Re: [Rdkit-discuss] Chirality wedge disappears in PNG depiction

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<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div dir="ltr"></div><div dir="ltr">Dear Jean-Marc.</div><div dir="ltr"><br></div><div dir="ltr">Then you only need addChiralHs=False:</div><div dir="ltr"><br></div><div dir="ltr"><table data-hpc="" class="highlight tab-size js-file-line-container js-code-nav-container js-tagsearch-file" data-tab-size="8" data-paste-markdown-skip="" data-tagsearch-lang="Python" data-tagsearch-path="msg11409.py" style="font-variant-caps: normal; border-spacing: 0px; border-collapse: collapse; tab-size: 8; caret-color: rgb(5, 12, 20); color: rgb(5, 12, 20); font-family: -apple-system, BlinkMacSystemFont, &quot;Segoe UI&quot;, &quot;Noto Sans&quot;, Helvetica, Arial, sans-serif, &quot;Apple Color Emoji&quot;, &quot;Segoe UI Emoji&quot;; font-size: 14px; -webkit-text-size-adjust: 100%;"><tbody style="box-sizing: border-box;"><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC1" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">from</span> <span class="pl-s1" style="box-sizing: border-box;">rdkit</span> <span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">import</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Chem</span></td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC2" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">from</span> <span class="pl-s1" style="box-sizing: border-box;">rdkit</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Chem</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Draw</span> <span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">import</span> <span class="pl-s1" style="box-sizing: border-box;">rdDepictor</span></td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC3" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">from</span> <span class="pl-s1" style="box-sizing: border-box;">rdkit</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Chem</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Draw</span> <span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">import</span> <span class="pl-s1" style="box-sizing: border-box;">rdMolDraw2D</span></td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC4" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">from</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">PIL</span> <span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">import</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Image</span></td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC5" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">from</span> <span class="pl-s1" style="box-sizing: border-box;">io</span> <span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">import</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">BytesIO</span></td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC6" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;">
</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC7" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">smi</span>  <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-s" style="box-sizing: border-box; color: var(--color-prettylights-syntax-string);">"C1CC[C@H]2CCCC[C@@H]2C1"</span></td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC8" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">filenameOut</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-s" style="box-sizing: border-box; color: var(--color-prettylights-syntax-string);">"img.png"</span></td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC9" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;">
</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC10" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">mol</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Chem</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">MolFromSmiles</span>(<span class="pl-s1" style="box-sizing: border-box;">smi</span>)</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC11" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;">
</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC12" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">rdDepictor</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">SetPreferCoordGen</span>(<span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">True</span>)</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC13" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;">
</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC14" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">rdDepictor</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Compute2DCoords</span>(<span class="pl-s1" style="box-sizing: border-box;">mol</span>)</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC15" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;">
</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC16" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">d2d</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-s1" style="box-sizing: border-box;">rdMolDraw2D</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">MolDraw2DCairo</span>(<span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">350</span>, <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">300</span>)</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC17" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">dopts</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-s1" style="box-sizing: border-box;">d2d</span>.<span class="pl-en" style="box-sizing: border-box; color: var(--color-prettylights-syntax-entity);">drawOptions</span>()</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC18" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">dopts</span>.<span class="pl-s1" style="box-sizing: border-box;">baseFontSize</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">0.6</span></td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC19" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">dopts</span>.<span class="pl-s1" style="box-sizing: border-box;">prepareMolsBeforeDrawing</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">False</span></td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC20" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">mol_draw</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-s1" style="box-sizing: border-box;">rdMolDraw2D</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">PrepareMolForDrawing</span>(<span class="pl-s1" style="box-sizing: border-box;">mol</span>, <span class="pl-s1" style="box-sizing: border-box;">addChiralHs</span><span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span><span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">False</span>)</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC21" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">d2d</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">DrawMolecule</span>(<span class="pl-s1" style="box-sizing: border-box;">mol_draw</span>, <span class="pl-s1" style="box-sizing: border-box;">legend</span><span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span><span class="pl-s" style="box-sizing: border-box; color: var(--color-prettylights-syntax-string);">''</span>, <span class="pl-s1" style="box-sizing: border-box;">highlightAtoms</span><span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span>[])</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC22" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">d2d</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">FinishDrawing</span>()</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC23" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">bio</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">BytesIO</span>(<span class="pl-s1" style="box-sizing: border-box;">d2d</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">GetDrawingText</span>())</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC24" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">draw_code</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Image</span>.<span class="pl-en" style="box-sizing: border-box; color: var(--color-prettylights-syntax-entity);">open</span>(<span class="pl-s1" style="box-sizing: border-box;">bio</span>)</td></tr><tr style="box-sizing: border-box;"><td id="file-msg11409-py-LC25" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">draw_code</span>.<span class="pl-en" style="box-sizing: border-box; color: var(--color-prettylights-syntax-entity);">save</span>(<span class="pl-s1" style="box-sizing: border-box;">filenameOut</span>)</td></tr></tbody></table></div><div dir="ltr"><br></div><div dir="ltr">Cheers,</div><div dir="ltr">p.</div><div dir="ltr"><br><blockquote type="cite">On 27 Jul 2023, at 12:01, Jean-Marc Nuzillard &lt;jm....@un...&gt; wrote:<br><br></blockquote></div><blockquote type="cite"><div dir="ltr">
  
