Rosetta Protocols  2014.35
protocols::dna::DnaInterfacePacker Member List

This is the complete list of members for protocols::dna::DnaInterfacePacker, including all inherited members.

add_complementary_sequence(ResTypeSequence &)protocols::dna::DnaInterfacePackerprivate
allowed_types() const protocols::dna::DnaInterfacePacker
allowed_types_protocols::dna::DnaInterfacePackerprivate
apply(Pose &)protocols::dna::DnaInterfacePackervirtual
protocols::moves::Mover::apply(core::io::serialization::PipeMap &pmap)protocols::moves::Movervirtual
base_only_protocols::dna::DnaInterfacePackerprivate
binding_E_protocols::dna::DnaInterfacePackerprivate
calculate_specificity(Pose const &, ResTypeSequence const &, SequenceScores const &)protocols::dna::DnaInterfacePackerprivate
clear_info()protocols::moves::Moverinlinevirtual
clear_initialization()protocols::dna::DnaInterfacePacker
clone() const protocols::dna::DnaInterfacePackervirtual
create()protocols::moves::Movervirtual
current_dna_design_string(Pose const &) const protocols::dna::DnaInterfacePacker
current_working_sequence(Pose const &) const protocols::dna::DnaInterfacePacker
dna_chains_protocols::dna::DnaInterfacePackerprivate
dna_seq_tag(Pose const &, ResTypeSequence const &) const protocols::dna::DnaInterfacePacker
dna_sequences_protocols::dna::DnaInterfacePackerprivate
DnaInterfacePacker()protocols::dna::DnaInterfacePacker
DnaInterfacePacker(ScoreFunctionOP, bool minimize=false, std::string filename_root="dnapacker")protocols::dna::DnaInterfacePacker
filename_root_protocols::dna::DnaInterfacePackerprivate
Filters_map typedefprotocols::moves::Mover
fresh_instance() const protocols::dna::DnaInterfacePackervirtual
get_additional_output()protocols::moves::Movervirtual
get_current_job() const protocols::moves::Mover
get_current_tag() const protocols::moves::Moverinline
get_input_pose() const protocols::moves::Mover
get_last_move_status() const protocols::moves::Mover
get_name() const protocols::dna::DnaInterfacePackervirtual
get_native_pose() const protocols::moves::Mover
get_targeted_sequence(Pose const &) const protocols::dna::DnaInterfacePacker
get_type() const protocols::moves::Moverinline
ig() const protocols::simple_moves::PackRotamersMover
include_dna_potentials_in_specificity_calculations_protocols::dna::DnaInterfacePackerprivate
info()protocols::moves::Moverinlinevirtual
info() const protocols::moves::Moverinlinevirtual
init_standard(Pose &)protocols::dna::DnaInterfacePackerprivate
initialization_state_protocols::dna::DnaInterfacePackerprivate
initialized() const protocols::dna::DnaInterfacePacker
InteractionGraphBaseCOP typedefprotocols::simple_moves::PackRotamersMover
InteractionGraphBaseOP typedefprotocols::simple_moves::PackRotamersMover
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
make_dna_sequence_combinations()protocols::dna::DnaInterfacePackerprivate
measure_bp_specificities(Pose &)protocols::dna::DnaInterfacePacker
measure_specificities(Pose &, ResTypeSequences const &)protocols::dna::DnaInterfacePacker
measure_specificity(Pose &)protocols::dna::DnaInterfacePacker
min_movemap_protocols::dna::DnaInterfacePackerprivate
minimize_protocols::dna::DnaInterfacePackerprivate
minimize_options_protocols::dna::DnaInterfacePackerprivate
Mover()protocols::moves::Mover
Mover(std::string const &type_name)protocols::moves::Mover
Mover(Mover const &other)protocols::moves::Mover
name()protocols::moves::Moverinlinestatic
nloop(core::Size nloop_in)protocols::simple_moves::PackRotamersMover
nloop() const protocols::simple_moves::PackRotamersMoverinline
note_packertask_settings(Pose const &)protocols::simple_moves::PackRotamersMoverprotectedvirtual
num_repacks_protocols::dna::DnaInterfacePackerprivate
operator=(Mover const &other)protocols::moves::Mover
PackerTaskCOP typedefprotocols::simple_moves::PackRotamersMover
PackRotamersMover()protocols::simple_moves::PackRotamersMover
PackRotamersMover(std::string const &)protocols::simple_moves::PackRotamersMover
PackRotamersMover(ScoreFunctionCOP scorefxn, PackerTaskCOP task=0, core::Size nloop=1)protocols::simple_moves::PackRotamersMover
PackRotamersMover(PackRotamersMover const &other)protocols::simple_moves::PackRotamersMover
parse_def(utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, protocols::moves::MoverCacheSP cache)protocols::simple_moves::PackRotamersMovervirtual
