Molecular Interaction Rules
Welcome to the Non-Covalent Molecular Interaction Rule Database. Molecules are recorded in their internal coordinate system and quantum mechanically optimized with mp2/aug-cc-pvdz geometry with manual community edits as needed on visual inspection. Monomers and Dimers for NCIs can be formed readily to the user.
Pip Installation
pip install molecular-interaction-rules
Local Installation
Clone the repository and run
python -m pip install -e .
Import MoleculerDatabase
from molecular_interaction_rules import MoleculerDatabase
molecules = MoleculerDatabase()
Get Full List of Molecules in Current Database
# Get Full List of Molecules in Current Database
all_molecules = molecules.get_molecule_list()
print (all_molecules)
Get Functional Group Family of Desired Molecule
# Get Functional Group Family of Desired Molecule
mol1= "benzene"
mol1_fg_family = molecules.get_molecule_fg_family(mol1)
print(mol1_fg_family)
Get Site Names in a Molecule for Interaction with Another Molecule
# Get Site Names in a Molecule for Interaction with Another Molecule
mol1_atom_names = molecules.get_atom_names(mol1)
print(mol1_atom_names)
Output:
['RC1', 'H1']
Get Monomer Z-Matrix for Site of Interest
# Get Monomer Z-Matrix for Site RC1
mol1_site_of_interest = "RC1"
mol1_zmat_for_site_of_interest = molecules.get_monomer_coordinates(mol1, mol1_site_of_interest)
print (mol1_zmat_for_site_of_interest)
Get Dimer Z-Matrix for Desired Interaction Type
Interaction Type 1 (pi-stacking)
# Get Benzene-Dimer Z-Matrix for pi- stacking
mol2 = 'benzene'
mol2_site_of_interest = 'RC1'
benzene_dimer_pistack = molecules.form_dimer_coordinates(mol1, mol1_site_of_interest, mol2, mol2_site_of_interest)
print (benzene_dimer_pistack)
Interaction Type 2 (C-H--pi interaction; T-shaped)
# Get Benzene-Dimer Z-Matrix for C-H--pi interaction mode
mol2 = 'benzene'
mol2_site_of_interest = 'H1'
benzene_dimer_chpi = molecules.form_dimer_coordinates(mol1, mol1_site_of_interest, mol2, mol2_site_of_interest)
print (benzene_dimer_chpi)
Moleculer Database
| Functional Group Class | Molecules |
|---|---|
| Aromatic | Azulene, Benzene, Bipyrrole, Bromobenzene, Chlorobenzene, Cytosine, Fluorobenzene, Four Pyridinone, Furan, Imidazole, Imidazolium, Indole, Indolizine, Iodobenzene, Isoxazole, Methylene Oxide, Nitrobenzene, 1 Phenyl-4-Pyridinone, Phenol, Phenoxazine, Pyridine, Pyridinium, Pyrimidine, Pyrrolidine, Thiophene, 3-Aminopyridine, 2-H-Pyran, Uracil |
| Alkanes | Cyclobutane, Cyclohexane, Cyclopropane, Neopentane, Propane |
| Alkenes | Cyclohexene, Cyclopentene, Methoxyethene, 1,3-dibutene, Propene, 2-Pyrroline |
| Alkynes | Propyne |
| Amides | Acetamide, Amidinium, Azetidinone, DimethylFormamide, Methylacetamide, Prolineamide, 2-pyrrolidinone |
| Amines | Ammonia, Dimethylamine, Ethyl Ammonium, Hydrazine, Methylamine, Piperidine, (Z)-N-methylethanimine, Tetramethylammonium, Trimethylamine, Triethylammonium |
| Carbonyls | Acetaldehyde, Acetate, Acetic Acid, Acetone, Carbon Dioxide, Formaldehyde, Methylacetate, Urea |
| Ethers | Dimethyl ether, Epoxide, Oxetane, Tetrahydrofuran, Tetrahydropyran |
| Imines | Ethenamine |
| Halogens | Bromoethane, Chloroethane, Dibromoethane, Dichloroethane, Fluoroethane, Difluoroethane, Tribromoethane, Trichloroethane, Trifluoroethane |
| Nitriles | Acetonitrile |
| Organophosphorus | Methyl Phosphate, Dimethyl Phosphate |
| Organosulfur | Dimethyl sulfone, Dimethyl Sulfoxide, Dimethyl trithiocarbonate, Dimethyl Disulfide, Ethylsulfanyl Phosphonic Acid, Methanethiol, Methylthiolate |
Contact
Lead Developer: Suliman Sharif Co-Authors: Anmol Kumar, Alexander D. MacKerell Jr.
© Copyright 2024 – University of Maryland School of Pharmacy, Computer-Aided Drug Design Center All Rights Reserved
1 maintainer
Metadata
1 maintainer
Release files for molecular-interaction-rules 1.2.0
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