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I am attempting to produce an SVG image from the package RDKit. A minimum reproducable example: 

from rdkit import Chem
from rdkit.Chem import Draw 
img = Draw.MolsToGridImage([Chem.MolFromSmiles(x) for x in ['C', 'CO', 'CN']], useSVG = True)
print(img)

The output is below, but doesn't render any image in any browser or image viewer I have tried. Is this a valid SVG file, or is the package producing an invalid format? Or is there some other error I cannot see? 

<?xml version='1.0' encoding='iso-8859-1'?>
<svg version='1.1' baseProfile='full'
              xmlns='http://www.w3.org/2000/svg'
                      xmlns:rdkit='http://www.rdkit.org/xml'
                      xmlns:xlink='http://www.w3.org/1999/xlink'
                  xml:space='preserve'
width='600px' height='200px' >
<!-- END OF HEADER -->
<rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='600' height='200' x='0' y='0'> </rect>
<text x='0' y='200' style='font-size:0px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#000000' ><tspan>CH</tspan><tspan style='baseline-shift:sub;font-size:0px;'>4</tspan><tspan></tspan></text>
<path class='bond-0' d='M 200,200 200,200' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path class='bond-0' d='M 200,200 200,200' style='fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<text x='200' y='200' style='font-size:0px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#FF0000' ><tspan>OH</tspan></text>
<path d='M 200,200 200,200 200,200 200,200 200,200' style='fill:none;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path class='bond-0' d='M 400,200 400,200' style='fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<path class='bond-0' d='M 400,200 400,200' style='fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
<text x='400' y='200' style='font-size:0px;font-style:normal;font-weight:normal;fill-opacity:1;stroke:none;font-family:sans-serif;text-anchor:start;fill:#0000FF' ><tspan>NH</tspan><tspan style='baseline-shift:sub;font-size:0px;'>2</tspan><tspan></tspan></text>
<path d='M 400,200 400,200 400,200 400,200 400,200' style='fill:none;stroke:#FF0000;stroke-width:2px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1' />
</svg>
cddt
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    The rect is fill with white, the font-size of the text is 0px, the paths are lines with length 0: `d='M 200,200 200,200'` – enxaneta Sep 11 '19 at 09:37

1 Answers1

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RDKit is for an unknown reason producing SVG code which doesn't show anything. However, changing the list of molecules does result in SVG code which produces a visible image.

This works: 

from rdkit import Chem
from rdkit.Chem import Draw 
img = Draw.MolsToGridImage([Chem.MolFromSmiles(x) for x in ['C', 'CO', 'CN', 'CCC']], useSVG = True)
print(img)

A bug has been opened here: https://github.com/rdkit/rdkit/issues/2641

cddt
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