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# Group4MoleculeDatabase

# Documentation

# Group4: Molecule Database

# Description: 

**How it was implemented:**

To execute the program via the command-line interface, navigate to the directory where the md file is located. Once in the directory, users can run one of the following commands:

To execute the program via the command-line interface, navigate to the directory where the md file is located. Once in the directory, users can run one of the following commands. Please ensure that the file or folder path provided is the complete path to the selected file or folder.

./md --addMolecule [FILE PATH]: This command adds the molecule specified in the file path to the database. For example, to add biotin from the file biotin.txt to the database, run: ./md --addMolecule /path/to/directory/biotin.txt. 

./md --addBulk [FOLDER PATH]: This command allows users to add multiple molecules in bulk from a specified folder. For example, to add all molecules inside the Molecules folder, simply run: ./md --addBulk path/to/Molecules.

./md --delete [FILE PATH]: This command deletes the molecule specified in the file path to the database. For example, to delete biotin from the file biotin.txt, run:./md --delete /path/to/directory/biotin.txt

./md --findMolecule [FILE PATH]: This command searches for the isomorphic molecule specified in the file path within the database. For instance, to find an isomorphic molecule to biotin within the database using the file biotin.txt, run: ./md --findMolecule /path/to/directory/biotin.txt. If the program finds an exact match, it will display “FOUND.” If not, it will show “NO EXACT MATCH FOUND” and return the most similar molecule to the given molecule within the database.

./md --addProteins [FILE PATH]: This command adds protein molecules generated by `--makeManySimple` command and `--makeFewComplex` command to the database. The default path for --makeManySimple is “../simple” and `--makeFewComplex` “../complex”. For instance, ./md --addproteins ../simple and ./md --addProteins ../complex.

./md --findSubgraph [FILE PATH]: This command finds and outputs all molecules containing a subgraph provided in the file path. If no subgraph is found, the program outputs "No subgraph found."

./md --downloadPubChem start,end: This command downloads molecules from the PubChem database. "start" and "end" are indices or Compound ID (CID) numbers of the molecules in the PubChem database. For example, to download molecules 20-27, type: ./md --downloadPubChem 20,27

./md --printName: This command prints the name of the database.

./md --makeManySimple: This command generates 10 million molecule files with between 52 and 136 atoms.

./md --makeManySimple: This command generates 10 million molecule files, each having between 52 and 136 atoms. Generated molecules are saved in a folder called `simple` which is located in the parent directory of the project folder. Users do not need to specify a file or folder path for this feature.

./md --makeFewComplex: This command generates 10,000 million molecule files with over 10,000 atoms each.

./md --makeFewComplex: This command creates 10,000 million molecule files, each with over 10,000 atoms. Generated molecules are saved in a folder called `complex` that is located in the parent directory of the project folder. Users do not need to specify a file or folder path for this feature.

./md --addProteins [FILE PATH]: This command adds proteins created by the `--makeManySimple` and `--makeFewComplex` commands. Please make sure to select a file path, which is either the Complex or Simple directory.

./md --marco: This command pings the server to check if it is still alive.

**Stand-alone GUI**

**Percentage:** 15%