rdkit / neo4j-rdkit Goto Github PK

I'm not enough of a Java wizard to figure out what's going on here and don't have an XCode10 machine available to try on my own, but the Travis-CI builds for XCode10 are regularly failing. Here's an example from the dev branch:
https://travis-ci.com/rdkit/neo4j-rdkit/jobs/232173334

@evgerher @sarmbruster : any thoughts on how we can deal with this? Given that the other CI builds are passing, I'm happy to either ignore it or disable the XCode10 builds, but that's not a great long-term solution. Something seems to have changed that is interfering with Evgeniy's code that extracts native libraries from the jar file and saves a temp copy.

Can anyone help me how to create a mol from an inchi passed as a string? I only see MolToInchi method in the API. Thank you so much !

Hello,

When I run "mvn package" the build is failing with the following error message:
[INFO] --- maven-shade-plugin:3.2.4:shade (default) @ rdkit-index --- [ERROR] The project main artifact does not exist. This could have the following [ERROR] reasons: [ERROR] - You have invoked the goal directly from the command line. This is not [ERROR] supported. Please add the goal to the default lifecycle via an [ERROR] <execution> element in your POM and use "mvn package" to have it run. [ERROR] - You have bound the goal to a lifecycle phase before "package". Please [ERROR] remove this binding from your POM such that the goal will be run in [ERROR] the proper phase. [ERROR] - You removed the configuration of the maven-jar-plugin that produces the main artifact. [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 41.605 s [INFO] Finished at: 2022-06-03T10:34:40+02:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-shade-plugin:3.2.4:shade (default) on project rdkit-index: Failed to create shaded artifact, project main artifact does not exist. -> [Help 1] [ERROR] [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch. [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException

the system information are:

• OS : Windows 10
• Apache Maven : 3.8.5
• Java : 11.0.15.1

Regards.

I used the neo4j-rdkit plugin in (neo4j desktop) windows environment without any issue. However, I tried the the same for the neo4j-rdkit plugin within the neo4j docker image but with no success. I have found here another related post but unfortunately it doesn't solve my issue. Other neo4j plugins such as APOC, GDS, etc. worked fine with me.

Here the detailed error:

`docker run --user="$(id -u):$(id -g)" --publish=7474:7474 --publish=7687:7687 -e NEO4J_dbms_security_procedures_unrestricted=apoc.,gds.,n10s.,rdkit. -e NEO4J_rdkit_index_sanitize=true --volume=$HOME/data/neo4j/data:/var/lib/neo4j/data --volume=$HOME/data/neo4j/logs:/var/lib/neo4j/logs --volume=$HOME/data/neo4j/plugins:/var/lib/neo4j/plugins --volume=$HOME/data/neo4j/import:/var/lib/neo4j/import --name neo4j neo4j

2022-02-07 17:13:52.340+0000 INFO Starting...
2022-02-07 17:13:52.753+0000 INFO This instance is ServerId{f2bc4375} (f2bc4375-4ffd-45e6-ab0a-9b108d516b64)
2022-02-07 17:13:54.369+0000 INFO ======== Neo4j 4.4.3 ========
2022-02-07 17:13:54.722+0000 INFO Loading libraries from JAR
2022-02-07 17:13:54.839+0000 INFO trying to load native library /tmp/rdkit-153718487753989773/libGraphMolWrap.so
2022-02-07 17:13:54.854+0000 ERROR Failed to start Neo4j on 0.0.0.0:7474.
java.lang.RuntimeException: Error starting Neo4j database server at /data/databases
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:228) ~[neo4j-4.4.3.jar:4.4.3]
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.build(DatabaseManagementServiceFactory.java:181) ~[neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.CommunityBootstrapper.createNeo(CommunityBootstrapper.java:36) ~[neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:142) [neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:95) [neo4j-4.4.3.jar:4.4.3]
at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:34) [neo4j-4.4.3.jar:4.4.3]
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.rdkit.neo4j.bin.LibraryLoaderLifecycle@6094de13' failed to initialize. Please see the attached cause exception "/tmp/rdkit-153718487753989773/libGraphMolWrap.so: libfreetype.so.6: cannot open shared object file: No such file or directory".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:424) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.extension.AbstractExtensions.init(AbstractExtensions.java:77) ~[neo4j-kernel-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:403) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:101) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.3.jar:4.4.3]
... 5 more
Caused by: java.lang.UnsatisfiedLinkError: /tmp/rdkit-153718487753989773/libGraphMolWrap.so: libfreetype.so.6: cannot open shared object file: No such file or directory
at java.lang.ClassLoader$NativeLibrary.load0(Native Method) ~[?:?]
at java.lang.ClassLoader$NativeLibrary.load(ClassLoader.java:2442) ~[?:?]
at java.lang.ClassLoader$NativeLibrary.loadLibrary(ClassLoader.java:2498) ~[?:?]
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:2694) ~[?:?]
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:2627) ~[?:?]
at java.lang.Runtime.load0(Runtime.java:768) ~[?:?]
at java.lang.System.load(System.java:1837) ~[?:?]
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.lambda$loadNativeLibraries$0(LibraryLoaderLifecycle.java:75) ~[rdkit-index-1.2.0-4.2.jar:?]
at java.util.ArrayList.forEach(ArrayList.java:1541) ~[?:?]
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.loadNativeLibraries(LibraryLoaderLifecycle.java:73) ~[rdkit-index-1.2.0-4.2.jar:?]
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.init(LibraryLoaderLifecycle.java:55) ~[rdkit-index-1.2.0-4.2.jar:?]
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:403) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.extension.AbstractExtensions.init(AbstractExtensions.java:77) ~[neo4j-kernel-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:403) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:101) ~[neo4j-common-4.4.3.jar:4.4.3]
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:219) ~[neo4j-4.4.3.jar:4.4.3]`

