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fbaensch-beilsteinJanCBrammer
fbaensch-beilstein
authored and
JanCBrammer
committed
Enable enhanced stereochmistry branch (WIP);
1 parent c9979a0 commit 30c9afe

5 files changed

Lines changed: 254 additions & 1 deletion

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‎pages/build_wasm_modules.sh‎

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@@ -18,6 +18,7 @@ source "${root_dir}/pages/utils.sh"
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build_inchi_wasm "1.06" "$inchi_versions_file" "$root_dir" "${root_dir}/inchi/util.c.patch"
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build_inchi_wasm "Latest" "$inchi_versions_file" "$root_dir"
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build_inchi_wasm "Latest with Molecular Inorganics" "$inchi_versions_file" "$root_dir"
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build_inchi_wasm "Latest with Enhanced Stereochemistry" "$inchi_versions_file" "$root_dir"
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# Build RInChI
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build_rinchi_wasm "$root_dir"

‎pages/components/components.js‎

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@@ -316,6 +316,16 @@ class InChIOptionsLatestMoInElement extends InChIOptionsElement {
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}
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}
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class InChIOptionsLatestEnhancedStereoElement extends InChIOptionsElement {
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constructor() {
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super();
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this.componentPaths = [
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"components/tautomer-options.html",
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"components/latest-enhanced-stereo-options.html",
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];
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}
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}
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function createAnnotation(text, color) {
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const annotation = document.createElement("div");
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annotation.textContent = text;
@@ -570,4 +580,9 @@ customElements.define(
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"inchi-options-latest-moin",
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InChIOptionsLatestMoInElement,
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);
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customElements.define(
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"inchi-options-latest-enhanced-stereo",
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InChIOptionsLatestEnhancedStereoElement,
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)
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customElements.define("inchi-ngl-viewer", NGLViewerElement);
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‎pages/components/latest-enhanced-stereo-options.html‎

