From 8930234bb4572268abf74fca2e80a74a6460f6f9 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 24 Mar 2022 13:12:01 +0100 Subject: [PATCH 1/6] New CDK and Cytoscape versions --- pom.xml | 123 +++++------------- .../internal/depict/SvgDrawVisitor.java | 2 +- .../chemViz2/internal/model/Compound.java | 9 +- 3 files changed, 39 insertions(+), 95 deletions(-) diff --git a/pom.xml b/pom.xml index 74c3cc8..61bcda5 100644 --- a/pom.xml +++ b/pom.xml @@ -4,10 +4,12 @@ chemViz2 edu.ucsf.rbvi.chemViz2.internal - 3.5.0 + 3.9.0 2.3.4 4.2.0 + 2.7.1 + 1.1 edu.ucsf.rbvi @@ -93,28 +95,6 @@ true - - - jni-inchi - JNI-InChI Maven Repository - http://jni-inchi.sourceforge.net/m2repo - - true - - - - jnati - http://jnati.sourceforge.net/m2repo - - true - - @@ -190,6 +170,11 @@ 1.11.11 provided + + com.google.guava + guava + 31.1-jre + org.osgi org.osgi.core @@ -200,122 +185,107 @@ org.openscience.cdk cdk-interfaces - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-core - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-smiles - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-smarts - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-inchi - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-qsar - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-qsarmolecular - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-render - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-renderbasic - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-renderextra - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-renderawt - 1.5.14 - true - - - org.openscience.cdk - cdk-smsd - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-builder3d - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-fingerprint - 1.5.14 + ${cdk.version} true org.openscience.cdk cdk-silent - 1.5.14 + ${cdk.version} true - org.openscience.cdk cdk-legacy - 1.5.14 - true - - - net.sf.jnati - jnati-core - 0.4 + ${cdk.version} true - - net.sf.jnati - jnati-deploy - 0.4 - true - - + + io.github.dan2097 + jna-inchi-api + ${jna-inchi.version} + + + io.github.dan2097 + jna-inchi-core + ${jna-inchi.version} + xom xom - 1.2.5 + 1.3.7 provided @@ -336,37 +306,12 @@ 2.4 true - - xml-apis xml-apis 1.3.03 provided - - - net.sf.jni-inchi - jni-inchi - 0.9-SNAPSHOT - true - - - org.apache.commons - commons-math3 - 3.0 - true - diff --git a/src/main/java/edu/ucsf/rbvi/chemViz2/internal/depict/SvgDrawVisitor.java b/src/main/java/edu/ucsf/rbvi/chemViz2/internal/depict/SvgDrawVisitor.java index 7819364..a50911a 100644 --- a/src/main/java/edu/ucsf/rbvi/chemViz2/internal/depict/SvgDrawVisitor.java +++ b/src/main/java/edu/ucsf/rbvi/chemViz2/internal/depict/SvgDrawVisitor.java @@ -353,7 +353,7 @@ private void visit(String id, String cls, LineElement elem) { private void visit(MarkedElement elem) { String id = elem.getId(); List classes = elem.getClasses(); - String cls = classes.isEmpty() ? null : Joiner.on(" ").join(classes); + String cls = classes.isEmpty() ? null : String.join(" ", classes); IRenderingElement marked = elem.element(); diff --git a/src/main/java/edu/ucsf/rbvi/chemViz2/internal/model/Compound.java b/src/main/java/edu/ucsf/rbvi/chemViz2/internal/model/Compound.java index 760dcfc..01a6408 100644 --- a/src/main/java/edu/ucsf/rbvi/chemViz2/internal/model/Compound.java +++ b/src/main/java/edu/ucsf/rbvi/chemViz2/internal/model/Compound.java @@ -18,6 +18,7 @@ import org.cytoscape.model.CyNetwork; import edu.ucsf.rbvi.chemViz2.internal.view.ViewUtils; +import io.github.dan2097.jnainchi.InchiStatus; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.CDKConstants; @@ -41,8 +42,6 @@ import org.openscience.cdk.tools.CDKHydrogenAdder; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import net.sf.jniinchi.INCHI_RET; - /** * The Compound class provides the main interface to molecule compounds. A * given node or edge in Cytoscape could have multiple Compounds, either @@ -394,10 +393,10 @@ private String convertInchiToSmiles(String inchi) { InChIToStructure intostruct = factory.getInChIToStructure(inchi, SilentChemObjectBuilder.getInstance()); // Get the structure - INCHI_RET ret = intostruct.getReturnStatus(); - if (ret == INCHI_RET.WARNING) { + InchiStatus ret = intostruct.getStatus(); + if (ret == InchiStatus.WARNING) { logger.warn("InChI warning: " + intostruct.getMessage()); - } else if (ret != INCHI_RET.OKAY) { + } else if (ret != InchiStatus.SUCCESS) { logger.warn("Structure generation failed: " + ret.toString() + " [" + intostruct.getMessage() + "]"); return null; From a6d5f7f4e842ea99c589a56071e9610a3c01b5dd Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 24 Mar 2022 13:16:59 +0100 Subject: [PATCH 2/6] Replaced some Guava with modern Java --- .../chemViz2/internal/depict/Depiction.java | 25 ++++++++++--------- 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/src/main/java/edu/ucsf/rbvi/chemViz2/internal/depict/Depiction.java b/src/main/java/edu/ucsf/rbvi/chemViz2/internal/depict/Depiction.java index beb9313..2727278 100644 --- a/src/main/java/edu/ucsf/rbvi/chemViz2/internal/depict/Depiction.java +++ b/src/main/java/edu/ucsf/rbvi/chemViz2/internal/depict/Depiction.java @@ -18,15 +18,8 @@ */ package edu.ucsf.rbvi.chemViz2.internal.depict; -import com.google.common.base.Charsets; -import org.openscience.cdk.renderer.RendererModel; -import org.openscience.cdk.renderer.elements.Bounds; -import org.openscience.cdk.renderer.elements.IRenderingElement; -import org.openscience.cdk.renderer.font.AWTFontManager; -import org.openscience.cdk.renderer.generators.BasicSceneGenerator; -import org.openscience.cdk.renderer.visitor.IDrawVisitor; +import static edu.ucsf.rbvi.chemViz2.internal.depict.DepictionGenerator.AUTOMATIC; -import javax.imageio.ImageIO; import java.awt.geom.AffineTransform; import java.awt.geom.Rectangle2D; import java.awt.image.BufferedImage; @@ -34,12 +27,20 @@ import java.io.FileOutputStream; import java.io.IOException; import java.io.OutputStream; +import java.nio.charset.StandardCharsets; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Locale; -import static edu.ucsf.rbvi.chemViz2.internal.depict.DepictionGenerator.AUTOMATIC; +import javax.imageio.ImageIO; + +import org.openscience.cdk.renderer.RendererModel; +import org.openscience.cdk.renderer.elements.Bounds; +import org.openscience.cdk.renderer.elements.IRenderingElement; +import org.openscience.cdk.renderer.font.AWTFontManager; +import org.openscience.cdk.renderer.generators.BasicSceneGenerator; +import org.openscience.cdk.renderer.visitor.IDrawVisitor; /** * Base class of a pre-rendered depiction. The class allows introspection of @@ -212,11 +213,11 @@ public final List listFormats() { */ public final void writeTo(String fmt, OutputStream out) throws IOException { if (fmt.equalsIgnoreCase(SVG_FMT)) { - out.write(toSvgStr().getBytes(Charsets.UTF_8)); + out.write(toSvgStr().getBytes(StandardCharsets.UTF_8)); } else if (fmt.equalsIgnoreCase(PS_FMT)) { - out.write(toEpsStr().getBytes(Charsets.UTF_8)); + out.write(toEpsStr().getBytes(StandardCharsets.UTF_8)); } else if (fmt.equalsIgnoreCase(PDF_FMT)) { - out.write(toPdfStr().getBytes(Charsets.UTF_8)); + out.write(toPdfStr().getBytes(StandardCharsets.UTF_8)); } else { ImageIO.write(toImg(), fmt, out); } From d2928a5d89855631c1f4b275a0a1a2e1f3165e90 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 24 Mar 2022 13:28:30 +0100 Subject: [PATCH 3/6] Updated the Bnd tool, to fix a build error --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 61bcda5..65f6df3 100644 --- a/pom.xml +++ b/pom.xml @@ -6,7 +6,7 @@ edu.ucsf.rbvi.chemViz2.internal 3.9.0 - 2.3.4 + 5.1.2 4.2.0 2.7.1 1.1 From dc110e7c7070594c9f6482bee8b9e634684b5349 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Thu, 24 Mar 2022 13:28:39 +0100 Subject: [PATCH 4/6] Bumped the version number --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 65f6df3..3fbe863 100644 --- a/pom.xml +++ b/pom.xml @@ -17,7 +17,7 @@ bundle ${bundle.symbolicName} - 1.1.1 + 1.2.0 From a63931f924ef2432ca4e1164626f3f94d5ee4234 Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Wed, 18 May 2022 19:43:45 +0200 Subject: [PATCH 5/6] Duh. It did not include the shared objects --- pom.xml | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/pom.xml b/pom.xml index 3fbe863..f54b404 100644 --- a/pom.xml +++ b/pom.xml @@ -272,16 +272,16 @@ ${cdk.version} true - - io.github.dan2097 - jna-inchi-api - ${jna-inchi.version} - - - io.github.dan2097 - jna-inchi-core - ${jna-inchi.version} - + + io.github.dan2097 + jna-inchi-api + ${jna-inchi.version} + + + io.github.dan2097 + jna-inchi-all + ${jna-inchi.version} + xom xom From fb0b7c931d3ffd1660d32ea2e0788b01f521ceed Mon Sep 17 00:00:00 2001 From: Egon Willighagen Date: Wed, 18 May 2022 19:44:10 +0200 Subject: [PATCH 6/6] Don't try to layout when the compoundType is null --- .../java/edu/ucsf/rbvi/chemViz2/internal/model/Compound.java | 1 + 1 file changed, 1 insertion(+) diff --git a/src/main/java/edu/ucsf/rbvi/chemViz2/internal/model/Compound.java b/src/main/java/edu/ucsf/rbvi/chemViz2/internal/model/Compound.java index 01a6408..6d748e4 100644 --- a/src/main/java/edu/ucsf/rbvi/chemViz2/internal/model/Compound.java +++ b/src/main/java/edu/ucsf/rbvi/chemViz2/internal/model/Compound.java @@ -200,6 +200,7 @@ public IAtomContainer getMolecule3D() { public void layoutStructure() { if (!laidOut) { + if (compoundType == null) {} else if (compoundType.equals(CompoundType.MOLECULE)) { if (iMolecule == null) return;