md

Bindings for protocols::md namespace

class pyrosetta.rosetta.protocols.md.CartesianMD

Bases: pyrosetta.rosetta.protocols.md.MDBase

Emin_obj(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::Emin_obj() const –> double

Gamma(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::Gamma() const –> double

Kappa(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::Kappa() const –> double

acc(*args, **kwargs)

Overloaded function.

  1. acc(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::acc() const –> class utility::vector1<double, class std::allocator<double> >

  1. acc(self: pyrosetta.rosetta.protocols.md.MDBase, idof: int) -> float

C++: protocols::md::MDBase::acc(unsigned long) –> double &

add_trj(self: pyrosetta.rosetta.protocols.md.MDBase, xyz: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::add_trj(class utility::vector1<double, class std::allocator<double> >) –> void

add_trj_scratch(self: pyrosetta.rosetta.protocols.md.MDBase, xyz: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::add_trj_scratch(class utility::vector1<double, class std::allocator<double> >) –> void

apply(self: pyrosetta.rosetta.protocols.md.CartesianMD, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::md::CartesianMD::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.md.CartesianMD, : pyrosetta.rosetta.protocols.md.CartesianMD) pyrosetta.rosetta.protocols.md.CartesianMD

C++: protocols::md::CartesianMD::operator=(const class protocols::md::CartesianMD &) –> class protocols::md::CartesianMD &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.md.CartesianMD) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::md::CartesianMD::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

context_update_step(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::context_update_step() const –> unsigned long

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

cst_on_pose_dynamic(self: pyrosetta.rosetta.protocols.md.CartesianMD, pose: pyrosetta.rosetta.core.pose.Pose, ref_xyz: pyrosetta.rosetta.utility.vector1_double, curr_eqxyz: pyrosetta.rosetta.utility.vector1_double, prv_eqxyz: pyrosetta.rosetta.utility.vector1_double, min_map: pyrosetta.rosetta.core.optimization.CartesianMinimizerMap) None

C++: protocols::md::CartesianMD::cst_on_pose_dynamic(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const class core::optimization::CartesianMinimizerMap &) const –> void

cst_on_pose_simple(self: pyrosetta.rosetta.protocols.md.CartesianMD, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::md::CartesianMD::cst_on_pose_simple(class core::pose::Pose &) const –> void

cst_sdev(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::cst_sdev() const –> double

cummulative_time(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::cummulative_time() const –> double

dt(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::dt() const –> double

dump_poses(self: pyrosetta.rosetta.protocols.md.CartesianMD, pose_ref: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_core_pose_Pose

C++: protocols::md::CartesianMD::dump_poses(const class core::pose::Pose &) const –> class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> >

fresh_instance(self: pyrosetta.rosetta.protocols.md.CartesianMD) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::md::CartesianMD::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_eqxyz(self: pyrosetta.rosetta.protocols.md.CartesianMD) pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::CartesianMD::get_current_eqxyz() const –> class utility::vector1<double, class std::allocator<double> >

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.md.CartesianMD) str

C++: protocols::md::CartesianMD::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

init(self: pyrosetta.rosetta.protocols.md.MDBase) None

C++: protocols::md::MDBase::init() –> void

kinetic_energy(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::kinetic_energy() const –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mass(*args, **kwargs)

Overloaded function.

  1. mass(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::mass() const –> class utility::vector1<double, class std::allocator<double> >

  1. mass(self: pyrosetta.rosetta.protocols.md.MDBase, iatm: int) -> float

C++: protocols::md::MDBase::mass(unsigned long) const –> double

md_energy_report_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::md_energy_report_stepsize() const –> unsigned long

md_report_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::md_report_stepsize() const –> unsigned long

md_rsr_update_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::md_rsr_update_stepsize() const –> unsigned long

mdsch(*args, **kwargs)

Overloaded function.

