从 RDKit 验证 SVG 文件

Question

我正在尝试从 RDKit 包中生成 SVG 图像。最小可重现示例：

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)

输出如下，但在我尝试过的任何浏览器或图像查看器中都没有呈现任何图像。 这是一个有效的 SVG 文件，还是生成的包格式无效？还是有其他我看不到的错误？

<?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>

Answer 1

RDKit 出于未知原因生成了不显示任何内容的 SVG 代码。但是，更改分子列表确实会生成生成可见图像的 SVG 代码。

这个有效：

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)

此处已打开错误：https://github.com/rdkit/rdkit/issues/2641

从 RDKit 验证 SVG 文件

Validating an SVG file from RDKit

svg

rdkit