feat: templates and sampler testing/fixing

data/kg/chembl33_preprocessed_filtered_bioactivity_dataset_w_fullprotnames_smiles/meta.yaml

@@ -77,10 +77,10 @@ templates:
     Protein{# name|!}: {protein_name#}
     {#Molecule |!}{SMILES__description}: {SMILES#}
     Constraint{#s|!}: The {#resulting|derived|calculated!} {standard_type#} {#value |!}should be in {standard_units#}. Even if you are {#uncertain|not sure!}, you must {#derive|estimate|come up with!} a {standard_type#} {#value |!}without using any {#other|additional!} words.
-    Result:<EOI> {standard_value#} {standard_units#}
+    Result: {standard_value#} {standard_units#}
   - |-
     Task: Please {#create|generate!} a {#molecule |!}{SMILES__description} that has a {#bioaffinity|affinity!} to {#the protein |!}{protein_name#} with a {standard_type#} {#value |!}of {standard_value#} {standard_units#}.
-    Result:<EOI> {SMILES#}
+    Result: {SMILES#}
   - |-
     Task: Please answer the multiple choice question.
     Question: What is the {#the bioaffinity|the affinity!} of a {#molecule to a protein|protein to a molecule!}?
@@ -98,4 +98,4 @@ templates:
     Constraint: The {#shown|listed!} {standard_type#} values {#below |!}are in {standard_units#}. Even if you are {#uncertain|not sure!}, you must pick either {%multiple_choice_enum%3-5%aA1} without using any other words.
     Options:
     {standard_value%}
-    Answer:<EOI> {%multiple_choice_result}
+    Answer: {%multiple_choice_result}

data/kg/compound_chebi/meta.yaml

@@ -61,4 +61,4 @@ templates:
     Result: {SMILES#}
   - |-
     Task: Please {#create|generate!} {#a compound |a !}{SMILES__description} that {rel1_type#} {node2_name#}.
-    Result:<EOI> {SMILES#}
+    Result: {SMILES#}

data/tabular/MUV_466/meta.yaml

@@ -31,3 +31,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-466#not &NULL}{MUV-466__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-466#not &NULL}{MUV-466__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-466__names__noun}?
+    Answer: {MUV-466#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-466__names__noun}.
+    Result: {MUV-466#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-466#not &NULL}{MUV-466__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_548/meta.yaml

@@ -33,3 +33,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-548#not &NULL}{MUV-548__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-548#not &NULL}{MUV-548__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-548__names__noun}?
+    Answer: {MUV-548#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-548__names__noun}.
+    Result: {MUV-548#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-548#not &NULL}{MUV-548__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_600/meta.yaml

@@ -32,3 +32,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-600#not &NULL}{MUV-600__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-600#not &NULL}{MUV-600__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-600__names__noun}?
+    Answer: {MUV-600#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-600__names__noun}.
+    Result: {MUV-600#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-600#not &NULL}{MUV-600__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_644/meta.yaml

@@ -32,3 +32,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-644#not &NULL}{MUV-644__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-644#not &NULL}{MUV-644__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-644__names__noun}?
+    Answer: {MUV-644#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-644__names__noun}.
+    Result: {MUV-644#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-644#not &NULL}{MUV-644__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_652/meta.yaml

@@ -31,3 +31,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-652#not &NULL}{MUV-652__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-652#not &NULL}{MUV-652__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-652__names__noun}?
+    Answer: {MUV-652#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-652__names__noun}.
+    Result: {MUV-652#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-652#not &NULL}{MUV-652__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_689/meta.yaml

@@ -31,3 +31,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-689#not &NULL}{MUV-689__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-689#not &NULL}{MUV-689__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-689__names__noun}?
+    Answer: {MUV-689#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-689__names__noun}.
+    Result: {MUV-689#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-689#not &NULL}{MUV-689__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_692/meta.yaml

@@ -32,3 +32,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-692#not &NULL}{MUV-692__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-692#not &NULL}{MUV-692__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-692__names__noun}?
+    Answer: {MUV-692#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-692__names__noun}.
+    Result: {MUV-692#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-692#not &NULL}{MUV-692__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_712/meta.yaml

@@ -32,3 +32,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-712#not &NULL}{MUV-712__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-712#not &NULL}{MUV-712__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-712__names__noun}?
+    Answer: {MUV-712#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-712__names__noun}.
+    Result: {MUV-712#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-712#not &NULL}{MUV-712__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_713/meta.yaml

@@ -32,3 +32,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-713#not &NULL}{MUV-713__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-713#not &NULL}{MUV-713__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-713__names__noun}?
+    Answer: {MUV-713#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-713__names__noun}.
+    Result: {MUV-713#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-713#not &NULL}{MUV-713__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_733/meta.yaml

