Posts

Showing posts with the label Python code - Molecular structure from .sdf file

Python code - Molecular structure from .sdf file

Image
Python code – Fetching structure of molecules from .sdf file with rdkit   Written by, Dr. M Kanagasabapathy Asst. Professor Department of Chemistry Rajapalayam Rajus’ College Madurai Kamaraj University Rajapalayam (TN) INDIA   .sdf stands for S tructural D ata F ile (SDF) of a molecule and it’s based on .mol format. .sdf files encoded for multiple molecular structure in a single file, whereas .mol file is encoded for a single molecule. In .sdf file format, either 2D or 3D structures of multiple molecules are delimited by $$$$ (4 dollars) and it is formatted with ASCII. .sdf data files are primarily used by chemical suppliers.   Sample .sdf file   F0244-0040   -MTS-   05272009262D 0   0.00000     0.00000     0    40 45  0  0  0  0  0  0  0  0999 V2000     0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0    -1.3070   -0.7190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0    -2.6140    0.0480    0.0000 N   0  0