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2176: add ACS style reaction layout #1

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a087650
2176: add ACS style reaction layout
AleksandrParamonoff Aug 26, 2024
bad3411
revert unit-test changes
AleksandrParamonoff Aug 29, 2024
dcd1f43
fix layout bugs
AleksandrParamonoff Sep 4, 2024
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18 changes: 8 additions & 10 deletions api/c/indigo-renderer/src/indigo_render2d.cpp
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Expand Up @@ -74,14 +74,6 @@ IndigoRenderer::~IndigoRenderer()
{
}

#define SET_POSITIVE_FLOAT_OPTION(option, error) \
[](float value) { \
if (value <= 0.0f) \
throw IndigoError(error); \
option = value; \
}, \
[](float& value) { value = option; }

#define CHECK_AND_SETTER_GETTER_COLOR_OPTION(option) \
[](float r, float g, float b) { \
CHECKRGB(r, g, b); \
Expand Down Expand Up @@ -689,9 +681,17 @@ void IndigoRenderer::setOptionsHandlers()
if (!options_set)
{
auto mgr = sf::xlock_safe_ptr(indigoGetOptionManager(indigo_id));
options_set = true;

#define rp indigoRendererGetInstance().renderParams
#define cdxmlContext getCdxmlContext()
#define indigo indigoGetInstance()

rp.cnvOpt.bondLength = indigo.layout_options.bondLength;
rp.cnvOpt.bondLengthUnit = indigo.layout_options.bondLengthUnit;
rp.rOpt.reactionComponentMarginSize = indigo.layout_options.reactionComponentMarginSize;
rp.rOpt.reactionComponentMarginSizeUnit = indigo.layout_options.reactionComponentMarginSizeUnit;
rp.rOpt.ppi = indigo.layout_options.ppi;

mgr->setOptionHandlerInt("render-comment-offset", SETTER_GETTER_INT_OPTION(rp.cnvOpt.commentOffset));
mgr->setOptionHandlerInt("render-image-width", SETTER_GETTER_INT_OPTION(rp.cnvOpt.width));
Expand Down Expand Up @@ -757,7 +757,5 @@ void IndigoRenderer::setOptionsHandlers()
mgr->setOptionHandlerString("render-cdxml-title-face", SETTER_GETTER_STR_OPTION(cdxmlContext.titleFace));

mgr->setOptionHandlerVoid("reset-render-options", indigoRenderResetOptions);

options_set = true;
}
}
2 changes: 1 addition & 1 deletion api/c/indigo-renderer/src/indigo_renderer_internal.h
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Expand Up @@ -36,7 +36,7 @@ class IndigoRenderer : public IndigoPluginContext
private:
void setOptionsHandlers();

bool options_set = false;
std::atomic<bool> options_set = false;
};

class IndigoHDCOutput : public IndigoObject
Expand Down
3 changes: 2 additions & 1 deletion api/c/indigo/src/indigo.cpp
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Expand Up @@ -207,10 +207,11 @@ void Indigo::initMoleculeJsonSaver(MoleculeJsonSaver& saver)
saver.use_native_precision = json_use_native_precision;
}

void Indigo::initReactionJsonSaver(ReactionJsonSaver& saver)
void Indigo::initReactionJsonSaver(ReactionJsonSaver& saver) const
{
saver.add_stereo_desc = json_saving_add_stereo_desc;
saver.pretty_json = json_saving_pretty;
saver.layout_options = layout_options;
}

void Indigo::initReactionJsonSaver(PathwayReactionJsonSaver& saver)
Expand Down
6 changes: 4 additions & 2 deletions api/c/indigo/src/indigo_internal.h
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Expand Up @@ -335,7 +335,7 @@ class DLLEXPORT Indigo
bool embedding_edges_uniqueness, find_unique_embeddings;
int max_embeddings;

int layout_max_iterations; // default is zero -- no limit
int layout_max_iterations = 0; // default is zero -- no limit
bool smart_layout = false;
float layout_horintervalfactor = ReactionLayout::DEFAULT_HOR_INTERVAL_FACTOR;
bool layout_preserve_existing = false;
Expand All @@ -351,7 +351,7 @@ class DLLEXPORT Indigo
void initMolfileSaver(MolfileSaver& saver);
void initRxnfileSaver(RxnfileSaver& saver);
void initMoleculeJsonSaver(MoleculeJsonSaver& saver);
void initReactionJsonSaver(ReactionJsonSaver& saver);
void initReactionJsonSaver(ReactionJsonSaver& saver) const;
void initReactionJsonSaver(PathwayReactionJsonSaver& saver);

bool preserve_ordering_in_serialize;
Expand All @@ -366,6 +366,8 @@ class DLLEXPORT Indigo

bool scsr_ignore_chem_templates;

indigo::LayoutOptions layout_options;

static const Array<char>& getErrorMessage();
static void clearErrorMessage();
static void setErrorMessage(const char* message);
Expand Down
6 changes: 2 additions & 4 deletions api/c/indigo/src/indigo_layout.cpp
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Expand Up @@ -58,7 +58,7 @@ CEXPORT int indigoLayout(int object)
}

ml.max_iterations = self.layout_max_iterations;
ml.bond_length = MoleculeLayout::DEFAULT_BOND_LENGTH;
ml.bond_length = LayoutOptions::DEFAULT_BOND_LENGTH;
ml.layout_orientation = (layout_orientation_value)self.layout_orientation;
if (self.layout_preserve_existing || mol->hasAtropoStereoBonds())
ml.respect_existing_layout = true;
Expand Down Expand Up @@ -104,11 +104,9 @@ CEXPORT int indigoLayout(int object)
bool no_layout = rxn.intermediateCount() || rxn.specialConditionsCount() || rxn.meta().getNonChemicalMetaCount();
if (!no_layout)
{
ReactionLayout rl(rxn, self.smart_layout);
ReactionLayout rl(rxn, self.smart_layout, self.layout_options);
rl.max_iterations = self.layout_max_iterations;
rl.layout_orientation = (layout_orientation_value)self.layout_orientation;
rl.bond_length = MoleculeLayout::DEFAULT_BOND_LENGTH;
rl.horizontal_interval_factor = self.layout_horintervalfactor;
if (self.layout_preserve_existing)
rl.preserve_molecule_layout = true;
rl.make();
Expand Down
64 changes: 64 additions & 0 deletions api/c/indigo/src/indigo_options.cpp
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Expand Up @@ -261,6 +261,62 @@ void indigoProductEnumeratorGetOneTubeMode(Array<char>& value)
value.readString("grid", true);
}

bool isEqual(const char* l, const char* r)
{
return strcmp(l, r) != 0;
}

IndigoOptionManager::optf_string_t indigoSetUnitsOfMeasure(UnitsOfMeasure::TYPE& result)
{
static auto func = [&result](const char* mode) {
if (isEqual(mode, "pt"))
{
result = UnitsOfMeasure::TYPE::PT;
}
else if (isEqual(mode, "px"))
{
result = UnitsOfMeasure::TYPE::PX;
}
else if (isEqual(mode, "inches"))
{
result = UnitsOfMeasure::TYPE::INCHES;
}
else if (isEqual(mode, "cm"))
{
result = UnitsOfMeasure::TYPE::CM;
}
else
{
throw IndigoError("Invalid label mode, should be 'none', 'hetero', 'terminal-hetero' or 'all'");
}
};

return [](const char* mode) -> void { return func(mode); };
}

IndigoOptionManager::get_optf_string_t indigoGetUnitsOfMeasure(const UnitsOfMeasure::TYPE input)
{
static auto func = [input](Array<char>& result) {
switch (input)
{
case UnitsOfMeasure::TYPE::PT:
result.readString("pt", true);
break;
case UnitsOfMeasure::TYPE::PX:
result.readString("px", true);
break;
case UnitsOfMeasure::TYPE::INCHES:
result.readString("inches", true);
break;
case UnitsOfMeasure::TYPE::CM:
result.readString("cm", true);
break;
}
};

return [](Array<char>& res) -> void { return func(res); };
}

void IndigoOptionHandlerSetter::setBasicOptionHandlers(const qword id)
{
auto mgr = sf::xlock_safe_ptr(indigoGetOptionManager(id));
Expand Down Expand Up @@ -384,4 +440,12 @@ void IndigoOptionHandlerSetter::setBasicOptionHandlers(const qword id)
mgr->setOptionHandlerInt("rpe-max-products-count", SETTER_GETTER_INT_OPTION(indigo.rpe_params.max_product_count));
mgr->setOptionHandlerBool("rpe-layout", SETTER_GETTER_BOOL_OPTION(indigo.rpe_params.is_layout));
mgr->setOptionHandlerBool("transform-layout", SETTER_GETTER_BOOL_OPTION(indigo.rpe_params.transform_is_layout));

