Update examples and README

Author: ben-clancy

README.md

@@ -1,20 +1,23 @@
 # MONSTROUS
 
+MOlecular traNSporT inhibitoR and substrate predictOr Utility Server (MONSTROUS) is a computational transporter profiler that predicts the potential of a chemical to interact with transporters recommended for testing in drug development by regulatory agencies. Currently, these transporters are considered to be a major player in determining the safety and efficacy of drugs. MONSTROUS utilizes either graph convolutional neural networks or similarity-based cheminformatics approaches to screen query chemicals against 12 transporters widely expressed in various tissues, including liver, brain, and kidney, and makes predictions as to their potential to be inhibitors as well as substrates.
+
 ##### Supporting information for paper:
 Title: 
 Authors: 
 Journal: 
 ### Intro
-This repository contains the data and models used to make MONSTROUS's predictions and has sorted this data into 3 sections:
+This repository contains the data and models used to make MONSTROUS's predictions and has sorted this data into 4 sections:
 - A GCNN folder containing the data for our GCNN transporters. This data includes csv files containing lists of compounds for each GCNN transporter as well as their GCNN models.
 - A Similarity Approach folder containing the data for our non-GCNN transporters. This data includes csv files containing lists of compounds for each transporter.
 - A python folder containing the code that will run the MONSTROUS command line tool.
+- An examples folder containing an example input as well as output files for each output format the tool supports.
 
 ### GCNN
-The GCNN folder contains two subfolders: compounds and models. In the compounds folder are CSV files for each transporter, containing a list of compounds that are _____ for the given transporter. These compounds are used in generating the applicability domain for that transporter. In the models folder we hold the models for each GCNN transporter. These models are used to generate the values for GCNN transporters
+The GCNN folder contains two subfolders: compounds and models. In the compounds folder are CSV files for each transport protein, containing a list of reference compounds that are known inhibitors or substrates for the given transporter. These compounds are used in generating the applicability domain for that transporter. In the models folder we hold the models for each GCNN transporter. These models are used to generate the values for GCNN transporters
 
 ### Similarity Approach
-The similarity approach folder contains CSV files for each transporter, containing a list of compounds that are _____ for the given transporter. These compounds are used in generating the applicability domain for that transporter, as well as generating the values for similarity approach transporters
+The similarity approach folder contains CSV files for each transport protein, containing a list of reference compounds that are known inhibitors or substrates for the given transporter. These compounds are used in generating the applicability domain for that transporter, as well as generating the values for similarity approach transporters
 
 ## MONSTROUS Command Line Tool
 
@@ -31,7 +34,7 @@ Next, navigate to this repository's folder and enter the following command to in
 
 ### Running the MONSTROUS command line tool
 
-Once everything is installed, you can then run the script by running `python python/monstrous_clt.py` followed by any of the following tags (and must include the `-i` , input file, tag):
+Once everything is installed, you can then run the script by running `python python/monstrous_clt.py` followed by any of the following tags (and must include the `-i` , input file and tag):
 - `-h` or `--help`: Shows a help message explaining these tags.
 - `-i [INPUT]` or `--input [INPUT]`: The file location of a .CSV file whose first column is 'Name' and whose second is 'SMILES' and contains the list of SMILES to be submitted.
 - `-o [OUTPUT]` or `--output [OUTPUT]`: The output file path

