Hi Peter,
Thanks for posting the startools, I think many developers can benefit from these.
[snip]
> One final point on this: line-by-line processing needs to allow for the fact that
> there is no requirement at the format specification level for reflection data to
> be one reflection per line, and that the CIF may contain multi-line text data
> (unlikely in categories containing reflection data, but quite possible
> elsewhere in the same file). I am sure that 99.99% of reflection CIF's will be
> one reflection per line, but that is a convention (aka dialect). When someone
> hits a case where it isn't things will go wrong with applications that don't take
> account of this.
There actually used to be quite a lot of reflection files that had reflections wrapped over two or three lines. Line-by-line reading is still possible, but you have check whether a line has the number of data items you expect. If this is not the case, you read the data from the next line as well. You only have to do this for the first data line in a loop. That is, iff the file is formatted consistently. I guess that's a matter of trust between the person who writes the parser and the person who wrote the program that wrote the input file ;)
Cheers,
Robbie
>
> > If you imagine someone corresponding to the XDS INTEGRATE.HKL file
> > with 120 characters/reflection, then a dataset with 10^7 reflections
> > (not outrageously large these days) occupies 1.2e9 bytes, over 1GB,
> > which seems a lot to add gratuitously to memory demands even on
> > today's computers
> >
> > Of course (in my opinion) a working format (as opposed to an archive
> > format) should be binary for size, accuracy (FP dynamic range) and
> > speed.
>
> Yes: this is also a good point, particularly for large amounts of tabular data
> that is easy to define, like reflection data. MTZ has served us well for a long
> time, and other binary formats like HDF5 have been designed partly with this
> consideration in mind. OTOH, a format like mmCIF is well suited to a working
> format for chemical restraint/geometry dictionaries (provided of course that
> dialects don't proliferate, and that developers use data names that are
> defined in a dictionary that is available to other developers, rather than just
> making them up). Coordinate data is somewhere in the middle, but that is
> another discussion......
>
> Regards,
> Peter.
>
> > A quick comparison (using Pointless)
> >
> > Read 5.3e6 reflections from a formatted XDS INTEGRATE.HKL file, 608MB,
> > 15 secs Read equivalent binary MTZ file, 262MB, 2.6 secs
> >
> > Phil
> >
> > On 18 Sep 2013, at 15:58, yayahjb <[log in to unmask]> wrote:
> >
> > > 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
> > >>>
> > >>
>
> --
> 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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