bumped selfies to v2 (#69)

ur-whitelab · Jan 21, 2022 · 05f204c · 05f204c
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Showing 6 changed files with 18 additions and 11 deletions.
diff --git a/README.md b/README.md
@@ -91,8 +91,8 @@ one of the following:
 * `'narrow'`: Only one change to molecular structure, reduced set of possible bonds/elements
 * `'medium'`: Default. One or two changes to molecular structure, reduced set of possible bonds/elements
 * `'wide'`: One through five changes to molecular structure, large set of possible bonds/elements
-* `'chemed'`: A restrictive set where only pubchem molecules are considered. *Experimental*
-* `'custom'`: A restrictive set where only molecules provided by the "data" key are considered. *Experimental*
+* `'chemed'`: A restrictive set where only pubchem molecules are considered.
+* `'custom'`: A restrictive set where only molecules provided by the "data" key are considered.
 
 You can also pass `num_samples` as a "request" for number of samples. You will typically end up with less due to
 degenerate molecules. See API for complete description.

diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst
@@ -1,6 +1,13 @@
 Change Log
 ==========
 
+v1.0.0 (2022-1-21)
+-------------------
+* Switched to SELFIES v2.0 release, which has a different token list
+* Removed "experimental" tag from Chemed and Custom methods
+* Type annotations now pass ``mypy``
+* Paper models now generate SVGs correctly and fixed token issues
+
 v0.6.0 (2022-1-17)
 -------------------
 * Changed behavior of num_samples so that it is not affected by mutation count in STONED

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -18,7 +18,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "exmol"
-copyright = "2021, Geemi Wellawatte, Andrew D White"
+copyright = "2022, Geemi Wellawatte, Andrew D White"
 author = "Geemi Wellawatte, Andrew D White"
 
 

diff --git a/exmol/exmol.py b/exmol/exmol.py
@@ -51,7 +51,7 @@ def get_basic_alphabet() -> Set[str]:
     to_remove.extend(["[P]", "[#P]", "[=P]"])
 
     a -= set(to_remove)
-    a.add("[O-1expl]")
+    a.add("[O-1]")
     return a
 
 
@@ -149,9 +149,9 @@ def run_chemed(
     :return: SMILES and SCORES
     """
     if _pbar:
-        _pbar.set_description("⚡CHEMED⚡ is Experimental ☠️")
+        _pbar.set_description("⚡CHEMED⚡")
     else:
-        print("⚡CHEMED⚡ is Experimental ☠️")
+        print("⚡CHEMED⚡")
     url = f"https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/smiles/{requests.utils.quote(origin_smiles)}/property/CanonicalSMILES/JSON"
     try:
         reply = requests.get(
@@ -204,9 +204,9 @@ def run_custom(
     :return: SMILES and SCORES
     """
     if _pbar:
-        _pbar.set_description("⚡CUSTOM⚡ is Experimental ☠️")
+        _pbar.set_description("⚡CUSTOM⚡")
     else:
-        print("⚡CUSTOM⚡ is Experimental ☠️")
+        print("⚡CUSTOM⚡")
     mol0 = smi2mol(origin_smiles)
     fp0 = stoned.get_fingerprint(mol0, fp_type)
     scores = []
@@ -246,7 +246,7 @@ def sample_space(
     :param origin_smiles: starting SMILES
     :param f: A function which takes in SMILES and SELFIES and returns predicted value. Assumed to work with lists of SMILES/SELFIES unless `batched = False`
     :param batched: If `f` is batched
-    :param preset: Can be wide, medium, or narrow. Determines how far across chemical space is sampled. Try `"chemed"` experimental preset to only sample commerically available compounds.
+    :param preset: Can be wide, medium, or narrow. Determines how far across chemical space is sampled. Try `"chemed"` preset to only sample commerically available compounds.
     :param data: If not None and preset is `"custom"` will use this data instead of generating new ones.
     :param method_kwargs: More control over STONED, CHEMED and CUSTOM can be set here. See :func:`run_stoned`, :func:`run_chemed` and  :func:`run_custom`
     :param num_samples: Number of desired samples. Can be set in `method_kwargs` (overrides) or here. `None` means default for preset

diff --git a/exmol/version.py b/exmol/version.py
@@ -1 +1 @@
-__version__ = "0.6.0"
+__version__ = "1.0.0"
diff --git a/setup.py b/setup.py
@@ -17,7 +17,7 @@
     license="MIT",
     packages=["exmol", "exmol.stoned"],
     install_requires=[
-        "selfies == 1.0.4",
+        "selfies >= 2.0.0",
         "numpy",
         "requests",
         "tqdm",