protocols::md::CartesianMD Member List

This is the complete list of members for protocols::md::CartesianMD, including all inherited members.

acc() const	protocols::md::MDBase	inline
acc(core::Size idof)	protocols::md::MDBase	inline
add_trj(core::optimization::Multivec xyz)	protocols::md::MDBase	inline
add_trj_scratch(core::optimization::Multivec xyz)	protocols::md::MDBase	inline
apply(core::pose::Pose &pose) override	protocols::md::CartesianMD	virtual
Berendsen_Integrator(core::pose::Pose &pose, core::optimization::CartesianMinimizerMap &min_map)	protocols::md::CartesianMD	private
CartesianMD()	protocols::md::CartesianMD
CartesianMD(core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP sfxn, core::kinematics::MoveMapCOP movemap=nullptr)	protocols::md::CartesianMD
CartesianMD(core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn)	protocols::md::CartesianMD
CartesianMD(core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::kinematics::MoveMap const &movemap)	protocols::md::CartesianMD
clear_info()	protocols::moves::Mover	inlinevirtual
clone() const override	protocols::md::CartesianMD	virtual
context_update_step() const	protocols::md::MDBase	inline
create()	protocols::moves::Mover	virtual
cst_on_pose_dynamic(core::pose::Pose &pose, core::optimization::Multivec const &ref_xyz, core::optimization::Multivec const &curr_eqxyz, core::optimization::Multivec &prv_eqxyz, core::optimization::CartesianMinimizerMap const &min_map) const	protocols::md::CartesianMD
cst_on_pose_simple(core::pose::Pose &pose) const	protocols::md::CartesianMD
cst_sdev() const	protocols::md::MDBase	inline
cummulative_time() const	protocols::md::MDBase	inline
do_initialize(core::pose::Pose &pose)	protocols::md::CartesianMD	private
do_MD(core::pose::Pose &pose, core::Size const &nstep, core::Real const &temp0=300, bool const &initialize=false)	protocols::md::CartesianMD	private
do_minimize(core::pose::Pose &pose, core::optimization::MinimizerOptions const &options, bool const &show_energy)	protocols::md::CartesianMD	private
dt() const	protocols::md::MDBase	inline
dump_poses(core::pose::Pose const &pose_ref) const	protocols::md::CartesianMD
Emin_obj() const	protocols::md::MDBase	inline
fresh_instance() const override	protocols::md::CartesianMD	inlinevirtual
Gamma() const	protocols::md::MDBase	inline
get_additional_output()	protocols::moves::Mover	virtual
get_current_eqxyz() const	protocols::md::CartesianMD
get_current_job() const	protocols::moves::Mover
get_current_tag() const	protocols::moves::Mover	inline
get_input_pose() const	protocols::moves::Mover
get_last_move_status() const	protocols::moves::Mover
get_name() const override	protocols::md::CartesianMD	virtual
get_native_info(core::pose::Pose const &pose)	protocols::md::CartesianMD	private
get_native_pose() const	protocols::moves::Mover
get_self_ptr() const	protocols::moves::Mover	inline
get_self_ptr()	protocols::moves::Mover	inline
get_self_weak_ptr() const	protocols::moves::Mover	inline
get_self_weak_ptr()	protocols::moves::Mover	inline
get_type() const	protocols::moves::Mover	inline
info()	protocols::moves::Mover	inlinevirtual
info() const	protocols::moves::Mover	inlinevirtual
init()	protocols::md::MDBase
initialize_velocity(core::Real const &temperature)	protocols::md::CartesianMD	private
inittime_	protocols::md::CartesianMD	private
Kappa() const	protocols::md::MDBase	inline
kinetic_energy() const	protocols::md::MDBase	inline
last_proposal_density_ratio()	protocols::moves::Mover	inlinevirtual
mass() const	protocols::md::MDBase	inline
mass(core::Size iatm) const	protocols::md::MDBase	inline
md_energy_report_stepsize() const	protocols::md::MDBase	inline
md_report_stepsize() const	protocols::md::MDBase	inline
md_rsr_update_stepsize() const	protocols::md::MDBase	inline
MDBase()	protocols::md::MDBase
mdsch() const	protocols::md::MDBase	inline
mdsch(core::Size istep) const	protocols::md::MDBase	inline
min_map_	protocols::md::CartesianMD	private
