schrodinger.application.peptide_workflow.moves module

class schrodinger.application.peptide_workflow.moves.AbstractMover

Bases: object

randomMoveOnce(peptide, amplitude=0.4)

class schrodinger.application.peptide_workflow.moves.ConformationSampler(random_seed)

Bases: AbstractMover

__init__(random_seed)

randomMoveOnce(peptide, amplitude=0.4)

class schrodinger.application.peptide_workflow.moves.ComplexDockingMover(random_seed)

Bases: AbstractMover

__init__(random_seed)

randomMoveOnce(peptide, amplitude=0.4)

schrodinger.application.peptide_workflow.moves.move_centroid_to_xyz(st, x, y, z)

move the structure to x, y, z

Parameters:

• st (Structure) – structure to be moved

• z (x y) – xyz of the destination

schrodinger.application.peptide_workflow.moves.random_translate_move(peptide, random_generator, amp=0.4)

randomly move the structure

Parameters:

• peptide (Peptide) – peptide to be moved

• random_generator (numpy.random.default_rng object) – random number generator object

• amp (float) – 1/5 * standard deviation of the move in each Cartesian direction (A)

schrodinger.application.peptide_workflow.moves.random_rotation_move(peptide, random_generator, amp=0.4)

randomly rotate the structure

Parameters:

• peptide (Peptide) – peptide to be moved

• random_generator (numpy.random.default_rng object) – random number generator object

• amp (float) – standard deviation of the rotation (radian)

schrodinger.application.peptide_workflow.moves.delete_ring_bond(st, atom_index, crankshaft_backbone)

delete the nearest ring bond from the specified atom :param st: structure to be rotated :type st: structure.Structure :param atom_index: atom index of the atom whose ring bond will be removed :type atom_index: int :param crankshaft_backbone: indices of atoms in the crankshaft backbone :type crankshaft_backbone: [int]

schrodinger.application.peptide_workflow.moves.crankshaft_move(peptide, atom1, atom2, moving_atoms, random_number_generator, amp=0.4)

Perform a crankshaft move for the peptide

Parameters:

• peptide (Peptide) – peptide to be moved

• atom1 – atom index of the first atom of the rotating axis

• atom2 (int) – atom index of the second atom of the rotating axis

• moving_atoms ([int]) – indices of atoms to be moved between atom 1 and atom2

• random_generator (numpy.random.default_rng object) – random number generator object

• amp (float) – standard deviation of the rotation (radian)

schrodinger.application.peptide_workflow.moves.crankshaft_move_for_complex_cycles(peptide, random_generator, amp=0.4)

Perform a crankshaft move for complex cycles (bi- tri- cycles)

Parameters:

• peptide (Peptide) – peptide to be moved

• random_generator (numpy.random.default_rng object) – random number generator object

• amp (float) – standard deviation of the rotation (radian)