Backmerge: #2458 The reaction with catalysts is displayed incorrect w…

…ith ACS style setting and after layout (#2561)
epam · Oct 17, 2024 · 73d9e08 · 73d9e08
1 parent 7d03fb4
commit 73d9e08
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Showing 16 changed files with 1,501 additions and 187 deletions.
diff --git a/.github/workflows/indigo-ci.yaml b/.github/workflows/indigo-ci.yaml
@@ -267,10 +267,10 @@ jobs:
           name: indigo-python
           path: dist/
       - name: Install Pillow
-        run: python -m pip install Pillow --break-system-packages
+        run: python3 -m pip install Pillow
       - name: Install wrappers Linux
         if: ${{ startsWith(matrix.os, 'ubuntu') }}
-        run: python3 -m pip install dist/*manylinux1_x86_64*.whl --break-system-packages
+        run: python3 -m pip install dist/*manylinux1_x86_64*.whl
       - name: Install wrappers Windows
         if: ${{ startsWith(matrix.os, 'windows') }}
         run: Get-ChildItem dist -Filter *win_amd64*.whl -Recurse | % { python3 -m pip install $_.FullName }

diff --git a/api/c/indigo-renderer/src/indigo_render2d.cpp b/api/c/indigo-renderer/src/indigo_render2d.cpp
@@ -186,54 +186,6 @@ void indigoRenderGetStereoStyle(Array<char>& value)
     }
 }
 
-void indigoRenderSetLabelMode(const char* mode)
-{
-    std::string mode_string(mode);
-    LABEL_MODE result;
-    if (mode_string == "none")
-    {
-        result = LABEL_MODE_NONE;
-    }
-    else if (mode_string == "hetero")
-    {
-        result = LABEL_MODE_HETERO;
-    }
-    else if (mode_string == "terminal-hetero")
-    {
-        result = LABEL_MODE_TERMINAL_HETERO;
-    }
-    else if (mode_string == "all")
-    {
-        result = LABEL_MODE_ALL;
-    }
-    else
-    {
-        throw IndigoError("Invalid label mode, should be 'none', 'hetero', 'terminal-hetero' or 'all'");
-    }
-    RenderParams& rp = indigoRendererGetInstance().renderParams;
-    rp.rOpt.labelMode = result;
-}
-
-void indigoRenderGetLabelMode(Array<char>& value)
-{
-    RenderParams& rp = indigoRendererGetInstance().renderParams;
-    switch (rp.rOpt.labelMode)
-    {
-    case LABEL_MODE_NONE:
-        value.readString("none", true);
-        break;
-    case LABEL_MODE_HETERO:
-        value.readString("hetero", true);
-        break;
-    case LABEL_MODE_TERMINAL_HETERO:
-        value.readString("terminal-hetero", true);
-        break;
-    case LABEL_MODE_ALL:
-        value.readString("all", true);
-        break;
-    }
-}
-
 void indigoRenderSetCatalystsPlacement(const char* mode)
 {
     int result;
@@ -454,6 +406,11 @@ static void setParams(RenderParams& rp, LayoutOptions& layout_options)
     rp.cnvOpt.bondLength = layout_options.bondLength;
     rp.cnvOpt.bondLengthUnit = layout_options.bondLengthUnit;
     rp.rOpt.ppi = layout_options.ppi;
+    rp.rOpt.fontSize = layout_options.fontSize;
+    rp.rOpt.fontSizeUnit = layout_options.fontSizeUnit;
+    rp.rOpt.fontSizeSub = layout_options.fontSizeSub;
+    rp.rOpt.fontSizeSubUnit = layout_options.fontSizeSubUnit;
+    rp.rOpt.labelMode = layout_options.labelMode;
     rp.rOpt.bond_length_px = layout_options.bondLength > EPSILON ? layout_options.getBondLengthPx() : LayoutOptions::DEFAULT_BOND_LENGTH_PX;
     if (rp.cnvOpt.outputSheetWidth > 0)
     {
@@ -732,7 +689,6 @@ void IndigoRenderer::setOptionsHandlers()
 
         mgr->setOptionHandlerString("render-output-format", indigoRenderSetOutputFormat, indigoRenderGetOutputFormat);
 