    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
  
  
    <div class="moz-cite-prefix">Dear Paolo,<br>
      <br>
      your code works perfectly well.<br>
      <br>
      Running it with the SMILES of trans-decalin,
      C1CC[C@H]2CCCC[C@@H]2C1,<br>
      I obtained<br>
      <div>&lt;F293bnUXx7pCSmb2.png&gt;</div>.<br>
      The code with ReapplyMolBlockWedging() inside (that you proposed
      me<br>
      in a previous post) was intended to have no H atom displayed at
      ring junctions.<br>
      Sure, the SMILES of trans-decalin I propose, generated by rdkit
      from a molblock<br>
      devoid of H atoms, has explicit H atoms inside at the ring
      junction.<br>
      So, starting from an isomeric SMILES, I would like to produce PNG
      drawings that retain<br>
      the existing configuration information and do not show H atoms at
      ring junctions.<br>
      <br>
      Best,<br>
      <br>
      Jean-Marc<br>
      <br>
      <br>
      Le 27/07/2023 à 10:33, Paolo Tosco a écrit&nbsp;:<br>
    </div>
    <blockquote type="cite" cite="mid:E4B...@gm...">
      <meta http-equiv="content-type" content="text/html; charset=UTF-8">
      <div dir="ltr">Dear Jean-Marc,</div>
      <div dir="ltr"><br>
      </div>
      <div dir="ltr">You are generating the molecule from SMILES,
        therefore it does not have molblock wedging information.</div>
      <div dir="ltr">When you call ReapplyMolBlockWedging(), first
        existing wedging info will be stripped.</div>
      <div dir="ltr">Then, the molblock wedging will be applied, but
        there is none.</div>
      <div dir="ltr">Hence, you get no wedging.</div>
      <div dir="ltr"><br>
      </div>
      <div dir="ltr">You may simplify your code and get the expected
        wedging as follows:</div>
      <div dir="ltr"><br>
      </div>
      <div dir="ltr">
        <table data-hpc="" class="highlight tab-size
          js-file-line-container js-code-nav-container
          js-tagsearch-file" data-tab-size="8" data-paste-markdown-skip="" data-tagsearch-lang="Python" data-tagsearch-path="msg11409.py" style="font-variant-caps:
          normal; border-spacing: 0px; border-collapse: collapse;
          tab-size: 8; caret-color: rgb(5, 12, 20); color: rgb(5, 12,
          20); font-family: -apple-system, BlinkMacSystemFont,
          &quot;Segoe UI&quot;, &quot;Noto Sans&quot;, Helvetica, Arial,
          sans-serif, &quot;Apple Color Emoji&quot;, &quot;Segoe UI
          Emoji&quot;; font-size: 14px; -webkit-text-size-adjust: 100%;">
          <tbody style="box-sizing: border-box;">
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC1" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">from</span> <span class="pl-s1" style="box-sizing: border-box;">rdkit</span> <span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">import</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Chem</span></td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC2" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">from</span> <span class="pl-s1" style="box-sizing: border-box;">rdkit</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Chem</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Draw</span> <span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">import</span> <span class="pl-s1" style="box-sizing: border-box;">rdDepictor</span></td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC3" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">from</span> <span class="pl-s1" style="box-sizing: border-box;">rdkit</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Chem</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Draw</span> <span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">import</span> <span class="pl-s1" style="box-sizing: border-box;">rdMolDraw2D</span></td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC4" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">from</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">PIL</span> <span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">import</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Image</span></td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC5" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">from</span> <span class="pl-s1" style="box-sizing: border-box;">io</span> <span class="pl-k" style="box-sizing: border-box; color: var(--color-prettylights-syntax-keyword);">import</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">BytesIO</span></td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC6" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;">
