schrodinger.test.build_test_structures module

Some convenience functions to quickly and reproducibly create structures for testing.

schrodinger.test.build_test_structures.structure_from_smiles(smiles: str)

Create a structure.Structure from a SMILES string. The structure is not energy minimized, so it will probably be distorted.

Parameters

smiles – SMILES string representation of the desired molecule.

Return type

structure.Structure

Returns

CT of the input SMILES string.

schrodinger.test.build_test_structures.create_fragment(resname, restype='organic', assign_atom_names=False)

Use mmfrag library to create arbitrary fragments. See the mmfrag documentation for a list of possible fragments that can are available and which “type” they belong to. By default the pdb atom names for all atoms are those set by mmfrag (usually blank), but setting assign_atom_names to True will set unique atom names in the manner described in _assignAtomNames.

See .bld files in mmfrag for resname and restype.

schrodinger.test.build_test_structures.shuffle_ct_atoms(ct)

Randomize the atom-ordering within a ct. This is useful for testing to make sure there is no atom-order dependence for a given function. The input ct is not changed and the reordered output ct is returned.

Parameters

ct (structure.Structure) – Structure to be shuffled. Atom order of this structure will be preserved.

Return type

structure.Structure

Returns

Structure with atom order shuffled.

schrodinger.test.build_test_structures.build_protein_helix(sequence)

Uses schrodinger.protein.helix to create an Alpha-helix protein based on the input sequence.

Ptype sequence

str

Parameters

sequence – String of single letter amino acid names.