-        mgr->setOptionHandlerString("render-label-mode", indigoRenderSetLabelMode, indigoRenderGetLabelMode);
         mgr->setOptionHandlerString("render-comment", SETTER_GETTER_STR_OPTION(rp.cnvOpt.comment));
         mgr->setOptionHandlerString("render-comment-position", indigoRenderSetCommentPosition, indigoRenderGetCommentPosition);
         mgr->setOptionHandlerString("render-stereo-style", indigoRenderSetStereoStyle, indigoRenderGetStereoStyle);
@@ -790,10 +746,6 @@ void IndigoRenderer::setOptionsHandlers()
         mgr->setOptionHandlerVoid("reset-render-options", indigoRenderResetOptions);
 
         // ACS style options
-        mgr->setOptionHandlerFloat("render-font-size", SETTER_GETTER_FLOAT_OPTION(rp.rOpt.fontSize));
-        mgr->setOptionHandlerString("render-font-size-unit", SETTER_GETTER_UNIT_OPTION(rp.rOpt.fontSizeUnit));
-        mgr->setOptionHandlerFloat("render-font-size-sub", SETTER_GETTER_FLOAT_OPTION(rp.rOpt.fontSizeSub));
-        mgr->setOptionHandlerString("render-font-size-sub-unit", SETTER_GETTER_UNIT_OPTION(rp.rOpt.fontSizeSubUnit));
         mgr->setOptionHandlerFloat("render-bond-thickness", SETTER_GETTER_FLOAT_OPTION(rp.rOpt.bondThickness));
         mgr->setOptionHandlerString("render-bond-thickness-unit", SETTER_GETTER_UNIT_OPTION(rp.rOpt.bondThicknessUnit));
         mgr->setOptionHandlerFloat("render-bond-spacing", SETTER_GETTER_FLOAT_OPTION(rp.rOpt.bondSpacing));

diff --git a/api/c/indigo/src/indigo_options.cpp b/api/c/indigo/src/indigo_options.cpp
@@ -262,6 +262,54 @@ void indigoProductEnumeratorGetOneTubeMode(Array<char>& value)
         value.readString("grid", true);
 }
 
