md¶
Bindings for protocols::md namespace
- class pyrosetta.rosetta.protocols.md.CartesianMD¶
Bases:
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.
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> >
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_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.
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> >
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.
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> >
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.
report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose) -> None
report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, rmsd: float) -> None
report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, rmsd: float, gdttm: float) -> None
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.
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
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.
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
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.
set_write_dynamic_rsr(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) -> None
C++: protocols::md::MDBase::set_write_dynamic_rsr(bool) –> void
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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
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> > > >
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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.
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> >
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.
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> >
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:
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
- class pyrosetta.rosetta.protocols.md.Constraint¶
Bases:
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:
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.
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> >
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_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.
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> >
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.
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> >
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.
report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose) -> None
report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, rmsd: float) -> None
report_silent(self: pyrosetta.rosetta.protocols.md.MDBase, pose: pyrosetta.rosetta.core.pose.Pose, rmsd: float, gdttm: float) -> None
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.
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
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.
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
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.
set_write_dynamic_rsr(self: pyrosetta.rosetta.protocols.md.MDBase, setting: bool) -> None
C++: protocols::md::MDBase::set_write_dynamic_rsr(bool) –> void
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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
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> > > >
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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.
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> >
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.
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> >
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_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_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_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