schrodinger.application.peptide_workflow.minimize module

schrodinger.application.peptide_workflow.minimize.get_interface_crankshaft_backbone_atoms(st, backbone, recep, cutoff=5.0)

Get the overlap between the crankshaft “backbone” and the interface. Here we used a non-traditional definition of iRMSD because CA,CB,N,O and other atom ptypes are not always present in a user input “peptide”. :param st: peptide structure :type st: Structure :param backbone: list of atom indices in crankshaft backbone :type backbone: list(int) :param recep: receptor structure :type recep: Structure :param cutoff: distance cutoff for defining interface :type cutoff: float

class schrodinger.application.peptide_workflow.minimize.AbstractMinimizer

Bases: object

Minimize class, used to minimize the peptide.st and report the energy

initStack()

Intializes the proper context management

setUpPeptide()

This initializes proper environment for the current minimizer, assign FF, etc

minimize()

Runs the actual minimization and write energy to peptide.st

class schrodinger.application.peptide_workflow.minimize.OPLSMinimizer(clash_tolerance=100, dielectric_constant=1.0)

Bases: AbstractMinimizer

Primary use case: conformational sampling This is the OPLS minimizer for conformational sampling without a receptor

__init__(clash_tolerance=100, dielectric_constant=1.0)

Parameters:

stack (contextlib.ExitStack) – An exit stack

initStack(stack)

Initialize environment using stack. :param stack: An exit stack :type stack: contextlib.ExitStack

setUpPeptide(stack, minimize_st)

Initiate the minimizer and structure assignment :param stack: An exit stack :type stack: contextlib.ExitStack :param minimize_st: structure to initiate the minimizer atomtyping, ff assignment, etc. :type minimize_st: structure.Structure

minimize(peptide_t)

Minimize the peptide_t :param peptide_t: peptide to be minimizaed :type peptide_t: Peptide

class schrodinger.application.peptide_workflow.minimize.SkateMinimizer(grid_file, glide_keywords)

Bases: AbstractMinimizer

Primary use case: rigid receptor docking Minimize with Skate/Glide, minimize the interaction with receptor using Glide scoring function

__init__(grid_file, glide_keywords)

Parameters:

• grid_file (string) – grid_file

• glide_keywords (dictionary) – glide keywords to use with glide.Config

initStack(stack)

Intializes the proper context management

setUpPeptide(stack, minimize_st)

Initiate the minimizer and structure assignment :param stack: An exit stack, which is not used. :type stack: contextlib.ExitStack :param minimize_st: structure to initiate the minimizer atomtyping, ff assignment, etc. :type minimize_st: structure.Structure

minimize(peptide_t)

Minimize the peptide_t :param peptide_t: peptide to be minimizaed :type peptide_t: Peptide

minimizeXyz(peptide_t)

Use glide.minimize_xyz to minimize and score the peptide_t This is similar to the Post docking minimization in Glide :param peptide_t: peptide to be minimizaed :type peptide_t: Peptide

minimizeTorsions(peptide_t)

Use TorsionAndPlacementMinimizer to minimize and score the peptide_t :param peptide_t: peptide to be minimizaed :type peptide_t: Peptide

scoreAndUpdatePeptide(peptide_t)

Score the self.peptide_pose and update the st and energy of peptide_t This assumes self.peptide_pose is already minimized :param peptide_t: peptide to be updated :type peptide_t: Peptide

rescaleSkateEmodel(energy)

This is to score “bad” poses either clashing with the receptor or partially out of box Those poses are kept to help with the sampling :param energy: raw energy :type energy: float

class schrodinger.application.peptide_workflow.minimize.PrimeMinimizer(recept_st, recept_asl=None)

Bases: AbstractMinimizer

Primary use case: docking and induced-fit docking Minimize with PrimeServer, this minimizer is not a grid-based scoring, so it’s slow. With this approach, we can model the receptor flexibility

__init__(recept_st, recept_asl=None)

Parameters:

• recept_st – receptor structure

• recept_asl (string) – receptor ASL to define movable protein atoms

initStack(stack)

Initialize environment using stack. :param stack: An exit stack :type stack: contextlib.ExitStack

setUpPeptide(stack, minimize_st)

Initiate the minimizer and structure assignment :param stack: An exit stack :type stack: contextlib.ExitStack :param minimize_st: structure to initiate the minimizer atomtyping, ff assignment, etc. :type minimize_st: structure.Structure

minimize(peptide_t)

Minimize the peptide_t :param peptide_t: peptide to be minimizaed :type peptide_t: Peptide