diff --git a/.idea/.gitignore b/.idea/.gitignore
new file mode 100644
index 0000000..26d3352
--- /dev/null
+++ b/.idea/.gitignore
@@ -0,0 +1,3 @@
+# Default ignored files
+/shelf/
+/workspace.xml
diff --git a/.idea/.name b/.idea/.name
new file mode 100644
index 0000000..11a5d8e
--- /dev/null
+++ b/.idea/.name
@@ -0,0 +1 @@
+main.py
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
new file mode 100644
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--- /dev/null
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\ No newline at end of file
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diff --git a/.idea/modules.xml b/.idea/modules.xml
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diff --git a/.idea/plas_app.iml b/.idea/plas_app.iml
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diff --git a/.streamlit/config.toml b/.streamlit/config.toml
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--- /dev/null
+++ b/.streamlit/config.toml
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+[theme]
+
+# Primary accent for interactive elements
+primaryColor = '#E694FF'
+
+# Background color for the main content area
+backgroundColor = '#00172B'
+
+# Background color for sidebar and most interactive widgets
+secondaryBackgroundColor = '#FFFFFF'
+
+# Color used for almost all text
+textColor = '#FFFFFF'
+
+# Font family for all text in the app, except code blocks
+# Accepted values (serif | sans serif | monospace)
+# Default: "sans serif"
+font = "sans serif"
diff --git a/PaDEL-Descriptor/.DS_Store b/PaDEL-Descriptor/.DS_Store
new file mode 100644
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diff --git a/PaDEL-Descriptor/AtomPairs2DFingerprintCount.xml b/PaDEL-Descriptor/AtomPairs2DFingerprintCount.xml
new file mode 100755
index 0000000..afe9ff1
--- /dev/null
+++ b/PaDEL-Descriptor/AtomPairs2DFingerprintCount.xml
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diff --git a/PaDEL-Descriptor/AtomPairs2DFingerprinter.xml b/PaDEL-Descriptor/AtomPairs2DFingerprinter.xml
new file mode 100755
index 0000000..765f1da
--- /dev/null
+++ b/PaDEL-Descriptor/AtomPairs2DFingerprinter.xml
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diff --git a/PaDEL-Descriptor/Descriptors.xls b/PaDEL-Descriptor/Descriptors.xls
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diff --git a/PaDEL-Descriptor/EStateFingerprinter.xml b/PaDEL-Descriptor/EStateFingerprinter.xml
new file mode 100755
index 0000000..49188f1
--- /dev/null
+++ b/PaDEL-Descriptor/EStateFingerprinter.xml
@@ -0,0 +1,86 @@
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diff --git a/PaDEL-Descriptor/ExtendedFingerprinter.xml b/PaDEL-Descriptor/ExtendedFingerprinter.xml
new file mode 100755
index 0000000..2a763e1
--- /dev/null
+++ b/PaDEL-Descriptor/ExtendedFingerprinter.xml
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diff --git a/PaDEL-Descriptor/Fingerprinter.xml b/PaDEL-Descriptor/Fingerprinter.xml
new file mode 100755
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--- /dev/null
+++ b/PaDEL-Descriptor/Fingerprinter.xml
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diff --git a/PaDEL-Descriptor/GraphOnlyFingerprinter.xml b/PaDEL-Descriptor/GraphOnlyFingerprinter.xml
new file mode 100755
index 0000000..bb85baf
--- /dev/null
+++ b/PaDEL-Descriptor/GraphOnlyFingerprinter.xml
@@ -0,0 +1,86 @@
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diff --git a/PaDEL-Descriptor/KlekotaRothFingerprintCount.xml b/PaDEL-Descriptor/KlekotaRothFingerprintCount.xml
new file mode 100755
index 0000000..d3870ea
--- /dev/null
+++ b/PaDEL-Descriptor/KlekotaRothFingerprintCount.xml
@@ -0,0 +1,86 @@
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diff --git a/PaDEL-Descriptor/KlekotaRothFingerprinter.xml b/PaDEL-Descriptor/KlekotaRothFingerprinter.xml
new file mode 100755
index 0000000..443f3a7
--- /dev/null