  1. mdsch(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData

C++: protocols::md::MDBase::mdsch() const –> class utility::vector1<struct protocols::md::MDscheduleData, class std::allocator<struct protocols::md::MDscheduleData> >

  1. mdsch(self: pyrosetta.rosetta.protocols.md.MDBase, istep: int) -> pyrosetta.rosetta.protocols.md.MDscheduleData

C++: protocols::md::MDBase::mdsch(unsigned long) const –> struct protocols::md::MDscheduleData

movemap(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::md::MDBase::movemap() const –> class std::shared_ptr<class core::kinematics::MoveMap>

static mover_name() str

C++: protocols::md::CartesianMD::mover_name() –> std::string

n_dof(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::n_dof() const –> unsigned long

n_dof_temp(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::n_dof_temp() const –> unsigned long

static name() str

C++: protocols::moves::Mover::name() –> std::string

ncyc_postmin(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::ncyc_postmin() const –> unsigned long

ncyc_premin(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::ncyc_premin() const –> unsigned long

nstep(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::nstep() const –> unsigned long

parse_movemap(self: pyrosetta.rosetta.protocols.md.CartesianMD, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::md::CartesianMD::parse_movemap(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.md.CartesianMD, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::md::CartesianMD::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_opts(self: pyrosetta.rosetta.protocols.md.CartesianMD, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::md::CartesianMD::parse_opts(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_schfile(self: pyrosetta.rosetta.protocols.md.MDBase, schfile: str) None

C++: protocols::md::MDBase::parse_schfile(const std::string) –> void

pose0(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.core.pose.Pose

C++: protocols::md::MDBase::pose0() const –> class core::pose::Pose

pose_minobj(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.core.pose.Pose

C++: protocols::md::MDBase::pose_minobj() const –> class core::pose::Pose

potential_energy(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::potential_energy() const –> double

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::md::CartesianMD::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

prv_eqxyz(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::prv_eqxyz() const –> const class utility::vector1<double, class std::allocator<double> > &

ref_xyz(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::ref_xyz() const –> const class utility::vector1<double, class std::allocator<double> > &

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

renew_trj_scratch(self: pyrosetta.rosetta.protocols.md.MDBase) None

C++: protocols::md::MDBase::renew_trj_scratch() –> void

report_as_silent(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::report_as_silent() const –> bool

report_scorecomp(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::report_scorecomp() const –> bool

report_silent(*args, **kwargs)

Overloaded function.

  1. report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, rmsd: float) -> None

  3. report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, rmsd: float, gdttm: float) -> None

  4. report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, rmsd: float, gdttm: float, gdtha: float) -> None

C++: protocols::md::MDBase::report_silent(class core::pose::Pose &, double, double, double) –> void

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

resize_natm_variables(self: pyrosetta.rosetta.protocols.md.MDBase) None

C++: protocols::md::MDBase::resize_natm_variables() –> void

rsrfilename(self: pyrosetta.rosetta.protocols.md.MDBase) str

C++: protocols::md::MDBase::rsrfilename() const –> std::string

scheduled(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::scheduled() const –> bool

scorefxn(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::md::MDBase::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn_obj(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::md::MDBase::scorefxn_obj() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

selectmode(self: pyrosetta.rosetta.protocols.md.MDBase) str

C++: protocols::md::MDBase::selectmode() const –> std::string

set_Emin_obj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_Emin_obj(double) –> void

set_Gamma(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_Gamma(double) –> void

set_Kappa(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_Kappa(double) –> void

set_acc(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::set_acc(class utility::vector1<double, class std::allocator<double> >) –> void

set_constraint(self: pyrosetta.rosetta.protocols.md.MDBase, sdev: float) None

C++: protocols::md::MDBase::set_constraint(const double) –> void

set_context_update_step(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_context_update_step(unsigned long) –> void

set_cst_sdev(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_cst_sdev(double) –> void

set_cummulative_time(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_cummulative_time(double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_defaults(self: pyrosetta.rosetta.protocols.md.MDBase) None

C++: protocols::md::MDBase::set_defaults() –> void

set_dt(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_dt(double) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_kinetic_energy(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_kinetic_energy(double) –> void

set_mass(self: pyrosetta.rosetta.protocols.md.MDBase, iatm: int, setting: float) None