examples/example_csv_output_inhibitor.csv

@@ -1,16 +1,16 @@
 Name,SMILES (original),SMILES (standardized),BCRP_inhibitor,BSEP_inhibitor,MRP1_inhibitor,OATP1B1_inhibitor,OATP1B3_inhibitor,PGP_inhibitor,MATE1_inhibitor,MATE2_inhibitor,OAT1_inhibitor,OAT3_inhibitor,OCT2_inhibitor,MRP2_inhibitor
 Verapamil,COC1=C(OC)C=C(CCN(C)CCCC(C#N)(C(C)C)C2=CC(OC)=C(OC)C=C2)C=C1,COc1ccc(CCN(C)CCCC(C#N)(c2ccc(OC)c(OC)c2)C(C)C)cc1OC,True,False,True,False,False,True,False,False,False,False,False,False
-Lopinavir,CC1=C(C(=CC=C1)C)OCC(=O)NC(CC2=CC=CC=C2)C(CC(CC3=CC=CC=C3)NC(=O)C(C(C)C)N4CCCNC4=O)O,Cc1cccc(C)c1OCC(=O)NC(Cc1ccccc1)C(O)CC(Cc1ccccc1)NC(=O)C(C(C)C)N1CCCNC1=O,False,False,True,True,True,True,False,False,False,False,False,False
+Lopinavir,CC1=C(C(=CC=C1)C)OCC(=O)NC(CC2=CC=CC=C2)C(CC(CC3=CC=CC=C3)NC(=O)C(C(C)C)N4CCCNC4=O)O,Cc1cccc(C)c1OCC(=O)NC(Cc1ccccc1)C(O)CC(Cc1ccccc1)NC(=O)C(C(C)C)N1CCCNC1=O,False,False,True,True,True,True,True,True,False,False,True,False
 Probenecid,CCCN(CCC)S(=O)(=O)C1=CC=C(C=C1)C(=O)O,CCCN(CCC)S(=O)(=O)c1ccc(C(=O)O)cc1,False,False,True,False,False,False,False,False,True,True,False,False
-Saquinavir,CC(C)(C)NC(=O)C1CC2CCCCC2CN1CC(C(CC3=CC=CC=C3)NC(=O)C(CC(=O)N)NC(=O)C4=NC5=CC=CC=C5C=C4)O,CC(C)(C)NC(=O)C1CC2CCCCC2CN1CC(O)C(Cc1ccccc1)NC(=O)C(CC(N)=O)NC(=O)c1ccc2ccccc2n1,False,False,True,False,False,True,False,False,False,False,False,False
+Saquinavir,CC(C)(C)NC(=O)C1CC2CCCCC2CN1CC(C(CC3=CC=CC=C3)NC(=O)C(CC(=O)N)NC(=O)C4=NC5=CC=CC=C5C=C4)O,CC(C)(C)NC(=O)C1CC2CCCCC2CN1CC(O)C(Cc1ccccc1)NC(=O)C(CC(N)=O)NC(=O)c1ccc2ccccc2n1,False,False,True,False,False,True,True,True,False,False,False,False
 Bromosulphophthalein,[O-]S(=O)(=O)c1c(O)ccc(c1)C3(OC(=O)c2c(Br)c(Br)c(Br)c(Br)c23)c4ccc(O)c(c4)S([O-])(=O)=O,O=C1OC(c2ccc(O)c(S(=O)(=O)O)c2)(c2ccc(O)c(S(=O)(=O)O)c2)c2c(Br)c(Br)c(Br)c(Br)c21,True,False,True,True,True,False,False,False,False,False,False,False
 Methotrexate,CN(CC1=CN=C2C(=N1)C(=NC(=N2)N)N)C3=CC=C(C=C3)C(=O)NC(CCC(=O)O)C(=O)O,CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)NC(CCC(=O)O)C(=O)O)cc1,False,False,True,False,False,False,False,False,False,False,False,False
 Furosemide,C1=COC(=C1)CNC2=CC(=C(C=C2C(=O)O)S(=O)(=O)N)Cl,NS(=O)(=O)c1cc(C(=O)O)c(NCc2ccco2)cc1Cl,False,False,True,False,False,False,False,False,False,False,False,False
 Metformin,CN(C)C(=N)N=C(N)N,CN(C)C(=N)N=C(N)N,False,False,True,False,False,False,False,False,False,False,False,False
 Cimetidine,CC1=C(N=CN1)CSCCNC(=NC)NC#N,CN=C(NC#N)NCCSCc1nc[nH]c1C,False,False,True,False,False,False,True,False,False,False,True,False
-Procainamide,CCN(CC)CCNC(=O)C1=CC=C(C=C1)N,CCN(CC)CCNC(=O)c1ccc(N)cc1,False,False,False,False,False,False,False,False,False,False,False,False
+Procainamide,CCN(CC)CCNC(=O)C1=CC=C(C=C1)N,CCN(CC)CCNC(=O)c1ccc(N)cc1,False,False,False,False,False,False,False,False,True,True,False,False
 Oestrone,CC12CCC3C(C1CCC2=O)CCC4=C3C=CC(=C4)O,CC12CCC3c4ccc(O)cc4CCC3C1CCC2=O,False,False,True,False,False,False,True,True,False,False,True,False
-Pravastatin,CCC(C)C(=O)OC1CC(C=C2C1C(C(C=C2)C)CCC(CC(CC(=O)O)O)O)O,CCC(C)C(=O)OC1CC(O)C=C2C=CC(C)C(CCC(O)CC(O)CC(=O)O)C21,False,False,True,True,True,False,False,False,False,True,False,False
+Pravastatin,CCC(C)C(=O)OC1CC(C=C2C1C(C(C=C2)C)CCC(CC(CC(=O)O)O)O)O,CCC(C)C(=O)OC1CC(O)C=C2C=CC(C)C(CCC(O)CC(O)CC(=O)O)C21,False,False,True,True,True,False,False,False,False,True,False,True
 Delaviridine,CC(C)NC1=C(N=CC=C1)N1CCN(CC1)C(=O)C1=CC2=C(N1)C=CC(NS(C)(=O)=O)=C2,CC(C)Nc1cccnc1N1CCN(C(=O)c2cc3cc(NS(C)(=O)=O)ccc3[nH]2)CC1,True,False,True,False,False,True,False,False,False,False,False,False
 Loperamide,CN(C)C(=O)C(CCN1CCC(O)(CC1)C1=CC=C(Cl)C=C1)(C1=CC=CC=C1)C1=CC=CC=C1,CN(C)C(=O)C(CCN1CCC(O)(c2ccc(Cl)cc2)CC1)(c1ccccc1)c1ccccc1,False,False,True,False,False,True,False,False,False,False,False,False
 Rifampicin,CC1C=CC=C(C(=O)NC2=C(C(=C3C(=C2O)C(=C(C4=C3C(=O)C(O4)(OC=CC(C(C(C(C(C(C1O)C)O)C)OC(=O)C)C)OC)C)C)O)O)C=NN5CCN(CC5)C)C,COC1C=COC2(C)Oc3c(C)c(O)c4c(O)c(c(C=NN5CCN(C)CC5)c(O)c4c3C2=O)NC(=O)C(C)=CC=CC(C)C(O)C(C)C(O)C(C)C(OC(C)=O)C1C,False,False,True,False,True,False,False,False,False,False,False,True