+void indigoRenderSetLabelMode(const char* mode)
+{
+    std::string mode_string(mode);
+    LABEL_MODE result;
+    if (mode_string == "none")
+    {
+        result = LABEL_MODE_NONE;
+    }
+    else if (mode_string == "hetero")
+    {
+        result = LABEL_MODE_HETERO;
+    }
+    else if (mode_string == "terminal-hetero")
+    {
+        result = LABEL_MODE_TERMINAL_HETERO;
+    }
+    else if (mode_string == "all")
+    {
+        result = LABEL_MODE_ALL;
+    }
+    else
+    {
+        throw IndigoError("Invalid label mode, should be 'none', 'hetero', 'terminal-hetero' or 'all'");
+    }
+    LayoutOptions& layout_options = indigoGetInstance().layout_options;
+    layout_options.labelMode = result;
+}
+
+void indigoRenderGetLabelMode(Array<char>& value)
+{
+    LayoutOptions& layout_options = indigoGetInstance().layout_options;
+    switch (layout_options.labelMode)
+    {
+    case LABEL_MODE_NONE:
+        value.readString("none", true);
+        break;
+    case LABEL_MODE_HETERO:
+        value.readString("hetero", true);
+        break;
+    case LABEL_MODE_TERMINAL_HETERO:
+        value.readString("terminal-hetero", true);
+        break;
+    case LABEL_MODE_ALL:
+        value.readString("all", true);
+        break;
+    }
+}
+
 void IndigoOptionHandlerSetter::setBasicOptionHandlers(const qword id)
 {
     auto mgr = sf::xlock_safe_ptr(indigoGetOptionManager(id));
@@ -391,4 +439,9 @@ void IndigoOptionHandlerSetter::setBasicOptionHandlers(const qword id)
     mgr->setOptionHandlerFloat("reaction-component-margin-size", SETTER_GETTER_FLOAT_OPTION(indigo.layout_options.reactionComponentMarginSize));
     mgr->setOptionHandlerString("reaction-component-margin-size-unit", SETTER_GETTER_UNIT_OPTION(indigo.layout_options.reactionComponentMarginSizeUnit));
     mgr->setOptionHandlerInt("image-resolution", SET_POSITIVE_INT_OPTION(indigo.layout_options.ppi, "image resolution ppi must be positive"));
+    mgr->setOptionHandlerFloat("render-font-size", SETTER_GETTER_FLOAT_OPTION(indigo.layout_options.fontSize));
+    mgr->setOptionHandlerString("render-font-size-unit", SETTER_GETTER_UNIT_OPTION(indigo.layout_options.fontSizeUnit));
+    mgr->setOptionHandlerFloat("render-font-size-sub", SETTER_GETTER_FLOAT_OPTION(indigo.layout_options.fontSizeSub));
+    mgr->setOptionHandlerString("render-font-size-sub-unit", SETTER_GETTER_UNIT_OPTION(indigo.layout_options.fontSizeSubUnit));
+    mgr->setOptionHandlerString("render-label-mode", indigoRenderSetLabelMode, indigoRenderGetLabelMode);
 }
diff --git a/api/tests/integration/ref/basic/options.py.out b/api/tests/integration/ref/basic/options.py.out
@@ -14,7 +14,7 @@ bool
 True
 true
 ***** Float *****
-0.800
+0.500
 float
 21.333
 21.333
diff --git a/api/tests/integration/ref/layout/acs_style_reaction.py.out b/api/tests/integration/ref/layout/acs_style_reaction.py.out
@@ -16,3 +16,14 @@
 
 *** 2389 wrong margin ***
 acs_issue_2389.ket:SUCCEED
+
+*** 2458 catalist margins margin ***
+  Result: Molecule #0: Success
+   Molecule #1: Success
+   Molecule #2: Success
+   Molecule #3: Success
+   Molecule #4: Success
+   Molecule #5: Success
+   Molecule #6: Success
+   Molecule #7: Success
+   Molecule #8: Success
diff --git a/api/tests/integration/tests/layout/acs_style_reaction.py b/api/tests/integration/tests/layout/acs_style_reaction.py
@@ -75,3 +75,31 @@ def find_diff(a, b):
 else:
     print(filename + ":FAILED")
     print(diff)
+
+
+print("\n*** 2458 catalist margins margin ***")
+filename = "acs_issue_2458.ket"
+rxn = indigo.loadReactionFromFile(os.path.join(root, filename))
+indigo.resetOptions()
+indigo.setOption("molfile-saving-skip-date", "1")
+indigo.setOption("json-saving-pretty", "1")
+indigo.setOption("json-use-native-precision", "1")
+indigo.setOption("smart-layout", "true")
+indigo.setOption("dearomatize-on-load", "false")
+indigo.setOption("render-font-size", "10")
+indigo.setOption("render-font-size-unit", "pt")
+indigo.setOption("image-resolution", "600")
+indigo.setOption("bond-length-unit", "pt")
+indigo.setOption("bond-length", "14.4")
+indigo.setOption("render-label-mode", "terminal-hetero")
+rxn.layout()
+# with open(os.path.join(ref, filename), "w") as file:
+#     file.write(rxn.json())
+res = reactionLayoutDiff(
+    indigo,
+    rxn,
+    filename,
+    update=upd,
+    update_format="ket",
+)
+print("  Result: {}".format(res))
-Original file line number
+Diff line change
@@ Expand Up / @@ -14,7 +14,7 @@ bool @@
     True
     true
     ***** Float *****
-.800
+.500
     float
 .333
 .333