C++: protocols::md::MDBase::set_mass(unsigned long, double) –> void

set_md_energy_report_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_md_energy_report_stepsize(unsigned long) –> void

set_md_report_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_md_report_stepsize(unsigned long) –> void

set_md_rsr_update_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_md_rsr_update_stepsize(unsigned long) –> void

set_mdsch(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData) None

C++: protocols::md::MDBase::set_mdsch(class utility::vector1<struct protocols::md::MDscheduleData, class std::allocator<struct protocols::md::MDscheduleData> >) –> void

set_movemap(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::md::MDBase::set_movemap(const class core::pose::Pose &, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_n_dof(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_n_dof(unsigned long) –> void

set_n_dof_temp(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_n_dof_temp(unsigned long) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_ncyc_postmin(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_ncyc_postmin(unsigned long) –> void

set_ncyc_premin(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_ncyc_premin(unsigned long) –> void

set_nstep(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_nstep(unsigned long) –> void

set_pose0(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::md::MDBase::set_pose0(class core::pose::Pose) –> void

set_pose_minobj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::md::MDBase::set_pose_minobj(class core::pose::Pose) –> void

set_potential_energy(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_potential_energy(double) –> void

set_prv_eqxyz(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::set_prv_eqxyz(class utility::vector1<double, class std::allocator<double> >) –> void

set_ref_xyz(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::set_ref_xyz(class utility::vector1<double, class std::allocator<double> >) –> void

set_report_as_silent(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_report_as_silent(bool) –> void

set_report_scorecomp(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_report_scorecomp(bool) –> void

set_rsrfilename(self: pyrosetta.rosetta.protocols.md.MDBase, setting: str) None

C++: protocols::md::MDBase::set_rsrfilename(std::string) –> void

set_scheduled(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_scheduled(bool) –> void

set_scorefxn(*args, **kwargs)

Overloaded function.

  1. set_scorefxn(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::md::MDBase::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

  1. set_scorefxn(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::md::MDBase::set_scorefxn(const class core::scoring::ScoreFunction &) –> void

set_scorefxn_obj(*args, **kwargs)

Overloaded function.

  1. set_scorefxn_obj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::md::MDBase::set_scorefxn_obj(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

  1. set_scorefxn_obj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::md::MDBase::set_scorefxn_obj(const class core::scoring::ScoreFunction &) –> void

set_selectmode(self: pyrosetta.rosetta.protocols.md.MDBase, setting: str) None

C++: protocols::md::MDBase::set_selectmode(std::string) –> void

set_silentname(self: pyrosetta.rosetta.protocols.md.MDBase, setting: str) None

C++: protocols::md::MDBase::set_silentname(std::string) –> void

set_store_trj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_store_trj(bool) –> void

set_temp0(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_temp0(double) –> void

set_temperature(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_temperature(double) –> void

set_time_minobj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_time_minobj(double) –> void

set_trj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) None

C++: protocols::md::MDBase::set_trj(class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >) –> void

set_trj_score_only(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_trj_score_only(bool) –> void

set_trj_scratch(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) None

C++: protocols::md::MDBase::set_trj_scratch(class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_uniform_coord_constrained(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_uniform_coord_constrained(bool) –> void

set_vel(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::set_vel(class utility::vector1<double, class std::allocator<double> >) –> void

set_write_dynamic_rsr(*args, **kwargs)

Overloaded function.

  1. set_write_dynamic_rsr(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) -> None

C++: protocols::md::MDBase::set_write_dynamic_rsr(bool) –> void

  1. set_write_dynamic_rsr(self: pyrosetta.rosetta.protocols.md.MDBase, filename: str) -> None

C++: protocols::md::MDBase::set_write_dynamic_rsr(const std::string) –> void

set_xyz(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::set_xyz(class utility::vector1<double, class std::allocator<double> >) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

silentname(self: pyrosetta.rosetta.protocols.md.MDBase) str

C++: protocols::md::MDBase::silentname() const –> std::string

store_trj(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::store_trj() const –> bool

temp0(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::temp0() const –> double

temperature(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::temperature() const –> double

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

time_minobj(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::time_minobj() const –> double

trj(*args, **kwargs)

Overloaded function.