</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC7" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">smi</span>  <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-s" style="box-sizing: border-box; color: var(--color-prettylights-syntax-string);">"C=C[C@@](/C=C/c1ccc(cc1)O)(CCC=C(C)C)C"</span></td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC8" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">filenameOut</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-s" style="box-sizing: border-box; color: var(--color-prettylights-syntax-string);">"img.png"</span></td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC9" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;">
</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC10" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">mol</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Chem</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">MolFromSmiles</span>(<span class="pl-s1" style="box-sizing: border-box;">smi</span>)</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC11" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;">
</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC12" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">rdDepictor</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">SetPreferCoordGen</span>(<span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">True</span>)</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC13" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">rdDepictor</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Compute2DCoords</span>(<span class="pl-s1" style="box-sizing: border-box;">mol</span>)</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC14" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;">
</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC15" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">d2d</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-s1" style="box-sizing: border-box;">rdMolDraw2D</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">MolDraw2DCairo</span>(<span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">350</span>, <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">300</span>)</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC16" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">dopts</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-s1" style="box-sizing: border-box;">d2d</span>.<span class="pl-en" style="box-sizing: border-box; color: var(--color-prettylights-syntax-entity);">drawOptions</span>()</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC17" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">dopts</span>.<span class="pl-s1" style="box-sizing: border-box;">baseFontSize</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">0.6</span></td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC18" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">d2d</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">DrawMolecule</span>(<span class="pl-s1" style="box-sizing: border-box;">mol</span>, <span class="pl-s1" style="box-sizing: border-box;">legend</span><span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span><span class="pl-s" style="box-sizing: border-box; color: var(--color-prettylights-syntax-string);">''</span>, <span class="pl-s1" style="box-sizing: border-box;">highlightAtoms</span><span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span>[])</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC19" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">d2d</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">FinishDrawing</span>()</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC20" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">bio</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">BytesIO</span>(<span class="pl-s1" style="box-sizing: border-box;">d2d</span>.<span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">GetDrawingText</span>())</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC21" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">draw_code</span> <span class="pl-c1" style="box-sizing: border-box; color: var(--color-prettylights-syntax-constant);">=</span> <span class="pl-v" style="box-sizing: border-box; color: var(--color-prettylights-syntax-variable);">Image</span>.<span class="pl-en" style="box-sizing: border-box; color: var(--color-prettylights-syntax-entity);">open</span>(<span class="pl-s1" style="box-sizing: border-box;">bio</span>)</td>
