<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.
<h2 align="center">Quickstart</h2>
#### Install
```bash
pip install molecular-interaction-rules
```
#### Get Atom Names
```python
from molecular_interaction_rules import MoleculerDatabase
molecules = MoleculerDatabase()
benzene_atom_names = molecules.get_atom_names('benzene')
print(benzene_atom_names)
```
Output:
```
['RC1', 'H1']
```
#### Get Monomer Coordinates
```python
from molecular_interaction_rules import MoleculerDatabase
molecules = MoleculerDatabase()
benzene_monomer = molecules.get_monomer_coordinates('benzene', 'RC1')
print (benzene_monomer)
```
Output:
```
X11
C11 X11 1.3940
C12 C11 1.3774 X11 60.0000
C13 C12 1.3774 C11 120.0000 X11 0.0000
C14 C13 1.3774 C12 120.0000 C11 0.0000
C15 C14 1.3774 C13 120.0000 C12 0.0000
C16 C15 1.3774 C14 120.0000 C13 0.0000
H11 C11 1.0756 C12 120.0000 C13 180.0000
H12 C12 1.0756 C11 120.0000 C13 180.0000
H13 C13 1.0756 C12 120.0000 C11 180.0000
H14 C14 1.0756 C13 120.0000 C12 180.0000
H15 C15 1.0756 C14 120.0000 C13 180.0000
H16 C16 1.0756 C15 120.0000 C11 180.0000
0 1
```
#### Get Dimer Coordinates
```python
from molecular_interaction_rules import MoleculerDatabase
molecules = MoleculerDatabase()
benzene_dimer = molecules.form_dimer_coordinates('benzene', 'RC1', 'benzene', 'RC1')
print (benzene_dimer)
```
Output
```
X11
C11 X11 1.3940
C12 C11 1.3774 X11 60.0000
C13 C12 1.3774 C11 120.0000 X11 0.0000
C14 C13 1.3774 C12 120.0000 C11 0.0000
C15 C14 1.3774 C13 120.0000 C12 0.0000
C16 C15 1.3774 C14 120.0000 C13 0.0000
H11 C11 1.0756 C12 120.0000 C13 180.0000
H12 C12 1.0756 C11 120.0000 C13 180.0000
H13 C13 1.0756 C12 120.0000 C11 180.0000
H14 C14 1.0756 C13 120.0000 C12 180.0000
H15 C15 1.0756 C14 120.0000 C13 180.0000
H16 C16 1.0756 C15 120.0000 C11 180.0000
0 1
--
X21 X11 DISTANCE C11 180.0000 C12 90.0000
C21 X21 1.3940 X11 90.0000 C11 180.0000
C22 C21 1.3774 X21 60.0000 X11 90.0000
C23 C22 1.3774 C21 120.0000 X21 0.0000
C24 C23 1.3774 C22 120.0000 C21 0.0000
C25 C24 1.3774 C23 120.0000 C22 0.0000
C26 C25 1.3774 C24 120.0000 C23 0.0000
H21 C21 1.0756 C22 120.0000 C23 180.0000
H22 C22 1.0756 C21 120.0000 C23 180.0000
H23 C23 1.0756 C22 120.0000 C21 180.0000
H24 C24 1.0756 C23 120.0000 C22 180.0000
H25 C25 1.0756 C24 120.0000 C23 180.0000
H26 C26 1.0756 C25 120.0000 C21 180.0000
0 1
```
<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
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"description": "<h1 align=\"center\">Molecular Interaction Rules</h1>\n\n<p align=\"center\">\n<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\">\n</p>\n\nWelcome 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. \n\n<h2 align=\"center\">Quickstart</h2>\n\n#### Install\n\n```bash\n\npip install molecular-interaction-rules \n\n```\n#### Get Atom Names\n\n```python\n\nfrom molecular_interaction_rules import MoleculerDatabase\n\nmolecules = MoleculerDatabase()\nbenzene_atom_names = molecules.get_atom_names('benzene')\n\nprint(benzene_atom_names)\n\n```\n\nOutput:\n\n```\n['RC1', 'H1']\n```\n\n#### Get Monomer Coordinates\n\n```python\n\nfrom molecular_interaction_rules import MoleculerDatabase\n\nmolecules = MoleculerDatabase()\nbenzene_monomer = molecules.get_monomer_coordinates('benzene', 'RC1')\n\nprint (benzene_monomer)\n\n```\n\nOutput:\n\n```\nX11\nC11 X11 1.3940\nC12 