examples/example_csv_output_substrate.csv

@@ -1,16 +1,16 @@
 Name,SMILES (original),SMILES (standardized),BCRP_substrate,MRP1_substrate,PGP_substrate,BSEP_substrate,MATE1_substrate,MATE2_substrate,OAT1_substrate,OAT3_substrate,OATP1B1_substrate,OATP1B3_substrate,OCT2_substrate,MRP2_substrate
 Verapamil,COC1=C(OC)C=C(CCN(C)CCCC(C#N)(C(C)C)C2=CC(OC)=C(OC)C=C2)C=C1,COc1ccc(CCN(C)CCCC(C#N)(c2ccc(OC)c(OC)c2)C(C)C)cc1OC,False,True,True,False,False,False,False,False,False,False,False,False
-Lopinavir,CC1=C(C(=CC=C1)C)OCC(=O)NC(CC2=CC=CC=C2)C(CC(CC3=CC=CC=C3)NC(=O)C(C(C)C)N4CCCNC4=O)O,Cc1cccc(C)c1OCC(=O)NC(Cc1ccccc1)C(O)CC(Cc1ccccc1)NC(=O)C(C(C)C)N1CCCNC1=O,False,False,True,False,False,False,False,False,False,False,False,True
-Probenecid,CCCN(CCC)S(=O)(=O)C1=CC=C(C=C1)C(=O)O,CCCN(CCC)S(=O)(=O)c1ccc(C(=O)O)cc1,True,False,False,False,False,False,False,False,False,False,False,True
+Lopinavir,CC1=C(C(=CC=C1)C)OCC(=O)NC(CC2=CC=CC=C2)C(CC(CC3=CC=CC=C3)NC(=O)C(C(C)C)N4CCCNC4=O)O,Cc1cccc(C)c1OCC(=O)NC(Cc1ccccc1)C(O)CC(Cc1ccccc1)NC(=O)C(C(C)C)N1CCCNC1=O,False,False,True,True,False,False,False,False,False,False,False,True
+Probenecid,CCCN(CCC)S(=O)(=O)C1=CC=C(C=C1)C(=O)O,CCCN(CCC)S(=O)(=O)c1ccc(C(=O)O)cc1,True,False,False,False,True,True,False,True,False,False,False,True
 Saquinavir,CC(C)(C)NC(=O)C1CC2CCCCC2CN1CC(C(CC3=CC=CC=C3)NC(=O)C(CC(=O)N)NC(=O)C4=NC5=CC=CC=C5C=C4)O,CC(C)(C)NC(=O)C1CC2CCCCC2CN1CC(O)C(Cc1ccccc1)NC(=O)C(CC(N)=O)NC(=O)c1ccc2ccccc2n1,False,False,True,True,False,False,False,False,False,True,False,True
 Bromosulphophthalein,[O-]S(=O)(=O)c1c(O)ccc(c1)C3(OC(=O)c2c(Br)c(Br)c(Br)c(Br)c23)c4ccc(O)c(c4)S([O-])(=O)=O,O=C1OC(c2ccc(O)c(S(=O)(=O)O)c2)(c2ccc(O)c(S(=O)(=O)O)c2)c2c(Br)c(Br)c(Br)c(Br)c21,True,True,False,False,False,False,False,False,True,True,False,True
 Methotrexate,CN(CC1=CN=C2C(=N1)C(=NC(=N2)N)N)C3=CC=C(C=C3)C(=O)NC(CCC(=O)O)C(=O)O,CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)NC(CCC(=O)O)C(=O)O)cc1,True,False,False,False,False,False,False,True,False,False,False,True
-Furosemide,C1=COC(=C1)CNC2=CC(=C(C=C2C(=O)O)S(=O)(=O)N)Cl,NS(=O)(=O)c1cc(C(=O)O)c(NCc2ccco2)cc1Cl,True,False,False,False,False,False,False,False,False,False,False,False
-Metformin,CN(C)C(=N)N=C(N)N,CN(C)C(=N)N=C(N)N,True,True,False,False,False,False,False,False,False,False,False,False