I attempt the following commands to start neo4j 4.1.3 CE with latest rdkit & apoc plugin

rm -r ~/docker_vols_neo4j_4.1.3

mkdir ~/docker_vols_neo4j_4.1.3
mkdir ~/docker_vols_neo4j_4.1.3/plugins
mkdir ~/docker_vols_neo4j_4.1.3/deb
mkdir ~/docker_vols_neo4j_4.1.3/data

cp ~/Downloads/neo4j_rdkit_docker/plugins/apoc-4.1.0.2-all.jar ~/docker_vols_neo4j_4.1.3/plugins/
cp ~/Downloads/neo4j_rdkit_docker/plugins/rdkit-index-1.1.0-SNAPSHOT-4.1.jar ~/docker_vols_neo4j_4.1.3/plugins/
cp ~/Downloads/neo4j_rdkit_docker/deb/libpng16-16_1.6.36-6_amd64.deb ~/docker_vols_neo4j_4.1.3/deb/
cp ~/Downloads/neo4j_rdkit_docker/deb/libfreetype6_2.9.1-3+deb10u2_amd64.deb ~/docker_vols_neo4j_4.1.3/deb/
cp ~/Downloads/neo4j_rdkit_docker/deb/install_debs.sh ~/docker_vols_neo4j_4.1.3/deb/

chmod 644 ~/docker_vols_neo4j_4.1.3/plugins/.jar
chmod 644 ~/docker_vols_neo4j_4.1.3/deb/.deb
chmod 755 ~/docker_vols_neo4j_4.1.3/deb/*.sh

docker run --rm
-p 127.0.0.1:7474:7474
-p 127.0.0.1:7687:7687
-v ~/docker_vols_neo4j_4.1.3/plugins:/var/lib/neo4j/plugins
-v ~/docker_vols_neo4j_4.1.3/data:/var/lib/neo4j/data
-e NEO4J_AUTH=none
-e NEO4J_dbms_memory_pagecache_size=8G
-e NEO4J_dbms_memory_heap_max__size=16G
-e NEO4J_dbms_security_procedures_unrestricted=\*
-e EXTENSION_SCRIPT=/deb/install_debs.sh
-e NEO4J_rdkit_index_sanitize=true
--user=$(id -u):$(id -g)
neo4j:4.1.3

and receive the following error:

Directories in use:
home: /var/lib/neo4j
config: /var/lib/neo4j/conf
logs: /logs
plugins: /var/lib/neo4j/plugins
import: /var/lib/neo4j/import
data: /var/lib/neo4j/data
certificates: /var/lib/neo4j/certificates
run: /var/lib/neo4j/run
Starting Neo4j.
APOC couln't set a URLStreamHandlerFactory since some other tool already did this (e.g. tomcat). This means you cannot use s3:// or hdfs:// style URLs in APOC. This is caused by a limitation of the JVM which we cannot fix.
2020-11-03 20:12:48.858+0000 INFO Starting...
2020-11-03 20:12:51.198+0000 INFO ======== Neo4j 4.1.3 ========
2020-11-03 20:12:51.641+0000 INFO Loading libraries from JAR
2020-11-03 20:12:51.775+0000 INFO trying to load native library /tmp/rdkit-5402050139939947324/libGraphMolWrap.so
2020-11-03 20:12:51.788+0000 ERROR Failed to start Neo4j on dbms.connector.http.listen_address, a socket address. If missing port or hostname it is acquired from dbms.default_listen_address. Error starting Neo4j database server at /data/databases
java.lang.RuntimeException: Error starting Neo4j database server at /data/databases
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:198)
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.build(DatabaseManagementServiceFactory.java:158)
at org.neo4j.server.CommunityBootstrapper.createNeo(CommunityBootstrapper.java:36)
at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:117)
at org.neo4j.server.NeoBootstrapper.start(NeoBootstrapper.java:87)
at org.neo4j.server.CommunityEntryPoint.main(CommunityEntryPoint.java:35)
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.rdkit.neo4j.bin.LibraryLoaderLifecycle@4c361f63' failed to initialize. Please see the attached cause exception "/tmp/rdkit-5402050139939947324/libGraphMolWrap.so: libfreetype.so.6: cannot open shared object file: No such file or directory".
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:424)
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65)
at org.neo4j.kernel.extension.AbstractExtensions.init(AbstractExtensions.java:76)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:403)
at org.neo4j.kernel.lifecycle.LifeSupport.init(LifeSupport.java:65)
at org.neo4j.kernel.lifecycle.LifeSupport.start(LifeSupport.java:101)
at org.neo4j.graphdb.facade.DatabaseManagementServiceFactory.startDatabaseServer(DatabaseManagementServiceFactory.java:189)
... 5 more
Caused by: java.lang.UnsatisfiedLinkError: /tmp/rdkit-5402050139939947324/libGraphMolWrap.so: libfreetype.so.6: cannot open shared object file: No such file or directory
at java.base/java.lang.ClassLoader$NativeLibrary.load0(Native Method)
at java.base/java.lang.ClassLoader$NativeLibrary.load(ClassLoader.java:2442)
at java.base/java.lang.ClassLoader$NativeLibrary.loadLibrary(ClassLoader.java:2498)
at java.base/java.lang.ClassLoader.loadLibrary0(ClassLoader.java:2694)
at java.base/java.lang.ClassLoader.loadLibrary(ClassLoader.java:2627)
at java.base/java.lang.Runtime.load0(Runtime.java:768)
at java.base/java.lang.System.load(System.java:1837)
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.lambda$loadNativeLibraries$0(LibraryLoaderLifecycle.java:78)
at java.base/java.util.ArrayList.forEach(ArrayList.java:1541)
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.loadNativeLibraries(LibraryLoaderLifecycle.java:76)
at org.rdkit.neo4j.bin.LibraryLoaderLifecycle.init(LibraryLoaderLifecycle.java:58)
at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:403)
... 11 more
2020-11-03 20:12:51.789+0000 INFO Neo4j Server shutdown initiated by request