            </tr>
            <tr style="box-sizing: border-box;">
              <td id="file-msg11409-py-LC22" class="blob-code blob-code-inner js-file-line" style="box-sizing: border-box; padding: 0px 10px; position: relative; line-height: 20px; vertical-align: top; overflow: visible; font-family: ui-monospace, SFMono-Regular, &quot;SF Mono&quot;, Menlo, Consolas, &quot;Liberation Mono&quot;, monospace; font-size: 12px; color: var(--color-fg-default); overflow-wrap: anywhere; white-space: pre;"><span class="pl-s1" style="box-sizing: border-box;">draw_code</span>.<span class="pl-en" style="box-sizing: border-box; color: var(--color-prettylights-syntax-entity);">save</span>(<span class="pl-s1" style="box-sizing: border-box;">filenameOut</span>)</td>
            </tr>
          </tbody>
        </table>
      </div>
      <div dir="ltr"><br>
      </div>
      <div dir="ltr">Cheers.</div>
      <div dir="ltr">p.</div>
      <div dir="ltr"><br>
        <blockquote type="cite">On 27 Jul 2023, at 07:31, Jean-Marc
          Nuzillard <a class="moz-txt-link-rfc2396E" href="mailto:jm....@un...">&lt;jm....@un...&gt;</a> wrote:<br>
          <br>
        </blockquote>
      </div>
      <blockquote type="cite">
        <div dir="ltr">
          <meta http-equiv="Content-Type" content="text/html;
            charset=UTF-8">
          <div class="moz-cite-prefix">Hi David,<br>
            <br>
            thank you for your suggestion.<br>
            Setting wedgeBonds=True does not change anything,<br>
            probably because wedging is performed later by <br>
            the call to Chem.ReapplyMolBlockWedging() <br>
            <br>
            Best,<br>
            <br>
            Jean-Marc<br>
            <br>
            Le 26/07/2023 à 22:28, David Cosgrove a écrit&nbsp;:<br>
          </div>
          <blockquote type="cite" cite="mid:CAJ...@ma...">
            <meta http-equiv="content-type" content="text/html;
              charset=UTF-8">
            <div dir="auto">Hi,</div>
            <div dir="auto">I’m away from my computer at the moment, so
              can’t try anything, but I wonder if it’s anything to do
              with the ‘wedgeBonds=False’ option you gave when preparing
              the drawing.&nbsp;</div>
            <div dir="auto">Dave</div>
            <div dir="auto"><br>
            </div>
            <div><br>
              <div class="gmail_quote">
                <div dir="ltr" class="gmail_attr">On Wed, 26 Jul 2023 at
                  20:45, Jean-Marc Nuzillard &lt;<a href="mailto:jm....@un..." moz-do-not-send="true" class="moz-txt-link-freetext">jm....@un...</a>&gt;
                  wrote:<br>
                </div>
                <blockquote class="gmail_quote" style="margin:0px 0px
                  0px
0.8ex;border-left-width:1px;border-left-style:solid;padding-left:1ex;border-left-color:rgb(204,204,204)">
                  <div> Dear all,<br>
                    <br>
                    I use the following code to produce PNG drawings. I
                    use RDKit version 2023.03.1 .<br>
                    The SMILES chain describes a molecule with a single
                    chiral center of defined configuration.<br>
                    <br>
                    <font style="font-family:monospace;color:rgb(0,0,0)" face="monospace">from rdkit import Chem<br>
                      from rdkit.Chem import rdCoordGen<br>
                      from rdkit.Chem.Draw import rdMolDraw2D<br>
                      from PIL import Image<br>
                      from io import BytesIO<br>
                      <br>
                      smi&nbsp; = "C=C[C@@](/C=C/c1ccc(cc1)O)(CCC=C(C)C)C"<br>
                      filenameOut = "img.png"<br>
                      <br>
                      mol = Chem.MolFromSmiles(smi)<br>
                      rdCoordGen.AddCoords(mol)<br>
                      print(Chem.MolToMolBlock(mol))<br>
                      d2d = rdMolDraw2D.MolDraw2DCairo(350, 300)<br>
                      dopts = d2d.drawOptions()<br>
                      dopts.baseFontSize = 0.6<br>
                      dopts.prepareMolsBeforeDrawing = False<br>
                      mol_draw = rdMolDraw2D.PrepareMolForDrawing(mol,
                      addChiralHs=False, wedgeBonds=False)<br>
                      Chem.ReapplyMolBlockWedging(mol_draw)<br>
                      d2d.DrawMolecule(mol_draw, legend='',