+Furosemide,C1=COC(=C1)CNC2=CC(=C(C=C2C(=O)O)S(=O)(=O)N)Cl,NS(=O)(=O)c1cc(C(=O)O)c(NCc2ccco2)cc1Cl,True,False,False,False,False,False,False,True,False,False,False,False
+Metformin,CN(C)C(=N)N=C(N)N,CN(C)C(=N)N=C(N)N,True,True,False,False,True,True,False,False,False,False,True,False
 Cimetidine,CC1=C(N=CN1)CSCCNC(=NC)NC#N,CN=C(NC#N)NCCSCc1nc[nH]c1C,True,False,False,False,True,True,True,True,False,False,True,False
-Procainamide,CCN(CC)CCNC(=O)C1=CC=C(C=C1)N,CCN(CC)CCNC(=O)c1ccc(N)cc1,False,False,True,False,True,True,False,False,False,False,False,False
-Oestrone,CC12CCC3C(C1CCC2=O)CCC4=C3C=CC(=C4)O,CC12CCC3c4ccc(O)cc4CCC3C1CCC2=O,True,False,False,False,True,True,False,True,True,False,False,True
-Pravastatin,CCC(C)C(=O)OC1CC(C=C2C1C(C(C=C2)C)CCC(CC(CC(=O)O)O)O)O,CCC(C)C(=O)OC1CC(O)C=C2C=CC(C)C(CCC(O)CC(O)CC(=O)O)C21,True,True,False,True,False,False,False,True,False,True,False,True
+Procainamide,CCN(CC)CCNC(=O)C1=CC=C(C=C1)N,CCN(CC)CCNC(=O)c1ccc(N)cc1,False,False,True,False,True,True,True,True,False,False,False,True
+Oestrone,CC12CCC3C(C1CCC2=O)CCC4=C3C=CC(=C4)O,CC12CCC3c4ccc(O)cc4CCC3C1CCC2=O,True,False,False,True,True,True,False,True,True,False,False,True
+Pravastatin,CCC(C)C(=O)OC1CC(C=C2C1C(C(C=C2)C)CCC(CC(CC(=O)O)O)O)O,CCC(C)C(=O)OC1CC(O)C=C2C=CC(C)C(CCC(O)CC(O)CC(=O)O)C21,True,True,False,True,False,False,False,True,True,True,False,True
 Delaviridine,CC(C)NC1=C(N=CC=C1)N1CCN(CC1)C(=O)C1=CC2=C(N1)C=CC(NS(C)(=O)=O)=C2,CC(C)Nc1cccnc1N1CCN(C(=O)c2cc3cc(NS(C)(=O)=O)ccc3[nH]2)CC1,True,False,True,False,False,False,False,False,False,False,False,False
-Loperamide,CN(C)C(=O)C(CCN1CCC(O)(CC1)C1=CC=C(Cl)C=C1)(C1=CC=CC=C1)C1=CC=CC=C1,CN(C)C(=O)C(CCN1CCC(O)(c2ccc(Cl)cc2)CC1)(c1ccccc1)c1ccccc1,False,False,True,False,False,False,False,False,False,False,False,False
+Loperamide,CN(C)C(=O)C(CCN1CCC(O)(CC1)C1=CC=C(Cl)C=C1)(C1=CC=CC=C1)C1=CC=CC=C1,CN(C)C(=O)C(CCN1CCC(O)(c2ccc(Cl)cc2)CC1)(c1ccccc1)c1ccccc1,False,False,True,False,False,False,False,True,True,False,False,False
 Rifampicin,CC1C=CC=C(C(=O)NC2=C(C(=C3C(=C2O)C(=C(C4=C3C(=O)C(O4)(OC=CC(C(C(C(C(C(C1O)C)O)C)OC(=O)C)C)OC)C)C)O)O)C=NN5CCN(CC5)C)C,COC1C=COC2(C)Oc3c(C)c(O)c4c(O)c(c(C=NN5CCN(C)CC5)c(O)c4c3C2=O)NC(=O)C(C)=CC=CC(C)C(O)C(C)C(O)C(C)C(OC(C)=O)C1C,True,True,True,False,False,False,False,False,True,True,False,True