movemap() const	protocols::md::MDBase	inline
movemap_factory_	protocols::md::CartesianMD	private
Mover()	protocols::moves::Mover
Mover(std::string const &type_name)	protocols::moves::Mover
mover_name()	protocols::md::CartesianMD	static
n_dof() const	protocols::md::MDBase	inline
n_dof_temp() const	protocols::md::MDBase	inline
name()	protocols::moves::Mover	inlinestatic
native_	protocols::md::CartesianMD	private
native_given_	protocols::md::CartesianMD	private
native_resmap_	protocols::md::CartesianMD	private
ncyc_postmin() const	protocols::md::MDBase	inline
ncyc_premin() const	protocols::md::MDBase	inline
nstep() const	protocols::md::MDBase	inline
parent typedef	protocols::md::MDBase
parse_movemap(TagCOP tag, basic::datacache::DataMap &data)	protocols::md::CartesianMD
parse_my_tag(TagCOP, basic::datacache::DataMap &) override	protocols::md::CartesianMD	virtual
parse_opts(TagCOP tag, basic::datacache::DataMap &data)	protocols::md::CartesianMD
parse_schfile(std::string const schfile)	protocols::md::MDBase
Pose typedef	protocols::moves::Mover
pose0() const	protocols::md::MDBase	inline
pose_minobj() const	protocols::md::MDBase	inline
PoseCOP typedef	protocols::moves::Mover
potential_energy() const	protocols::md::MDBase	inline
provide_citation_info(basic::citation_manager::CitationCollectionList &) const	protocols::moves::Mover	virtual
provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd)	protocols::md::CartesianMD	static
prv_eqxyz() const	protocols::md::MDBase	inline
ref_xyz() const	protocols::md::MDBase	inline
register_options()	protocols::moves::Mover	inlinestatic
reinitialize_for_each_job() const	protocols::moves::Mover	virtual
reinitialize_for_new_input() const	protocols::moves::Mover	virtual
renew_trj_scratch()	protocols::md::MDBase	inline
report_as_silent() const	protocols::md::MDBase	inline
report_MD(core::pose::Pose &pose, core::optimization::CartesianMinimizerMap const &min_map, bool const report_trj)	protocols::md::CartesianMD	private
report_scorecomp() const	protocols::md::MDBase	inline
report_silent(core::pose::Pose &pose, core::Real rmsd=-1.0, core::Real gdttm=-1.0, core::Real gdtha=-1.0)	protocols::md::MDBase
reset_status()	protocols::moves::Mover
resize_natm_variables()	protocols::md::MDBase
rsrfilename() const	protocols::md::MDBase	inline
scheduled() const	protocols::md::MDBase	inline
scorefxn() const	protocols::md::MDBase	inline
scorefxn_obj() const	protocols::md::MDBase	inline
selectmode() const	protocols::md::MDBase	inline
set_acc(core::optimization::Multivec setting)	protocols::md::MDBase	inline
set_constraint(core::Real const sdev)	protocols::md::MDBase
set_context_update_step(core::Size setting)	protocols::md::MDBase	inline
set_cst_sdev(core::Real setting)	protocols::md::MDBase	inline
set_cummulative_time(core::Real setting)	protocols::md::MDBase	inline
set_current_job(protocols::jobdist::BasicJobCOP job)	protocols::moves::Mover
set_current_tag(std::string const &new_tag)	protocols::moves::Mover	inlinevirtual
set_defaults()	protocols::md::MDBase	inline
set_dt(core::Real setting)	protocols::md::MDBase	inline
set_Emin_obj(core::Real setting)	protocols::md::MDBase	inline
set_Gamma(core::Real setting)	protocols::md::MDBase	inline
set_input_pose(PoseCOP pose)	protocols::moves::Mover	virtual
set_Kappa(core::Real setting)	protocols::md::MDBase	inline
set_kinetic_energy(core::Real setting)	protocols::md::MDBase	inline
set_last_move_status(MoverStatus status)	protocols::moves::Mover	protected
set_mass(core::Size iatm, core::Real setting)	protocols::md::MDBase	inline
set_md_energy_report_stepsize(core::Size setting)	protocols::md::MDBase	inline
set_md_report_stepsize(core::Size setting)	protocols::md::MDBase	inline
set_md_rsr_update_stepsize(core::Size setting)	protocols::md::MDBase	inline
set_mdsch(utility::vector1< MDscheduleData > setting)	protocols::md::MDBase	inline
set_movemap(core::pose::Pose const &pose, core::kinematics::MoveMapCOP movemap)	protocols::md::MDBase	virtual
