diff --git a/CHANGELOG.md b/CHANGELOG.md index db8ef10..3a5014a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ The file is formatted as described on http://keepachangelog.com/. ## Changed +* Allow proteins to be in mol2 format (#14) * Switched from 3Dmol to NGL (https://github.com/3D-e-Chem/molviewer-tsx/issues/4) ## [0.1.4] - 2016-11-25 diff --git a/examples/molviewer-ligands-and-proteins-example.knwf b/examples/molviewer-ligands-and-proteins-example.knwf index ec4a31b..e501520 100755 Binary files a/examples/molviewer-ligands-and-proteins-example.knwf and b/examples/molviewer-ligands-and-proteins-example.knwf differ diff --git a/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerDialog.java b/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerDialog.java index a6ddf3f..7464eb5 100644 --- a/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerDialog.java +++ b/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerDialog.java @@ -33,7 +33,7 @@ protected LigandsAndProteinsViewerDialog() { addDialogComponent(new DialogComponentColumnNameSelection( new SettingsModelString(LigandsAndProteinsViewerModel.CFGKEY_LIGAND, null), - "Column with SDF formatted molecules", LigandsAndProteinsViewerModel.LIGAND_PORT, SdfValue.class, + "Column with SDF or Mol2 formatted molecules", LigandsAndProteinsViewerModel.LIGAND_PORT, SdfValue.class, Mol2Value.class)); addDialogComponent(new DialogComponentColumnNameSelection( @@ -44,7 +44,8 @@ protected LigandsAndProteinsViewerDialog() { addDialogComponent(new DialogComponentColumnNameSelection( new SettingsModelString(LigandsAndProteinsViewerModel.CFGKEY_PROTEIN, null), - "Column with PDB formatted molecules", LigandsAndProteinsViewerModel.PROTEIN_PORT, PdbValue.class)); + "Column with PDB or Mol2 formatted molecules", LigandsAndProteinsViewerModel.PROTEIN_PORT, PdbValue.class, + Mol2Value.class)); addDialogComponent(new DialogComponentColumnNameSelection( new SettingsModelColumnName(LigandsAndProteinsViewerModel.CFGKEY_PROTEIN_LABEL, null), diff --git a/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerFactory.xml b/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerFactory.xml index 643163c..f5269a8 100644 --- a/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerFactory.xml +++ b/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerFactory.xml @@ -23,14 +23,14 @@ - + Table containing Ligands in SDF or Mol2 format - Table containing Proteins in PDB format + Table containing Proteins in PDB or Mol2 format Display web browser launcher diff --git a/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerModel.java b/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerModel.java index b45ad24..03a932e 100644 --- a/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerModel.java +++ b/plugin/src/main/java/nl/esciencecenter/e3dchem/knime/molviewer/ligandsandproteins/LigandsAndProteinsViewerModel.java @@ -148,7 +148,8 @@ protected void reset() { protected DataTableSpec[] configure(final DataTableSpec[] inSpecs) throws InvalidSettingsException { isCompatibleLambda compatibleLigand = (DataColumnSpec s) -> s.getType().isCompatible(SdfValue.class) || s.getType().isCompatible(Mol2Value.class); - isCompatibleLambda compatibleProtein = (DataColumnSpec s) -> s.getType().isCompatible(PdbValue.class); + isCompatibleLambda compatibleProtein = (DataColumnSpec s) -> s.getType().isCompatible(PdbValue.class) + || s.getType().isCompatible(Mol2Value.class); // as PDB, SDF and Mol2 are also string compatible exclude them for // label isCompatibleLambda compatibleLabel = (DataColumnSpec s) -> s.getType().isCompatible(StringValue.class) diff --git a/tests/pom.xml b/tests/pom.xml index 8792aa2..e4c623b 100644 --- a/tests/pom.xml +++ b/tests/pom.xml @@ -18,6 +18,7 @@ tycho-surefire-plugin ${tycho.version} + true ${tycho.test.jvmArgs} diff --git a/tests/src/knime/molviewer-test/.savedWithData b/tests/src/knime/molviewer-test/.savedWithData index 732715c..c74fc22 100644 --- a/tests/src/knime/molviewer-test/.savedWithData +++ b/tests/src/knime/molviewer-test/.savedWithData @@ -1,4 +1,4 @@ Do not delete this file! This file serves to indicate that the workflow was written as part of the usual save routine (not exported). -Workflow was last saved by user verhoes on Fri Nov 25 13:30:08 CET 2016 \ No newline at end of file +Workflow was last saved