Publication release

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+extend-ignore = E501

.gitignore

@@ -127,3 +127,10 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# vscode settings
+/.vscode
+
+# Ignore figures and tables
+/figures/svg/*
+/figures/tables/*

bin/rbt-canonicalize.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+import click
+from rxn_biocatalysis_tools import EnzymaticReaction, tokenize_smiles
+
+
+@click.command()
+@click.argument("input_file", type=click.Path(exists=True))
+@click.argument("output_file", type=click.Path())
+@click.option("--pipe", is_flag=True)
+def main(input_file: str, output_file: str, pipe: bool):
+    pipe_char = ""
+    if pipe:
+        pipe_char = " |"
+
+    smiles = []
+    with open(input_file, "r") as f:
+        for line in f:
+            smiles.append(line.strip())
+
+    with open(output_file, "w+") as f:
+        for original_smiles in smiles:
+            # In case of a predicted source which includes the EC number (always starting with "[v")
+            # we need to take care of this
+            smiles_part = original_smiles.replace(" ", "")
+            ec_part = ""
+
+            # Writing non-sense items that occur in the backward prediction as is
+            try:
+                ec_index = smiles_part.find("[v")
+                if ec_index > -1:
+                    ec_part = f" {smiles_part[ec_index:].strip()}".replace("][", "] [")
+                    smiles_part = smiles_part[:ec_index].strip()
+
+                # Using the EnzymaticReaction class here to get canonicalisation + ordering
+                # ">>" is needed for it to be recoganised as a valid rxn smiles / smarts
+                rxn = EnzymaticReaction(smiles_part + ">>")
+                rxn.sort()
+                sorted_canonicalised_smiles = ".".join(rxn.get_reactants_as_smiles())
+                f.write(
+                    f"{tokenize_smiles(sorted_canonicalised_smiles)}{pipe_char}{ec_part}\n"
+                )
+            except:
+                f.write(f"{original_smiles}\n")
+
+
+if __name__ == "__main__":
+    main()