  1. trj(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

C++: protocols::md::MDBase::trj() const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

  1. trj(self: pyrosetta.rosetta.protocols.md.MDBase, itrj: int) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::trj(unsigned long) const –> class utility::vector1<double, class std::allocator<double> >

trj_score_only(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::trj_score_only() const –> bool

trj_scratch(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

C++: protocols::md::MDBase::trj_scratch() const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

uniform_coord_constrained(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::uniform_coord_constrained() const –> bool

update_restraint(self: pyrosetta.rosetta.protocols.md.CartesianMD, pose: pyrosetta.rosetta.core.pose.Pose, min_map: pyrosetta.rosetta.core.optimization.CartesianMinimizerMap) None

C++: protocols::md::CartesianMD::update_restraint(class core::pose::Pose &, const class core::optimization::CartesianMinimizerMap &) –> void

use_rattle(self: pyrosetta.rosetta.protocols.md.CartesianMD, value: bool) None

C++: protocols::md::CartesianMD::use_rattle(const bool) –> void

vel(*args, **kwargs)

Overloaded function.

  1. vel(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::vel() const –> class utility::vector1<double, class std::allocator<double> >

  1. vel(self: pyrosetta.rosetta.protocols.md.MDBase, idof: int) -> float

C++: protocols::md::MDBase::vel(unsigned long) –> double &

write_dynamic_rsr(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::write_dynamic_rsr() const –> bool

xyz(*args, **kwargs)

Overloaded function.

  1. xyz(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::xyz() const –> class utility::vector1<double, class std::allocator<double> >

  1. xyz(self: pyrosetta.rosetta.protocols.md.MDBase, idof: int) -> float

C++: protocols::md::MDBase::xyz(unsigned long) –> double &

class pyrosetta.rosetta.protocols.md.CartesianMDCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.md.CartesianMDCreator, : pyrosetta.rosetta.protocols.md.CartesianMDCreator) pyrosetta.rosetta.protocols.md.CartesianMDCreator

C++: protocols::md::CartesianMDCreator::operator=(const class protocols::md::CartesianMDCreator &) –> class protocols::md::CartesianMDCreator &

create_mover(self: pyrosetta.rosetta.protocols.md.CartesianMDCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::md::CartesianMDCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.md.CartesianMDCreator) str

C++: protocols::md::CartesianMDCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.md.CartesianMDCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::md::CartesianMDCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.md.Constraint

Bases: pybind11_builtins.pybind11_object

property a
assign(self: pyrosetta.rosetta.protocols.md.Constraint, : pyrosetta.rosetta.protocols.md.Constraint) pyrosetta.rosetta.protocols.md.Constraint

C++: protocols::md::Constraint::operator=(const struct protocols::md::Constraint &) –> struct protocols::md::Constraint &

property b
property k
class pyrosetta.rosetta.protocols.md.MDBase

Bases: pyrosetta.rosetta.protocols.moves.Mover

Emin_obj(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::Emin_obj() const –> double

Gamma(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::Gamma() const –> double

Kappa(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::Kappa() const –> double

acc(*args, **kwargs)

Overloaded function.

  1. acc(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::acc() const –> class utility::vector1<double, class std::allocator<double> >

  1. acc(self: pyrosetta.rosetta.protocols.md.MDBase, idof: int) -> float

C++: protocols::md::MDBase::acc(unsigned long) –> double &

add_trj(self: pyrosetta.rosetta.protocols.md.MDBase, xyz: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::add_trj(class utility::vector1<double, class std::allocator<double> >) –> void

add_trj_scratch(self: pyrosetta.rosetta.protocols.md.MDBase, xyz: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::add_trj_scratch(class utility::vector1<double, class std::allocator<double> >) –> void

apply(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::md::MDBase::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.md.MDBase, : pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.protocols.md.MDBase

C++: protocols::md::MDBase::operator=(const class protocols::md::MDBase &) –> class protocols::md::MDBase &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

context_update_step(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::context_update_step() const –> unsigned long

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

cst_sdev(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::cst_sdev() const –> double

cummulative_time(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::cummulative_time() const –> double

dt(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::dt() const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.md.MDBase) str

C++: protocols::md::MDBase::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

init(self: pyrosetta.rosetta.protocols.md.MDBase) None

C++: protocols::md::MDBase::init() –> void

kinetic_energy(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::kinetic_energy() const –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

mass(*args, **kwargs)

Overloaded function.