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<div class="form-check">
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<input
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data-id="mobileH"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-off="FixedH"
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data-default-checked
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checked
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/>
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<label class="form-check-label">Mobile H Perception</label>
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</div>
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<div class="form-check">
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<input
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data-id="doNotAddH"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-on="DoNotAddH"
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/>
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<label class="form-check-label"
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>Do not add implicit H atoms
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<i
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class="bi bi-question-circle-fill colored-icon"
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data-bs-toggle="tooltip"
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data-bs-custom-class="custom-tooltip"
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data-bs-html="true"
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data-bs-title="If enabled all hydrogens in input structure will be treated as explicit hydrogens. Reflects the <i>doNotAddH</i> option in the InChI command line tool. If disabled, implicit hydrogens will be added to the structure before InChI generation. <p><b>Note: </b> The Ketcher structural drawing tool does not take this option into account. Therefore, implicit hydrogen atoms are displayed based on the Ketcher settings.</p>"
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></i
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></label>
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</div>
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<div class="row">
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<div class="col">
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<div class="form-check">
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<input
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data-id="includeStereo"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-off="SNon"
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data-default-checked
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checked
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/>
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<label class="form-check-label">Include Stereo:</label>
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</div>
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</div>
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<div class="col">
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<div class="form-check ms-xl-0 ms-lg-4">
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<input
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data-id="EnhancedStereochemistry"
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class="form-check-input"
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type="radio"
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name="stereoRadio"
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data-inchi-option-on="EnhancedStereochemistry"
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data-inchi-stereo-option
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data-default-checked
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checked
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/>
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<label class="form-check-label">
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Enhanced Stereochemistry
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<i
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class="bi bi-question-circle-fill colored-icon"
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data-bs-toggle="tooltip"
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data-bs-custom-class="custom-tooltip"
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data-bs-html="true"
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data-bs-title="The functionality for enhanced stereochemistry is a work in progress. You can expect to encounter warnings."
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></i>
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</label>
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</div>
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<div class="form-check ms-xl-0 ms-lg-4">
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<input
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data-id="SAbs"
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class="form-check-input"
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type="radio"
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name="stereoRadio"
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data-inchi-stereo-option
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/>
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<label class="form-check-label">Absolute</label>
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</div>
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<div class="form-check ms-xl-0 ms-lg-4">
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<input
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data-id="SRel"
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class="form-check-input"
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type="radio"
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name="stereoRadio"
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data-inchi-option-on="SRel"
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data-inchi-stereo-option
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/>
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<label class="form-check-label">Relative</label>
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</div>
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<div class="form-check ms-xl-0 ms-lg-4">
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<input
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data-id="SRac"
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class="form-check-input"
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type="radio"
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name="stereoRadio"
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data-inchi-option-on="SRac"
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data-inchi-stereo-option
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/>
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<label class="form-check-label">Racemic</label>
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</div>
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<div class="form-check ms-xl-0 ms-lg-4">
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<input
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data-id="SUCF"
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class="form-check-input"
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type="radio"
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name="stereoRadio"
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data-inchi-option-on="SUCF"
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data-inchi-stereo-option
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/>
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<label class="form-check-label">From chiral flag</label>
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</div>
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</div>
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</div>
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<div class="form-check ms-4">
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<input
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data-id="SUU"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-on="SUU"
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data-inchi-stereo-option
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/>
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<label class="form-check-label"
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>Always include omitted/undefined stereo</label
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>
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</div>
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<div class="form-check ms-4">
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<input
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data-id="SLUUD"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-on="SLUUD"
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data-inchi-stereo-option
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/>
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<label class="form-check-label"
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>Different marks for unknown/undefined stereo</label
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>
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</div>
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<div class="form-check ms-4">
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<input
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data-id="NEWPSOFF"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-on="NEWPSOFF"
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data-inchi-stereo-option
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/>
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<label class="form-check-label"
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>Both ends of wedge point to stereocenters</label
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>
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</div>
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<div class="form-check">
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<input
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data-id="RecMet"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-on="RecMet"
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/>
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<label class="form-check-label">Include Bonds to Metal</label>
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</div>
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<div class="form-check">
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<input
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data-id="treatPolymers"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-on="Polymers"
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/>
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<label class="form-check-label">Treat polymers:</label>
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</div>
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<div class="form-check ms-4">
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<input
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data-id="NoEdits"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-on="NoEdits"
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data-inchi-polymer-option
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data-default-disabled
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disabled
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/>
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<label class="form-check-label"
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>No pre-edits of original polymer structure</label
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>
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</div>
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<div class="form-check ms-4">
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<input
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data-id="FoldCRU"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-on="FoldCRU"
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data-inchi-polymer-option
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data-default-disabled
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disabled
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/>
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<label class="form-check-label">Enable CRU folding</label>
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</div>
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<div class="form-check ms-4">
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<input
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data-id="NoFrameShift"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-on="NoFrameShift"
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data-inchi-polymer-option
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data-default-disabled
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disabled
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/>
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<label class="form-check-label">Disable CRU frame shift</label>
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</div>
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<div class="form-check">
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<input
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data-id="NPZz"
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class="form-check-input"
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type="checkbox"
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data-inchi-option-on="NPZz"
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/>
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<label class="form-check-label"
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>Allow non-polymer Zz pseudoatoms
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<i
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class="bi bi-question-circle-fill colored-icon"
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data-bs-toggle="tooltip"
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data-bs-custom-class="custom-tooltip"
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data-bs-html="true"
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data-bs-title='The "Zz" or "*" ("star") pseudoatom is a generic placeholder designating an entity of undefined/unknown/variable nature. It is typically used for handling polymers, but may also be used outside the polymer context with this InChI option (<i>NPZz</i>). See the InChI Technical Manual, section IV. "g. Zz (star, pseudo element) atoms", for details.<br /><br />How to draw?<br />"*" pseudoatoms can be selected within the Ketcher structure editor either via the <i>Extended Table</i> in the right toolbar or using the hotkey "*".'
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></i
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></label>
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</div>
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<div class="mt-2">
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<a style="text-decoration: none" role="button" data-reset-inchi-options
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><i class="bi bi-arrow-clockwise pe-2"></i>Reset InChI Options</a
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>
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</div>

‎pages/inchi_versions.json‎

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"optionsTemplateId": "inchi-options-latest-moin",
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"commit": "35059dc4d1065224b3fd46df1a3094a98ed69b4d",
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"url": "https://github.com/IUPAC-InChI/InChI/pull/107"
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},
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"Latest with Enhanced Stereochemistry": {
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"module": "inchiModuleLatestEnhancedStereo",
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"name": "inchi-web-latest-enhanced-stereo",
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"optionsTemplateId": "inchi-options-latest-enhanced-stereo",
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"commit": "cf6d7ce3c5de92fe4382f70875783192b760c629",
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"url": "https://github.com/IUPAC-InChI/InChI/pull/185"
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}
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}

‎pages/index.html‎

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<!DOCTYPE html>
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<!doctype html>
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<html>
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<head>
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<meta charset="utf-8" />
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src="inchi/inchi-web-latest-moin.js"
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></script>
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<script type="text/javascript" src="inchi/inchi-web106.js"></script>
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<script
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type="text/javascript"
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src="inchi/inchi-web-latest-enhanced-stereo.js"
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></script>
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<!-- RInChI modules -->
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<script type="text/javascript" src="rinchi/librinchi-1.1.js"></script>

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