schrodinger.test.hypothesis.strategies.proteins module

schrodinger.test.hypothesis.strategies.proteins.generated_aln_annotations()

schrodinger.test.hypothesis.strategies.proteins.generated_seq_annotations()

schrodinger.test.hypothesis.strategies.proteins.generated_res_prop_annotations()

schrodinger.test.hypothesis.strategies.proteins.generated_annotation_lists()

Returns a strategy providing a list of annotations

class schrodinger.test.hypothesis.strategies.proteins.AlignmentInfo(seqs=(), cysteines_to_bond=(), anchor_residues=())

Bases: object

__init__(seqs=(), cysteines_to_bond=(), anchor_residues=())

An object that can be used in alignment tests

This object can be used to create an alignment, along with fixtures adapted to the alignment that can be used in testing it. We use this object so that different tests can create different kinds of alignments (regular kinds and undoable alignments).

Parameters

seqs – List of sequences to be used in constructing an alignment

schrodinger.test.hypothesis.strategies.proteins.generated_residues(residue_types=None, gaps=True)

Parameters

• draw (function) – A function supplied by hypothesis

• residue_types (list(residue.ElementType)) – Alphabet to use for residues. By default, it will use 95% standard and 5% nonstandard protein amino acids.

• gaps (bool) – Whether to include gaps in default residue types

Returns

A residue suitable for testing

Return type

schrodinger.protein.residue.Residue

schrodinger.test.hypothesis.strategies.proteins.cysteine_pair_lists(residues)

Given an iterable of residues, returns a list of tuples of cysteine pairs

Parameters

• draw (function) – A function supplied by hypothesis

• residues (iterable) – An iterable of residues

Return type

list(tuple)

Returns

A list of tuples of cysteine pairs

schrodinger.test.hypothesis.strategies.proteins.generated_sequences(min_size=0, max_size=None, residue_types=None, include_gaps=True, add_cysteine_bonds=True)

Parameters

• draw (function) – A function supplied by hypothesis

• min_size (int) – Minimum length for sequences

• max_size (int) – Maximum number of residues to include in the sequence

• residue_types (list(residue.ElementType)) – Alphabet to use for residues

• include_gaps (bool) – Whether to generate gaps in the sequence

Returns

A protein sequence suitable for testing

Return type

schrodinger.protein.sequence.ProteinSequence

schrodinger.test.hypothesis.strategies.proteins.generated_multichain_sequences(min_chain_size=0, max_chain_size=None, min_num_chains=1, max_num_chains=None, residue_types=None, include_gaps=True)

Generates multiple sequences that represent different chains of a single protein.

Parameters

• draw (function) – A function supplied by hypothesis

• min_chain_size (int) – The minimum length of each chain’s sequence

• max_chain_size (int) – The maximum length of each chain’s sequence

• min_num_chains – The minimum number of chains in the protein. Must be positive.

• max_num_chains – The maximum number of chains in the protein. Must be less than or equal to 62 since each chain needs a unique single-character name.

• residue_types (list(residue.ElementType)) – Alphabet to use for residues

• include_gaps (bool) – Whether to generate gaps in the sequence

Returns

The generated sequences

Return type

list[schrodinger.protein.sequence.ProteinSequence[

schrodinger.test.hypothesis.strategies.proteins.alignment_infos(include_interseq_ss_bonds=True, include_anchor_residues=False, **kwargs)

Returns everything we need to create an alignment. Takes in kwargs to pass to strategies.lists().

We return an alignment_info instead of an alignment in order to allow tests to create different kinds of alignments and also to pass along additional test data customized to the alignment that the test will create.

Returns

A test fixture for alignment tests

Return type

AlignmentInfo