  1. mass(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::mass() const –> class utility::vector1<double, class std::allocator<double> >

  1. mass(self: pyrosetta.rosetta.protocols.md.MDBase, iatm: int) -> float

C++: protocols::md::MDBase::mass(unsigned long) const –> double

md_energy_report_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::md_energy_report_stepsize() const –> unsigned long

md_report_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::md_report_stepsize() const –> unsigned long

md_rsr_update_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::md_rsr_update_stepsize() const –> unsigned long

mdsch(*args, **kwargs)

Overloaded function.

  1. mdsch(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData

C++: protocols::md::MDBase::mdsch() const –> class utility::vector1<struct protocols::md::MDscheduleData, class std::allocator<struct protocols::md::MDscheduleData> >

  1. mdsch(self: pyrosetta.rosetta.protocols.md.MDBase, istep: int) -> pyrosetta.rosetta.protocols.md.MDscheduleData

C++: protocols::md::MDBase::mdsch(unsigned long) const –> struct protocols::md::MDscheduleData

movemap(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::md::MDBase::movemap() const –> class std::shared_ptr<class core::kinematics::MoveMap>

n_dof(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::n_dof() const –> unsigned long

n_dof_temp(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::n_dof_temp() const –> unsigned long

static name() str

C++: protocols::moves::Mover::name() –> std::string

ncyc_postmin(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::ncyc_postmin() const –> unsigned long

ncyc_premin(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::ncyc_premin() const –> unsigned long

nstep(self: pyrosetta.rosetta.protocols.md.MDBase) int

C++: protocols::md::MDBase::nstep() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_schfile(self: pyrosetta.rosetta.protocols.md.MDBase, schfile: str) None

C++: protocols::md::MDBase::parse_schfile(const std::string) –> void

pose0(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.core.pose.Pose

C++: protocols::md::MDBase::pose0() const –> class core::pose::Pose

pose_minobj(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.core.pose.Pose

C++: protocols::md::MDBase::pose_minobj() const –> class core::pose::Pose

potential_energy(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::potential_energy() const –> double

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

prv_eqxyz(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::prv_eqxyz() const –> const class utility::vector1<double, class std::allocator<double> > &

ref_xyz(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::ref_xyz() const –> const class utility::vector1<double, class std::allocator<double> > &

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

renew_trj_scratch(self: pyrosetta.rosetta.protocols.md.MDBase) None

C++: protocols::md::MDBase::renew_trj_scratch() –> void

report_as_silent(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::report_as_silent() const –> bool

report_scorecomp(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::report_scorecomp() const –> bool

report_silent(*args, **kwargs)

Overloaded function.

  1. report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, rmsd: float) -> None

  3. report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, rmsd: float, gdttm: float) -> None

  4. report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, rmsd: float, gdttm: float, gdtha: float) -> None

C++: protocols::md::MDBase::report_silent(class core::pose::Pose &, double, double, double) –> void

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

resize_natm_variables(self: pyrosetta.rosetta.protocols.md.MDBase) None

C++: protocols::md::MDBase::resize_natm_variables() –> void

rsrfilename(self: pyrosetta.rosetta.protocols.md.MDBase) str

C++: protocols::md::MDBase::rsrfilename() const –> std::string

scheduled(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::scheduled() const –> bool

scorefxn(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::md::MDBase::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn_obj(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::md::MDBase::scorefxn_obj() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

selectmode(self: pyrosetta.rosetta.protocols.md.MDBase) str

C++: protocols::md::MDBase::selectmode() const –> std::string

set_Emin_obj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_Emin_obj(double) –> void

set_Gamma(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_Gamma(double) –> void

set_Kappa(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_Kappa(double) –> void

set_acc(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::set_acc(class utility::vector1<double, class std::allocator<double> >) –> void

set_constraint(self: pyrosetta.rosetta.protocols.md.MDBase, sdev: float) None

C++: protocols::md::MDBase::set_constraint(const double) –> void

set_context_update_step(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_context_update_step(unsigned long) –> void

set_cst_sdev(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_cst_sdev(double) –> void

set_cummulative_time(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_cummulative_time(double) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_defaults(self: pyrosetta.rosetta.protocols.md.MDBase) None