                      highlightAtoms=[])<br>
                      d2d.FinishDrawing()<br>
                      bio = BytesIO(d2d.GetDrawingText())<br>
                      draw_code = Image.open(bio)<br>
                      draw_code.save(filenameOut)<br>
                    </font><br>
                    The resulting image does not show the chirality
                    wedge:<br>
                    <div>&lt;wAS5dAnxRREFAFxp.png&gt;</div>
                    <br>
                    <br>
                    The script prints the MolBlock that comes from the
                    SMILES and the calculation of the 2D atomic
                    coordinates:<br>
                    _________________<br>
                    <font style="font-family:monospace;color:rgb(0,0,0)" face="monospace"><br>
                      &nbsp;&nbsp;&nbsp;&nbsp; RDKit&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2D<br>
                      <br>
                      &nbsp;19 19&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0999 V2000<br>
                      &nbsp;&nbsp;&nbsp; 2.0515&nbsp;&nbsp;&nbsp; 1.2242&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp;&nbsp; 1.0515&nbsp;&nbsp;&nbsp; 1.2214&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp;&nbsp; 0.5539&nbsp;&nbsp;&nbsp; 0.3540&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp; -0.4459&nbsp;&nbsp;&nbsp; 0.3512&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp; -0.9435&nbsp;&nbsp; -0.5162&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp; -1.9435&nbsp;&nbsp; -0.5190&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp; -2.4411&nbsp;&nbsp; -1.3866&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp; -3.4411&nbsp;&nbsp; -1.3892&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp; -3.9435&nbsp;&nbsp; -0.5246&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp; -3.4459&nbsp;&nbsp;&nbsp; 0.3428&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp; -2.4459&nbsp;&nbsp;&nbsp; 0.3456&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp; -4.9435&nbsp;&nbsp; -0.5274&nbsp;&nbsp;&nbsp; 0.0000 O&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp;&nbsp; 1.4215&nbsp;&nbsp; -0.1436&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp;&nbsp; 2.2861&nbsp;&nbsp;&nbsp; 0.3588&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp;&nbsp; 3.1535&nbsp;&nbsp; -0.1388&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp;&nbsp; 4.0181&nbsp;&nbsp;&nbsp; 0.3636&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp;&nbsp; 4.0153&nbsp;&nbsp;&nbsp; 1.3636&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp;&nbsp; 4.8855&nbsp;&nbsp; -0.1338&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp;&nbsp;&nbsp; 0.5567&nbsp;&nbsp; -0.6460&nbsp;&nbsp;&nbsp; 0.0000 C&nbsp;&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp;
                      0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0&nbsp; 0<br>
                      &nbsp; 1&nbsp; 2&nbsp; 2&nbsp; 0<br>
                      &nbsp; 2&nbsp; 3&nbsp; 1&nbsp; 0<br>
                      &nbsp; 3&nbsp; 4&nbsp; 1&nbsp; 0<br>
                      &nbsp; 4&nbsp; 5&nbsp; 2&nbsp; 0<br>
                      &nbsp; 5&nbsp; 6&nbsp; 1&nbsp; 0<br>
                      &nbsp; 6&nbsp; 7&nbsp; 2&nbsp; 0<br>
                      &nbsp; 7&nbsp; 8&nbsp; 1&nbsp; 0<br>
                      &nbsp; 8&nbsp; 9&nbsp; 2&nbsp; 0<br>
                      &nbsp; 9 10&nbsp; 1&nbsp; 0<br>
                      &nbsp;10 11&nbsp; 2&nbsp; 0<br>
                      &nbsp; 9 12&nbsp; 1&nbsp; 0<br>
                      &nbsp; 3 13&nbsp; 1&nbsp; 0<br>
                      &nbsp;13 14&nbsp; 1&nbsp; 0<br>
                      &nbsp;14 15&nbsp; 1&nbsp; 0<br>
                      &nbsp;15 16&nbsp; 2&nbsp; 0<br>
                      &nbsp;16 17&nbsp; 1&nbsp; 0<br>
                      &nbsp;16 18&nbsp; 1&nbsp; 0<br>
                      &nbsp; 3 19&nbsp; 1&nbsp; 1<br>
                      &nbsp;11&nbsp; 6&nbsp; 1&nbsp; 0<br>
                      M&nbsp; END<br>
                    </font>_____________________<br>
                    <br>
                    The wedge bond (3-19) is apparently here but is not
                    drawn as such.<br>
                    <br>
                    Is there a remedy for that?<br>
                    <br>
                    Best regards,<br>
                    <br>
                    Jean-Marc<br>
                    <pre cols="72" style="font-family:monospace">-- 
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

