From 85001f57a619086298af2c283d0e19e426b75dc3 Mon Sep 17 00:00:00 2001
From: Navan Chauhan <navanchauhan@gmail.com>
Date: Thu, 10 Sep 2020 00:49:32 +0530
Subject: [PATCH] created a pdbqt convertor utility

---
 app/forms.py                  |  6 +++
 app/templates/home.html       |  1 +
 app/templates/pdbqt_form.html | 42 ++++++++++++++++++++
 app/views.py                  | 75 ++++++++++++++++++++++++++++++++++-
 4 files changed, 122 insertions(+), 2 deletions(-)
 create mode 100644 app/templates/pdbqt_form.html

diff --git a/app/forms.py b/app/forms.py
index 4a3f880..eaaf547 100644
--- a/app/forms.py
+++ b/app/forms.py
@@ -45,5 +45,11 @@ class generateSMILES(FlaskForm):
     n = IntegerField('Number of Molecules to Generate',default=1,validators=[DataRequired()])
     #modelSelection = SelectField('Model',choices=[("alpha","Alpha"),("beta","Beta")])
 
+class generatePDBQTS(FlaskForm):
+    jobType = SelectField(u'Generate for Protein or Ligand', choices=[("", "Protein or Ligand"),('protein', 'Protein (PDB)'), ('ligand', 'Ligand (SMILES)')], default='SelectOption')
+    pdb = StringField('PDB ID')
+    smiles = StringField('SMILES')
+    name = StringField('Compound Name (Optional)')
+
 class PyMedSearch(FlaskForm):
     query = StringField('Search Query for PubMed',default="Covid-19",validators=[DataRequired()])
\ No newline at end of file
diff --git a/app/templates/home.html b/app/templates/home.html
index bf4cf32..f1f340a 100644
--- a/app/templates/home.html
+++ b/app/templates/home.html
@@ -23,6 +23,7 @@
 
     <h3>Misc.</h3>
     <ul>
+        <li><a href="{{url_for('generate_pdbqts')}}">Generate PDBQTs</a> - Generate PDBQTs for your compounds or proteins</li>
         <li><a href="{{url_for('editor')}}">Editor</a> - Simple Molecular Editor powered by Kekule.js</li>
         <li><a href="{{ url_for('status')}}">Job Status</a> - Check the job status </li>
         <li><a href="{{ url_for('visualise')}}">Visualise</a> - Molecular Viewer </li>
diff --git a/app/templates/pdbqt_form.html b/app/templates/pdbqt_form.html
new file mode 100644
index 0000000..09cd1b0
--- /dev/null
+++ b/app/templates/pdbqt_form.html
@@ -0,0 +1,42 @@
+
+{% extends 'base.html' %}
+
+{% block main %}
+    <h2>Generate PDBQTs</h2>
+
+    <script>
+        function makeVisible() {
+
+            var val = document.getElementById("jobType").value;
+
+            if (val === "protein") {
+            document.getElementById("pdb").disabled = false;
+            document.getElementById('smiles').disabled = true;
+            document.getElementById('name').disabled = true;
+            }
+            else if (val=='ligand') {
+                document.getElementById('smiles').disabled = false;
+                document.getElementById("pdb").disabled = true;
+                document.getElementById("name").disabled = false;
+            }
+}
+    </script>
+
+    <form method="post" action="{{ url_for('generate_pdbqts') }}">
+        {% include 'flash_messages.html' %}
+        {{ form.csrf_token }}
+        <div class="form-group">
+            {{ form.jobType.label }} {{ form.jobType(**{"onchange":"makeVisible()","class":"form-control"}) }}
+        </div>
+        <div class="form-group">
+            {{ form.pdb.label }} {{ form.pdb(**{"disabled":"false","class":"form-control"}) }}
+        </div>
+        <div class="form-group">
+            {{ form.smiles.label }} {{ form.smiles(**{"disabled":"true","class":"form-control"}) }}
+        </div>
+        <div class="form-group">
+            {{ form.name.label }} {{ form.name(**{"disabled":"true","class":"form-control"}) }}
+        </div>
+    <button type="submit" class="btn btn-primary">Submit</button>
+</form>
+{% endblock %}
\ No newline at end of file
diff --git a/app/views.py b/app/views.py
index 86a01fd..1e6b269 100644
--- a/app/views.py
+++ b/app/views.py
@@ -5,7 +5,7 @@ Werkzeug Documentation:  http://werkzeug.pocoo.org/documentation/
 """
 import os
 from app import app
-from flask import render_template, request, flash
+from flask import render_template, request, flash, send_file
 from werkzeug.utils import secure_filename
 from random import choice, shuffle
 from string import digits, ascii_lowercase
@@ -16,7 +16,7 @@ import subprocess
 
