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-rw-r--r--app/views.py90
1 files changed, 89 insertions, 1 deletions
diff --git a/app/views.py b/app/views.py
index 47a37ac..bf2d401 100644
--- a/app/views.py
+++ b/app/views.py
@@ -17,6 +17,8 @@ import subprocess
import mysql.connector as con
from mysql.connector.errors import InterfaceError,DatabaseError
+
+
import requests
import logging
@@ -31,6 +33,8 @@ import configparser
misc = configparser.ConfigParser()
misc.read('app/misc.ini')
errors = misc['ERRORS']
+AlertSMARTS = misc['ALERT_SMARTS']
+AlertDescription = misc['ALERT_DESCRIPTION']
base = os.getcwd()
@@ -121,6 +125,47 @@ def pubchem():
return render_template('search-pubchem.html',result=search,form=form)
return render_template('search-pubchem.html',form=form)
+@app.route('/Properties',methods=['GET','POST'])
+def propalert():
+ form = PyMedSearch()
+
+ if request.method == 'POST' and form.validate_on_submit():
+ q = form.query.data
+ result = []
+ perfect = False
+ complete = False
+
+ try:
+ from rdkit import Chem
+ except ImportError:
+ return render_template('error.html',code="RD00",description=errors["RD00"])
+
+ if Chem.MolFromSmiles(q.strip()) is None:
+ print("invalid smiles")
+ return render_template('error.html',code="RD01",description=errors["RD01"])
+
+ for alert in AlertSMARTS:
+ print("Checking",alert,AlertSMARTS[alert])
+ records = {}
+ records['Name'] = alert
+ try:
+ records['SVG'] = get_svg(q,AlertSMARTS[alert])
+ except:
+ continue
+ records['Description'] = AlertDescription[alert]
+ result.append(records)
+
+ prop = get_prop(q)
+ print(prop)
+
+ complete = True
+
+ if len(result) == 0:
+ perfect = True
+
+ return render_template('mol-characteristics.html',complete=complete,result=result,form=form,perfect=perfect,prop=prop)
+ return render_template('mol-characteristics.html',form=form)
+
@app.route('/Status',methods=['GET','POST'])
def status():
taskStatusForm = statusForm()
@@ -426,4 +471,47 @@ def page_not_found(error):
if __name__ == '__main__':
- app.run(debug=True, host="0.0.0.0", port="8080") \ No newline at end of file
+ app.run(debug=True, host="0.0.0.0", port="8080")
+
+def get_svg(base,pattern):
+ try:
+ from rdkit.Chem.Draw import rdMolDraw2D
+ from rdkit import Chem
+ except:
+ return None # Need to add logic
+
+ mol = Chem.MolFromSmiles(base)
+ patt = Chem.MolFromSmarts(pattern)
+ hit_ats = list(mol.GetSubstructMatch(patt))
+ hit_bonds = []
+ for bond in patt.GetBonds():
+ aid1 = hit_ats[bond.GetBeginAtomIdx()]
+ aid2 = hit_ats[bond.GetEndAtomIdx()]
+ hit_bonds.append(mol.GetBondBetweenAtoms(aid1,aid2).GetIdx())
+ d = rdMolDraw2D.MolDraw2DSVG(500, 500)
+ rdMolDraw2D.PrepareAndDrawMolecule(d, mol, highlightAtoms=hit_ats, highlightBonds=hit_bonds)
+ return d.GetDrawingText().replace("width='500' height='500'","").replace("width='500px' height='500px'","")
+
+def get_prop(base):
+ try:
+ from rdkit import Chem
+ from rdkit.Chem import Crippen
+ from rdkit.Chem import Descriptors
+ from rdkit.Chem import rdMolDescriptors
+ from rdkit.Chem import Lipinski
+ except:
+ return None # Need to add logic
+ result = {}
+
+ mol = Chem.MolFromSmiles(base)
+ result["cLogP"] = Crippen.MolLogP(mol)
+ result["Molecular Weight"] = Descriptors.MolWt(mol)
+ result["TPSA"] = rdMolDescriptors.CalcTPSA(mol)
+ result["Hydrogen Bond Acceptors"] = Lipinski.NumHAcceptors(mol)
+ result["Hydrogen Bond Donors"] = Lipinski.NumHDonors(mol)
+ result["Rotable Bonds"] = Lipinski.NumRotatableBonds(mol)
+ result["Fraction SP3"] = Lipinski.FractionCSP3(mol)
+
+
+ return result
+