proteins.bst

% PROTEINS bibliography style (3-Mar-93 version)
%
%    History
%       4/22/92	Cindy Fisher---Original version for BibTeX 0.99c
%                       THIS `proteins' VERSION DOES NOT WORK WITH BIBTEX 0.98i.
%                       For Proteins: Struct. Func. Genet. journal
%
%       3/3/93      Cindy Fisher---Fixed editors bug in function "inproceedings"
%

ENTRY
  { address
    author
    booktitle
    chapter
    edition
    editor
    howpublished
    institution
    journal
    key
    month
    note
    number
    organization
    pages
    publisher
    school
    series
    title
    type
    volume
    year
  }
  {}
  { label }

INTEGERS { output.state before.all mid.sentence after.sentence after.block }

FUNCTION {init.state.consts}
{ #0 'before.all :=
  #1 'mid.sentence :=
  #2 'after.sentence :=
  #3 'after.block :=
}

STRINGS { s t }

FUNCTION {output.nonnull}
{ 's :=
  output.state mid.sentence =
    { " " * write$ }
    { output.state after.block =
        { add.period$ write$
          newline$
          "\newblock " write$
        }
        { output.state before.all =
            'write$
            { add.period$ " " * write$ }
          if$
        }
      if$
      mid.sentence 'output.state :=
    }
  if$
  s
}

FUNCTION {output}
{ duplicate$ empty$
    'pop$
    'output.nonnull
  if$
}

FUNCTION {output.check}
{ 't :=
  duplicate$ empty$
    { pop$ "empty " t * " in " * cite$ * warning$ }
    'output.nonnull
  if$
}

FUNCTION {output.bibitem}
{ newline$
  "\bibitem{" write$
  cite$ write$
  "}" write$
  newline$
  ""
  before.all 'output.state :=
}

FUNCTION {fin.entry}
{ add.period$
  write$
  newline$
}

FUNCTION {new.block}
{ output.state before.all =
    'skip$
    { after.block 'output.state := }
  if$
}

FUNCTION {new.sentence}
{ output.state after.block =
    'skip$
    { output.state before.all =
        'skip$
        { after.sentence 'output.state := }
      if$
    }
  if$
}

FUNCTION {not}
{   { #0 }
    { #1 }
  if$
}

FUNCTION {and}
{   'skip$
    { pop$ #0 }
  if$
}

FUNCTION {or}
{   { pop$ #1 }
    'skip$
  if$
}

FUNCTION {new.block.checka}
{ empty$
    'skip$
    'new.block
  if$
}

FUNCTION {new.block.checkb}
{ empty$
  swap$ empty$
  and
    'skip$
    'new.block
  if$
}

FUNCTION {field.or.null}
{ duplicate$ empty$
    { pop$ "" }
    'skip$
  if$
}

FUNCTION {emphasize}
{ duplicate$ empty$
    { pop$ "" }
    { "{\em " swap$ * "}" * }
  if$
}

FUNCTION {emphasizeic}
{ duplicate$ empty$
    { pop$ "" }
    { "{\em " swap$ * "\/}" * }
  if$
}

FUNCTION {scapify}
{ duplicate$ empty$
    { pop$ "" }
    { "{\sc " swap$ * "}" * }
  if$
}

FUNCTION {boldface}
{ duplicate$ empty$
    { pop$ "" }
    { "{\bf " swap$ * "}" * }
  if$
}

FUNCTION {boldfaceic}
{ duplicate$ empty$
    { pop$ "" }
    { "{\bf " swap$ * "\/}" * }
  if$
}

INTEGERS { nameptr namesleft numnames }

FUNCTION {format.names}
{ 's :=
  #1 'nameptr :=
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { s nameptr "{vv~}{ll}{, f.}{~jj}" format.name$ 't :=
      nameptr #1 >
        { namesleft #1 >
            { ", " * t * }
            { t "others" =
                { " {\em et~al}." * }
                { ", " * t * }
              if$
            }
          if$
        }
        't
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

% For names inside entries (e.g., editors of an "In ...");
% this is exactly ABBRV.BST's `format.names' function.
FUNCTION {format.innames}
{ 's :=
  #1 'nameptr :=
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { s nameptr "{f.~}{vv~}{ll}{, jj}" format.name$ 't :=
      nameptr #1 >
        { namesleft #1 >
            { ", " * t * }
            { numnames #2 >
                { "," * }
                'skip$
              if$
              t "others" =
                { " {\em et~al}." * }
                { " \& " * t * }
              if$
            }
          if$
        }
        't
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