set_n_dof(core::Size setting)	protocols::md::MDBase	inline
set_n_dof_temp(core::Size setting)	protocols::md::MDBase	inline
set_native_pose(PoseCOP pose)	protocols::moves::Mover	virtual
set_ncyc_postmin(core::Size setting)	protocols::md::MDBase	inline
set_ncyc_premin(core::Size setting)	protocols::md::MDBase	inline
set_nstep(core::Size setting)	protocols::md::MDBase	inline
set_pose0(core::pose::Pose setting)	protocols::md::MDBase	inline
set_pose_minobj(core::pose::Pose setting)	protocols::md::MDBase	inline
set_potential_energy(core::Real setting)	protocols::md::MDBase	inline
set_prv_eqxyz(core::optimization::Multivec setting)	protocols::md::MDBase	inline
set_ref_xyz(core::optimization::Multivec setting)	protocols::md::MDBase	inline
set_report_as_silent(bool setting)	protocols::md::MDBase	inline
set_report_scorecomp(bool setting)	protocols::md::MDBase	inline
set_rsrfilename(std::string setting)	protocols::md::MDBase	inline
set_scheduled(bool setting)	protocols::md::MDBase	inline
set_scorefxn(core::scoring::ScoreFunctionCOP setting)	protocols::md::MDBase	inline
set_scorefxn(core::scoring::ScoreFunction const &setting)	protocols::md::MDBase	inline
set_scorefxn_obj(core::scoring::ScoreFunctionCOP setting)	protocols::md::MDBase	inline
set_scorefxn_obj(core::scoring::ScoreFunction const &setting)	protocols::md::MDBase	inline
set_selectmode(std::string setting)	protocols::md::MDBase	inline
set_silentname(std::string setting)	protocols::md::MDBase	inline
set_store_trj(bool setting)	protocols::md::MDBase	inline
set_temp0(core::Real setting)	protocols::md::MDBase	inline
set_temperature(core::Real setting)	protocols::md::MDBase	inline
set_time_minobj(core::Real setting)	protocols::md::MDBase	inline
set_trj(utility::vector1< core::optimization::Multivec > setting)	protocols::md::MDBase	inline
set_trj_score_only(bool setting)	protocols::md::MDBase	inline
set_trj_scratch(utility::vector1< core::optimization::Multivec > setting)	protocols::md::MDBase	inline
set_type(std::string const &setting)	protocols::moves::Mover	inline
set_uniform_coord_constrained(bool setting)	protocols::md::MDBase	inline
set_vel(core::optimization::Multivec setting)	protocols::md::MDBase	inline
set_write_dynamic_rsr(bool setting)	protocols::md::MDBase	inline
set_write_dynamic_rsr(std::string const filename)	protocols::md::MDBase	inline
set_xyz(core::optimization::Multivec setting)	protocols::md::MDBase	inline
show(std::ostream &output=std::cout) const	protocols::moves::Mover	virtual
silentname() const	protocols::md::MDBase	inline
store_trj() const	protocols::md::MDBase	inline
Strings typedef	protocols::moves::Mover
TagCOP typedef	protocols::moves::Mover
temp0() const	protocols::md::MDBase	inline
temperature() const	protocols::md::MDBase	inline
test_move(Pose &pose)	protocols::moves::Mover	inlinevirtual
time_minobj() const	protocols::md::MDBase	inline
trj() const	protocols::md::MDBase	inline
trj(core::Size itrj) const	protocols::md::MDBase	inline
trj_score_only() const	protocols::md::MDBase	inline
trj_scratch() const	protocols::md::MDBase	inline
type(const std::string &type_in)	protocols::moves::Mover	inline
type() const	protocols::moves::Mover	inline
uniform_coord_constrained() const	protocols::md::MDBase	inline
update_restraint(core::pose::Pose &pose, core::optimization::CartesianMinimizerMap const &min_map)	protocols::md::CartesianMD
use_rattle(bool const value)	protocols::md::CartesianMD
use_rattle_	protocols::md::CartesianMD	private
vel() const	protocols::md::MDBase	inline
vel(core::Size idof)	protocols::md::MDBase	inline
VelocityVerlet_Integrator(core::pose::Pose &pose, core::optimization::CartesianMinimizerMap &min_map, md::Rattle &rattle, bool const update_score=false)	protocols::md::CartesianMD	private
write_dynamic_rsr() const	protocols::md::MDBase	inline
xyz() const	protocols::md::MDBase	inline
xyz(core::Size idof)	protocols::md::MDBase	inline
~CartesianMD() override	protocols::md::CartesianMD
~MDBase() override	protocols::md::MDBase