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Re: [ddlm-group] The Grazulis eliding proposal: how to incorporateinto CIF?. .. .

To avoid any misunderstanding and have us all working from the same base 
please send the proposal we are discussing as one self-contained document
   -- Herbert
=====================================================
  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  +1-631-244-3035
                  [email protected]
=====================================================

On Tue, 26 Jul 2011, James Hester wrote:

> Dear DDLm-ers,
> 
> I agree that we should try and resolve any outstanding issues with CIF2 at the Madrid
> meeting.� However, to make that approach workable we need to have exposed all the issues in
> this forum so that we are not blindsided by new information in Madrid and left with no time
> to process it.� I would therefore suggest that this discussion continues so that we can
> identify precisely what the particular issues and alternatives are.� The less we have to
> deal with in Madrid the more likely we will be able to converge on a solution.
> 
> So, to pursue Herbert's comments below:
> (1) In what sense is John's draft an 'either-or' approach to prefixes and line folding?�
> Doesn't it require both to be recognised?
> (2) Are there any other reasons John's draft is not an improvement?
> 
> James.
> 
> On Wed, Jun 29, 2011 at 4:45 AM, Herbert J. Bernstein <[email protected]> wrote:
>       Dear Colleagues,
>
>       � I fear we are not comunicating very effectively. �I am
>       _not_ comfortable with the current state of the CIF2
>       document, and I do not find the current emendation to
>       be an improvement. �Much as I would dearly love to have
>       the current line-folding protocol in CIF2, I think it
>       is much more important to work on making CIF2 into
>       something clear and coherent. �I for one find the
>       either-or approach to prefixes and line-folding unnecessary
>       and confusing. �When working with old fortran compilers,
>       I _need_ the line folding protocol. �If the prefixes
>       are bing introduced, I need a way to deal with both the
>       prefixes _and_ the line-folding protocol, not have it
>       be either-or. �I understand that mose people don't
>       see a problem, but I work with software both on new computers
>       and very, very old computers (e.g. I just brought an Indigo
>       back to life).
>
>       � I repeat my suggestion that we need to meet and talk things
>       out. �Maybe then I will understand what the rest of you are trying
>       to do, and maybe I will be able to explain what I am trying
>       to do.
>
>       � Regards,
>       � � Herbert
>
>       =====================================================
>       �Herbert J. Bernstein, Professor of Computer Science
>       � �Dowling College, Kramer Science Center, KSC 121
>       � � � � Idle Hour Blvd, Oakdale, NY, 11769
>
>       � � � � � � � � �+1-631-244-3035
>       � � � � � � � � �[email protected]
>       =====================================================
> 
> On Tue, 28 Jun 2011, Bollinger, John C wrote:
> 
> >
> > On Tuesday, June 28, 2011 9:07 AM, Herbert J. Bernstein wrote:
> >
> > [...]
> >
> >> � For CIF2, I would urge that we try to make something
> >> coherent and clear. �I don't think we are there yet.
> >> Maybe, if time permits and enough of us are present,
> >> we can converge on something in Madrid.
> >
> >
> > No need to wait for Madrid. �Please find below a concrete realization of my most
> preferred alternative. �I think it's coherent and clear, though suggestions for
> improvement on that front are welcome.
> >
> >
> > =====
> >
> > 1. In Change 6, section (3) of the CIF 2.0 syntax changes document:
> >
> > a) Before the sentence "CIF2 does not specify any interpretation of the contents of
> the string," insert: "The string is interpreted according to the CIF Line-Folding
> Protocol (Appendix 1) when its signature is present, and according to the CIF Text
> Prefix Protocol (Appendix 2) when its signature is present. �Otherwise, "
> >
> > b) Insert this text after "The string value is Sugar\nFlour\nButter, where \n is
> the literal newline sequence." as a new paragraph:
> >
> > When the Line-Folding Protocol and Text Prefix Protocol are applied to the same
> value, the value shall appear in CIF as if line-folding had been performed first,
> followed by prefixing.
> >
> >
> > 2. Add a definition of the Line-Folding Protocol as Appendix 1 of the CIF 2.0
> syntax changes document:
> >
> > Appendix 1. � � The CIF Line-Folding Protocol
> >
> > The CIF line-folding protocol is a mechanism for splitting logical lines of text
> across two or more physical lines of a CIF semicolon-delimited data value ("text
> field"). �A version of this protocol appears among the "Common Semantic Features" of
> CIF 1.1 and is in wide use in that context; in CIF 2.0 line-folding is part of the
> CIF syntax, as described below.
> >
> > The protocol applies to text fields whose contents (after interpretation of the
> text protocol, if applicable) begin with a backslash, followed by any number of
> whitespace characters other than newline, followed by newline or the end of the text
> field; that sequence is designated \<ws>*\n below. �There must not be any whitespace
> preceding the initial backslash.
> >
> > Given un-prefixed (Appendix 2) text field contents to which the line-folding
> protocol applies, the logical text it represents is derived from it by removing each
> occurrence of \<ws>*\n, including the initial one. �Different lines may have
> different amounts of whitespace between the trailing backslash and newline.
> >
> > Note that the line-folding protocol cannot elide the terminating \n; of a text
> field because the \n of that delimiter is not accounted part of the field contents.
> �It follows from the above definition of \<ws>*\n, however, that if the last line
> ends with \<ws>* then that will not appear in the unfolded value.
> >
> >
> > 3. Add a definition of the of the Text Prefix Protocol as Appendix 2 of the CIF 2.0
> syntax changes document:
> >
> > The CIF text-prefix protocol is a mechanism for formatting the logical content of a
> CIF semicolon-delimited value ("text field") so as to avoid misinterpretation of
> embedded appearances of \n;. It may also be useful for improving human readability of
> some CIFs.
> >
> > The protocol applies to text fields whose physical contents begin with a prefix
> (see below), followed by one or two backslashes, optionally followed by any amount of
> whitespace other than a newline, followed by a newline. �A prefix consists of a
> sequence of one or more characters that are permitted in a text field, except for
> backslash or newline, and does not begin with a semicolon.
> >
> > The second and all subsequent physical lines of the contents of a prefixed text
> field must begin with the designated prefix for that field. �The line containing the
> terminating semicolon is not part of the contents for this purpose. �The logical
> (i.e. "un-prefixed") contents of the field is derived from the physical contents by
> the following procedure:
> >
> > a) remove the prefix from each line, including the first
> > b) if the first line starts with two backslashes then remove the first of them;
> otherwise remove the whole line
> >
> > Example 1:
> >
> > data_providing_example
> > _example
> > ;CIF>\
> > CIF>data_example
> > CIF>_text
> > CIF>;This is an embedded multiline value
> > CIF>;
> > ; # here the field terminates.
> >
> > Example 2:
> >
> > data_providing_example
> > _example
> > ; \
> > data_example
> > _text
> > ;This is an embedded multiline value
> > ;
> > ; # here the field terminates.
> >
> >
> > =====
> >
> >
> > Regards,
> >
> > John
> >
> > --
> > John C. Bollinger, Ph.D.
> > Department of Structural Biology
> > St. Jude Children's Research Hospital
> >
> >
> > Email Disclaimer: �www.stjude.org/emaildisclaimer
> >
> > _______________________________________________
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> > [email protected]
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> >
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