FUNCTION {format.authors}
{ author empty$
    { "" }
    { author format.names }
  if$
}

FUNCTION {format.editors}
{ editor empty$
    { "" }
    { editor format.names 
      editor num.names$ #1 >
        { ", eds. " * }
        { ", ed. " * }
      if$
    }
  if$
}

FUNCTION {format.ineditors}
{ editor empty$
    { "" }
    { editor num.names$ #1 >
        { editor format.names * " eds. " * }
        { editor format.names * " ed. " * }
      if$
    }    
  if$
}

FUNCTION {format.title}
{ title empty$
    { "" }
    { title "t" change.case$ }
  if$
}

FUNCTION {n.dashify}
{ 't :=
  ""
    { t empty$ not }
    { t #1 #1 substring$ "-" =
        { t #1 #2 substring$ "--" = not
            { "--" *
              t #2 global.max$ substring$ 't :=
            }
            {   { t #1 #1 substring$ "-" = }
                { "-" *
                  t #2 global.max$ substring$ 't :=
                }
              while$
            }
          if$
        }
        { t #1 #1 substring$ *
          t #2 global.max$ substring$ 't :=
        }
      if$
    }
  while$
}

FUNCTION {format.date}
{ year empty$
    { month empty$
        { "" }
        { "there's a month but no year in " cite$ * warning$
          month
        }
      if$
    }
    { month empty$
        'year
        { month " " * year * }
      if$
    }
  if$
}

FUNCTION {format.btitle}
{ title 
}

FUNCTION {tie.or.space.connect}
{ duplicate$ text.length$ #3 <
    { "~" }
    { " " }
  if$
  swap$ * *
}

FUNCTION {either.or.check}
{ empty$
    'pop$
    { "can't use both " swap$ * " fields in " * cite$ * warning$ }
  if$
}

FUNCTION {format.bvolume}
{ volume empty$
    { "" }
    { "Vol.~" volume * ". " *
      series empty$
        'skip$
        { " of " * series emphasize * }
      if$
      "volume and number" number either.or.check
    }
  if$
}

FUNCTION {format.number.series}
{ volume empty$
    { number empty$
        { series field.or.null }
        { output.state mid.sentence =
            { "no.~" }
            { "No.~" }
          if$
          number *
          series empty$
            { "there's a number but no series in " cite$ * warning$ }
            { " in " * series * }
          if$
        }
      if$
    }
    { "" }
  if$
}

FUNCTION {format.edition}
{ edition empty$
    { "" }
    { output.state mid.sentence =
        { edition "l" change.case$ "~Ed." * }
        { edition "t" change.case$ "~Ed." * }
      if$
    }
  if$
}

FUNCTION {format.pages}
{ pages empty$
    { "" }
    { pages n.dashify }
  if$
}

INTEGERS { multiresult }

FUNCTION {multi.page.check}
{ 't :=
  #0 'multiresult :=
    { multiresult not
      t empty$ not
      and
    }
    { t #1 #1 substring$
      duplicate$ "-" =
      swap$ duplicate$ "," =
      swap$ "+" =
      or or
        { #1 'multiresult := }
        { t #2 global.max$ substring$ 't := }
      if$
    }
  while$
  multiresult
}

INTEGERS {char.num}

STRINGS {current.char}

FUNCTION {take.first.page}
{ 't :=
  #1 'char.num :=
      { t char.num #1 substring$ 'current.char :=
	 current.char "," =
	 current.char "-" =
	 current.char "" = or or not
      }
      { char.num #1 + 'char.num := }
  while$
  char.num #1 - 'char.num :=
  t #1 char.num substring$
}

FUNCTION {format.pp.pages}
{ pages empty$
    { "" }
    { pages multi.page.check
        { "~" pages n.dashify * }
        { "~" pages * }
      if$
    }
  if$
}

FUNCTION {format.vol.num.pages.date}
{ volume field.or.null
  number empty$
    'skip$
    { "(" number * ")" * *
      volume empty$
        { "there's a number but no volume in " cite$ * warning$ }
        'skip$
      if$
    }    
  if$
  pages empty$
    'skip$
    { duplicate$ empty$
        { pop$ format.pages }
        { ":" * pages n.dashify * }
      if$
      year empty$
        { "empty year in " cite$ * warning$ }
        { ", " * format.date * }
      if$
    }
  if$
}

