V0.0.2

DocMinus · DocMinus · commit e39cf8eab9c8 · 2023-05-19T18:21:57.000+02:00
diff --git a/.gitignore b/.gitignore
@@ -1,9 +1,6 @@
-# Pycharm IDE
 **/.idea/
 **/__pycache__
-
-# Jupyter
-**/.ipynb_checkpoints
+**/.vscode/
 
 **/image*.svg
 **/*.log
diff --git a/README.md b/README.md
@@ -5,6 +5,7 @@
 # ChemDash
 ## Proof of concept small molecule (web) GUI
 Here is a proof of concept of a "small molecule chemistry centric gui", running in a web-browser<br>
+Some basic calculations are done which can be easiliy expanded upon. A practical, non standard one concerns process safety, the so called "oxygene balance". See for example https://en.wikipedia.org/wiki/Oxygen_balance for more info.
 It's build in Pyton and uses the Plotly Dash components.<br>
 For installation, see the environment folder.<br>
 
@@ -23,3 +24,6 @@ Dash is a somewhat straightforward way to make a GUI, especially in context of d
 A number of tutorials helped me, among them I want to thank and highlight:<br> 
 * [ArjanCodes dash tutorial](https://github.com/ArjanCodes/2022-dash), including the Youtube videos
 * [Algorithms](https://github.com/siddharthajuprod07/algorithms), including the Youtube videos
+<br>
+### Updates
+* Minor refactoring in code 0.0.1 -> 0.0.2
diff --git a/multi_page_example.py b/multi_page_example.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 """
 Chemical Dashboard for reactions
 Version 0.3.7 (Jan 03, 14:15:00 2023)
@@ -12,8 +10,8 @@
 """
 
 import dash
-from dash import html
 import dash_bootstrap_components as dbc
+from dash import html
 
 app = dash.Dash(
     __name__,
diff --git a/pages/calculations_jsme.py b/pages/calculations_jsme.py
@@ -1,17 +1,17 @@
+# Update: small refactor and added a round to the moldescriptors
 import dash
-from dash import html, Input, Output, dcc
 import dash_bio as dashbio
+import pandas as pd
 import plotly.graph_objects as go
 import plotly.subplots as sp
+from dash import Input, Output, dcc, html
 
-import pandas as pd
-
-from . import navigation
-
+from src.calculations.molecule import Molecule
 from src.calculations.oxybalance import oxy_balance
-from src.calculations.mol_properties import molecule
-from src.mol_img import mol_image
 from src.ids import *
+from src.mol_img import mol_image
+
+from . import navigation
 
 dash.register_page(__name__, path=MENU1SUB1_HREF)
 
@@ -23,7 +23,7 @@
         html.Div(
             [
                 dashbio.Jsme(
-                    width="25%",
+                    width="40%",
                     height="36vh",
                     id="jsme",
                     smiles="",
@@ -62,7 +62,7 @@ def calc_and_display(jsme_smiles):
     o_balance = 0
     sum_formula = "C0H0"
     calc_image = mol_image(jsme_smiles)
-    alt_text = "No/invalid smiles. "
+    alt_text = "No/invalid structure. "
     descriptors = pd.DataFrame()
     fig = sp.make_subplots(rows=1, cols=1, specs=[[{"type": "table"}]])
     show_first_x_props = 5
@@ -72,9 +72,9 @@ def calc_and_display(jsme_smiles):
 
     if len(calc_image):
         o_balance = oxy_balance(jsme_smiles)
-        _mol = molecule(jsme_smiles)
+        _mol = Molecule(jsme_smiles)
         sum_formula = _mol.sumformula()
-        descriptors = _mol.moldescriptors()
+        descriptors = _mol.moldescriptors().round(3)  # the round is optional
         # only selected few properties shown; again, only proof of concept.
         # slicing from 1:x instead of 0:x removes the ID
         descriptors = descriptors.iloc[:1, 1:show_first_x_props]
@@ -95,7 +95,7 @@ def calc_and_display(jsme_smiles):
         )
 
     # can't get displayModeBar False to work, probably doing it wrong.
-    #fig.update_layout(displayModeBar=False, width=800, height=400)
+    # fig.update_layout(displayModeBar=False, width=800, height=400)
     fig.update_layout(width=800, height=400)
 
     _image = html.Img(
diff --git a/pages/calculations_smi.py b/pages/calculations_smi.py
@@ -1,12 +1,13 @@
+# Update small refactor
 import dash
-from dash import dcc, html, Input, Output, State, ctx
+from dash import Input, Output, State, ctx, dcc, html
 
