Support for Open Babel v2.4.1

[aminophen]

The behavior of SVG output of Open Babel 2.4.1 seems different from that of Open Babel 2.3.2. With the new version, the output image always has a square bounding box and the margins around the structure are bigger. Should I crop the margins (using pdfcrop?) before including it to the LaTeX document?

[marijnschraagen]

For a question on TeX.SE I implemented this suggestion. You can probably find a cleaner way but maybe it is a starting point. The main issue is that pdfcrop does not work on eps files so this should be conditional on the image extension. My implementation (only for \smilesobabel):

\DeclareOption{pdf}{\def\chemob@belimgExt{pdf}\def\chemob@bel@cropcmd#1{pdfcrop #1 #1}}
\DeclareOption{eps}{\def\chemob@belimgExt{eps}\let\chemob@bel@cropcmd\@undefined}

\newcommand\@smilesobabel[2]{%
  \endgroup
  \chemob@bel@exec{%
    \smilesob@bel@obabelcmd{#1}{#2} 2>\smilesob@belGetName.log
    && \chemob@bel@svgtoimgcmd{\smilesob@belGetName}{\chemob@belimgExt} 2>>\smilesob@belGetName.log
    || rm -f \smilesob@belGetName.\chemob@belimgExt}%
  \ifcsname chemob@bel@cropcmd\endcsname%
  \chemob@bel@exec{\chemob@bel@cropcmd{\smilesob@belGetName.pdf}}\fi%
  \chemob@bel@common@maybeimg{\smilesobabel@next}{\smilesob@belGetName}{SMILES string}%
  \addtocounter{smilesob@belCounter}{1}% select next name
}

See the question on https://tex.stackexchange.com/questions/655477/how-to-draw-structures-from-smiles-using-latex.

[aminophen]

Thanks for your advice!

For EPS, the program ps2eps can crop the margin, and it's installed via TeX Live. I will add "pdfcrop" and "ps2eps" into the package.

Note: with "ps2eps" the white background remains, but adding "clip" to the optional argument the image is properly cropped (similar to \includegraphics).

[aminophen]

Implemented 21cf582af1f2930b1c7bb9f1515f526f6d706d64. Default crop, and the package option "nocrop" restores the old behavior without crop.

Documentation to be written (including the above "clip" for eps).

[aminophen]

Memo: https://github.com/openbabel/openbabel/issues/338

[aminophen]

Documentation done. 874ca5f4961e2f78dfcb5d7d6ab454de7edffc19