C11 1.3774 X11 60.0000\nC13 C12 1.3774 C11 120.0000 X11 0.0000\nC14 C13 1.3774 C12 120.0000 C11 0.0000\nC15 C14 1.3774 C13 120.0000 C12 0.0000\nC16 C15 1.3774 C14 120.0000 C13 0.0000\nH11 C11 1.0756 C12 120.0000 C13 180.0000\nH12 C12 1.0756 C11 120.0000 C13 180.0000\nH13 C13 1.0756 C12 120.0000 C11 180.0000\nH14 C14 1.0756 C13 120.0000 C12 180.0000\nH15 C15 1.0756 C14 120.0000 C13 180.0000\nH16 C16 1.0756 C15 120.0000 C11 180.0000\n0 1\n\n```\n\n#### Get Dimer Coordinates \n\n```python\n\nfrom molecular_interaction_rules import MoleculerDatabase\n\nmolecules = MoleculerDatabase()\nbenzene_dimer = molecules.form_dimer_coordinates('benzene', 'RC1', 'benzene', 'RC1')\n\nprint (benzene_dimer)\n\n```\n\nOutput\n```\nX11\nC11 X11 1.3940\nC12 C11 1.3774 X11 60.0000\nC13 C12 1.3774 C11 120.0000 X11 0.0000\nC14 C13 1.3774 C12 120.0000 C11 0.0000\nC15 C14 1.3774 C13 120.0000 C12 0.0000\nC16 C15 1.3774 C14 120.0000 C13 0.0000\nH11 C11 1.0756 C12 120.0000 C13 180.0000\nH12 C12 1.0756 C11 120.0000 C13 180.0000\nH13 C13 1.0756 C12 120.0000 C11 180.0000\nH14 C14 1.0756 C13 120.0000 C12 180.0000\nH15 C15 1.0756 C14 120.0000 C13 180.0000\nH16 C16 1.0756 C15 120.0000 C11 180.0000\n0 1\n--\nX21 X11 DISTANCE C11 180.0000 C12 90.0000\nC21 X21 1.3940 X11 90.0000 C11 180.0000\nC22 C21 1.3774 X21 60.0000 X11 90.0000\nC23 C22 1.3774 C21 120.0000 X21 0.0000\nC24 C23 1.3774 C22 120.0000 C21 0.0000\nC25 C24 1.3774 C23 120.0000 C22 0.0000\nC26 C25 1.3774 C24 120.0000 C23 0.0000\nH21 C21 1.0756 C22 120.0000 C23 180.0000\nH22 C22 1.0756 C21 120.0000 C23 180.0000\nH23 C23 1.0756 C22 120.0000 C21 180.0000\nH24 C24 1.0756 C23 120.0000 C22 180.0000\nH25 C25 1.0756 C24 120.0000 C23 180.0000\nH26 C26 1.0756 C25 120.0000 C21 180.0000\n0 1\n```\n\n<h2 align=\"center\">Moleculer Database</h2>\n\n\n| Functional Group Class | Molecules |\n|-|-|\n| 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 | \n| Alkanes | Cyclobutane, Cyclohexane, Cyclopropane, Neopentane, Propane | \n| Alkenes | Cyclohexene, Cyclopentene, Methoxyethene, 1,3-dibutene, Propene, 2-Pyrroline | \n| Alkynes | Propyne | \n| Amides | Acetamide, Amidinium, Azetidinone, DimethylFormamide, Methylacetamide, Prolineamide, 2-pyrrolidinone | \n| Amines | Ammonia, Dimethylamine, Ethyl Ammonium, Hydrazine, Methylamine, Piperidine, (Z)-N-methylethanimine, Tetramethylammonium, Trimethylamine, Triethylammonium | \n| Carbonyls | Acetaldehyde, Acetate, Acetic Acid, Acetone, Carbon Dioxide, Formaldehyde, Methylacetate, Urea | \n| Ethers | Dimethyl ether, Epoxide, Oxetane, Tetrahydrofuran, Tetrahydropyran | \n| Imines | Ethenamine | \n| Halogens | Bromoethane, Chloroethane, Dibromoethane, Dichloroethane, Fluoroethane, Difluoroethane, Tribromoethane, Trichloroethane, Trifluoroethane | \n| Nitriles | Acetonitrile | \n| Organophosphorus | Methyl Phosphate, Dimethyl Phosphate | \n| Organosulfur | Dimethyl sulfone, Dimethyl Sulfoxide, Dimethyl trithiocarbonate, Dimethyl Disulfide, Ethylsulfanyl Phosphonic Acid, Methanethiol, Methylthiolate | \n\n<h2 align=\"center\">Contact</h2>\n\nLead Developer: Suliman Sharif\nCo-Authors: Anmol Kumar, Alexander D. MacKerell Jr.\n\n\n\n\n\u00a9 Copyright 2024 \u2013 University of Maryland School of Pharmacy, Computer-Aided Drug Design Center All Rights Reserved",
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