Merge pull request #12 from ncats/apply_parameters

Create the ability to pass parameters to a ChemicalImplFactory class
ncats · May 9, 2024 · cddbf47 · cddbf47
2 parents ad468a0 + 5918f6d
commit cddbf47
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Showing 85 changed files with 95 additions and 89 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,4 @@
 witch.iml
 molwitch.iml
 /target/
+
diff --git a/LICENSE b/LICENSE
@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2023 ncats
+   Copyright 2024 ncats
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

diff --git a/pom.xml b/pom.xml
@@ -2,7 +2,7 @@
 <!--
   ~ NCATS-MOLWITCH
   ~
-  ~ Copyright 2023 NIH/NCATS
+  ~ Copyright 2024 NIH/NCATS
   ~
   ~    Licensed under the Apache License, Version 2.0 (the "License");
   ~    you may not use this file except in compliance with the License.
@@ -24,7 +24,7 @@
 
     <groupId>gov.nih.ncats</groupId>
     <artifactId>molwitch</artifactId>
-    <version>0.6.6</version>
+    <version>0.6.7</version>
 
     <name>ncats-molwitch</name>
 

diff --git a/src/main/java/gov/nih/ncats/molwitch/Atom.java b/src/main/java/gov/nih/ncats/molwitch/Atom.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/AtomCoordinates.java b/src/main/java/gov/nih/ncats/molwitch/AtomCoordinates.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/Bond.java b/src/main/java/gov/nih/ncats/molwitch/Bond.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/BondTable.java b/src/main/java/gov/nih/ncats/molwitch/BondTable.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/Chemical.java b/src/main/java/gov/nih/ncats/molwitch/Chemical.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/ChemicalBuilder.java b/src/main/java/gov/nih/ncats/molwitch/ChemicalBuilder.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/ChemicalSource.java b/src/main/java/gov/nih/ncats/molwitch/ChemicalSource.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/Chirality.java b/src/main/java/gov/nih/ncats/molwitch/Chirality.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/DoubleBondStereochemistry.java b/src/main/java/gov/nih/ncats/molwitch/DoubleBondStereochemistry.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/ElementData.java b/src/main/java/gov/nih/ncats/molwitch/ElementData.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/ExtendedTetrahedralChirality.java b/src/main/java/gov/nih/ncats/molwitch/ExtendedTetrahedralChirality.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/FileSource.java b/src/main/java/gov/nih/ncats/molwitch/FileSource.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/GraphInvariant.java b/src/main/java/gov/nih/ncats/molwitch/GraphInvariant.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/ImplUtil.java b/src/main/java/gov/nih/ncats/molwitch/ImplUtil.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/MolWitch.java b/src/main/java/gov/nih/ncats/molwitch/MolWitch.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/MolwitchException.java b/src/main/java/gov/nih/ncats/molwitch/MolwitchException.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/PathVisitor.java b/src/main/java/gov/nih/ncats/molwitch/PathVisitor.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/SGroup.java b/src/main/java/gov/nih/ncats/molwitch/SGroup.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/SmartsSource.java b/src/main/java/gov/nih/ncats/molwitch/SmartsSource.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/SmilesSource.java b/src/main/java/gov/nih/ncats/molwitch/SmilesSource.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/Stereocenter.java b/src/main/java/gov/nih/ncats/molwitch/Stereocenter.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/TetrahedralChirality.java b/src/main/java/gov/nih/ncats/molwitch/TetrahedralChirality.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/datastores/ChemicalDataStore.java b/src/main/java/gov/nih/ncats/molwitch/datastores/ChemicalDataStore.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/datastores/FileChemicalDataStore.java b/src/main/java/gov/nih/ncats/molwitch/datastores/FileChemicalDataStore.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/datastores/SimpleChemicalDataStore.java b/src/main/java/gov/nih/ncats/molwitch/datastores/SimpleChemicalDataStore.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/fingerprint/Fingerprint.java b/src/main/java/gov/nih/ncats/molwitch/fingerprint/Fingerprint.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/fingerprint/Fingerprinter.java b/src/main/java/gov/nih/ncats/molwitch/fingerprint/Fingerprinter.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/fingerprint/Fingerprinters.java b/src/main/java/gov/nih/ncats/molwitch/fingerprint/Fingerprinters.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/fingerprint/package-info.java b/src/main/java/gov/nih/ncats/molwitch/fingerprint/package-info.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKey.java b/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKey.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKeyBag.java b/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKeyBag.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKeyUtil.java b/src/main/java/gov/nih/ncats/molwitch/inchi/BinaryInchiKeyUtil.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/DefaultInchiKeyBag.java b/src/main/java/gov/nih/ncats/molwitch/inchi/DefaultInchiKeyBag.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/InChiResult.java b/src/main/java/gov/nih/ncats/molwitch/inchi/InChiResult.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/Inchi.java b/src/main/java/gov/nih/ncats/molwitch/inchi/Inchi.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.
@@ -163,13 +163,13 @@ public static Chemical toChemical(String inchi) throws IOException{
 		}
 		Throwable throwable = null;
 		for(InchiImplFactory impl : implLoaders.get()) {
-
 			try {
 				Chemical result = impl.parseInchi(input);
 				if (result != null) {
 					return result;
 				}
 			}catch(Throwable t){
+				System.err.printf("Error running impl: %s\n", t.getMessage());
 				throwable = t;
 			}
 		}

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/InchiKey.java b/src/main/java/gov/nih/ncats/molwitch/inchi/InchiKey.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/InchiKeyBag.java b/src/main/java/gov/nih/ncats/molwitch/inchi/InchiKeyBag.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/inchi/InchiUtil.java b/src/main/java/gov/nih/ncats/molwitch/inchi/InchiUtil.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.

diff --git a/src/main/java/gov/nih/ncats/molwitch/internal/InternalUtil.java b/src/main/java/gov/nih/ncats/molwitch/internal/InternalUtil.java
@@ -1,7 +1,7 @@
 /*
  * NCATS-MOLWITCH
  *
- * Copyright 2023 NIH/NCATS
+ * Copyright 2024 NIH/NCATS
  *
  *    Licensed under the Apache License, Version 2.0 (the "License");
  *    you may not use this file except in compliance with the License.