Metadata-Version: 2.1
Name: molecular-interaction-rules
Version: 1.2.0
Summary: UNKNOWN
Home-page: https://www.github.com/mackerell-lab/Non-Covalent-Molecular-Interaction-Rules
Author: Suliman Sharif
Author-email: sharifsuliman1@gmail.com
License: GPL
Description: <h1 align="center">Molecular Interaction Rules</h1>
        
        <p align="center">
        <img width="784" alt="Screenshot 2024-05-29 at 10 14 28 PM" src="https://github.com/mackerell-lab/Non-Covalent-Molecular-Interaction-Rules/assets/11812946/880e237a-f9a3-43d5-bb75-c7aeb756f28a">
        </p>
        
        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.  
        
        ![Downloads](https://pepy.tech/badge/molecular-interaction-rules)
        
        #### Pip Installation
        
        
        ```bash
        
        pip install molecular-interaction-rules 
        
        ```
        
        #### Local Installation
        
        Clone the repository and run
        
        ```
        python -m pip install -e .
        ```
        
        #### Import MoleculerDatabase
        
        ```python
        from molecular_interaction_rules import MoleculerDatabase
        
        molecules = MoleculerDatabase()
        ```
        
        #### Get Full List of Molecules in Current Database
        
        ```python
        # Get Full List of Molecules in Current Database
        all_molecules = molecules.get_molecule_list()
        print (all_molecules)
        ```
        
        #### Get Functional Group Family of Desired Molecule
        
        ```python
        # 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
        
        ```python
        # 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
        
        ```python
        # 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)
        
        ```python
        # 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)
        
        ```python
        # 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)
        ```
        
        <h2 align="center">Moleculer Database</h2>
        
        
        | 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 |    | Alcohols      | Methanol |  
        | 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 |  
        
        <h2 align="center">Contact</h2>
        
        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
        
Keywords: molcules non-covalent interactions rules geometry
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: Mozilla Public License 2.0 (MPL 2.0)
Classifier: Intended Audience :: Developers
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Description-Content-Type: text/markdown
