Module build_test_structures

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

Functions

[hide private]

structure.Structure

structure_from_smiles(smiles)
Create a structure.Structure from a SMILES string.

create_fragment(resname, restype="organic", assign_atom_names=False)
Use mmfrag library to create arbitrary fragments.

_assign_atom_names(ct)
Assign unique atom names by residue for a structure.

structure.Structure

shuffle_ct_atoms(ct)
Randomize the atom-ordering within a ct.

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

Function Details

[hide private]

structure_from_smiles(smiles)

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.

Returns: structure.Structure

CT of the input SMILES string.

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.

_assign_atom_names(ct)

Assign unique atom names by residue for a structure. Atom names consist of the element (2 character) followed by a unique number for that element. (ie C1,C2,H1)

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 to be shuffled. Atom order of this structure will be preserved.

Returns: structure.Structure

Structure with atom order shuffled.

build_protein_helix(sequence)

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

Parameters:

sequence - String of single letter amino acid names.