adapted snake_case in doc and ipynbs

rinikerlab · Apr 4, 2024 · 44483ee · 44483ee
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commit 44483ee
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Showing 4 changed files with 11 additions and 11 deletions.
diff --git a/demos/02_computational_experiment_1.ipynb b/demos/02_computational_experiment_1.ipynb
@@ -314,7 +314,7 @@
    ],
    "source": [
     "# now bulk register. We want to also collect IDs of compounds which were already registered.\n",
-    "reg_ids = lwreg.bulk_register(mols=ms,failOnDuplicate=False)\n",
+    "reg_ids = lwreg.bulk_register(mols=ms,fail_on_duplicate=False)\n",
     "reg_ids = set(reg_ids)\n",
     "print(f'Registered {len(reg_ids)} unique compounds.')"
    ]

diff --git a/demos/03_computational_experiment_2.ipynb b/demos/03_computational_experiment_2.ipynb
@@ -380,7 +380,7 @@
    ],
    "source": [
     "# now bulk register. We want to also collect IDs of compounds which were already registered.\n",
-    "reg_ids = lwreg.bulk_register(mols=ms_3d,failOnDuplicate=False)\n",
+    "reg_ids = lwreg.bulk_register(mols=ms_3d,fail_on_duplicate=False)\n",
     "print(f'Registered {len(reg_ids)} unique conformers.')"
    ]
   },

diff --git a/lwreg/utils.py b/lwreg/utils.py
@@ -395,7 +395,7 @@ def _register_one_conformer(mrn,
                             cn,
                             curs,
                             config,
-                            failOnDuplicate,
+                            fail_on_duplicate,
                             confId=-1):
     try:
         chash = _get_conformer_hash(sMol,
@@ -422,7 +422,7 @@ def _register_one_conformer(mrn,
         cn.commit()
     except _violations:
         cn.rollback()
-        if failOnDuplicate:
+        if fail_on_duplicate:
             raise
         else:
             curs.execute(
@@ -636,7 +636,7 @@ def register(config=None,
     molblock   -- MOL or SDF block
     smiles     -- smiles
     escape     -- the escape layer
-    failOnDuplicate -- if true then an exception is raised when trying to register a duplicate
+    fail_on_duplicate -- if true then an exception is raised when trying to register a duplicate
     confId     -- the conformer ID to use when in registerConformers mode
     no_verbose -- if this is False then the registry number will be printed
     """
@@ -688,7 +688,7 @@ def register_multiple_conformers(config=None,
     config     -- configuration dict
     mol        -- RDKit molecule object (must have at least one conformer)
     escape     -- the escape layer
-    failOnDuplicate -- if true then an exception is raised when trying to register a duplicate
+    fail_on_duplicate -- if true then an exception is raised when trying to register a duplicate
     no_verbose -- if this is False then the registry number will be printed
     """
     if not config:
@@ -774,7 +774,7 @@ def bulk_register(config=None,
     The result tuple includes a single entry for each molecule in the input.
     That entry can be one of the following:
       - the registry number (molregno) of the registered molecule
-      - RegistrationFailureReasons.DUPLICATE if failOnDuplicate is True and a
+      - RegistrationFailureReasons.DUPLICATE if fail_on_duplicate is True and a
         molecule is a duplicate
       - RegistrationFalureReasons.PARSE_FAILURE if there was a problem processing
         the molecule 
@@ -785,8 +785,8 @@ def bulk_register(config=None,
     config         -- configuration dict
     mols           -- an iterable of RDKit molecule objects
     sdfile         -- SDF filename
-    escapeProperty -- the molecule property to use as the escape layer
-    failOnDuplicate -- if true then RegistraionFailureReasons.DUPLICATE will be returned 
+    escape_property -- the molecule property to use as the escape layer
+    fail_on_duplicate -- if true then RegistraionFailureReasons.DUPLICATE will be returned 
                        for each already-registered molecule, otherwise the already existing
                        structure ID will be returned
     no_verbose     -- if this is False then the registry numbers will be printed

diff --git a/tutorial/Machine learning experiment.ipynb b/tutorial/Machine learning experiment.ipynb
@@ -340,7 +340,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mrns = lwreg.bulk_register(mols=df.mol.to_list(),failOnDuplicate=False)"
+    "mrns = lwreg.bulk_register(mols=df.mol.to_list(),fail_on_duplicate=False)"
    ]
   },
   {
@@ -390,7 +390,7 @@
     "simpd_name = 'CHEMBL217-1'\n",
     "ds = catalog[simpd_name]\n",
     "df = ds.read()\n",
-    "mrns = lwreg.bulk_register(mols=df.mol.to_list(),failOnDuplicate=False)\n",
+    "mrns = lwreg.bulk_register(mols=df.mol.to_list(),fail_on_duplicate=False)\n",
     "chembl_target = ds.metadata[\"url\"].split(\"/\")[-2]\n",
     "ds_uid = str(uuid.uuid4())\n",
     "cn = utils.connect(config=config)\n",