Structures with the arrow lose their integrity when pressing 'Layout' #…

…938 (#939) * bingo removed * bump to 1.9.0-rc.1 * npm enable * misc fixes * misc fixes * misc changes * clang fix * cdx test fix * bump version to 1.9.0.rc.1 * clang fix * text size fix * unordered map fix Co-authored-by: Roman Porozhnetov <roman_porozhnetov@epam.com>
epam · Dec 19, 2022 · 9dd0dfc · 9dd0dfc
1 parent 3574cdc
commit 9dd0dfc
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Showing 26 changed files with 710 additions and 403 deletions.
diff --git a/.ci/version.txt b/.ci/version.txt
@@ -1,5 +1,5 @@
 1.9.0
-dev
-0
+rc
+1
 
-61934d47141baa775cf6b3f9e02f8ad132b3c364ad613e4c4df45497e2278cbd
+db544139e56560177275ed6d7e8525f955e4949d53bbae0a47d13c807e1374f5
diff --git a/.github/workflows/indigo-ci.yaml b/.github/workflows/indigo-ci.yaml
diff --git a/api/c/indigo/src/indigo_layout.cpp b/api/c/indigo/src/indigo_layout.cpp
@@ -101,6 +101,7 @@ CEXPORT int indigoLayout(int object)
             bool no_layout = rxn.catalystCount() || rxn.intermediateCount() || rxn.specialConditionsCount() || rxn.meta().getNonChemicalMetaCount();
             if (!no_layout)
             {
+                rxn.meta().resetMetaData();
                 ReactionLayout rl(rxn, self.smart_layout);
                 rl.max_iterations = self.layout_max_iterations;
                 rl.layout_orientation = (layout_orientation_value)self.layout_orientation;

diff --git a/api/dotnet/src/Indigo.Net.csproj b/api/dotnet/src/Indigo.Net.csproj
@@ -2,7 +2,7 @@
 
 	<PropertyGroup>
 		<TargetFrameworks>netstandard2.0</TargetFrameworks>
-		<Version>1.9.0-dev.0</Version>
+		<Version>1.9.0-rc.1</Version>
 		<Authors>EPAM Systems Life Science Department</Authors>
 		<Company>EPAM Systems</Company>
 		<Description>Universal cheminformatics toolkit</Description>

diff --git a/api/http/requirements.txt b/api/http/requirements.txt
@@ -1,7 +1,7 @@
 anyio==3.3.4
 asgiref==3.4.1
 click==8.0.3
-epam.indigo==1.9.0.dev0
+epam.indigo==1.9.0.rc1
 fastapi==0.70.0
 h11==0.12.0
 idna==3.3

diff --git a/api/http/setup.py b/api/http/setup.py
@@ -19,7 +19,7 @@
 
 setup_kwargs = {
     "name": "indigo-service",
-    "version": "1.9.0.dev0",
+    "version": "1.9.0.rc1",
     "description": "",
     "long_description": None,
     "author": "Ruslan Khyurri",

diff --git a/api/indigo-version.cmake b/api/indigo-version.cmake
@@ -1,4 +1,4 @@
-set(INDIGO_DEFAULT_VERSION "1.9.0-dev.0")
+set(INDIGO_DEFAULT_VERSION "1.9.0-rc.1")
 set(INDIGO_MAX_REVISION 1000)
 find_package(Git)
 if(GIT_EXECUTABLE)

diff --git a/api/java/pom.xml b/api/java/pom.xml
@@ -17,7 +17,7 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>${maven.compiler.source}</maven.compiler.target>
-        <revision>1.9.0-dev.0</revision>
+        <revision>1.9.0-rc.1</revision>
     </properties>
 
     <licenses>

diff --git a/api/python/indigo/__init__.py b/api/python/indigo/__init__.py
@@ -3,4 +3,4 @@
 from .indigo.indigo_exception import IndigoException  # noqa
 from .indigo.indigo_object import IndigoObject  # noqa
 