 # Note: that when using Flask-WTF we need to import the Form Class that we created
 # in forms.py
-from .forms import MyForm, curieForm, statusForm, generateSMILES, PyMedSearch, dockSingleForm
+from .forms import MyForm, curieForm, statusForm, generateSMILES, PyMedSearch, dockSingleForm, generatePDBQTS
 
 def gen_word(N, min_N_dig, min_N_low):
     choose_from = [digits]*min_N_dig + [ascii_lowercase]*min_N_low
@@ -143,6 +143,77 @@ def wtform():
         flash_errors(myform)
     return render_template('wtform.html', form=myform)
 
+@app.route('/PDBQTs',methods=['GET','POST'])
+def generate_pdbqts():
+    myform = generatePDBQTS()
+
+    if request.method == 'POST':
+        if myform.validate_on_submit():
+            pdbId = myform.pdb.data
+            smiles = myform.smiles.data
+            name = myform.name.data
+            if (len(pdbId)==0) and (len(smiles)==0):
+                print("Nothing Submitted!")
+                flash("Invalid Submission!",'danger')
+            if len(smiles) != 0:
+                import oddt
+                try:
+                    mol = oddt.toolkit.readstring('smi', smiles)
+                except:
+                    return render_template('error.html',code="OD01",description="Could not convert SMILES to molecule, please check the SMILES")
+                try:
+                    mol.make3D()
+                    mol.calccharges()
+                except:
+                    return render_template('error.html',code="OD02",description="Failed to add charges to molecule")
+                from oddt.docking.AutodockVina import write_vina_pdbqt
+                
+                try:
+                    write_vina_pdbqt(mol,'app',flexible=False)
+                except:
+                    return render_template('error.html',code="OD03",description="Failed to write the converted PDBQT file")
+                path = ".pdbqt"
+                if ".pdbqt" in name:
+                    fname = name
+                else:
+                    fname = name + ".pdbqt"
+                return send_file(path,attachment_filename=fname,as_attachment=True)
+            if len(pdbId) != 0:
+                from plip.basic import config
+                from plip.exchange.webservices import fetch_pdb
+                from plip.structure.preparation import create_folder_if_not_exists, extract_pdbid
+                from plip.structure.preparation import tilde_expansion, PDBComplex
+
+                try:
+                    pdbfile, pdbid = fetch_pdb(pdbId.lower())
+                except:
+                    return render_template('error.html',code="PL01",description="Failed to fetch the PDB, please check the PDB Code")
+                pdbpath = tilde_expansion('%s/%s.pdb' % (config.BASEPATH.rstrip('/'), pdbid))
+                create_folder_if_not_exists(config.BASEPATH)
+                with open(pdbpath, 'w') as g:
+                    g.write(pdbfile)
+                import oddt
+                from oddt.docking.AutodockVina import write_vina_pdbqt
+                try:
+                    receptor = next(oddt.toolkit.readfile("pdb",pdbpath.split("./")[1]))
+                    receptor.calccharges()
+                except Exception:
+                    receptor = next(oddt.toolkits.rdk.readfile("pdb",pdbpath.split("./")[1]))
+                    receptor.calccharges()
+
+                try:
+                    path = write_vina_pdbqt(receptor,'app',flexible=False)
+                except:
+                    return render_template('error.html',code="OD03",description="Failed to write the converted PDBQT file")
+                os.rename(path,"app/.pdbqt")
+                path = ".pdbqt"
+                fname = pdbId.upper() + ".pdqbt"
+                return send_file(path,attachment_filename=fname,as_attachment=True) 
+        flash_errors(myform)
+    return render_template('pdbqt_form.html',form=myform)
+            
+
+
 tfWorking = 0
 
 if tfWorking == -1: