Fix syntax problems in CIF files

[vaitkus]

This PR fixes several minor CIF syntax issues in example files that prevented them from being parsed.

[BobHanson]

Ah -- I had forgotten that these were part of the automated system. I will revert those. They will be undergoing several changes over the next few days. Along with the dictionary.

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On Wed, Sep 1, 2021 at 6:52 AM Antanas Vaitkus ***@***.***> wrote: This PR fixes several minor CIF syntax issues in example files that prevented them from being parsed. ------------------------------ You can view, comment on, or merge this pull request online at: #39 Commit Summary - Fix syntax problems in CIF files. File Changes - *M* examples/example_1.cif <https://github.com/COMCIFS/TopoCif/pull/39/files#diff-3326ca3248764c54ead2883df27b5a133191466873aca88e5759da0a4a78e57e> (1) - *M* examples/example_2.cif <https://github.com/COMCIFS/TopoCif/pull/39/files#diff-96fe1ac7102001a56ade4914c3d4df1428cd64a4443cc43f68d185f63f3684bc> (1) - *M* examples/example_3.cif <https://github.com/COMCIFS/TopoCif/pull/39/files#diff-67385bae926030c89860750b372dd64823bcd59cde6121af352dc7c0b54ccaf2> (1) - *M* examples/example_4.cif <https://github.com/COMCIFS/TopoCif/pull/39/files#diff-144c9bc9ffec79cee71c85c0236148bbd6f28807fd0cf35f51cfc1b98c222fe2> (1) - *M* more_examples/MOF5-v2b.cif <https://github.com/COMCIFS/TopoCif/pull/39/files#diff-b37c8cd26a676835e808bc38a07bcd98e09c3b244806047141c3c980bc692a65> (4) - *M* more_examples/MOF5-v2c.cif <https://github.com/COMCIFS/TopoCif/pull/39/files#diff-55edbc7d93de52739ed5025541e426993dbb47af0809cff7ec86253fdb39af10> (4) - *M* more_examples/MOF5-v2d.cif <https://github.com/COMCIFS/TopoCif/pull/39/files#diff-8e4030f9d2f842f8741e599587c0aba0ff4a71371e4f1da3cce8413aa9d1bb4c> (4) - *M* more_examples/MOF5-v2e.cif <https://github.com/COMCIFS/TopoCif/pull/39/files#diff-41b8546a56b8cd2561209aaad3abfb900b00dc5880f31674f3215c3fcf173e79> (4) Patch Links: - https://github.com/COMCIFS/TopoCif/pull/39.patch - https://github.com/COMCIFS/TopoCif/pull/39.diff — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#39>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHNCW3GRWFCAKLTPSVYQVTT7YHYNANCNFSM5DGJNMOQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.*

[vaitkus]

Thank you for clarifying. There are still, however, several minor syntactic issues in the files from the more_examples directory. Feel free to close the PR without merging if the proposed fixes are not relevant (i.e. if these file will also be changed in the near future).

[BobHanson]

Yes, we are aware of that. OK, I will move those files out of examples/ so that they are not checked. Am I right that it is only that directory that is being processed?

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On Wed, Sep 1, 2021 at 10:59 AM Antanas Vaitkus ***@***.***> wrote: Thank you for clarifying. There are still, however, several minor syntactic issues in the files from the more_examples directory. Feel free to close the PR without merging if the proposed fixes are not relevant (i.e. if these file will also be changed in the near future). — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#39 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEHNCWYO377YOLJUEPBNPZLT7ZEV5ANCNFSM5DGJNMOQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.*

[BobHanson]

No, I guess not. more examples/ is a top-level directory as well. OK, if it's OK with you, just ignore this for a while. We had to do some minor changes in the dictionary after this last chapter review.

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On Wed, Sep 1, 2021 at 4:01 PM Robert Hanson ***@***.***> wrote: Yes, we are aware of that. OK, I will move those files out of examples/ so that they are not checked. Am I right that it is only that directory that is being processed? On Wed, Sep 1, 2021 at 10:59 AM Antanas Vaitkus ***@***.***> wrote: > Thank you for clarifying. There are still, however, several minor > syntactic issues in the files from the more_examples directory. Feel > free to close the PR without merging if the proposed fixes are not relevant > (i.e. if these file will also be changed in the near future). > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#39 (comment)>, or > unsubscribe > <https://github.com/notifications/unsubscribe-auth/AEHNCWYO377YOLJUEPBNPZLT7ZEV5ANCNFSM5DGJNMOQ> > . > Triage notifications on the go with GitHub Mobile for iOS > <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> > or Android > <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.*

-- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 *We stand on the homelands of the Wahpekute Band of the Dakota Nation. We honor with gratitude the people who have stewarded the land throughout the generations and their ongoing contributions to this region. We acknowledge the ongoing injustices that we have committed against the Dakota Nation, and we wish to interrupt this legacy, beginning with acts of healing and honest storytelling about this place.*

[vaitkus]

Actually, neither examples nor more-examples directories are currently automatically checked by GitHub actions (syntax, validity, style checks). These checks only apply to CIF/DDL files on the top-most directory (.). I do agree that eventually it would be a great idea to automatically validate test CIF files as well and have now raised an appropriate GitHub issue [1].

I detected the issues in the CIF files by manually running the cif_parse and ddlm_validate programs from the cod-tools package against these files out of simple curiosity. I apologise if my reporting was premature or annoying.

One thing that I noticed is that the JMol CIF parser seems to be slightly more permissive when dealing with CIF_2.0 files than is allowed by the CIF_2.0 grammar. Namely, JMol allows to:

• Omit the "##CIF_2.0" comment header that is mandatory in CIF_2.0 files.
• Have the delimiter symbol inside the delimited string ('O'Keeffe M.' was OK in CIF_1.1, but is no longer OK in CIF_2.0).
• Have trailing symbols that are silently ignored (i.e. the $ symbols that are addressed by this PR).

Of course, it is great that JMol is able to properly read slightly incorrect CIF files, but such syntactic mistakes should probably still not appear in example CIF files.

I will close the PR now since it will most likely not have any relevance after the planned changes to the files.

[1] COMCIFS/dictionary_check_action#7