parse_my_tag(TagCOP, basic::datacache::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, Pose const &)protocols::dna::DnaInterfacePackervirtual
parse_score_function(TagCOP, basic::datacache::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)protocols::simple_moves::PackRotamersMovervirtual
parse_state(SerializableState const &state)protocols::moves::Movervirtual
parse_task_operations(TagCOP, basic::datacache::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)protocols::simple_moves::PackRotamersMovervirtual
pdbname()protocols::dna::DnaInterfacePackerinline
pdbname_protocols::dna::DnaInterfacePackerprivate
pdboutput(PDBOutputOP)protocols::dna::DnaInterfacePacker
pdboutput_protocols::dna::DnaInterfacePackerprivate
Pose typedefprotocols::moves::Mover
PoseCOP typedefprotocols::moves::Mover
post_packing(Pose &, ResTypeSequence const &, Size)protocols::dna::DnaInterfacePackerprivate
probe_specificity_protocols::dna::DnaInterfacePackerprivate
protein_scan(Pose &)protocols::dna::DnaInterfacePackerprivate
protein_scan_protocols::dna::DnaInterfacePackerprivate
reference_pose(Pose const &)protocols::dna::DnaInterfacePacker
reference_pose() const protocols::dna::DnaInterfacePacker
reference_pose_protocols::dna::DnaInterfacePackerprivate
reference_residue_types_protocols::dna::DnaInterfacePackerprivate
register_options()protocols::moves::Moverinlinestatic
reinitialize_for_each_job() const protocols::moves::Movervirtual
reinitialize_for_new_input() const protocols::moves::Movervirtual
reset_status()protocols::moves::Mover
reversion_scan(Pose &, core::Real bound_score=0., core::Real binding_score=0., std::pair< core::Real, core::Real > specificities=std::make_pair(0., 0.))protocols::dna::DnaInterfacePacker
reversion_scan_protocols::dna::DnaInterfacePackerprivate
rotamer_sets() const protocols::simple_moves::PackRotamersMover
RotamerSetsCOP typedefprotocols::simple_moves::PackRotamersMover
RotamerSetsOP typedefprotocols::simple_moves::PackRotamersMover
run(Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const protocols::simple_moves::PackRotamersMoverprotectedvirtual
save_state(SerializableState &state)protocols::moves::Movervirtual
score_function(ScoreFunctionCOP sf)protocols::simple_moves::PackRotamersMover
score_function() const protocols::simple_moves::PackRotamersMover
ScoreFunctionCOP typedefprotocols::simple_moves::PackRotamersMover
ScoreFunctionOP typedefprotocols::dna::DnaInterfacePacker
set_current_job(protocols::jobdist::BasicJobCOP job)protocols::moves::Mover
set_current_tag(std::string const &new_tag)protocols::moves::Moverinline
set_filename_root(std::string const &name)protocols::dna::DnaInterfacePackerinline
set_input_pose(PoseCOP pose)protocols::moves::Movervirtual
set_last_move_status(MoverStatus status)protocols::moves::Moverprotected
set_native_pose(PoseCOP pose)protocols::moves::Movervirtual
set_type(std::string const &setting)protocols::moves::Moverinline
setup(Pose &pose)protocols::simple_moves::PackRotamersMoverprotectedvirtual
show(std::ostream &output=std::cout) const protocols::simple_moves::PackRotamersMovervirtual
specificity_repacks_protocols::dna::DnaInterfacePackerprivate
standard_packing(Pose &)protocols::dna::DnaInterfacePackerprivate
Strings typedefprotocols::moves::Mover
TagCOP typedefprotocols::dna::DnaInterfacePacker
targeted_dna(DnaDesignDefOPs const &)protocols::dna::DnaInterfacePacker
targeted_dna() const protocols::dna::DnaInterfacePacker
targeted_dna_protocols::dna::DnaInterfacePackerprivate
task(PackerTaskCOP t)protocols::simple_moves::PackRotamersMover
task() const protocols::simple_moves::PackRotamersMover
task_factory(TaskFactoryCOP tf)protocols::simple_moves::PackRotamersMover
task_factory() const protocols::simple_moves::PackRotamersMover
task_is_valid(Pose const &pose) const protocols::simple_moves::PackRotamersMover
TaskFactoryCOP typedefprotocols::simple_moves::PackRotamersMover
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
type() const protocols::moves::Moverinline
type(const std::string &type_in)protocols::moves::Moverinline
unbound_score(Pose const &, bool output_pdb=false, std::string pdbname="")protocols::dna::DnaInterfacePacker
~DnaInterfacePacker()protocols::dna::DnaInterfacePackervirtual
~Mover()protocols::moves::Movervirtual
~PackRotamersMover()protocols::simple_moves::PackRotamersMovervirtual