C++: protocols::md::MDBase::set_defaults() –> void

set_dt(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_dt(double) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_kinetic_energy(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_kinetic_energy(double) –> void

set_mass(self: pyrosetta.rosetta.protocols.md.MDBase, iatm: int, setting: float) None

C++: protocols::md::MDBase::set_mass(unsigned long, double) –> void

set_md_energy_report_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_md_energy_report_stepsize(unsigned long) –> void

set_md_report_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_md_report_stepsize(unsigned long) –> void

set_md_rsr_update_stepsize(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_md_rsr_update_stepsize(unsigned long) –> void

set_mdsch(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_protocols_md_MDscheduleData) None

C++: protocols::md::MDBase::set_mdsch(class utility::vector1<struct protocols::md::MDscheduleData, class std::allocator<struct protocols::md::MDscheduleData> >) –> void

set_movemap(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::md::MDBase::set_movemap(const class core::pose::Pose &, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_n_dof(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_n_dof(unsigned long) –> void

set_n_dof_temp(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_n_dof_temp(unsigned long) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_ncyc_postmin(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_ncyc_postmin(unsigned long) –> void

set_ncyc_premin(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_ncyc_premin(unsigned long) –> void

set_nstep(self: pyrosetta.rosetta.protocols.md.MDBase, setting: int) None

C++: protocols::md::MDBase::set_nstep(unsigned long) –> void

set_pose0(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::md::MDBase::set_pose0(class core::pose::Pose) –> void

set_pose_minobj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::md::MDBase::set_pose_minobj(class core::pose::Pose) –> void

set_potential_energy(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_potential_energy(double) –> void

set_prv_eqxyz(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::set_prv_eqxyz(class utility::vector1<double, class std::allocator<double> >) –> void

set_ref_xyz(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::set_ref_xyz(class utility::vector1<double, class std::allocator<double> >) –> void

set_report_as_silent(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_report_as_silent(bool) –> void

set_report_scorecomp(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_report_scorecomp(bool) –> void

set_rsrfilename(self: pyrosetta.rosetta.protocols.md.MDBase, setting: str) None

C++: protocols::md::MDBase::set_rsrfilename(std::string) –> void

set_scheduled(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_scheduled(bool) –> void

set_scorefxn(*args, **kwargs)

Overloaded function.

  1. set_scorefxn(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::md::MDBase::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

  1. set_scorefxn(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::md::MDBase::set_scorefxn(const class core::scoring::ScoreFunction &) –> void

set_scorefxn_obj(*args, **kwargs)

Overloaded function.

  1. set_scorefxn_obj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::md::MDBase::set_scorefxn_obj(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

  1. set_scorefxn_obj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::md::MDBase::set_scorefxn_obj(const class core::scoring::ScoreFunction &) –> void

set_selectmode(self: pyrosetta.rosetta.protocols.md.MDBase, setting: str) None

C++: protocols::md::MDBase::set_selectmode(std::string) –> void

set_silentname(self: pyrosetta.rosetta.protocols.md.MDBase, setting: str) None

C++: protocols::md::MDBase::set_silentname(std::string) –> void

set_store_trj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_store_trj(bool) –> void

set_temp0(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_temp0(double) –> void

set_temperature(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_temperature(double) –> void

set_time_minobj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: float) None

C++: protocols::md::MDBase::set_time_minobj(double) –> void

set_trj(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) None

C++: protocols::md::MDBase::set_trj(class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >) –> void

set_trj_score_only(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_trj_score_only(bool) –> void

set_trj_scratch(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) None

C++: protocols::md::MDBase::set_trj_scratch(class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_uniform_coord_constrained(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) None

C++: protocols::md::MDBase::set_uniform_coord_constrained(bool) –> void

set_vel(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::set_vel(class utility::vector1<double, class std::allocator<double> >) –> void

set_write_dynamic_rsr(*args, **kwargs)

Overloaded function.