+++ b/PaDEL-Descriptor/KlekotaRothFingerprinter.xml
@@ -0,0 +1,86 @@
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diff --git a/PaDEL-Descriptor/MACCSFingerprinter.xml b/PaDEL-Descriptor/MACCSFingerprinter.xml
new file mode 100755
index 0000000..69be5e9
--- /dev/null
+++ b/PaDEL-Descriptor/MACCSFingerprinter.xml
@@ -0,0 +1,86 @@
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diff --git a/PaDEL-Descriptor/PaDEL-Descriptor.jar b/PaDEL-Descriptor/PaDEL-Descriptor.jar
new file mode 100755
index 0000000..fe75e22
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diff --git a/PaDEL-Descriptor/PubchemFingerprinter.xml b/PaDEL-Descriptor/PubchemFingerprinter.xml
new file mode 100755
index 0000000..d521f37
--- /dev/null
+++ b/PaDEL-Descriptor/PubchemFingerprinter.xml
@@ -0,0 +1,86 @@
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diff --git a/PaDEL-Descriptor/SubstructureFingerprintCount.xml b/PaDEL-Descriptor/SubstructureFingerprintCount.xml
new file mode 100755
index 0000000..ed52d2f
--- /dev/null
+++ b/PaDEL-Descriptor/SubstructureFingerprintCount.xml
@@ -0,0 +1,86 @@
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diff --git a/PaDEL-Descriptor/SubstructureFingerprinter.xml b/PaDEL-Descriptor/SubstructureFingerprinter.xml
new file mode 100755
index 0000000..681efd6
--- /dev/null
+++ b/PaDEL-Descriptor/SubstructureFingerprinter.xml
@@ -0,0 +1,86 @@
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diff --git a/PaDEL-Descriptor/config b/PaDEL-Descriptor/config
new file mode 100755
index 0000000..18f9bbd
--- /dev/null
+++ b/PaDEL-Descriptor/config
@@ -0,0 +1,20 @@
+#Fri Jul 08 10:37:03 ICT 2016
+MaxThreads=-1
+DescriptorFile=/home/server1/Desktop/Nut/HTS/SMILES/ER_Alpha-SubStructureCount.csv
+Compute3D=false
+TautomerFile=
+ComputeFingerprints=true
+Directory=/home/server1/Desktop/Nut/HTS/SMILES
+MaxCpdPerFile=0
+StandardizeTautomers=true
+StandardizeNitro=true
+RetainOrder=true
+RemoveSalt=true
+MaxJobsWaiting=-1
+MaxRunTime=-1
+UseFilenameAsMolName=false
+Log=true
+DetectAromaticity=true
+Compute2D=false
+Retain3D=false
+Convert3D=No
diff --git a/PaDEL-Descriptor/descriptors.xml b/PaDEL-Descriptor/descriptors.xml
new file mode 100755
index 0000000..550e2c5
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+++ b/PaDEL-Descriptor/descriptors.xml
@@ -0,0 +1,86 @@
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diff --git a/PaDEL-Descriptor/lib/ambit2-base-2.4.7-SNAPSHOT.jar b/PaDEL-Descriptor/lib/ambit2-base-2.4.7-SNAPSHOT.jar
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diff --git a/PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT(1).jar b/PaDEL-Descriptor/lib/ambit2-core-2.4.7-SNAPSHOT(1).jar
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diff --git a/PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(1).jar b/PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(1).jar
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diff --git a/PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(2).jar b/PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(2).jar
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diff --git a/PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(3).jar b/PaDEL-Descriptor/lib/ambit2-smarts-2.4.7-SNAPSHOT(3).jar
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\ No newline at end of file
diff --git a/PaDEL-Descriptor/license/README - CDK b/PaDEL-Descriptor/license/README - CDK
new file mode 100755
index 0000000..8fa17d8
--- /dev/null
+++ b/PaDEL-Descriptor/license/README - CDK
@@ -0,0 +1,117 @@
+CDK The Chemical Development Kit
+
+Copyright 1997-2007 The CDK Development Team
+License: LGPL, see doc/lgpl.license
+
+1. Introduction
+
+You are currently reading the README file for the Chemistry Development Project (CDK).
+This project is hosted under http://cdk.sourceforge.net
+Please refer to these pages for updated information and the latest version of the CDK.
