmented DDL dictionary (p. 520) | html | pdf |
    - 5.3.7.2.3. Input to a C application program (p. 521) | html | pdf |
    - 5.3.7.2.4. Input to a Fortran application program (pp. 521-522) | html | pdf |
- 5.3.8. Tools for mmCIF (pp. 522-525) | html | pdf |
  - 5.3.8.1. CIFOBJ and related libraries (p. 522) | html | pdf |
  - 5.3.8.2. OpenMMS (pp. 522-523) | html | pdf |
    - 5.3.8.2.1. The OpenMMS toolkit (p. 523) | html | pdf |
  - 5.3.8.3. mmLib: a Python toolkit for bioinformatics applications (pp. 523-525) | html | pdf |
- 5.3.9. Concluding remarks (p. 525) | html | pdf |
- References | html | pdf |
- Figures
  - Fig. 5.3.2.1. (a) An example CIF with a number of syntax errors and (b) the report of the errors produced by vcif (p. 500) | html | pdf |
  - Fig. 5.3.2.2. Verbose error listing from vcif when run with the `-v' option on the example of Fig. 5.3.2.1 (p. 500) | html | pdf |
  - Fig. 5.3.3.1. The enCIFer graphical user interface (p. 501) | html | pdf |
  - Fig. 5.3.3.2. The enCIFer loop editor (p. 503) | html | pdf |
  - Fig. 5.3.3.3. The enCIFer publication data wizard (p. 503) | html | pdf |
  - Fig. 5.3.3.4. The enCIFer chemical and crystal data wizard (p. 503) | html | pdf |
  - Fig. 5.3.3.5. Visualization of a molecular and crystal three-dimensional structure with enCIFer (p. 503) | html | pdf |
  - Fig. 5.3.3.6. The use of CIFEDIT to display and alter the contents of a CIF (p. 504) | html | pdf |
  - Fig. 5.3.3.7. Row-based loop editing with CIFEDIT (p. 504) | html | pdf |
  - Fig. 5.3.3.8. Control window of the HICCuP application (p. 505) | html | pdf |
  - Fig. 5.3.3.9. HICCuP edit window and error description (p. 505) | html | pdf |
  - Fig. 5.3.3.10. HICCuP dictionary browser window (p. 505) | html | pdf |
  - Fig. 5.3.3.11. A category view in the beCIF editor of a CIF with navigation by tabs (p. 506) | html | pdf |
  - Fig. 5.3.3.12. Representation by the beCIF editor of looped data within a category (here ATOM_SITE) in spreadsheet style (p. 507) | html | pdf |
  - Fig. 5.3.3.13. The dual RTF/CIF editing windows in the printCIF for Word application (p. 507) | html | pdf |
  - Fig. 5.3.4.1. Sample output from CYCLOPS (p. 509) | html | pdf |
  - Fig. 5.3.5.1. An example request list for QUASAR (p. 510) | html | pdf |
  - Fig. 5.3.5.2. Example CIF for demonstrating the use of QUASAR (p. 510) | html | pdf |
  - Fig. 5.3.5.3. Result of running QUASAR with the example request list of Fig. 5.3.5.1 on the CIF listed in Fig. 5.3.5.2 (p. 510) | html | pdf |
  - Fig. 5.3.5.4. Sample CIF data input to ciftex (p. 513) | html | pdf |
  - Fig. 5.3.5.5. Output from ciftex run on the data of Fig. 5.3.5.4 (p. 513) | html | pdf |
  - Fig. 5.3.5.6. $[\hbox{\TeX}]$ markup for typesetting a table of atomic coordinates (p. 513) | html | pdf |
  - Fig. 5.3.5.7. Example map file for use with ciftex (p. 514) | html | pdf |
  - Fig. 5.3.5.8. Example format file for ciftex (p. 514) | html | pdf |
  - Fig. 5.3.6.1. Skeleton version of an application to format a CIF dictionary for publication (p. 516) | html | pdf |
  - Fig. 5.3.6.2. Structure of the imgCIF dictionary (Chapter 4.6 ) as described by the get_keys method of the STAR::DataBlock module (p. 517) | html | pdf |
  - Fig. 5.3.7.1. ZINC transformation of CIF (p. 518) | html | pdf |
  - Fig. 5.3.7.2. Two example files in CIF format differing greatly in layout but little in content: (a) sample1.cif, (b) sample2.cif (p. 519) | html | pdf |
  - Fig. 5.3.7.3. Output from cifdiff comparing files sample1.cif and sample2.cif of Fig. 5.3.7.2 (p. 519) | html | pdf |
  - Fig. 5.3.7.4. Extracts from an augmented DDL1 dictionary (version 1.0 of the core CIF dictionary) (p. 520) | html | pdf |
  - Fig. 5.3.7.5. Header file cifvars.h for a C application built by BuildSiv from the augmented DDL dictionary of Fig. 5.3.7.4 (p. 521) | html | pdf |
  - Fig. 5.3.7.6. An example C program designed to read CIF data as tagged in the augmented DDL dictionary of Fig. 5.3.7.4 (p. 521) | html | pdf |
  - Fig. 5.3.7.7. Fortran include file forcif.inc for an application built by BuildSiv from the augmented DDL dictionary of Fig. 5.3.7.4 (p. 522) | html | pdf |
  - Fig. 5.3.7.8. An example Fortran program designed to read CIF data as tagged in the augmented DDL dictionary of Fig. 5.3.7.4 (p. 522) | html | pdf |
  - Fig. 5.3.8.1. The OpenMMS metamodel and data flow (p. 523) | html | pdf |
  - Fig. 5.3.8.2. Sample XML output from the OpenMMS XML generator (p. 524) | html | pdf |
  - Fig. 5.3.8.3. A snippet of code illustrating mmCIF/PDB file format conversion with the mmLib toolkit (p. 524) | html | pdf |
- Tables
  - Table 5.3.6.1. Object methods provided by the STAR::DataBlock Perl module (p. 516) | html | pdf |
  - Table 5.3.8.1. The modules provided by the mmLib toolkit (p. 524) | html | pdf |

Chapter 5.3. Syntactic utilities for CIF

Contents