CREATE (n:Entity:Chemical:Compound:Structure {
luri: 'test1',
preferred_name: 'chloro benzene',
smiles: 'ClC1=CC=CC=C1'})
creates a node the chemical structure for chloro benzene:

The query
CALL org.rdkit.search.exact.smiles(['Chemical', 'Structure'], 'ClC1=CC=CC=C1')
yields:

{ "columns" : [ "name", "luri", "canonical_smiles" ], "data" : [ [ "chloro benzene", "test1", "Clc1ccccc1" ] ] }

in CREATE the property "preferred_name" was set, query delivers a property "name". Suggestion: eliminate "name" from output of any search query (org.rdkit.search.exact.smiles, org.rdkit.search.exact.mol, org.rdkit.search.substructure.smiles, org.rdkit.search.substructure.mol). treat preferred_name in CREATE statement as any other property

Would it be possible to update this for Neo4j 5.x?

I believe some full-text indexing commands also need to fixed to be compatible with the new version.

For example, a 5 coordinate neutral carbon will generate errors if you attempt to sanitize it normally, but can be handled if you turn off the appropriate pieces. For example:

In [2]: m = Chem.MolFromSmiles('ClC(C)(C)Br')
[04:56:25] Explicit valence for atom # 1 C, 5, is greater than permitted

In [3]: m = Chem.MolFromSmiles('ClC(C)(C)Br',sanitize=False)

In [4]: Chem.SanitizeMol(m,Chem.SanitizeFlags.SANITIZE_ALL^Chem.SanitizeFlags.SANITIZE_PROPERTIES)
Out[4]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE

In [5]: m.HasSubstructMatch(Chem.MolFromSmarts('ClCBr'))
Out[5]: True

I'm using Java 11 now and the native libraries I generated can only work with Java 11, not other versions. Is there anyways to generate native libraries to work with all Java version?

CREATE (n:Entity:Chemical:Compound:Structure {
luri: 'test1',
preferred_name: 'chloro benzene',
smiles: 'ClC1=CC=CC=C1'})
creates a node the chemical structure for chloro benzene:

The property "luri" is supposed to be a unique resource identifier for the node (originally: legacy uri). I believe it makes sense to have such resource identifier on nodes bearing structures. Suggestion: if luri-attribute is not deliberately set by user upon data ingestion the plugin should create the luri-property and assign a UUID to it

The query
CALL org.rdkit.search.exact.smiles(['Chemical', 'Structure'], 'ClC1=CC=CC=C1')
yields:

{ "columns" : [ "name", "luri", "canonical_smiles" ], "data" : [ [ "chloro benzene", "test1", "Clc1ccccc1" ] ] }

in CREATE the property "preferred_name" was set, query delivers a property "name". Suggestion: eliminate "name" from output of any search query (org.rdkit.search.exact.smiles, org.rdkit.search.exact.mol, org.rdkit.search.substructure.smiles, org.rdkit.search.substructure.mol). treat preferred_name in CREATE statement as any other property

CALL org.rdkit.search.createIndex(['Structure', 'Chemical'])

yields:

Neo.ClientError.Procedure.ProcedureCallFailed

Failed to invoke procedure org.rdkit.search.createIndex: Caused by: java.lang.NoClassDefFoundError: Could not initialize class org.rdkit.neo4j.procedures.SubstructureSearch

did the syntax change from 3.5 to 4.1?