+
+The CDK is an open-source library of algorithms for structural chemo- and bioinformatics, implemented in
+the programming language Java(tm). The library is published under terms of the the
+GNU Lesser General Public License. This has implications on what you can do with sources and
+binaries of the CDK library. For details, please refer to the file LICENSE, which should have been
+provided with this distribution.
+
+PLEASE NOTE: This is a library of useful data structures and algorithms to manipulated them
+from the area of structural chemo- and bioinformatics. As such, it is intended for the use by
+programmers, who wish to save some effort by reusing code. It is not intended for the enduser.
+If you consider yourself to be more like user, you might not find what you wanted.
+Please refer to other projects like the JChemPaint project (http://jchempaint.sourceforge.net)
+or the Jmol project (http://jmol.sourceforge.net) for programs that actually take advantage of the
+CDK library.
+
+2. Compiling
+
+Compiling and jar-ing the software is done with Jakarta's
+Ant (http://jakarta.apache.org/ant/) and requires Java 1.5.0 or better:
+
+cdk/$ ls build.xml
+build.xml
+cdk/$ ant
+
+"ant -p" gives a list of possible compilation targets. The default target is 'dist-all', which
+creates a number of .jar files in the 'dist' directory corresponding to subsets of the CDK
+functionality. For convenience, one large .jar file containing everything can be created using the
+target 'dist-large' (using the command "ant dist-large"). This is also created in dist/jar and is
+typically named something like 'cdk-cvs-20060303.jar'.
+
+2.1 Creating the JavaDoc documentation for the API
+
+The JavaDoc documentation for the API describes all of the CDK classes in detail. It functions as
+the user manual for the CDK, although you should also look at the list of examples and tutorials
+below. This documentation is created by 'ant' from the Java source code for the CDK as follows:
+
+cdk/$ ls javadoc.xml
+javadoc.xml
+cdk/$ ant -buildfile javadoc.xml
+
+The documenation is created as a series of .html pages in doc/api. If you use firefox, you can read
+the documentation using the following command:
+
+cdk/$ firefox doc/api/index.html
+
+3. Running tests
+
+After you compiled the code, you can do "ant test-all" to run the test suite of non-interactive, automated
+tests. You might need to copy an appropriate junit.jar into your $ANT_HOME/lib
+directory or somewhere else in your classpath.
+Upon "ant dist-all test-dist-all test-all", you should see something like:
+
+test:
+Running org.openscience.cdk.test.CDKTests
+Tests run: 1065, Failures: 7, Errors: 1, Time elapsed: 27,55 sec
+
+As you can see, the vast majority of tests ran successfully, but that there
+are failures and errors. The $CDK_HOME/reports/results.txt file contains
+information about the outcome of the tests. Some tests might fail intentionally
+to mark know issues in CDK.
+
+There are also run interactive tests, like the Controller2DTest. In order to try them, you can edit the "run"
+target in the build.xml file to look like this:
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+Then, a "ant run" should give you a window where you can add bonds to a given structure.
+Currently, there are more than 2500 test, of which a large part tests the data, datadebug and
+nonotify classes.
+
+4. Using CDK
+
+CDK is a class library intended to be used by other programs. It will not run
+as a stand-alone program, although it contains some GUI- and command
+line applications. In order to use the CDK in your program, you need to build
+the distribution jars by running "ant dist-all". They will end up in
+$CDK_HOME/dist/jar. Copy all cdk-*.jars as well as all jars from $CDK_HOME/jar
+to the lib directory of the project for which you intend to have CDK support and
+use them as you would use any other third party jar.
+
+Alternatively, run "ant dist-large" to create a jar cdk-svn-YYYYMMDD.jar in
+$CDK_HOME/dist/jar. This large jar contains all the CDK code and all third
+party libraries that code depends on.
+
+5. Examples and tutorials
+
+To get started using the CDK, you may be interested in the following websites which contain
+examples and tutorials:
+* http://www.chemistry-development-kit.org
+* http://blue.chem.psu.edu/~rajarshi/code/java
+* http://www.redbrick.dcu.ie/~noel/CDKJython.html
+
+Further examples can also be found in issues of the CDK News:
+* http://cdknews.org/
+
diff --git a/PaDEL-Descriptor/license/lgpl-2.1.txt b/PaDEL-Descriptor/license/lgpl-2.1.txt
new file mode 100755
index 0000000..4362b49
--- /dev/null
+++ b/PaDEL-Descriptor/license/lgpl-2.1.txt
@@ -0,0 +1,502 @@
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+[This is the first released version of the Lesser GPL. It also counts
+ as the successor of the GNU Library Public License, version 2, hence
+ the version number 2.1.]
