CommonUseCases

List of common use cases

This is a list of common use cases, which are or should/will be supported by libaas.

Complex use cases in one example

Create an amino acid sequence using custom amino acids with custom modifications and a custom element configuration

1. create/add custom element
2. create/add stoichiometry configuration
3. create/add custom raw modification
4. create/add custom amino acid
5. create amino acid sequence using the peptide sequence and modification string
6. set custom stoichiometry configuration on amino acid sequence

Amino acid sequence

Create an amino acid sequence

Add a standard modification

Add a custom modification

Create an amino acid sequence with a modification string

Create an amino acid sequence with a modification string, containing custom modifications

1. custom modifications - not present in unimod
2. custom modifications - present in unimod but with different properties

Remove a (custom) modification

Retrieve the stoichiometry

Residue

Create a residue

Set/Change the amino acid

Set/Change the modification

Apply stoichiometry configurations

Retrieve the stoichiometry

Amino acid

Create an amino acid

Set a stoichiometry configuration

Retrieve the stoichiometry

Raw Amino acid

Retrieve a standard raw amino acid

Create a custom raw amino acid

Add a custom raw amino acid

Override a standard raw amino acid

Retrieve the stoichiometry

Modification

Use a standard modification

Create a custom modification

Add a custom specificity

Use a custom modification

Retrieve the stoichiometry

Set a stoichiometry configuration

in order to use custom elements

Raw modification

Retrieve a standard modification

Create a custom modification

Add a custom specificity

Add a custom modification

Retrieve a custom modification

Retrieve the stoichiometry

a) manually

b) by convenience functions

Override a standard modification

a) from scratch

b) using standard modification

Specificity

Create a custom specificity

Stoichiometry

Add a stoichiometry entry

Retrieve a stoichiometry entry

Stoichiometry configuration

Retrieve default stoichiometry configuration

The default stoichiometry configuration contains the mapping (symbol to key) of all standard elements. Custom elements are not present in the default stoichiometry configuration!

Create a custom stoichiometry configuration

It is not necessary to add all standard elements in a stoichiometry configuration since all methods using the configuration automatically fall back to the default mapping in case an element is not present in the custom configuration.

Add a custom stoichiometry configuration

a) manually

b) by convenience functions

Retrieve a custom stoichiometry configuration

Override the default stoichiometry configuration

a) from scratch It is not recommended to create the stoichiometry configuration from scratch since the default configuration is used when a custom mapping does not contain an element. But, the default configuration does not contain all element (only standard elements).

b) using standard mapping

Elements

Retrieve a standard element

Create a custom element

Add a custom element

a) manually

b) by convenience functions

Retrieve a custom element

Override a standard element

a) from scratch

1. create ElementImpl
2. add like a custom element

b) using standard element

1. create ElementImpl using ElementImpl(Key) - this will initialize the element with its default properties
2. add like a custom element

Isotope

Create an isotope