01_import

Module imports and RDkit functions

Install the package from pip (skip this step if the package is already installed)

! pip install ligning

Collecting ligning
  Downloading ligning-0.1.1-py3-none-any.whl (32 kB)
Requirement already satisfied: openpyxl>=3.0.7 in /opt/anaconda3/lib/python3.8/site-packages (from ligning) (3.0.9)
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Collecting networkx>=2.5
  Downloading networkx-2.8.3-py3-none-any.whl (2.0 MB)
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Collecting rdkit-pypi>=2021.9.2.1
  Downloading rdkit_pypi-2022.3.2.1-cp38-cp38-macosx_10_9_x86_64.whl (17.9 MB)
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Installing collected packages: networkx, rdkit-pypi, ligning
  Attempting uninstall: networkx
    Found existing installation: networkx 2.4
    Uninstalling networkx-2.4:
      Successfully uninstalled networkx-2.4
Successfully installed ligning-0.1.1 networkx-2.8.3 rdkit-pypi-2022.3.2.1

Test LigninGraphs (ligning) and RDKit import

# set ligning path (optional if installed via pip)
import sys, os
project_path = os.path.abspath(os.path.join(os.getcwd(), '..\..\..'))
print(project_path)
sys.path.insert(0, project_path)


from ligning.monomer import Monomer
from ligning.utils import graph_to_mol
from rdkit.Chem.Descriptors import ExactMolWt
from rdkit.Chem.rdMolDescriptors import CalcMolFormula

c:\Users\yifan\Documents\GitHub\LigninGraphs

Create a H monomer Visualize the H monomer using the mol object

H_G = Monomer('H').create()
H_mol = graph_to_mol(H_G)
H_mol

Calculate the molecule weight and chemical formula

H_mw = ExactMolWt(H_mol)
print('The molecular weight is {}'.format(H_mw))

H_formula = CalcMolFormula(H_mol)
print('The chemcial formula is {}'.format(H_formula))

The molecular weight is 150.06807956
The chemcial formula is C9H10O2