-from . import navigation
-
-from src.calculations.oxybalance import oxy_balance, n_count
-from src.calculations.mol_properties import molecule
-from src.mol_img import mol_image
+from src.calculations.molecule import Molecule
+from src.calculations.oxybalance import n_count, oxy_balance
 from src.ids import *
+from src.mol_img import mol_image
+
+from . import navigation
 
 dash.register_page(__name__, path=MENU1SUB2_HREF)
 
@@ -68,7 +69,7 @@ def calc_and_display(calc_button_, calc_smiles_, reset):
     if len(calc_image):
         o_balance = oxy_balance(calc_smiles_)
         num_of_n = n_count(calc_smiles_)
-        _mol = molecule(calc_smiles_)
+        _mol = Molecule(calc_smiles_)
         sum_formula = _mol.sumformula()
         mol_weight = _mol.molwt()
 
diff --git a/pages/home.py b/pages/home.py
@@ -1,5 +1,6 @@
 import dash
 from dash import html
+
 from . import navigation
 
 dash.register_page(__name__, path="/")
@@ -13,6 +14,6 @@
         html.Br(),
         html.Label("For details, check out the README or have a look into the code."),
         html.Br(),
-        html.Label("Written early January 2023 by DocMinus"),
+        html.Label("Written January 2023 by DocMinus"),
     ]
 )
diff --git a/pages/links_of_interest.py b/pages/links_of_interest.py
@@ -1,9 +1,9 @@
 import dash
 from dash import html
 
-from . import navigation
 from src.ids import *
 
+from . import navigation
 
 dash.register_page(__name__, path=MENU2SUB1_HREF)
 
@@ -19,7 +19,8 @@
         "https://www.acsgcipr.org/tools-for-innovation-in-chemistry/",
     ),
     ("Chemix - editor for labdiagrams, etc", "https://chemix.org"),
-    ("Docminus's Gibthub:", "https://github.com/DocMinus"),
+    ("Docminus's Gibthub", "https://github.com/DocMinus"),
+    ("Oxygene Balance, Wikipedia", "https://en.wikipedia.org/wiki/Oxygen_balance"),
 ]
 
 links = [
diff --git a/single_page_example.py b/single_page_example.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 """
 Chemical Dashboard for reactions
 Version 0.1.1 (Jan 03, 14:15:00 2023)
@@ -13,14 +11,13 @@
 """
 
 
-from dash import Dash, dcc, html, Input, Output, State, ctx
 import dash_bootstrap_components as dbc
+from dash import Dash, Input, Output, State, ctx, dcc, html
+from rdkit import RDLogger
 
-from src.calculations.oxybalance import oxy_balance, n_count
-from src.mol_img import mol_image
+from src.calculations.oxybalance import n_count, oxy_balance
 from src.ids import *
-
-from rdkit import RDLogger
+from src.mol_img import mol_image
 
 RDLogger.logger().setLevel(RDLogger.CRITICAL)
 
diff --git a/src/calculations/__init__.py b/src/calculations/__init__.py
diff --git a/src/calculations/chemtools.py b/src/calculations/chemtools.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 """
 Reduced chemtools module for use in ChemDash proof of concept based on
 Version 0.5.6 (May 24, 07:30:00 2021)
@@ -9,13 +7,13 @@
 """
 
 import re
+
 import pandas as pd
 
 # RDkit stuff
-from rdkit import Chem
+from rdkit import Chem, RDLogger
 from rdkit.Chem.MolStandardize import rdMolStandardize
 from rdkit.ML.Descriptors.MoleculeDescriptors import MolecularDescriptorCalculator
-from rdkit import RDLogger
 
 # Important, or else waaaay too many RDkit details in output
 RDLogger.logger().setLevel(RDLogger.CRITICAL)
@@ -184,7 +182,6 @@ def clean_step4(mol_object: list) -> list:
         # name = mol.GetProp("_Name")
         # using name here seems to mess things up;
         # on the other hand, not necessary anyway since rdkit takes care of it at this stage
-        # print("3rd round, ID: ", mol.GetProp("_Name"), " ", Chem.rdmolfiles.MolToSmiles(mol))
         mol = uncharger.uncharge(rdMolStandardize.FragmentParent(mol))
         mol = md.Disconnect(mol)
 
diff --git a/src/calculations/molecule.py b/src/calculations/molecule.py
@@ -1,15 +1,11 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
+# Updated: Corrected spelling of class name & renamed file for clarity.
 import pandas as pd
-from rdkit import Chem
+from rdkit import Chem, RDLogger
 from rdkit.Chem import Descriptors
 
-from rdkit import RDLogger
-
 RDLogger.logger().setLevel(RDLogger.CRITICAL)
 
