Fix dependencies and code

Dockerfile

@@ -1,11 +1,12 @@
-FROM bentoml/model-server:0.11.0-py37
+FROM bentoml/model-server:0.11.0-py38
 MAINTAINER ersilia
 
 RUN pip install rdkit==2023.3.2 
 RUN pip install mordred==1.2
 RUN pip install timeout-decorator==0.5.0
 RUN pip install pandas==1.3.5
-RUN conda install -c conda-forge xorg-libxrender xorg-libxtst
+RUN pip install numpy==1.19.5
+RUN pip install networkx==2.0.0
 
 WORKDIR /repo
 COPY ./repo

model/framework/code/main.py

@@ -34,6 +34,9 @@ def one_molecule(mol):
         r = [None for _ in range(len(columns))]
     R += [r]
 
-df = pd.DataFrame(R, columns=columns)
-
+# We read as float dtype because mordred gives us errors for many of the MAX... type descriptors
+# Refer to https://github.com/mordred-descriptor/mordred/issues/68
+df = pd.DataFrame(R, columns=columns, dtype=float)
+# Then we fill those empty columns with 0.0
+df.fillna(0.0, inplace=True)
 df.to_csv(outfile, index=False)

model/framework/examples/input.csv

@@ -0,0 +1,4 @@
+smiles
+CC(C)CC1=CC=C(C=C1)C(C)C(=O)O
+CC1(OC2C(OC(C2O1)(C#N)C3=CC=C4N3N=CN=C4N)CO)C
+COC1=CC23CCCN2CCC4=CC5=C(C=C4C3C1O)OCO5