by user verhoes on Fri Dec 02 17:48:25 CET 2016 \ No newline at end of file diff --git a/tests/src/knime/molviewer-test/Ligands and Proteins Viewer (#20)/settings.xml b/tests/src/knime/molviewer-test/Ligands and Proteins Viewer (#20)/settings.xml index 89f2280..c4c7675 100644 --- a/tests/src/knime/molviewer-test/Ligands and Proteins Viewer (#20)/settings.xml +++ b/tests/src/knime/molviewer-test/Ligands and Proteins Viewer (#20)/settings.xml @@ -59,11 +59,11 @@ - + - + diff --git a/tests/src/knime/molviewer-test/Ligands and Proteins Viewer (#27)/settings.xml b/tests/src/knime/molviewer-test/Ligands and Proteins Viewer (#27)/settings.xml new file mode 100644 index 0000000..4d3277c --- /dev/null +++ b/tests/src/knime/molviewer-test/Ligands and Proteins Viewer (#27)/settings.xml @@ -0,0 +1,76 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/src/knime/molviewer-test/Ligands and Proteins Viewer (#4)/settings.xml b/tests/src/knime/molviewer-test/Ligands and Proteins Viewer (#4)/settings.xml index 8a66d0f..40cd376 100644 --- a/tests/src/knime/molviewer-test/Ligands and Proteins Viewer (#4)/settings.xml +++ b/tests/src/knime/molviewer-test/Ligands and Proteins Viewer (#4)/settings.xml @@ -59,11 +59,11 @@ - + - + diff --git a/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/data.xml b/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/data.xml index 316d3df..43ab5eb 100644 --- a/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/data.xml +++ b/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/data.xml @@ -1,22 +1,22 @@ - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/data.zip b/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/data.zip index b9afd2e..21d1cab 100644 Binary files a/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/data.zip and b/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/data.zip differ diff --git a/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/spec.xml b/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/spec.xml index 927c6e7..8af8de7 100644 --- a/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/spec.xml +++ b/tests/src/knime/molviewer-test/PDB Loader (#12)/port_1/spec.xml @@ -1,37 +1,37 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/src/knime/molviewer-test/PDB Loader (#12)/settings.xml b/tests/src/knime/molviewer-test/PDB Loader (#12)/settings.xml index 614332e..1151974 100644 --- a/tests/src/knime/molviewer-test/PDB Loader (#12)/settings.xml +++ b/tests/src/knime/molviewer-test/PDB Loader (#12)/settings.xml @@ -1,63 +1,63 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/data.xml b/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/data.xml index 7d42e5a..7bfa244 100644 --- a/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/data.xml +++ b/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/data.xml @@ -1,6 +1,6 @@ - - - - - + + + + + diff --git a/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/data.zip b/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/data.zip index 0968983..2851e61 100644 Binary files a/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/data.zip and b/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/data.zip differ diff --git a/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/spec.xml b/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/spec.xml index 4a18c52..8d9b9f7 100644 --- a/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/spec.xml +++ b/tests/src/knime/molviewer-test/Table Creator (#13)/port_1/spec.xml @@ -1,26 +1,26 @@ - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/src/knime/molviewer-test/Table Creator (#13)/settings.xml b/tests/src/knime/molviewer-test/Table Creator (#13)/settings.xml index 8caab6d..e779cda 100644 --- a/tests/src/knime/molviewer-test/Table Creator (#13)/settings.xml +++ b/tests/src/knime/molviewer-test/Table Creator (#13)/settings.xml @@ -1,83 +1,83 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/src/knime/molviewer-test/workflow.knime b/tests/src/knime/molviewer-test/workflow.knime index fbc50b4..68e0422 100644 --- a/tests/src/knime/molviewer-test/workflow.knime +++ b/tests/src/knime/molviewer-test/workflow.knime @@ -7,7 +7,7 @@ - + @@ -135,7 +135,7 @@ - + @@ -151,7 +151,7 @@ - + @@ -167,7 +167,23 @@ - + + + + + + + + + + + + + + + + + @@ -213,17 +229,29 @@ - + + + + + + + + + + + + + - +