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epam / ketcher

Web-based molecule sketcher
https://lifescience.opensource.epam.com/ketcher/demo.html
Apache License 2.0
503 stars 174 forks source link

SVGs for molecules with extend smiles have non-unique symbol IDs, messing up inline on page of multiple SVG outputs from Ketcher #1254

Open emripka opened 2 years ago

emripka commented 2 years ago

Steps to Reproduce

  1. Create a molecule in Ketcher-standalone (2.4) with the "HAR" query atom: image

  2. Save this as an SVG: Save As > Image > SVG Document: image

  3. View the source of the SVG:

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    • Notice that the three symbols defined at the top which correspond to the H A and R symbols have the IDs: glyph0-0, glyph0-1, and glyph0-2.

  4. Add the "A" query atom the the molecule in Ketcher: image

  5. Download this molecule as an SVG as before: image

  6. View the source of the SVG:

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</symbol>
</g>
</defs>
<g id="surface19">
<path style="fill:none;stroke-width:0.0333333;stroke-linecap:butt;stroke-linejoin:miter;stroke:rgb(0%,0%,0%);stroke-opacity:1;stroke-miterlimit:10;" d="M 0.504824 -0.00832039 L -0.00482422 0.874336 " transform="matrix(100,0,0,100,4.126953,4.066414)"/>
<path style="fill:none;stroke-width:0.0333333;stroke-linecap:butt;stroke-linejoin:miter;stroke:rgb(0%,0%,0%);stroke-opacity:1;stroke-miterlimit:10;" d="M -0.00482422 0.857695 L 0.504824 1.740351 " transform="matrix(100,0,0,100,4.126953,4.066414)"/>
<path style="fill:none;stroke-width:0.0333333;stroke-linecap:butt;stroke-linejoin:miter;stroke:rgb(0%,0%,0%);stroke-opacity:1;stroke-miterlimit:10;" d="M 0.187637 0.857695 L 0.601035 1.573672 " transform="matrix(100,0,0,100,4.126953,4.066414)"/>
<path style="fill:none;stroke-width:0.0333333;stroke-linecap:butt;stroke-linejoin:miter;stroke:rgb(0%,0%,0%);stroke-opacity:1;stroke-miterlimit:10;" d="M 0.490371 1.732031 L 1.28502 1.732031 " transform="matrix(100,0,0,100,4.126953,4.066414)"/>
<path style="fill:none;stroke-width:0.0333333;stroke-linecap:butt;stroke-linejoin:miter;stroke:rgb(0%,0%,0%);stroke-opacity:1;stroke-miterlimit:10;" d="M 1.645488 1.480039 L 2.00002 0.866016 " transform="matrix(100,0,0,100,4.126953,4.066414)"/>
<path style="fill:none;stroke-width:0.0333333;stroke-linecap:butt;stroke-linejoin:miter;stroke:rgb(0%,0%,0%);stroke-opacity:1;stroke-miterlimit:10;" d="M 1.501152 1.396719 L 1.807559 0.866016 " transform="matrix(100,0,0,100,4.126953,4.066414)"/>
<path style="fill:none;stroke-width:0.0333333;stroke-linecap:butt;stroke-linejoin:miter;stroke:rgb(0%,0%,0%);stroke-opacity:1;stroke-miterlimit:10;" d="M 2.004824 0.874336 L 1.495215 -0.00832039 " transform="matrix(100,0,0,100,4.126953,4.066414)"/>
<path style="fill:none;stroke-width:0.0333333;stroke-linecap:butt;stroke-linejoin:miter;stroke:rgb(0%,0%,0%);stroke-opacity:1;stroke-miterlimit:10;" d="M 1.509629 -0.0000000762194 L 0.490371 -0.0000000762194 " transform="matrix(100,0,0,100,4.126953,4.066414)"/>
<path style="fill:none;stroke-width:0.0333333;stroke-linecap:butt;stroke-linejoin:miter;stroke:rgb(0%,0%,0%);stroke-opacity:1;stroke-miterlimit:10;" d="M 1.413418 0.16668 L 0.586621 0.16668 " transform="matrix(100,0,0,100,4.126953,4.066414)"/>
<path style="fill:none;stroke-width:0.0333333;stroke-linecap:butt;stroke-linejoin:miter;stroke:rgb(0%,0%,0%);stroke-opacity:1;stroke-miterlimit:10;" d="M 1.99041 0.866016 L 2.79002 0.866016 " transform="matrix(100,0,0,100,4.126953,4.066414)"/>
<g style="fill:rgb(0%,0%,0%);fill-opacity:1;">
  <use xlink:href="#glyph0-0" x="141.628906" y="190.265625"/>
</g>
<g style="fill:rgb(0%,0%,0%);fill-opacity:1;">
  <use xlink:href="#glyph0-1" x="292.128906" y="103.667969"/>
</g>
<g style="fill:rgb(0%,0%,0%);fill-opacity:1;">
  <use xlink:href="#glyph0-0" x="311.796875" y="103.667969"/>
</g>
<g style="fill:rgb(0%,0%,0%);fill-opacity:1;">
  <use xlink:href="#glyph0-2" x="334.460938" y="103.667969"/>
</g>
</g>
</svg>
    • Notice that again, we have three IDs for the 3 different atoms of H A and R, with IDs: glyph0-0, glyph0-1, and glyph0-2.