-from .chemtools import clean_smiles, RDKIT_DESCRIPS, RDKIT_DESCRIPS_HEADERS
-
+from .chemtools import RDKIT_DESCRIPS, RDKIT_DESCRIPS_HEADERS, clean_smiles
 
 
 def get_clean_ids(_mollist: list) -> list:
@@ -38,7 +34,6 @@ def rdkit_calc(cleaned_mol_list: list) -> pd.DataFrame:
     :return: pandas df containing calculated properties (no structures, but now with ID)
     """
 
-    print("\nCalculating RDkit")
     calcrdk = [RDKIT_DESCRIPS.CalcDescriptors(mol) for mol in cleaned_mol_list]
     transposed_properties = zip(*calcrdk)
     headers = RDKIT_DESCRIPS_HEADERS
@@ -51,14 +46,17 @@ def rdkit_calc(cleaned_mol_list: list) -> pd.DataFrame:
     return pd.concat([properties_ids_df, properties_df1], axis=1)
 
 
-class molecule:
+class Molecule:
     """
     Simple clean and convert of smiles to rdkit object
-    Addition of different calculations as required.
-    Only ene of many ways to use this.
-
-    :param molecule: mol as smiles
-    :rtype:
+    Adding more stuff possible, but not necessary for this proof of concept.
+
+    :param molecule: mol as smiles \n
+    :rtype: cleanmolobj() = rdkit object \n
+            cleansmiles() = rkdit object as smiles \n
+            sumformula() \n
+            molwt() \n
+            moldescriptors() = rdkit calculated descriptors
     """
 
     def __init__(self, schmiles: str):
@@ -70,10 +68,10 @@ def __init__(self, schmiles: str):
         self._mol_list = clean_smiles(self._in_mols_df)
         self._mol = self._mol_list[0]
 
-    def cleanmolobj(self):
+    def clean_molobj(self):
         return self._mol
 
-    def cleansmiles(self):
+    def cleaned_smiles(self):
         return Chem.rdmolfiles.MolToSmiles(self._mol)
 
     def sumformula(self):
diff --git a/src/calculations/oxybalance.py b/src/calculations/oxybalance.py
@@ -1,17 +1,16 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 # changed do work without files, now SVG only in memory
+# oxygenbalance cutoffs:
 # -22 red; -233 green
 
-from rdkit import Chem
-from rdkit import RDLogger
+from rdkit import Chem, RDLogger
 
 RDLogger.logger().setLevel(RDLogger.CRITICAL)
 
 
+from collections import defaultdict
+
 from rdkit import Chem
 from rdkit.Chem import Descriptors
-from collections import defaultdict
 
 
 def elemental_composition(smiles: str) -> dict:
@@ -47,7 +46,6 @@ def elemental_composition(smiles: str) -> dict:
 
 
 def oxy_balance(smiles: str) -> str:
-
     composition = elemental_composition(smiles)
     o_balance = 0
     if composition:
diff --git a/src/ids.py b/src/ids.py
@@ -1,11 +1,12 @@
 # define diverse permanent variables accessible/used in multiple places.
-import os, sys
-
+import os
+import sys
 
 CURRENT_SRC_DIR = os.path.abspath(os.path.abspath(sys.argv[0]))
 TMP_DIR = os.path.abspath(os.path.join(os.path.dirname(CURRENT_SRC_DIR), "assets"))
 MENU_LOGO = "navbar_logo.png"
 
+
 # menu names and hrefs
 MENU1_NAME = "Calculations"
 MENU1SUB1_NAME = "Single Molecule (editor)"
diff --git a/src/mol_img.py b/src/mol_img.py
@@ -1,11 +1,9 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 # changed do work without files, now SVG only in memory
 
 import base64
-from rdkit import Chem
-from rdkit.Chem.Draw import rdMolDraw2D, rdDepictor
-from rdkit import RDLogger
+
+from rdkit import Chem, RDLogger
+from rdkit.Chem.Draw import rdDepictor, rdMolDraw2D
 
 RDLogger.logger().setLevel(RDLogger.CRITICAL)
 

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,6 @@`
`1`	`1`	`import dash`
`2`	`2`	`from dash import html`
	`3`	`+`
`3`	`4`	`from . import navigation`
`4`	`5`
`5`	`6`	`dash.register_page(__name__, path="/")`
`@@ -13,6 +14,6 @@`
`13`	`14`	`html.Br(),`
`14`	`15`	`html.Label("For details, check out the README or have a look into the code."),`
`15`	`16`	`html.Br(),`
`16`		`- html.Label("Written early January 2023 by DocMinus"),`
	`17`	`+ html.Label("Written January 2023 by DocMinus"),`
`17`	`18`	`]`
`18`	`19`	`)`