-__version__ = "1.9.0.dev0"
+__version__ = "1.9.0.rc1"
diff --git a/api/python/setup.py b/api/python/setup.py
@@ -98,7 +98,7 @@
 
 setup(
     name="epam.indigo",
-    version="1.9.0.dev0",
+    version="1.9.0.rc1",
     description="Indigo universal cheminformatics toolkit",
     author="EPAM Systems Life Science Department",
     author_email="lifescience.opensource@epam.com",

diff --git a/api/r/DESCRIPTION b/api/r/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: rindigo
-Version: 1.9.0-dev.0
+Version: 1.9.0-rc.1
 Date: 2020-12-10
 Title: R Package for Indigo Toolkit
 Authors@R: c(person(given = "Mikhail", family = "Kviatkovskii", role = c("cre"),

diff --git a/api/wasm/indigo-ketcher/package.json b/api/wasm/indigo-ketcher/package.json
@@ -1,6 +1,6 @@
 {
   "name": "indigo-ketcher",
-  "version": "1.9.0-dev.0",
+  "version": "1.9.0-rc.1",
   "description": "WASM implementation of Indigo organic chemistry toolkit web service for Ketcher",
   "main": "indigo-ketcher.js",
   "files": [

diff --git a/api/wasm/indigo-ketcher/test64.ket b/api/wasm/indigo-ketcher/test64.ket
@@ -1 +1 @@
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+{"root":{"nodes":[{"$ref":"mol0"}]},"mol0":{"type":"molecule","atoms":[{"label":"C","location":[3.4810001850128176,-6.519333839416504,0.0]},{"label":"C","location":[4.3470001220703129,-6.019333839416504,0.0]},{"label":"C","location":[4.3470001220703129,-5.019333839416504,0.0]},{"label":"O","location":[2.6150004863739015,-6.019333839416504,0.0]},{"label":"N","location":[3.4810001850128176,-4.519333839416504,0.0]},{"label":"C","location":[4.3470001220703129,-8.019333839416504,0.0],"stereoLabel":"abs"},{"label":"C","location":[5.213000297546387,-7.519333839416504,0.0]},{"label":"N","location":[3.4810001850128176,-7.519333839416504,0.0]},{"label":"O","location":[6.078999996185303,-8.019333839416504,0.0]},{"label":"C","location":[2.258333444595337,-8.161665916442871,0.0]},{"label":"C","location":[1.280333399772644,-7.9536662101745609,0.0]},{"label":"C","location":[0.6110000610351563,-8.696667671203614,0.0]},{"label":"C","location":[0.9200001955032349,-9.647665977478028,0.0]},{"label":"C","location":[2.567333459854126,-9.112667083740235,0.0]},{"label":"C","location":[1.8983337879180909,-9.855666160583496,0.0]},{"label":"N","location":[2.398333787918091,-10.721667289733887,0.0]},{"label":"C","location":[3.376333713531494,-10.513998985290528,0.0]},{"label":"C","location":[3.4810001850128176,-9.519333839416504,0.0]},{"label":"C","location":[4.3470001220703129,-9.019333839416504,0.0]},{"label":"C","location":[6.078999996185303,-6.019333839416504,0.0],"stereoLabel":"abs"},{"label":"C","location":[6.078999996185303,-5.019333839416504,0.0]},{"label":"N","location":[5.213000297546387,-6.519333839416504,0.0]},{"label":"O","location":[6.945000171661377,-4.519333839416504,0.0]},{"label":"C","location":[9.033666610717774,-7.376999855041504,0.0]},{"label":"C","location":[10.011667251586914,-7.585000514984131,0.0]},{"label":"C","location":[10.680999755859375,-6.842000484466553,0.0]},{"label":"C","location":[10.371999740600586,-5.891000270843506,0.0]},{"label":"C","location":[8.7246675491333,-6.426000118255615,0.0]},{"label":"C","location":[9.39366626739502,-5.682999610900879,0.0]},{"label":"N","location":[8.89366626739502,-4.817000389099121,0.0]},{"label":"C","location":[7.915666580200195,-5.0246663093566898,0.0]},{"label":"C","location":[7.811000347137451,-6.019333839416504,0.0]},{"label":"C","location":[6.945000171661377,-6.519333839416504,0.0]},{"label":"C","location":[3.4810001850128176,-3.519333839416504,0.0]},{"label":"N","location":[4.3470001220703129,-2.019333839416504,0.0]},{"label":"C","location":[4.3470001220703129,-3.019333839416504,0.0],"stereoLabel":"abs"},{"label":"C","location":[5.213000297546387,-3.519333839416504,0.0],"stereoLabel":"abs"},{"label":"C","location":[6.078999996185303,-3.019333839416504,0.0]},{"label":"O","location":[5.213000297546387,-4.519333839416504,0.0]},{"label":"O","location":[2.6150004863739015,-3.019333839416504,0.0]},{"label":"C","location":[3.4810001850128176,-1.5193339586257935,0.0]},{"label":"O","location":[3.4810001850128176,-0.5193338990211487,0.0]},{"label":"C","location":[2.6150004863739015,-2.019333839416504,0.0]},{"label":"C","location":[1.749000072479248,-1.5193339586257935,0.0]},{"label":"C","location":[1.749000072479248,-0.5193338990211487,0.0]},{"label":"C","location":[0.8830001950263977,-0.01933390274643898,0.0]},{"label":"C","location":[0.01666666753590107,-0.5193338990211487,0.0]},{"label":"C","location":[0.01666666753590107,-1.5193339586257935,0.0]},{"label":"C","location":[0.8830001950263977,-2.019333839416504,0.0]}],"bonds":[{"type":1,"atoms":[0,7]},{"type":1,"atoms":[6,21]},{"type":1,"atoms":[20,38]},{"type":1,"atoms":[33,4]},{"type":1,"atoms":[0,1]},{"type":1,"atoms":[1,2]},{"type":2,"atoms":[0,3]},{"type":1,"atoms":[2,4]},{"type":1,"atoms":[13,9]},{"type":2,"atoms":[10,9]},{"type":1,"atoms":[11,10]},{"type":2,"atoms":[12,11]},{"type":1,"atoms":[14,12]},{"type":1,"atoms":[17,13]},{"type":2,"atoms":[14,13]},{"type":1,"atoms":[15,14]},{"type":1,"atoms":[16,15]},{"type":2,"atoms":[17,16]},{"type":1,"atoms":[5,18],"stereo":1},{"type":1,"atoms":[5,6]},{"type":1,"atoms":[5,7]},{"type":2,"atoms":[6,8]},{"type":1,"atoms":[18,17]},{"type":1,"atoms":[27,23]},{"type":2,"atoms":[24,23]},{"type":1,"atoms":[25,24]},{"type":2,"atoms":[26,25]},{"type":1,"atoms":[28,26]},{"type":1,"atoms":[31,27]},{"type":2,"atoms":[28,27]},{"type":1,"atoms":[29,28]},{"type":1,"atoms":[30,29]},{"type":2,"atoms":[31,30]},{"type":1,"atoms":[19,32],"stereo":6},{"type":1,"atoms":[19,20]},{"type":1,"atoms":[19,21]},{"type":2,"atoms":[20,22]},{"type":1,"atoms":[32,31]},{"type":1,"atoms":[35,34],"stereo":1},{"type":1,"atoms":[33,35]},{"type":1,"atoms":[35,36]},{"type":1,"atoms":[36,37],"stereo":1},{"type":1,"atoms":[36,38]},{"type":2,"atoms":[33,39]},{"type":2,"atoms":[40,41]},{"type":1,"atoms":[40,42]},{"type":1,"atoms":[43,44]},{"type":2,"atoms":[44,45]},{"type":1,"atoms":[45,46]},{"type":2,"atoms":[46,47]},{"type":1,"atoms":[47,48]},{"type":2,"atoms":[43,48]},{"type":1,"atoms":[42,43]},{"type":1,"atoms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diff --git a/bingo/bingo-elastic/java/pom.xml b/bingo/bingo-elastic/java/pom.xml
@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>com.epam.indigo</groupId>
     <artifactId>bingo-elastic</artifactId>
-    <version>1.9.0-dev.0</version>
+    <version>1.9.0-rc.1</version>
     <packaging>jar</packaging>
 