mgr->setOptionHandlerFloat("bond-length", SET_POSITIVE_FLOAT_OPTION(indigo.layout_options.bondLength, "bond length must be positive"));
mgr->setOptionHandlerString("bond-length-units", indigoSetUnitsOfMeasure(indigo.layout_options.bondLengthUnit),
indigoGetUnitsOfMeasure(indigo.layout_options.bondLengthUnit));
mgr->setOptionHandlerFloat("reaction-component-margin-size", SETTER_GETTER_FLOAT_OPTION(indigo.layout_options.reactionComponentMarginSize));
mgr->setOptionHandlerString("reaction-component-margin-size-unit", indigoSetUnitsOfMeasure(indigo.layout_options.reactionComponentMarginSizeUnit),
indigoGetUnitsOfMeasure(indigo.layout_options.reactionComponentMarginSizeUnit));
mgr->setOptionHandlerInt("image-resolution", SET_POSITIVE_INT_OPTION(indigo.layout_options.ppi, "image resolution ppi must be positive"));
}
16 changes: 16 additions & 0 deletions api/c/indigo/src/option_manager.h
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Original file line number Diff line number Diff line change
Expand Up @@ -89,6 +89,22 @@ using namespace indigo;
value.push(0); \
}

#define SET_POSITIVE_FLOAT_OPTION(option, error) \
[](float value) { \
if (value <= 0.0f) \
throw IndigoError(error); \
option = value; \
}, \
[](float& value) { value = option; }

#define SET_POSITIVE_INT_OPTION(option, error) \
[](int32_t value) { \
if (value <= 0) \
throw IndigoError(error); \
option = value; \
}, \
[](int32_t& value) { value = option; }

class DLLEXPORT IndigoOptionManager
{
public:
Expand Down
94 changes: 94 additions & 0 deletions api/c/tests/unit/tests/layout.cpp
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Original file line number Diff line number Diff line change
@@ -0,0 +1,94 @@
/****************************************************************************
* Copyright (C) from 2009 to Present EPAM Systems.
*
* This file is part of Indigo toolkit.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
***************************************************************************/

#include <thread>

#include <gtest/gtest.h>

#include <base_cpp/exception.h>

#include <algorithm>
#include <fstream>
#include <indigo-renderer.h>
#include <indigo.h>

#include "common.h"

using namespace indigo;

class IndigoApiLayoutTest : public IndigoApiTest
{
protected:
void SetUp() final
{
IndigoApiTest::SetUp();
indigoRendererInit(session);
}

void TearDown() final
{
indigoRendererDispose(session);
IndigoApiTest::TearDown();
}
};

TEST_F(IndigoApiLayoutTest, one_reactant_one_product)
{
indigoSetErrorHandler(errorHandler, nullptr);

indigoSetOption("render-coloring", "true");
indigoSetOption("render-stereo-style", "none");
indigoSetOptionXY("render-image-size", 400, 400);
indigoSetOption("render-output-format", "png");

indigoSetOptionBool("json-saving-pretty", true);
try
{
auto rc = indigoLoadReactionFromFile(dataPath("molecules/basic/before_layout.ket").c_str());

indigoLayout(rc);

const char* res = indigoJson(rc);
// printf("res=%s", res);
std::ifstream is(dataPath("molecules/basic/after_layout.ket"), std::ios::binary | std::ios::ate);
auto size = is.tellg();
std::string str(size, '\0'); // construct string to stream size
is.seekg(0);
is.read(&str[0], size);
str.erase(std::remove(str.begin(), str.end(), '\r'), str.end());

// ASSERT_STREQ(res, str.c_str());
indigoSaveJsonToFile(rc, "res_after_layout.ket");
{
indigoSetOption("reaction-component-margin-size", "0.0");
indigoLayout(rc);
indigoSaveJsonToFile(rc, "res_after_layout2.ket");
}
{
indigoSetOption("reaction-component-margin-size", "3.2");
indigoLayout(rc);
indigoSaveJsonToFile(rc, "res_after_layout3.ket");
}

indigoFree(rc);
}
catch (Exception& e)
{
ASSERT_STREQ("", e.message());
}
}
42 changes: 21 additions & 21 deletions api/tests/integration/ref/arom/basic.py.out
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Expand Up @@ -402,14 +402,14 @@ NC1=NC=NC2NC=NC=21
-INDIGO-01000000002D

8 8 0 0 0 0 0 0 0 0999 V2000
0.8000 1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4000 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8000 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4000 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4000 1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
Expand All @@ -424,14 +424,14 @@ M END
-INDIGO-01000000002D

8 8 0 0 0 0 0 0 0 0999 V2000
0.8000 1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4000 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8000 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4000 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4000 1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
Expand All @@ -446,14 +446,14 @@ M END
-INDIGO-01000000002D

8 8 0 0 0 0 0 0 0 0999 V2000
0.8000 1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4000 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8000 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4000 -1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4000 1.3856 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5000 -0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5000 0.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
Expand Down
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