From dc8a12d713fa2f01193cb391891dc13fdf2cd147 Mon Sep 17 00:00:00 2001 From: Mitch Miller Date: Mon, 30 Sep 2024 14:39:23 -0400 Subject: [PATCH 1/3] new method in ChemicalImpl interface: List permuteEpimers() --- pom.xml | 2 +- src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImpl.java | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 19332ca..9b48598 100644 --- a/pom.xml +++ b/pom.xml @@ -24,7 +24,7 @@ gov.nih.ncats molwitch - 0.6.9 + 0.6.12-SNAPSHOT ncats-molwitch diff --git a/src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImpl.java b/src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImpl.java index 3fdda8d..91ef112 100644 --- a/src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImpl.java +++ b/src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImpl.java @@ -230,5 +230,11 @@ public String toString() { void generateCoordinates() throws MolwitchException; void flipChirality(Stereocenter s); + ChemicalImpl flipAllChiralCenters(); + + ChemicalImpl flipEpimericChiralCenters(); + + List permuteEpimers(); + List getSGroupWarnings(); } From 16b821895f04ba1f1ac72b804bbfbf652cb960c0 Mon Sep 17 00:00:00 2001 From: Mitch Miller Date: Thu, 13 Feb 2025 13:28:08 -0500 Subject: [PATCH 2/3] added permuteEpimersAndEnantiomers, and made flipEpimericChiralCenters and flipAllChiralCenters return Chemical objects --- src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImpl.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImpl.java b/src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImpl.java index 91ef112..935ef77 100644 --- a/src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImpl.java +++ b/src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImpl.java @@ -230,11 +230,13 @@ public String toString() { void generateCoordinates() throws MolwitchException; void flipChirality(Stereocenter s); - ChemicalImpl flipAllChiralCenters(); + Chemical flipAllChiralCenters(); - ChemicalImpl flipEpimericChiralCenters(); + Chemical flipEpimericChiralCenters(); List permuteEpimers(); + List permuteEpimersAndEnantiomers(); + List getSGroupWarnings(); } From 3cab669e94382e5261c5f08b6d37fbebf57e9a61 Mon Sep 17 00:00:00 2001 From: Mitch Miller Date: Fri, 14 Feb 2025 19:27:16 -0500 Subject: [PATCH 3/3] changed version to 0.6.10 updated copyright year to 2025 --- pom.xml | 4 ++-- src/main/java/gov/nih/ncats/molwitch/Atom.java | 2 +- src/main/java/gov/nih/ncats/molwitch/AtomCoordinates.java | 2 +- src/main/java/gov/nih/ncats/molwitch/Bond.java | 2 +- src/main/java/gov/nih/ncats/molwitch/BondTable.java | 2 +- src/main/java/gov/nih/ncats/molwitch/Chemical.java | 2 +- src/main/java/gov/nih/ncats/molwitch/ChemicalBuilder.java | 2 +- src/main/java/gov/nih/ncats/molwitch/ChemicalSource.java | 2 +- src/main/java/gov/nih/ncats/molwitch/Chirality.java | 2 +- .../gov/nih/ncats/molwitch/DoubleBondStereochemistry.java | 2 +- src/main/java/gov/nih/ncats/molwitch/ElementData.java | 2 +- .../gov/nih/ncats/molwitch/ExtendedTetrahedralChirality.java | 2 +- src/main/java/gov/nih/ncats/molwitch/FileSource.java | 2 +- src/main/java/gov/nih/ncats/molwitch/GraphInvariant.java | 2 +- src/main/java/gov/nih/ncats/molwitch/ImplUtil.java | 2 +- src/main/java/gov/nih/ncats/molwitch/MolWitch.java | 2 +- src/main/java/gov/nih/ncats/molwitch/MolwitchException.java | 2 +- src/main/java/gov/nih/ncats/molwitch/PathVisitor.java | 2 +- src/main/java/gov/nih/ncats/molwitch/SGroup.java | 2 +- src/main/java/gov/nih/ncats/molwitch/SmartsSource.java | 2 +- src/main/java/gov/nih/ncats/molwitch/SmilesSource.java | 2 +- src/main/java/gov/nih/ncats/molwitch/Stereocenter.java | 2 +- .../java/gov/nih/ncats/molwitch/TetrahedralChirality.java | 2 +- .../gov/nih/ncats/molwitch/datastores/ChemicalDataStore.java | 2 +- .../nih/ncats/molwitch/datastores/FileChemicalDataStore.java | 2 +- .../ncats/molwitch/datastores/SimpleChemicalDataStore.java | 2 +- .../java/gov/nih/ncats/molwitch/fingerprint/Fingerprint.java | 2 +- .../gov/nih/ncats/molwitch/fingerprint/Fingerprinter.java | 2 +- .../gov/nih/ncats/molwitch/fingerprint/Fingerprinters.java | 2 +- .../java/gov/nih/ncats/molwitch/fingerprint/package-info.java | 2 +- .../java/gov/nih/ncats/molwitch/inchi/BinaryInchiKey.java | 2 +- .../java/gov/nih/ncats/molwitch/inchi/BinaryInchiKeyBag.java | 2 +- .../java/gov/nih/ncats/molwitch/inchi/BinaryInchiKeyUtil.java | 2 +- .../java/gov/nih/ncats/molwitch/inchi/DefaultInchiKeyBag.java | 2 +- src/main/java/gov/nih/ncats/molwitch/inchi/InChiResult.java | 2 +- src/main/java/gov/nih/ncats/molwitch/inchi/Inchi.java | 2 +- src/main/java/gov/nih/ncats/molwitch/inchi/InchiKey.java | 2 +- src/main/java/gov/nih/ncats/molwitch/inchi/InchiKeyBag.java | 2 +- src/main/java/gov/nih/ncats/molwitch/inchi/InchiUtil.java | 2 +- .../java/gov/nih/ncats/molwitch/internal/InternalUtil.java | 2 +- .../java/gov/nih/ncats/molwitch/internal/OpsinHelper.java | 2 +- .../java/gov/nih/ncats/molwitch/internal/package-info.java | 2 +- .../gov/nih/ncats/molwitch/internal/source/LazySource.java | 2 +- .../gov/nih/ncats/molwitch/internal/source/MolFileInfo.java | 2 +- .../nih/ncats/molwitch/internal/source/MolStringSource.java | 2 +- .../gov/nih/ncats/molwitch/internal/source/StringSource.java | 2 +- src/main/java/gov/nih/ncats/molwitch/io/ChemFormat.java | 2 +- src/main/java/gov/nih/ncats/molwitch/io/ChemicalReader.java | 2 +- .../java/gov/nih/ncats/molwitch/io/ChemicalReaderFactory.java | 2 +- src/main/java/gov/nih/ncats/molwitch/io/ChemicalWriter.java | 2 +- .../java/gov/nih/ncats/molwitch/io/ChemicalWriterFactory.java | 2 +- src/main/java/gov/nih/ncats/molwitch/io/CtTableCleaner.java | 2 +- .../gov/nih/ncats/molwitch/io/DelegateChemicalWriter.java | 2 +- .../gov/nih/ncats/molwitch/io/PushbackBufferedReader.java | 2 +- src/main/java/gov/nih/ncats/molwitch/io/SdfUtil.java | 2 +- .../java/gov/nih/ncats/molwitch/io/StandardChemFormats.java | 2 +- src/main/java/gov/nih/ncats/molwitch/io/WriterOptions.java | 2 +- .../java/gov/nih/ncats/molwitch/io/WriterOptionsBuilder.java | 2 +- src/main/java/gov/nih/ncats/molwitch/io/package-info.java | 2 +- .../java/gov/nih/ncats/molwitch/isotopes/ElementData.java | 2 +- src/main/java/gov/nih/ncats/molwitch/isotopes/Elements.java | 2 +- src/main/java/gov/nih/ncats/molwitch/isotopes/Isotope.java | 2 +- .../java/gov/nih/ncats/molwitch/isotopes/IsotopeFactory.java | 2 +- .../gov/nih/ncats/molwitch/isotopes/NISTIsotopeFactory.java | 2 +- .../gov/nih/ncats/molwitch/isotopes/ValueWithUncertainty.java | 2 +- .../java/gov/nih/ncats/molwitch/isotopes/WeightInterval.java | 2 +- src/main/java/gov/nih/ncats/molwitch/search/MolSearcher.java | 2 +- .../gov/nih/ncats/molwitch/search/MolSearcherFactory.java | 2 +- .../nih/ncats/molwitch/spi/AgnosticChemicalImplFactory.java | 2 +- src/main/java/gov/nih/ncats/molwitch/spi/ChemicalImpl.java | 2 +- .../java/gov/nih/ncats/molwitch/spi/ChemicalImplFactory.java | 2 +- .../java/gov/nih/ncats/molwitch/spi/ChemicalImplReader.java | 2 +- .../java/gov/nih/ncats/molwitch/spi/ChemicalWriterImpl.java | 2 +- .../gov/nih/ncats/molwitch/spi/ChemicalWriterImplFactory.java | 2 +- .../java/gov/nih/ncats/molwitch/spi/FingerprinterImpl.java | 2 +- .../java/gov/nih/ncats/molwitch/spi/InchiImplFactory.java | 2 +- .../gov/nih/ncats/molwitch/spi/MolSearcherImplFactory.java | 2 +- src/main/java/gov/nih/ncats/molwitch/spi/WitchModule.java | 2 +- src/main/java/gov/nih/ncats/molwitch/spi/package-info.java | 2 +- src/test/java/CleanSdfTest.java | 2 +- src/test/java/InchiKeyBagTest.java | 2 +- src/test/java/InchiKeyTest.java | 2 +- src/test/java/TestNISTIsotopeFactory.java | 2 +- 83 files changed, 84 insertions(+), 84 deletions(-) diff --git a/pom.xml b/pom.xml index 9b48598..d7aecad 100644 --- a/pom.xml +++ b/pom.xml @@ -2,7 +2,7 @@