buf chemical

Subcommand Description

buf chemical allows you to access and modify your chemical library, i.e. your personal list of chemicals and their molar masses. Before making solutions that specify a chemical’s concentration in molar, that chemical’s molar mass must first be added to your chemical library.

Adding Chemicals

To add a chemical to your library, use buf -a <molar_mass> <chemical_names>..., where the chemical’s molar mass is in g/mol. For example, after adding NaCl to your library with buf add -a 58.44 NaCl, you can then buf make 2L 1M NaCl to calculate the mass of salt you would need to add to a 2L solution to raise the salt concentration to 1M (see buf make for more information on performing solution calculations).

Chemicals can have multiple names, which can be listed upon addition to your library. For example, using buf chemical -a 58.44 NaCl salt allows you use either the name ‘salt’ or ‘NaCl’ when making buffers (i.e. buf make 2L 1M NaCl is equivalent to buf make 2L 1M salt, since both expressions refer to the same molar mass.

Nicknaming Chemicals

To add additional names to an existing entry in your chemical library (also known as ‘nicknaming’ the chemical), use buf chemical -n <existing_chemical_name> <nicknames>.... For example, if you added NaCl to your library with buf chemical -a 58.44 NaCl, and then nicknamed the chemical with buf chemical -n NaCl salt table_salt, you could use any of ‘NaCl’, ‘salt’, or ‘table_salt’ to refer to the same molar mass. Note that using buf chemical -a 58.44 NaCl table_salt salt is equivalent to using buf chemical -a 58.44 NaCl followed by buf chemical -n NaCl table_salt salt.

Adding Chemicals From a Text File

Another way to add chemicals to your library is by specifying a list of them in a text file. This file should contain one chemical per line, where the first word on each line specifies the chemical’s molar mass, followed by the list of the chemical’s names. Spaces should separate each item on a line. For example, if a file ‘chemicals.txt’ contains the following:

58.44 NaCl salt
68.08 Imidazole imi
74.55 KCl

Using buf chemical -a chemicals.txt would add these three chemicals to your library.

Deleting Chemicals

To delete a chemical, use buf chemical -d <chemical_name>. By default, chemical deletion is shallow/incomplete; the same chemical can still be accessed through its other names after one name has been deleted. For example, if buf chemical -a 58.44 NaCl salt was used to add a chemical to our library, and then the name ‘NaCl’ was deleted with buf chemical -d NaCl, the name ‘salt’ would still be bound to a molar mass of 58.44 g/mol in your chemical library. To delete a chemical entirely (i.e. delete all its names), use the --complete option. Using the example above, buf chemical -d NaCl --complete would remove both the names ‘NaCl’ and ‘salt’ from our chemical library. To skip the program asking you to confirm your decision, use the --confirm option.

Viewing Your Library

To view information about a specific chemical (its molar mass and additional names), use buf chemical <chemical_name>. To view your entire chemical library, use buf chemical.