FUNCTION {format.chapter.pages}
{ chapter empty$
    'format.pp.pages
    { type empty$
        { "ch.~" chapter * }
        { type "l" change.case$ chapter tie.or.space.connect }
      if$
      pages empty$
        'skip$
        { ", " * format.pp.pages * }
      if$
    }
  if$
}

FUNCTION {format.in.booktitle.ed}
{ booktitle empty$
    { "" }
    { "In: " booktitle * ". " *
        volume empty$
          'skip$
          { "Vol. " * volume * ". " *}
        if$
        editor empty$
          'skip$
         { format.ineditors }
        if$
    }
  if$
}

FUNCTION {format.in.ed.booktitle}
{ booktitle empty$
    { "" }
    { "In " booktitle *
      editor empty$
        'skip$
        { ", " * format.ineditors * }
      if$
    }
  if$
}

FUNCTION {format.address.publisher.date.pages}
{ address empty$
    { "empty address in " cite$ * warning$ }
    { address }
  if$
  publisher empty$
    { "empty publisher in " cite$ * warning$ }
    { ": " * publisher * }
  if$
  year empty$
    { "empty year in " cite$ * warning$ }
    { ". " * format.date * }
  if$
  pages empty$
	'skip$
	{ ": " * format.pages *}
  if$
}

FUNCTION {format.address.publisher.date}
{ address empty$
    { "empty address in " cite$ * warning$ }
    { address }
  if$
  publisher empty$
    { "empty publisher in " cite$ * warning$ }
    { ": " * publisher * }
  if$
  year empty$
    { "empty year in " cite$ * warning$ }
    { ". " * format.date * }
  if$
}

FUNCTION {format.proc.date}
{ duplicate$ empty$
    { pop$ "" }
    { year empty$
        { "empty year in " cite$ * warning$
          address empty$
            'emphasize
            { emphasizeic
              " (" address * ")" *
            }
          if$
        }
        { emphasizeic *
          " (" 
          address empty$
            'skip$
            { address * ", " * }
          if$
          format.date *
          ")"  *
        }
      if$
    }
  if$
}

FUNCTION {format.in.proc.date}
{ booktitle empty$
    { "" }
    { "In " booktitle format.proc.date * }
  if$
}

FUNCTION {empty.misc.check}
{ author empty$ title empty$ howpublished empty$
  month empty$ year empty$ note empty$
  and and and and and
  key empty$ not and
    { "all relevant fields are empty in " cite$ * warning$ }
    'skip$
  if$
}

FUNCTION {format.thesis.type}
{ type empty$
    'skip$
    { pop$
      type "t" change.case$
    }
  if$
}

FUNCTION {format.tr.number}
{ type empty$
    { "Tech. Rep." }
    'type
  if$
  number empty$
    { "t" change.case$ }
    { number tie.or.space.connect }
  if$
}

FUNCTION {format.article.crossref}
{ key empty$
    { journal empty$
        { "need key or journal for " cite$ * " to crossref " * crossref *
          warning$
          ""
        }
        { "In {\em " journal * "\/}" * }
      if$
    }
    { "In " key * }
  if$
  " \cite{" * crossref * "}" *
}

FUNCTION {format.crossref.editor}
{ editor #1 "{vv~}{ll}" format.name$
  editor num.names$ duplicate$
  #2 >
    { pop$ " {\em et~al}." * }
    { #2 <
        'skip$
        { editor #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
            { " {\em et~al}." * }
            { " and " * editor #2 "{vv~}{ll}" format.name$ * }
          if$
        }
      if$
    }
  if$
}

FUNCTION {format.book.crossref}
{ volume empty$
    { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
      "In "
    }
    { "vol.~" volume *
      " of " *
    }
  if$
  editor empty$
  editor field.or.null author field.or.null =
  or
    { key empty$
        { series empty$
            { "need editor, key, or series for " cite$ * " to crossref " *
              crossref * warning$
              "" *
            }
            { "{\em " * series * "\/}" * }
          if$
        }
        { key * }
      if$
    }
    { format.crossref.editor * }
  if$
  " \cite{" * crossref * "}" *
}

FUNCTION {format.incoll.inproc.crossref}
{ editor empty$
  editor field.or.null author field.or.null =
  or
    { key empty$
        { booktitle empty$
            { "need editor, key, or booktitle for " cite$ * " to crossref " *
              crossref * warning$
              ""
            }
            { "In {\em " booktitle * "\/}" * }
          if$
        }
        { "In " key * }
      if$
    }
    { "In " format.crossref.editor * }
  if$
  " \cite{" * crossref * "}" *
}