  1. set_write_dynamic_rsr(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) -> None

C++: protocols::md::MDBase::set_write_dynamic_rsr(bool) –> void

  1. set_write_dynamic_rsr(self: pyrosetta.rosetta.protocols.md.MDBase, filename: str) -> None

C++: protocols::md::MDBase::set_write_dynamic_rsr(const std::string) –> void

set_xyz(self: pyrosetta.rosetta.protocols.md.MDBase, setting: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::MDBase::set_xyz(class utility::vector1<double, class std::allocator<double> >) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

silentname(self: pyrosetta.rosetta.protocols.md.MDBase) str

C++: protocols::md::MDBase::silentname() const –> std::string

store_trj(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::store_trj() const –> bool

temp0(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::temp0() const –> double

temperature(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::temperature() const –> double

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

time_minobj(self: pyrosetta.rosetta.protocols.md.MDBase) float

C++: protocols::md::MDBase::time_minobj() const –> double

trj(*args, **kwargs)

Overloaded function.

  1. trj(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

C++: protocols::md::MDBase::trj() const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

  1. trj(self: pyrosetta.rosetta.protocols.md.MDBase, itrj: int) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::trj(unsigned long) const –> class utility::vector1<double, class std::allocator<double> >

trj_score_only(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::trj_score_only() const –> bool

trj_scratch(self: pyrosetta.rosetta.protocols.md.MDBase) pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

C++: protocols::md::MDBase::trj_scratch() const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

uniform_coord_constrained(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::uniform_coord_constrained() const –> bool

vel(*args, **kwargs)

Overloaded function.

  1. vel(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::vel() const –> class utility::vector1<double, class std::allocator<double> >

  1. vel(self: pyrosetta.rosetta.protocols.md.MDBase, idof: int) -> float

C++: protocols::md::MDBase::vel(unsigned long) –> double &

write_dynamic_rsr(self: pyrosetta.rosetta.protocols.md.MDBase) bool

C++: protocols::md::MDBase::write_dynamic_rsr() const –> bool

xyz(*args, **kwargs)

Overloaded function.

  1. xyz(self: pyrosetta.rosetta.protocols.md.MDBase) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::md::MDBase::xyz() const –> class utility::vector1<double, class std::allocator<double> >

  1. xyz(self: pyrosetta.rosetta.protocols.md.MDBase, idof: int) -> float

C++: protocols::md::MDBase::xyz(unsigned long) –> double &

class pyrosetta.rosetta.protocols.md.MDscheduleData

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.md.MDscheduleData, : pyrosetta.rosetta.protocols.md.MDscheduleData) pyrosetta.rosetta.protocols.md.MDscheduleData

C++: protocols::md::MDscheduleData::operator=(const struct protocols::md::MDscheduleData &) –> struct protocols::md::MDscheduleData &

property nstep
property temp0
property type
class pyrosetta.rosetta.protocols.md.Rattle

Bases: pybind11_builtins.pybind11_object

ncst(self: pyrosetta.rosetta.protocols.md.Rattle) int

C++: protocols::md::Rattle::ncst() –> unsigned long

run_rattle1(self: pyrosetta.rosetta.protocols.md.Rattle, dt: float, xyz: pyrosetta.rosetta.utility.vector1_double, vel: pyrosetta.rosetta.utility.vector1_double, mass: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::Rattle::run_rattle1(const double &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

run_rattle2(self: pyrosetta.rosetta.protocols.md.Rattle, dt: float, xyz: pyrosetta.rosetta.utility.vector1_double, vel: pyrosetta.rosetta.utility.vector1_double, mass: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::Rattle::run_rattle2(const double &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

class pyrosetta.rosetta.protocols.md.Thermostat

Bases: pybind11_builtins.pybind11_object

get_temperature(self: pyrosetta.rosetta.protocols.md.Thermostat, vel: pyrosetta.rosetta.utility.vector1_double, mass: pyrosetta.rosetta.utility.vector1_double) float

C++: protocols::md::Thermostat::get_temperature(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> double

nstep_per_update(self: pyrosetta.rosetta.protocols.md.Thermostat) int

C++: protocols::md::Thermostat::nstep_per_update() –> unsigned long

rescale(self: pyrosetta.rosetta.protocols.md.Thermostat, vel: pyrosetta.rosetta.utility.vector1_double, dt: float, mass: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::md::Thermostat::rescale(class utility::vector1<double, class std::allocator<double> > &, const double &, const class utility::vector1<double, class std::allocator<double> > &) –> void