@@ -31,3 +31,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-733#not &NULL}{MUV-733__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-733#not &NULL}{MUV-733__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-733__names__noun}?
+    Answer: {MUV-733#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-733__names__noun}.
+    Result: {MUV-733#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-733#not &NULL}{MUV-733__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_737/meta.yaml

@@ -32,3 +32,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-737#not &NULL}{MUV-737__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-737#not &NULL}{MUV-737__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-737__names__noun}?
+    Answer: {MUV-737#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-737__names__noun}.
+    Result: {MUV-737#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-737#not &NULL}{MUV-737__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_810/meta.yaml

@@ -32,3 +32,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-810#not &NULL}{MUV-810__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-810#not &NULL}{MUV-810__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-810__names__noun}?
+    Answer: {MUV-810#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-810__names__noun}.
+    Result: {MUV-810#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-810#not &NULL}{MUV-810__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_832/meta.yaml

@@ -31,3 +31,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-832#not &NULL}{MUV-832__names__noun}.
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-832#not &NULL}{MUV-832__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-832__names__noun}?
+    Answer: {MUV-832#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-832__names__noun}.
+    Result: {MUV-832#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-832#not &NULL}{MUV-832__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_846/meta.yaml

@@ -33,17 +33,13 @@ templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-846#not &NULL}{MUV-846__names__noun}.
   - |-
     Question: Is the {SMILES__description} {SMILES#} {MUV-846__names__noun}?
-
-    Answer:<EOI>{MUV-846#no&yes}
+    Answer:{MUV-846#no&yes}
   - |-
     Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-846__names__noun}.
-
-    Result:<EOI>{MUV-846#no&yes}
+    Result: {MUV-846#no&yes}
   - |-
     Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-846#not &NULL}{MUV-846__names__noun} and report its {SMILES__description}.
-
-    Result:<EOI>{SMILES#}
+    Result: {SMILES#}
   - |-
     {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-846#not &NULL}{MUV-846__names__noun} and report its {SMILES__description}.
-
     Result: {SMILES#}

data/tabular/MUV_852/meta.yaml

@@ -31,3 +31,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-852#not &NULL}{MUV-852__names__noun}.
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-852__names__noun}?
+    Answer:{MUV-852#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-852__names__noun}.
+    Result: {MUV-852#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-852#not &NULL}{MUV-852__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-852#not &NULL}{MUV-852__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_858/meta.yaml

@@ -32,3 +32,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-858#not &NULL}{MUV-858__names__noun}.
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-858__names__noun}?
+    Answer:{MUV-858#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-858__names__noun}.
+    Result: {MUV-858#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-858#not &NULL}{MUV-858__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-858#not &NULL}{MUV-858__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/MUV_859/meta.yaml

@@ -32,3 +32,15 @@ bibtex:
     URL = {https://doi.org/10.1021/ci8002649}}
 templates:
   - The {#molecule|compound|chemical|molecular species|chemical compound!} with the {SMILES__description} {#representation of |!}{SMILES#} is {MUV-859#not &NULL}{MUV-859__names__noun}.
+  - |-
+    Question: Is the {SMILES__description} {SMILES#} {MUV-859__names__noun}?
+    Answer:{MUV-859#no&yes}
+  - |-
+    Task: Please {#determine|predict|estimate!} if the {#molecule|compound!} with the {SMILES__description} {SMILES#} is {MUV-859__names__noun}.
+    Result: {MUV-859#no&yes}
+  - |-
+    Task: Please {#create|generate!} a {#molecule|compound!} that is {MUV-859#not &NULL}{MUV-859__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}
+  - |-
+    {#Create|Generate|Propose|Suggest|Design|Invent!} a {#molecule|compound!} that is {MUV-859#not &NULL}{MUV-859__names__noun} and report its {SMILES__description}.
+    Result: {SMILES#}

data/tabular/RedDB/transform.py

@@ -280,8 +280,8 @@ def str_presenter(dumper, data):
         str, str_presenter
     )  # to use with safe_dum
     fn_meta = "meta.yaml"
-    with open(fn_meta, "w") as f:
-        yaml.dump(meta, f, sort_keys=False)
+    #with open(fn_meta, "w") as f:
+        #yaml.dump(meta, f, sort_keys=False)
 
     print(f"Finished processing {meta['name']} dataset!")
 

data/tabular/SIDER/transform.py

@@ -138,8 +138,8 @@ def str_presenter(dumper, data):
         str, str_presenter
     )  # to use with safe_dum
     fn_meta = "meta.yaml"
-    with open(fn_meta, "w") as f:
-        yaml.dump(meta, f, sort_keys=False)
+    #with open(fn_meta, "w") as f:
+        #yaml.dump(meta, f, sort_keys=False)
 
     print(f"Finished processing {meta['name']} dataset!")