  7. Create a very simple component to display both of these SVGs inline:

    import React from 'react';
import SVG from 'react-inlinesvg';

// Not actual pasting here in this demo for simplicity, but I
// just copy-paste from the above snippits.
const test1 = `<paste-first-svg-text-here>`;
const test2 = `<paste-second-svg-text-here>`;

const Test = () => {
  return (
    <>
      <SVG src={test1} />
      <SVG src={test2} />
    </>
  );
};

    image

    • Notice that the second SVG has incorrectly displayed the symbols of it's query features; swapping the H + A symbols.

    Or if you reverse the order of rendering:

    import React from 'react';
import SVG from 'react-inlinesvg';

// Not actual pasting here in this demo for simplicity, but I
// just copy-paste from the above snippits.
const test1 = `<paste-first-svg-text-here>`;
const test2 = `<paste-second-svg-text-here>`;

const Test = () => {
  return (
    <>
      <SVG src={test2} />
      <SVG src={test1} />
    </>
  );
};

    image

    • Now the first is rendered correctly, but again, the H + A have swapped places.

Expected behavior

Unfortunately, when you inline SVGs on a single page, the first definition of a given symbol is referenced. There is no guarantee that these IDs correspond between molecules.

I would expect that there would be unique IDs for each SVG's symbol definitions, such that we can uniquely display the symbols, independent from one another.

I am using a hack currently to get this to work, which uniquifies the IDs of each symbol:

const molFileString = await ketcher.getMolfile('v3000');
const svgBlob = await ketcher.generateImage(
  molFileString,
  {outputFormat: 'svg'},
);
const svg = await svgBlob.text();
// glyph ids are reused, so we need to make them unique, or else "H"
// can be shown as "A" etc.
// Yes, this is necessary. Yes, it is messy and annoying, but it
// works.
const ids = [];
const splitSvg = svg.split('<defs>')[1].split('<');
splitSvg.forEach(line => {
  if (line.includes('id') && line.includes('glyph')) {
    const [unused, glyph] = line.split('id');
    const splits = glyph.split('"');
    ids.push(splits[1]);
  };
});
let uniqueIdsSvg = svg;
ids.forEach(oldId => {
  const newId = `${uuid()}-${oldId}`;
  uniqueIdsSvg = uniqueIdsSvg.replaceAll(oldId, newId);
});

Which will produce something like:

<?xml version="1.0" encoding="UTF-8"?>
<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="362pt" height="197pt" viewBox="0 0 362 197" version="1.1">
<defs>
<g>
<symbol overflow="visible" id="SIgzBJqWpsKDl7fe-glyph0-0">
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Desktop:

AndreiMazol commented 2 years ago

Dear @emripka,

Thank you for your interest to Ketcher. SVGs are generated on server side so your request has been redirected to Indigo team.

Regards, Andrei

ElenaOdnoshivkina commented 2 years ago

Related issue https://github.com/epam/Indigo/issues/656