+
+ Preamble
+
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diff --git a/PaDEL-Descriptor/license/lgpl.license b/PaDEL-Descriptor/license/lgpl.license
new file mode 100755
index 0000000..25a95e2
--- /dev/null
+++ b/PaDEL-Descriptor/license/lgpl.license
@@ -0,0 +1,504 @@
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diff --git a/lipinsky_model.pkl b/lipinsky_model.pkl
new file mode 100644
index 0000000..46d6590
Binary files /dev/null and b/lipinsky_model.pkl differ
diff --git a/main.py b/main.py
new file mode 100644
index 0000000..afbe66f
--- /dev/null
+++ b/main.py
@@ -0,0 +1,187 @@
+import pandas as pd
+from rdkit import Chem
+from rdkit.Chem import Descriptors
+import pickle
+import streamlit as st
+import subprocess
+import csv
+from pypdb import *
+
+
+@st.cache_data
+def calculate_lipinski_descriptors(smiles):
+ """
+ Calculate Lipinski descriptors for a given SMILES string.
+
+ Parameters:
+ smiles (str): Canonical SMILES string of a compound.
+
+ Returns:
+ pandas.DataFrame: DataFrame containing the calculated Lipinski descriptors.
+ """
+ mol = Chem.MolFromSmiles(smiles)
+ if mol is None:
+ raise ValueError("Invalid SMILES string")
+
+ descriptors = {
+ 'MW': Descriptors.MolWt(mol),
+ 'LogP': Descriptors.MolLogP(mol),
+ 'NumHDonors': Descriptors.NumHDonors(mol),
+ 'NumHAcceptors': Descriptors.NumHAcceptors(mol)
+ }
+
+ return pd.DataFrame(descriptors, index=[0])
+
+
+def generate_csv_file(string1, string2, filename):
+ """
+ Generate a CSV file with a single row containing the concatenated string of string1 and string2.
+
+ Parameters:
+ string1 (str): First string.
+ string2 (str): Second string.
+ filename (str): Name of the output CSV file.
+ """
+ data = [[string1 + '\t' + string2]] # Create a list of lists containing the strings
+
+ with open(filename, 'w', newline='') as file:
+ writer = csv.writer(file)
+ writer.writerows(data)
+
+
+# Set page title and initial layout
+st.set_page_config(page_title="Plasmodium Drug Prediction System", page_icon='🦟', layout="wide")
+
+# Apply custom CSS to modify app appearance
+st.markdown(
+ """
+
+ """,
+ unsafe_allow_html=True
+)
+
+# App title
+st.title("A Plasmodium faliparum Drug Prediction System")
+
+# ---Use local CSS---
+def local_css(file_name):
+ with open(file_name) as f:
+ st.markdown(f"", unsafe_allow_html=True)
+
+
+local_css("style/style.css")
+
+
+# Main function
+def main():
+ """
+ Main function for the Plasmodium faliparum Drug Prediction System web application.
