e0984a43a9
This deprecates the use of the external pandoc-citeproc
filter; citation processing is now built in to pandoc.
* Add dependency on citeproc library.
* Add Text.Pandoc.Citeproc module (and some associated unexported
modules under Text.Pandoc.Citeproc). Exports `processCitations`.
[API change]
* Add data files needed for Text.Pandoc.Citeproc: default.csl
in the data directory, and a citeproc directory that is just
used at compile-time. Note that we've added file-embed as a mandatory
rather than a conditional depedency, because of the biblatex
localization files. We might eventually want to use readDataFile
for this, but it would take some code reorganization.
* Text.Pandoc.Loging: Add `CiteprocWarning` to `LogMessage` and use it
in `processCitations`. [API change]
* Add tests from the pandoc-citeproc package as command tests (including
some tests pandoc-citeproc did not pass).
* Remove instructions for building pandoc-citeproc from CI and
release binary build instructions. We will no longer distribute
pandoc-citeproc.
* Markdown reader: tweak abbreviation support. Don't insert a
nonbreaking space after a potential abbreviation if it comes right before
a note or citation. This messes up several things, including citeproc's
moving of note citations.
* Add `csljson` as and input and output format. This allows pandoc
to convert between `csljson` and other bibliography formats,
and to generate formatted versions of CSL JSON bibliographies.
* Add module Text.Pandoc.Writers.CslJson, exporting `writeCslJson`. [API
change]
* Add module Text.Pandoc.Readers.CslJson, exporting `readCslJson`. [API
change]
* Added `bibtex`, `biblatex` as input formats. This allows pandoc
to convert between BibLaTeX and BibTeX and other bibliography formats,
and to generated formatted versions of BibTeX/BibLaTeX bibliographies.
* Add module Text.Pandoc.Readers.BibTeX, exporting `readBibTeX` and
`readBibLaTeX`. [API change]
* Make "standalone" implicit if output format is a bibliography format.
This is needed because pandoc readers for bibliography formats put
the bibliographic information in the `references` field of metadata;
and unless standalone is specified, metadata gets ignored.
(TODO: This needs improvement. We should trigger standalone for the
reader when the input format is bibliographic, and for the writer
when the output format is markdown.)
* Carry over `citationNoteNum` to `citationNoteNumber`. This was just
ignored in pandoc-citeproc.
* Text.Pandoc.Filter: Add `CiteprocFilter` constructor to Filter.
[API change] This runs the processCitations transformation.
We need to treat it like a filter so it can be placed
in the sequence of filter runs (after some, before others).
In FromYAML, this is parsed from `citeproc` or `{type: citeproc}`,
so this special filter may be specified either way in a defaults file
(or by `citeproc: true`, though this gives no control of positioning
relative to other filters). TODO: we need to add something to the
manual section on defaults files for this.
* Add deprecation warning if `upandoc-citeproc` filter is used.
* Add `--citeproc/-C` option to trigger citation processing.
This behaves like a filter and will be positioned
relative to filters as they appear on the command line.
* Rewrote the manual on citatations, adding a dedicated Citations
section which also includes some information formerly found in
the pandoc-citeproc man page.
* Look for CSL styles in the `csl` subdirectory of the pandoc user data
directory. This changes the old pandoc-citeproc behavior, which looked
in `~/.csl`. Users can simply symlink `~/.csl` to the `csl`
subdirectory of their pandoc user data directory if they want
the old behavior.
* Add support for CSL bibliography entry formatting to LaTeX, HTML,
Ms writers. Added CSL-related CSS to styles.html.
4.4 KiB
4.4 KiB
% pandoc -f biblatex -t markdown -s
@comment{
Adapted from biblatex-example.bib
Formatted with pandoc and chicago-author-date.csl, 2013-10-23:
(Sigfridsson and Ryde 1998)
Sigfridsson, Emma, and Ulf Ryde. 1998. “Comparison of Methods for
Deriving Atomic Charges from the Electrostatic Potential and Moments.”