FUNCTION {article}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  crossref missing$
    { journal "journal" output.check
      format.vol.num.pages.date output
    }
    { format.article.crossref output.nonnull
      format.pages output
    }
  if$
  new.block
  note output
  fin.entry
}

FUNCTION {book}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check }
    { format.authors output.nonnull
      crossref missing$
        { "author and editor" editor either.or.check }
        'skip$
      if$
    }
  if$
  format.btitle "title" output.check
  new.block
  format.edition output
  crossref missing$
    { format.bvolume output
      format.number.series output
      format.address.publisher.date output
    }
    { new.block
      format.book.crossref output.nonnull
    }
  if$
  new.block
  note output
  fin.entry
}

FUNCTION {booklet}
{ output.bibitem
  format.authors output
  new.block
  format.title "title" output.check
  howpublished address new.block.checkb
  howpublished output
  address output
  format.date output
  new.block
  note output
  fin.entry
}

FUNCTION {inbook}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check }
    { format.authors output.nonnull
      crossref missing$
        { "author and editor" editor either.or.check }
        'skip$
      if$
    }
  if$
  format.title output
  new.block
  format.in.booktitle.ed output
  format.edition output
  crossref missing$
    { format.number.series output
      format.address.publisher.date.pages "address and publisher" output.check
    }
    { new.block
      format.book.crossref output.nonnull
    }
  if$
  new.block
  note output
  fin.entry
}

FUNCTION {incollection}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  crossref missing$
    { format.in.booktitle.ed output
      format.edition output
      format.bvolume output
      format.number.series output
      new.sentence
      publisher "publisher" output.check
      address output
      format.date "year" output.check
    }
    { format.incoll.inproc.crossref output.nonnull }
  if$
  format.chapter.pages output
  new.block
  note output
  fin.entry
}

FUNCTION {inproceedings}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title output
  new.block
  crossref missing$
    { format.in.proc.date output
      new.block
      format.editors output
      format.bvolume output
      format.number.series output
      organization output
      new.block
      publisher output
      new.block
    }
    { format.incoll.inproc.crossref output.nonnull }
  if$
%  format.pp.pages output
%  new.block
%  note output
  fin.entry
}

FUNCTION {conference} { inproceedings }

FUNCTION {manual}
{ output.bibitem
  author empty$
    { organization scapify output }
    { format.authors output.nonnull }
  if$
  new.block
  format.title "title" output.check
  format.edition output
  author empty$
    { address new.block.checka }
    { organization address new.block.checkb
      organization output
    }
  if$
  address output
  format.date output
  new.block
  note output
  fin.entry
}

FUNCTION {mastersthesis}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  "Master's thesis" format.thesis.type output.nonnull
  new.block
  school "school" output.check
  new.block
  address output
  new.block
  format.date "year" output.check
  new.block
  note output
  fin.entry
}

FUNCTION {misc}
{ output.bibitem
  format.authors output
  title howpublished new.block.checkb
  format.title output
  new.block
  howpublished new.block.checka
  howpublished output
  new.block
  format.date output
  new.block
  note output
  fin.entry
  empty.misc.check
}

FUNCTION {phdthesis}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  "PhD thesis" format.thesis.type output.nonnull
  new.block
  school "school" output.check
  new.block
  address output
  new.block
  format.date "year" output.check
  new.block
  note output
  fin.entry
}

FUNCTION {proceedings}
{ output.bibitem
  editor empty$
    { organization output }
    { format.editors output.nonnull }
  if$
  new.block
  title format.proc.date "title" output.check
  format.bvolume output
  format.number.series output
  editor empty$
    'skip$
    { organization output }
  if$
  publisher output
  new.block
  note output
  fin.entry
}

FUNCTION {techreport}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  format.tr.number output.nonnull
  new.block
  institution "institution" output.check
  address output
  new.block
  format.date "year" output.check
  new.block
  note output
  fin.entry
}

FUNCTION {unpublished}
{ output.bibitem
  format.authors "author" output.check
  new.block
  format.title "title" output.check
  new.block
  note "note" output.check
  format.date output
  fin.entry
}