+ """
+ # Text input
+ smiles_input = st.text_input("Enter Canonical SMILES")
+
+ # Selectbox options
+ options = [
+ "Compute Lipinski's Descriptors",
+ "Predict the Compound's Activity",
+ "Predict the Compound's pIC50",
+ "Retrieve interacting proteins"
+ ]
+
+ # Selectbox
+ selected_option = st.selectbox("Select the program to run", options)
+
+ # Button to run the selected option
+ if st.button("Run"):
+ if not smiles_input:
+ st.text("Enter Canonical SMILES")
+ else:
+ try:
+ if selected_option == "Compute Lipinski's Descriptors":
+ # Calculate Lipinski's descriptors and display the result
+ df = calculate_lipinski_descriptors(smiles_input)
+ df.columns = ['Molecular Weight', 'Octanol-Water Partition Coefficient (LogP)',
+ 'Number of Hydrogen Bond Donors', 'Number of Hydrogen Bond Acceptors']
+ hide_table_row_index = """
+
+ """
+ st.markdown(hide_table_row_index, unsafe_allow_html=True)
+ st.table(df)
+ elif selected_option == "Predict the Compound's Activity":
+ # Load the model and predict the compound's activity
+ filename = 'lipinsky_model.pkl'
+ loaded_model = pickle.load(open(filename, 'rb'))
+ y_pred = loaded_model.predict(calculate_lipinski_descriptors(smiles_input))
+ if y_pred == [1]:
+ st.text('Active')
+ else:
+ st.text('Inactive')
+ elif selected_option == "Predict the Compound's pIC50":
+ # Generate a CSV file and compute pIC50
+ string1 = smiles_input
+ string2 = 'Compound_name'
+
+ filename = "molecule.smi"
+ generate_csv_file(string1, string2, filename)
+
+ script_path = "./padel.sh"
+ subprocess.call(['bash', script_path])
+
+ data = pd.read_csv('descriptors_output.csv')
+ X = data.drop(columns=['Name'])
+
+ loaded_model = pickle.load(open('model.pkl', 'rb'))
+ y_pred = loaded_model.predict(X)
+ predicted_value = y_pred[0]
+ predicted_value = format(predicted_value, ".2f")
+ st.text("The pIC50 of your compound is " + str(predicted_value))
+ elif selected_option == "Retrieve interacting proteins":
+ # Retrieve interacting proteins from PDB database
+ result = Query(smiles_input).search()
+ ids = []
+ for pdb_id in result:
+ if len(ids) < 10:
+ ids.append(pdb_id)
+ ids_str = ", ".join(ids)
+ st.markdown(ids_str)
+
+ except ValueError as e:
+ st.error(str(e))
+ # ---- CONTACT ----
+ with st.container():
+ st.write("---")
+ st.header("Please contact us!")
+
+ # Documention: https://formsubmit.co/ !!! CHANGE EMAIL ADDRESS !!!
+ contact_form = """
+
+ """
+ left_column, right_column = st.columns(2)
+ with left_column:
+ st.markdown(contact_form, unsafe_allow_html=True)
+ with right_column:
+ st.empty()
+
+
+if __name__ == "__main__":
+ main()
diff --git a/padel.sh b/padel.sh
new file mode 100755
index 0000000..01f5d65
--- /dev/null
+++ b/padel.sh
@@ -0,0 +1 @@
+java -Xms1G -Xmx1G -Djava.awt.headless=true -jar ./PaDEL-Descriptor/PaDEL-Descriptor.jar -removesalt -standardizenitro -fingerprints -descriptortypes ./PaDEL-Descriptor/PubchemFingerprinter.xml -dir ./ -file descriptors_output.csv
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..beba740
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,4 @@
+pandas==2.0.2
+pypdb==2.2
+rdkit==2023.3.2
+streamlit==1.24.0
diff --git a/style/style.css b/style/style.css
new file mode 100644
index 0000000..2533b12
--- /dev/null
+++ b/style/style.css
@@ -0,0 +1,33 @@
+/* CSS Snippet from W3schools: https://www.w3schools.com/howto/howto_css_contact_form.asp */
+/* Style inputs with type="text", select elements and textareas */
+input[type=message], input[type=email], input[type=text], textarea {
+ width: 100%; /* Full width */
+ padding: 12px; /* Some padding */
+ border: 1px solid #ccc; /* Gray border */
+ border-radius: 4px; /* Rounded borders */
+ box-sizing: border-box; /* Make sure that padding and width stays in place */
+ margin-top: 6px; /* Add a top margin */
+ margin-bottom: 16px; /* Bottom margin */
+ resize: vertical /* Allow the user to vertically resize the textarea (not horizontally) */
+}
+
+/* Style the submit button with a specific background color etc */
+button[type=submit] {
+ background-color: #04AA6D;
+ color: white;
+ padding: 12px 20px;
+ border: none;
+ border-radius: 4px;
+ cursor: pointer;
+}
+
+/* When moving the mouse over the submit button, add a darker green color */
+button[type=submit]:hover {
+ background-color: #45a049;
+}
+
+
+/* Hide Streamlit Branding */
+#MainMenu {visibility: hidden;}
+footer {visibility: hidden;}
+header {visibility: hidden;}