     <name>Bingo Elastic</name>

diff --git a/bingo/bingo-elastic/python/bingo_elastic/__init__.py b/bingo/bingo-elastic/python/bingo_elastic/__init__.py
@@ -1 +1 @@
-__version__ = "1.9.0.dev0"
+__version__ = "1.9.0.rc1"
diff --git a/bingo/bingo-elastic/python/setup.py b/bingo/bingo-elastic/python/setup.py
@@ -21,7 +21,7 @@
 
 setup(
     name="bingo_elastic",
-    version="1.9.0.dev0",
+    version="1.9.0.rc1",
     description="Cartridge that provides fast, scalable, and efficient storage and searching solution for chemical information using Elasticsearch",
     author="Ruslan Khyurri",
     author_email="ruslan_khyurri@epam.com",
@@ -35,7 +35,7 @@
     download_url="https://pypi.org/project/bingo_elastic",
     python_requires=">=3.7",
     packages=["bingo_elastic", "bingo_elastic.model"],
-    install_requires=["epam.indigo==1.9.0.dev0", "elasticsearch==7.16.2"],
+    install_requires=["epam.indigo==1.9.0.rc1", "elasticsearch==7.16.2"],
     extras_require={
         "async": ["elasticsearch[async]==7.16.2"],
         "dev": [
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
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