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 install molecular-interaction-rules
Clone the repository and run
python -m pip install -e .
from molecular_interaction_rules import MoleculerDatabase
molecules = MoleculerDatabase()all_molecules = molecules.get_molecule_list()
print (all_molecules)molecule_a= "benzene"
molecule_a_fg_family = molecules.get_molecule_fg_family(molecule_a)
print(molecule_a_fg_family)molecule_a= "benzene"
molecule_a_site_names = molecules.get_atom_names(molecule_a)
print(molecule_a_site_names)Output:
['RC1', 'H1']
molecule_a_interaction_site = "RC1"
molecule_a_zmatrix_for_siteRC1 = molecules.get_monomer_coordinates(molecule_a, molecule_a_interaction_site)
print (molecule_a_zmatrix_for_siteRC1)molecule_b = 'benzene'
molecule_b_interaction_site = 'RC1'
benzene_dimer_pi_stack = molecules.form_dimer_coordinates(molecule_a, molecule_a_interaction_site, molecule_b, molecule_b_interaction_site)
print (benzene_dimer_pi_stack)molecule_b = 'benzene'
molecule_b_interaction_site = 'H1'
benzene_dimer_t_shaped = molecules.form_dimer_coordinates(molecule_a, molecule_a_interaction_site, molecule_b, molecule_b_interaction_site)
print (benzene_dimer_t_shaped)| 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 |
Lead Developer: Suliman Sharif Co-Authors: Anmol Kumar, Alexander D. MacKerell Jr.
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