FUNCTION {default.type} { misc }

MACRO {jan} {"Jan."}

MACRO {feb} {"Feb."}

MACRO {mar} {"Mar."}

MACRO {apr} {"Apr."}

MACRO {may} {"May"}

MACRO {jun} {"June"}

MACRO {jul} {"July"}

MACRO {aug} {"Aug."}

MACRO {sep} {"Sept."}

MACRO {oct} {"Oct."}

MACRO {nov} {"Nov."}

MACRO {dec} {"Dec."}

MACRO {jacs} {"J. Am. Chem. Soc."}

MACRO {bbrc} {"Biochem. Biophys. Res. Commun."}

MACRO {jbc} {"J. Biol. Chem."}

MACRO {pnas} {"Proc. Natl. Acad. Sci. U.S.A."}

MACRO {jmb} {"J. Mol. Biol."}

MACRO {embo} {"EMBO J."}

MACRO {tibs} {"Trends Biochem. Sci."}

MACRO {protsfg} {"Proteins: Struct. Func. Gen."}

READ

FUNCTION {sortify}
{ purify$
  "l" change.case$
}

INTEGERS { len }

FUNCTION {chop.word}
{ 's :=
  'len :=
  s #1 len substring$ =
    { s len #1 + global.max$ substring$ }
    's
  if$
}

FUNCTION {sort.format.names}
{ 's :=
  #1 'nameptr :=
  ""
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { nameptr #1 >
        { "   " * }
        'skip$
      if$
      s nameptr "{vv{ } }{ll{ }}{  f{ }}{  jj{ }}" format.name$ 't :=
      nameptr numnames = t "others" = and
        { "{\em et al}." * }
        { t sortify * }
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

FUNCTION {sort.format.title}
{ 't :=
  "A " #2
    "An " #3
      "The " #4 t chop.word
    chop.word
  chop.word
  sortify
  #1 global.max$ substring$
}

FUNCTION {author.sort}
{ author empty$
    { key empty$
        { "to sort, need author or key in " cite$ * warning$
          ""
        }
        { key sortify }
      if$
    }
    { author sort.format.names }
  if$
}

FUNCTION {author.editor.sort}
{ author empty$
    { editor empty$
        { key empty$
            { "to sort, need author, editor, or key in " cite$ * warning$
              ""
            }
            { key sortify }
          if$
        }
        { editor sort.format.names }
      if$
    }
    { author sort.format.names }
  if$
}

FUNCTION {author.organization.sort}
{ author empty$
    { organization empty$
        { key empty$
            { "to sort, need author, organization, or key in " cite$ * warning$
              ""
            }
            { key sortify }
          if$
        }
        { "The " #4 organization chop.word sortify }
      if$
    }
    { author sort.format.names }
  if$
}

FUNCTION {editor.organization.sort}
{ editor empty$
    { organization empty$
        { key empty$
            { "to sort, need editor, organization, or key in " cite$ * warning$
              ""
            }
            { key sortify }
          if$
        }
        { "The " #4 organization chop.word sortify }
      if$
    }
    { editor sort.format.names }
  if$
}

FUNCTION {presort}
{ type$ "book" =
  type$ "inbook" =
  or
    'author.editor.sort
    { type$ "proceedings" =
        'editor.organization.sort
        { type$ "manual" =
            'author.organization.sort
            'author.sort
          if$
        }
      if$
    }
  if$
  "    "
  *
  year field.or.null sortify
  *
  "    "
  *
  title field.or.null
  sort.format.title
  *
  #1 entry.max$ substring$
  'sort.key$ :=
}

ITERATE {presort}

%SORT

STRINGS { longest.label }

INTEGERS { number.label longest.label.width }

FUNCTION {initialize.longest.label}
{ "" 'longest.label :=
  #1 'number.label :=
  #0 'longest.label.width :=
}

FUNCTION {longest.label.pass}
{ number.label int.to.str$ 'label :=
  number.label #1 + 'number.label :=
  label width$ longest.label.width >
    { label 'longest.label :=
      label width$ 'longest.label.width :=
    }
    'skip$
  if$
}

EXECUTE {initialize.longest.label}

ITERATE {longest.label.pass}

FUNCTION {begin.bib}
{ preamble$ empty$
    'skip$
    { preamble$ write$ newline$ }
  if$
  "\begin{thebibliography}{"  longest.label  * "}" * write$ newline$
}

EXECUTE {begin.bib}

EXECUTE {init.state.consts}

ITERATE {call.type$}

FUNCTION {end.bib}
{ newline$
  "\end{thebibliography}" write$ newline$
}

EXECUTE {end.bib}