bolierplate-codes
Openbable Docker

How to use openbabel in python 🐍 in docker 🐋

To install openbabel use conda then import pybel from openbabel or else it will not work, in case when used from openbabel bable all package were safe and sound.

conda install -c conda-forge openbabel
>python3
from openbabel import pybel

and to install conda in Google collab run the following code.

!pip install -q condacolab
import condacolab
condacolab.install()
!conda install -c conda-forge openbabel

To get started i asked ChatGPT to create me course on Cheminformatics.

Certainly! Here's an advanced course outline for using Pybel, a Python wrapper for Open Babel, in cheminformatics:

Course Title: Advanced Pybel for Cheminformatics

Module 1: Introduction to Pybel

  • Overview of Pybel and Open Babel
  • Installing Pybel and its dependencies
  • Pybel data structures and molecule representations
  • Reading and writing molecular file formats using Pybel

Module 2: Molecular Manipulation with Pybel

  • Molecular property calculations using Pybel
  • Conformer generation and optimization
  • Substructure searching with SMARTS patterns
  • Fragmentation and scaffold extraction
  • Molecular similarity and clustering analysis

Module 3: Molecular Descriptors and Fingerprints

  • Introduction to molecular descriptors and fingerprints
  • Calculation and utilization of molecular descriptors using Pybel
  • Generation and analysis of fingerprints with Pybel
  • Similarity searching and virtual screening using fingerprints

Module 4: Pharmacophore Modeling with Pybel

  • Overview of pharmacophore modeling
  • Feature mapping and pharmacophore generation with Pybel
  • Pharmacophore-based virtual screening using Pybel
  • Analysis and interpretation of pharmacophore models

Module 5: Molecular Docking with Pybel

  • Introduction to molecular docking
  • Preparing receptor and ligand structures for docking with Pybel
  • Performing molecular docking using Pybel and AutoDock Vina
  • Analyzing and visualizing docking results with Pybel

Module 6: QSAR/QSPR Modeling with Pybel

  • Introduction to QSAR/QSPR modeling
  • Dataset preparation and feature generation using Pybel
  • Building predictive models with machine learning algorithms in Pybel
  • Model evaluation and validation techniques in Pybel

Module 7: Cheminformatics Workflows and Integration

  • Designing and automating cheminformatics workflows with Pybel
  • Integration of Pybel with other cheminformatics libraries and tools
  • Pybel in pipeline development and data processing
  • Case studies and practical examples of advanced cheminformatics workflows

Module 8: Advanced Topics and Future Directions

  • Advanced topics in Pybel and Open Babel
  • Recent developments and future directions in cheminformatics
  • Exploring the Pybel source code and contributing to the project

And good thing is that it also coded me examples on each and every topic.

Module 1: Introduction to Pybel

This example demonstrates how to read file and get basic properties of molecules

import pybel
 
# Load a molecule from a file
molecule = pybel.readfile("sdf", "input.sdf")
mol = next(molecule)
# Access molecule properties
print("Formula:", mol.formula)
print("Molecular weight:", mol.molwt)
 
# Write the molecule to a different file format
mol.write("mol2", "output.mol2")

and to get all the properties of the loaded molecule

# Get all properties of the molecule
properties = mol.data
# Print all properties
for key, value in properties.items():
    print(f"{key}: {value}")
output
 