ORCID : 0000-0002-5120-2556
Tel : +33 (0)3 26 91 82 10

<a href="http://www.univ-reims.fr/icmr" target="_blank" style="font-family:monospace" moz-do-not-send="true" class="moz-txt-link-freetext">http://www.univ-reims.fr/icmr</a>

<a href="https://nuzillard.github.io/PyLSD" target="_blank" style="font-family:monospace" moz-do-not-send="true" class="moz-txt-link-freetext">https://nuzillard.github.io/PyLSD</a></pre>
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            <span class="gmail_signature_prefix">-- </span><br>
            <div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature">
              <div dir="ltr">
                <div>
                  <div>David Cosgrove<br>
                  </div>
                  Freelance computational chemistry and chemoinformatics
                  developer<br>
                </div>
                <a href="http://cozchemix.co.uk" target="_blank" moz-do-not-send="true" class="moz-txt-link-freetext">http://cozchemix.co.uk</a><br>
                <br>
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          <br>
          <br>
          <pre class="moz-signature" cols="72">-- 
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

ORCID : 0000-0002-5120-2556
Tel : +33 (0)3 26 91 82 10

<a class="moz-txt-link-freetext" href="http://www.univ-reims.fr/icmr" moz-do-not-send="true">http://www.univ-reims.fr/icmr</a>

<a class="moz-txt-link-freetext" href="https://nuzillard.github.io/PyLSD" moz-do-not-send="true">https://nuzillard.github.io/PyLSD</a></pre>
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    <br>
    <br>
    <pre class="moz-signature" cols="72">-- 
Jean-Marc Nuzillard
Directeur de Recherches au CNRS

Institut de Chimie Moléculaire de Reims
CNRS UMR 7312
Moulin de la Housse
CPCBAI, Bâtiment 18
BP 1039
51687 REIMS Cedex 2
France

ORCID : 0000-0002-5120-2556
Tel : +33 (0)3 26 91 82 10

<a class="moz-txt-link-freetext" href="http://www.univ-reims.fr/icmr">http://www.univ-reims.fr/icmr</a>

<a class="moz-txt-link-freetext" href="https://nuzillard.github.io/PyLSD">https://nuzillard.github.io/PyLSD</a></pre>
  
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Re: [Rdkit-discuss] Chirality wedge disappears in PNG depiction

Open-Source Cheminformatics and Machine Learning

Re: [Rdkit-discuss] Chirality wedge disappears in PNG depiction