Dear Colleagues,
There are two major issues that tend to trip up CIF programmers:
1. Dealing with the order independence of CIF. Unlike PDB format,
tags in CIF can validly
be presented in any order. This means you cannot simply scan a CIF for
a tag you want and
start processing from that point forward as you do with a PDB file. In
general to read
a CIF properly, you need to read all of it into memory before you can do
anything with it.
A common mistake is to assume that just because many CIFs have been
written with tags in
a given order, the next CIF you encounter will also have the tags in
that order.
2. Doing the lexical scan (the tokenizing) correctly. CIF uses a
context sensitive grammar,
so lexers based on simple BNF tend to make mistakes, and most reliable
CIF lexers are
hand-written rather than being generated from a grammar. The advice to
use a pre-written
and tested lexer is sensible.
The bottom line is that, while it is relatively easy to write a valid
CIF, reading CIFs reliably
can be a very challenging programming task, because you need to write
code that will handle
the very complex general case, rather than just specific examples.
Fortunately there are
software packages to help you do this.
Herbert J. Bernstein
On 9/18/13 10:41 AM, Peter Keller wrote:
> Hi Phil,
>
> I agree that the issue that you raise (about the need to define the
> data items and categories propery) is an important one that needs
> proper consideration. However, your mail could be read to suggest that
> correct parsing of CIF-format data is a secondary issue that doesn't
> deserve the same attention from developers.
>
> I hope that this isn't quite what you meant.... There are already
> mutually-incompatible CIF dialects out there that have been created by
> developers coding to their own understanding and interpretations of
> the CIF/STAR format. I am sure that you would not want to be the
> creator of yet another one :-) Correct tokenising is a necessary (but
> not sufficient) condition for preventing the problem getting worse.
>
> In practice, the code and applications that I have seen, and the
> discussions about this that I have had, all suggest that developers
> find it more difficult to write code that tokenises CIF/STAR-format
> data correctly than code that handles other text formats that they
> have to deal with in this field. My experience suggests that this is
> an important practical issue with real-world ramifications, and it is
> worthwhile devoting some effort to it.
>
> Regards,
> Peter.
>
> On Wed, 18 Sep 2013, Phil Evans wrote:
>
>> Date: Wed, 18 Sep 2013 13:38:07 +0100
>> From: Phil Evans <[log in to unmask]>
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] Code to handle the syntax of (mm)CIF data
>> correctly.
>>
>> As a novice looking at mmCIF from a developers point of view, for
>> reflection data, the complication is not so much tokenising
>> (parsing), but what items to write or to expect to read. For example
>> as far as I can see an observed intensity may be encoded in a
>> reflection loop (merged or unmerged) as any one of the following, and
>> there seem to be similar choices for other items:-
>>
>>
>> _refln_intensity_meas
>> _refln.F_squared_meas
>> _refln.pdbx_I_plus, _refln.pdbx_I_minus
>>
>> _diffrn_refln.counts_net
>> _diffrn_refln.intensity_net
>>
>> If I'm writing a file, which should I use, and if I'm reading one
>> which ones should I expect? And is there a distinction between merged
>> and unmerged data?
>>
>> confused (easily)
>> Phil
>>
>>
>>
>> On 17 Sep 2013, at 15:30, Peter Keller <[log in to unmask]>
>> wrote:
>>
>>> Dear all,
>>>
>>> At Global Phasing, we have seen that there are still issues with the
>>> way that different applications deal with mmCIF-format data, and
>>> this continues to cause problems for users. I believe that part of
>>> the reason for this is that the underlying syntax (the STAR format)
>>> is not universally understood, and that a common and complete
>>> understanding of the full STAR syntax amongst programmers who deal
>>> with the format will help with some of the existing problems.
>>>
>>> I wrote some code for low-level handling of the STAR format a while
>>> ago that I have been meaning to release for over a year. Garry
>>> Battle's announcement on 23 August about the mmCIF/PDBx workshop at
>>> the EBI has prompted me into action: I have written a short article
>>> that discusses some examples of the issues that we have encountered,
>>> and made my code available for download. The references in the
>>> article are given primarily as web links: more conventional
>>> citations can usually be found in the pages that I link to. This
>>> code has not been used in any released products, but it has had some
>>> internal use at Global Phasing. There is an MX bias in the article's
>>> discussion, but the issues are not restricted to MX.
>>>
>>> As I explain in the article, the handling of the input data is based
>>> on an enourmous regular expression that matches STAR data, with only
>>> a little logic in the code itself. The regular expression should be
>>> usable with a variety of other languages, not only in Java (which I
>>> have used in this case). The code, or the regular expression on its
>>> own, may be freely used in other projects: see the included
>>> licencing for details, but basically you should: (i) give credit for
>>> using it, and (ii) if you choose to modify the regular expression,
>>> state that you have done so in that credit.
>>>
>>> The article, which contains links to a tar file containing the code,
>>> and the documentation, is here:
>>>
>>> <http://www.globalphasing.com/startools/>
>>>
>>> Hoping that others will find this useful and/or help to resolve or
>>> clarify outstanding questions,
>>>
>>> Peter.
>>>
>>> --
>>> Peter Keller Tel.: +44 (0)1223
>>> 353033
>>> Global Phasing Ltd., Fax.: +44 (0)1223
>>> 366889
>>> Sheraton House,
>>> Castle Park,
>>> Cambridge CB3 0AX
>>> United Kingdom
>>
>
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