molecular-interaction-rules 1.2.0

No project description provided

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