Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: CIF 2.0 syntax proposal for retaining backwards CIF 1.xcompatibility

  • To: "Discussion list of the IUCr Committee for the Maintenance of the CIF Standard (COMCIFS)" <comcifs@iucr.org>
  • Subject: Re: CIF 2.0 syntax proposal for retaining backwards CIF 1.xcompatibility
  • From: James Hester <jamesrhester@gmail.com>
  • Date: Mon, 16 Sep 2013 12:58:47 +1000
  • DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20120113;h=mime-version:in-reply-to:references:date:message-id:subject:from:to:content-type; bh=AXV1d+J6oteZWbOsEOq6Zlvi0a/jwIu0Im6CuEr63W4=;b=P9rKzZ8QX2aWub0Fy9QI04nNRUXXth4E1JjzlOq5PdGLy6KF0VQ0syw75ILRrdpmI4vj7DSukJNTke9adGj++KGz5c517GrT/dsdi1+Fh6FK30kQSVPtuCZ2KtTyQH0J72XlLdH/xswQ1HqlrHTCKK7Qx8HQwMsm9c2E9olGTtAt9AXoEmDjxk6bY0vQ8B8nRnFglbq9dp+m17bMFYr0SOSPs5y2kCCY0iJxibC2X9P/qtp3Ey0RCsE0ugS5GBbxKkzaxCvBdjJZsvdJOOA1PoTLX0HkCyLbdIqHYQgmJcQYfxIxfh0Uj5ztHZlPPCw3jhbQEybj8bEjmQRWArjrWw==
  • In-Reply-To: <521F284F.4000203@ibt.lt>
  • References: <521F284F.4000203@ibt.lt>
Reply to Saulius's suggestions of altered syntax.

It was decided early on that the CIF2 standard would not be backwards
compatible with the original standard. Rather, we would allow
ourselves to be disruptive in order to add the new datastructures for
DDLm and to fix deficiencies in CIF1. We therefore called the new
standard CIF2, rather than (for example) CIF1.2.  In addition, we
undertook to allow CIF1 to exist for as long as necessary, with no
coercion to move to CIF2. For background, see the messages in the DDLm
list dating from September/October 2009.

So incompatibility with CIF1 is not, in itself, news and is not
sufficient to justify changes to a syntax that has been sweated over
for many years.

In particular, the drawbacks identified by Saulius are:

(1) Users will need to learn different rules. 

Yes, we have accepted this as part of the change

(2) Developers will need to produce two distinct grammars and parsers

Yes, we have accepted that this will be the case.

(3) Auto-choosing between CIF1 files and CIF2 files is problematic for non-seekable
files if the header is lost

The CIF2.0 header is a required part of CIF2. I do not believe that
the first line of a file is lost that often, if ever.

Regarding the syntax suggestion itself: while it is likely to be the
most elegant way to maintain CIF1 compatibility (if we felt that
worthwhile) while still making it possible to present something
that looks vaguely like a table, it still falls short of a compelling idea, because it gives
'[ [' and '[[' different meanings, which is counter-intuitive and a step
backward towards the CIF1 approach of giving whitespace extra significance.

It is to avoid such contortions that we agreed to allow
incompatibility between CIF1 and CIF2.

We need to avoid any further major syntax changes in CIF2. Closing
the book on syntax changes results in a precise understanding of
the differences between CIF1 and CIF2, so we can meaningfully explore
managing CIF1-CIF2 transitions in alternative ways, e.g. through
documentation and policy.

On Thu, Aug 29, 2013 at 8:54 PM, Saulius Gražulis <grazulis@ibt.lt> wrote:
Dear COMCIFS members,

as we have discussed during the recent IUCr Data Management workshop, I
have put together a proposal for the CIF 2.0 syntax that is fully
backwards compatible with CIF 1.1. I attach a draft of this proposal
(see the attached "CIF1-CIF2-compatibility.txt" file). The new proposal
uses '[[' and ']] to delimit tables (instead of '{' and '}'), and
retains the syntax of CIF 1.x quoted strings.

James has offered to try to "break" the proposed syntax, i.e. to see if
it can be parsed correctly in all kinds of unusual cases. I have done
preliminary tests of this kind using my sample implementation; the tests
I have used are attached as the "breakit.zip" file (it features 6
correct cases and 5 incorrect syntax examples). My impression is that
the proposed '[['/']]' syntax can always be parsed as expected, and
syntax errors an be unambiguously detected.

I would be grateful for comments from the COMCIFS members and, if the
proposal is found to be acceptable, for consideration of its inclusion
into the forthcoming CIF 2.0 standard.

Sicnerely yours,

Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Graiciuno 8
LT-02241 Vilnius, Lietuva (Lithuania)
fax: (+370-5)-2602116 / phone (office): (+370-5)-2602556
mobile: (+370-684)-49802, (+370-614)-36366

comcifs mailing list

T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148
comcifs mailing list

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Science Council (admitted 1947). Member of CODATA, the ISC Committee on Data. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

International Science Council Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.