*Journal of Computational Chemistry* 19 (4): 377–395.
doi:[10.1002/(SICI)1096-987X(199803)19:4\<377::AID-JCC1\>3.0.CO;2-P](https://doi.org/10.1002/(SICI)1096-987X(199803)19:4<377::AID-JCC1>3.0.CO;2-P "10.1002/(SICI)1096-987X(199803)19:4<377::AID-JCC1>3.0.CO;2-P").
Formatted with pandoc and apa.csl, 2013-10-23:
(Sigfridsson & Ryde, 1998)
Sigfridsson, E., & Ryde, U. (1998). Comparison of methods for deriving
atomic charges from the electrostatic potential and moments. *Journal of
Computational Chemistry*, *19*(4), 377–395.
doi:[10.1002/(SICI)1096-987X(199803)19:4\<377::AID-JCC1\>3.0.CO;2-P](https://doi.org/10.1002/(SICI)1096-987X(199803)19:4<377::AID-JCC1>3.0.CO;2-P "10.1002/(SICI)1096-987X(199803)19:4<377::AID-JCC1>3.0.CO;2-P")
NOTES:
- biblio2xaml
- the string "doi:" should not appear as part of the content of the "doi" field
}
@Article{sigfridsson,
author = {Sigfridsson, Emma and Ryde, Ulf},
title = {Comparison of methods for deriving atomic charges from the
electrostatic potential and moments},
journaltitle = {Journal of Computational Chemistry},
date = 1998,
volume = 19,
number = 4,
pages = {377-395},
doi = {10.1002/(SICI)1096-987X(199803)19:4<377::AID-JCC1>3.0.CO;2-P},
hyphenation = {american},
indextitle = {Methods for deriving atomic charges},
annotation = {An article entry with volume,
number, and doi fields. Note that the
\textsc{doi} is transformed into a clickable link if
hyperref support has been enabled},
abstract = {Four methods for deriving partial atomic charges from the
quantum chemical electrostatic potential (CHELP, CHELPG,
Merz-Kollman, and RESP) have been compared and critically
evaluated. It is shown that charges strongly depend on how and
where the potential points are selected. Two alternative
methods are suggested to avoid the arbitrariness in the
point-selection schemes and van der Waals exclusion radii:
CHELP-BOW, which also estimates the charges from the
electrostatic potential, but with potential points that are
Boltzmann-weighted after their occurrence in actual
simulations using the energy function of the program in which
the charges will be used, and CHELMO, which estimates the
charges directly from the electrostatic multipole
moments. Different criteria for the quality of the charges are
discussed.},
}
^D
---
nocite: '[@*]'
references:
- abstract: 'Four methods for deriving partial atomic charges from the
quantum chemical electrostatic potential (CHELP, CHELPG,
Merz-Kollman, and RESP) have been compared and critically evaluated.
It is shown that charges strongly depend on how and where the
potential points are selected. Two alternative methods are suggested
to avoid the arbitrariness in the point-selection schemes and van
der Waals exclusion radii: CHELP-BOW, which also estimates the
charges from the electrostatic potential, but with potential points
that are Boltzmann-weighted after their occurrence in actual
simulations using the energy function of the program in which the
charges will be used, and CHELMO, which estimates the charges
directly from the electrostatic multipole moments. Different
criteria for the quality of the charges are discussed.'
annote: 'An article entry with volume, number, and doi fields. Note
that the [doi]{.smallcaps} is transformed into a clickable link if
hyperref support has been enabled'
author:
- family: Sigfridsson
given: Emma
- family: Ryde
given: Ulf
container-title: Journal of Computational Chemistry
doi: '10.1002/(SICI)1096-987X(199803)19:4\<377::AID-JCC1\>3.0.CO;2-P'
id: sigfridsson
issue: 4
issued: 1998
language: 'en-US'
page: '377-395'
title: Comparison of methods for deriving atomic charges from the
electrostatic potential and moments
type: 'article-journal'
volume: 19
---