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Molecules input

Every single virtual screening campaign initiates with the identification of a chemical space that is intended to be explored. This chemical space may vary significantly in size, ranging from a single molecule to a large set of hundred millions compounds.

In this respect, the most simple procedure to read a set of compound into TidyScreen is by using a .csv file structured in the following way:

field_#1: SMILES notation indicating the structure of the molecule/s to be read.

field_#2: name of the molecule/s

field_#3: Flag used for general purposes (such as filtering, etc)

In order to read a .csv file, the corresponding function should be invoked using the generated chemspace_object as follows:

# Step #1: It is assumed that TidyScreen packages have been activated
# Step #2: A project named `tutorial` has been generated
# Step #3: A chemspace object named `tutorial_chemspace` has been created
$ tutorial_chemspace.input_csv($PATH_TO_FILE)

When the above function is executed, the first line of the .csv file is written to the console, asking the user to indicate if the files has a header or not (y/n).

Once the input files containing valid SMILES notations, a table named after the read .csv file will be created in the chemspace.db.

Molecules tables contained within the chemspace.db can be listed as follows:

# Step #1: It is assumed that TidyScreen packages have been activated
# Step #2: A project named `tutorial` has been generated
# Step #3: A chemspace object named `tutorial_chemspace` has been created
$ tutorial_chemspace.list_ligand_tables()

Also a table can be deleted from chemspace.db using:

# Step #1: It is assumed that TidyScreen packages have been activated
# Step #2: A project named `tutorial` has been generated
# Step #3: A chemspace object named `tutorial_chemspace` has been created
$ tutorial_chemspace.delete_table(TABLE_NAME)

In case a 2D depiction of compounds stored in a given table is required, the following function can be invoked:

# Step #1: It is assumed that TidyScreen packages have been activated
# Step #2: A project named `tutorial` has been generated
# Step #3: A chemspace object named `tutorial_chemspace` has been created
$ tutorial_chemspace.depict_ligand_table(TABLE_NAME)

The depiction of a table of molecules will generate a set of .png files that will be stored within the $PROJECT_PATH/chemspace/misc/$TABLE_NAME folder.

note

Frequently, during virtual screening campaigns a high number of molecules are stored within a table. Consequently, depicting all of them may lead to a large number or .png files. In those cases, the following are usefull

  • max_mols_ppage: indicates the number of depictions included per .png file. Default: 25
  • limit: set the maximum number of molecules to depict. Default: 0 ; depicts all molecules stored in the table.
  • random: If set to True will depict the required molecules indicated with limit picking a randomized selection. Default: False