# asprin was loaded by sdf file
 
MOL Chiral Flag: 0
PUBCHEM_COMPOUND_CID: 2244
PUBCHEM_COMPOUND_CANONICALIZED: 1
PUBCHEM_CACTVS_COMPLEXITY: 212
PUBCHEM_CACTVS_HBOND_ACCEPTOR: 4
PUBCHEM_CACTVS_HBOND_DONOR: 1
PUBCHEM_CACTVS_ROTATABLE_BOND: 3
PUBCHEM_CACTVS_SUBSKEYS: AAADccBwOAAAAAAAAAAAAAAAAAAAAAAAAAAwAAAAAAAAAAABAAAAGgAACAAADASAmAAyDoAABgCIAiDSCAACCAAkIAAIiAEGCMgMJzaENRqCe2Cl4BEIuYeIyCCOAAAAAAAIAAAAAAAAABAAAAAAAAAAAA==
PUBCHEM_IUPAC_OPENEYE_NAME: 2-acetoxybenzoic acid
PUBCHEM_IUPAC_CAS_NAME: 2-acetyloxybenzoic acid
PUBCHEM_IUPAC_NAME_MARKUP: 2-acetyloxybenzoic acid
PUBCHEM_IUPAC_NAME: 2-acetyloxybenzoic acid
PUBCHEM_IUPAC_SYSTEMATIC_NAME: 2-acetyloxybenzoic acid
PUBCHEM_IUPAC_TRADITIONAL_NAME: 2-acetoxybenzoic acid
PUBCHEM_IUPAC_INCHI: InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)
PUBCHEM_IUPAC_INCHIKEY: BSYNRYMUTXBXSQ-UHFFFAOYSA-N
PUBCHEM_XLOGP3: 1.2
PUBCHEM_EXACT_MASS: 180.04225873
PUBCHEM_MOLECULAR_FORMULA: C9H8O4
PUBCHEM_MOLECULAR_WEIGHT: 180.16
PUBCHEM_OPENEYE_CAN_SMILES: CC(=O)OC1=CC=CC=C1C(=O)O
PUBCHEM_OPENEYE_ISO_SMILES: CC(=O)OC1=CC=CC=C1C(=O)O
PUBCHEM_CACTVS_TPSA: 63.6
PUBCHEM_MONOISOTOPIC_WEIGHT: 180.04225873
PUBCHEM_TOTAL_CHARGE: 0
PUBCHEM_HEAVY_ATOM_COUNT: 13
PUBCHEM_ATOM_DEF_STEREO_COUNT: 0
PUBCHEM_ATOM_UDEF_STEREO_COUNT: 0
PUBCHEM_BOND_DEF_STEREO_COUNT: 0
PUBCHEM_BOND_UDEF_STEREO_COUNT: 0
PUBCHEM_ISOTOPIC_ATOM_COUNT: 0
PUBCHEM_COMPONENT_COUNT: 1
PUBCHEM_CACTVS_TAUTO_COUNT: -1
PUBCHEM_COORDINATE_TYPE: 1
5
255
PUBCHEM_BONDANNOTATIONS: 5  6  8
5  7  8
6  8  8
7  9  8
8  10  8
9  10  8
OpenBabel Symmetry Classes: 10 9 3 7 16 13 12 17 14 11 15 18 19 5 4 2 6 8 8 8 1
Formula: C9H8O4
PartialCharges: Gasteiger

Module 2: Molecular Manipulation with Pybel

Basics: to view the molecule in 3d viewer install & py3Dmol is entire library will lots of different fetures like surface to set background color etc...

!conda install py3Dmol
import py3Dmol
# Create a Py3Dmol view
view = py3Dmol.view(width=400, height=400)
mol = pybel.readfile("sdf","./asprin.sdf")
mol = next(mol)
mol.make3D()
mol.localopt()
pdb_block = mol.write("pdb")
view.addModel(pdb_block, "pdb")
# view.setStyle({'cartoon': {'color': 'spectrum'}})
# view.zoomTo()
# view.show()

Topic Material:

  • require rdkit
!pip install rdkit
from rdkit import Chem
# Generate conformers for a molecule
molecule = pybel.readfile("sdf", "input.sdf")
molecule = next(molecule)
molecule.make3D()
 
# Optimize the molecule's geometry
molecule.localopt()
 
# convert to RdKit Molecule
rdkit_mol = Chem.MolFromMolBlock(molecule.write("mol"))
 
 
 
# # Perform substructure searching
# pattern = pybel.Smarts("[#6][#6]")
# matches = molecule.findall(pattern)
# for match in matches:
#     print("Substructure found at atom indices:", match)
 
# # Fragment the molecule
# fragments = molecule.split()
 
# # Perform molecular similarity analysis
# other_molecule = pybel.readfile("sdf", "other.sdf").next()
# similarity = molecule.calcdesc(["similarity"], other_molecule)
# print("Similarity:", similarity["similarity"])

Force Field 🤕

from openbabel import pybel
from rdkit import Chem
import pandas as pd
import numpy as np
import py3Dmol
 
compound = "CC(=O)OC1=CC=CC=C1C(=O)O"
mol = pybel.readstring("smi",compound)
 
mol.localopt(forcefield="mmff94",steps=900000)
 
view = py3Dmol.view()
view.setBackgroundColor("black")
view.addModel(mol.write("pdb"),"pdb")
GitHub Ssh ConnectionsQuntitative Structure Property Relationships