protocols::stepwise::modeler::packer Namespace Reference

Classes
class	SideChainCopier
class	StepWiseMasterPacker
class	StepWisePacker

Typedefs
typedef utility::pointer::owning_ptr < SideChainCopier >	SideChainCopierOP
typedef utility::pointer::owning_ptr < SideChainCopier const >	SideChainCopierCOP
typedef utility::pointer::owning_ptr < StepWiseMasterPacker >	StepWiseMasterPackerOP
typedef utility::pointer::owning_ptr < StepWiseMasterPacker const >	StepWiseMasterPackerCOP
typedef utility::pointer::owning_ptr < StepWisePacker >	StepWisePackerOP
typedef utility::pointer::owning_ptr < StepWisePacker const >	StepWisePackerCOP

Functions
StepWisePackerOP	get_packer (core::scoring::ScoreFunctionCOP pack_scorefxn, utility::vector1< core::Size > const &moving_res_list, protocols::stepwise::modeler::options::StepWiseModelerOptionsCOP options)
utility::vector1< core::Size >	figure_out_working_interface_res (core::pose::Pose const &pose, core::Size const working_moving_res)
utility::vector1< Size >	figure_out_working_interface_res (core::pose::Pose const &pose, utility::vector1< Size > const &working_moving_res_list)
bool	check_o2prime_contact (pose::Pose const &pose, Size const i, Size const j)
void	figure_out_working_interface_res (core::pose::Pose const &pose, core::Size const working_moving_res, utility::vector1< bool > &interface_res, utility::vector1< utility::vector1< bool > > &checked_pair)

Typedef Documentation

typedef utility::pointer::owning_ptr< SideChainCopier const > protocols::stepwise::modeler::packer::SideChainCopierCOP

typedef utility::pointer::owning_ptr< SideChainCopier > protocols::stepwise::modeler::packer::SideChainCopierOP

typedef utility::pointer::owning_ptr< StepWiseMasterPacker const > protocols::stepwise::modeler::packer::StepWiseMasterPackerCOP

typedef utility::pointer::owning_ptr< StepWiseMasterPacker > protocols::stepwise::modeler::packer::StepWiseMasterPackerOP

typedef utility::pointer::owning_ptr< StepWisePacker const > protocols::stepwise::modeler::packer::StepWisePackerCOP

typedef utility::pointer::owning_ptr< StepWisePacker > protocols::stepwise::modeler::packer::StepWisePackerOP

Function Documentation

bool protocols::stepwise::modeler::packer::check_o2prime_contact	(	pose::Pose const &	pose,
		Size const	i,
		Size const	j
	)

References core::conformation::Residue::is_virtual(), core::conformation::Residue::nheavyatoms(), core::chemical::rna::RNA_ResidueType::o2prime_index(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::ResidueType::RNA_type(), and core::conformation::Residue::xyz().

Referenced by figure_out_working_interface_res().

utility::vector1< core::Size > protocols::stepwise::modeler::packer::figure_out_working_interface_res	(	core::pose::Pose const &	pose,
		core::Size const	working_moving_res
	)

References figure_out_working_interface_res(), and utility::tools::make_vector1().

Referenced by protocols::stepwise::monte_carlo::mover::DeleteMover::apply(), protocols::stepwise::monte_carlo::mover::ResampleMover::apply(), protocols::stepwise::modeler::packer::StepWisePacker::figure_out_neighbors(), protocols::stepwise::modeler::StepWiseModeler::initialize_working_parameters_and_root(), and protocols::stepwise::modeler::StepWiseMinimizer::let_neighboring_side_chains_minimize().

utility::vector1< core::Size > protocols::stepwise::modeler::packer::figure_out_working_interface_res	(	core::pose::Pose const &	pose,
		utility::vector1< Size > const &	working_moving_res_list
	)

References figure_out_working_interface_res(), and core::pose::Pose::total_residue().

void protocols::stepwise::modeler::packer::figure_out_working_interface_res	(	core::pose::Pose const &	pose,
		core::Size const	working_moving_res,
		utility::vector1< bool > &	interface_res,
		utility::vector1< utility::vector1< bool > > &	checked_pair
	)

References check_o2prime_contact(), core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), protocols::stepwise::sampler::rigid_body::figure_out_moving_partition_res(), core::graph::Edge::get_node(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_RNA(), and core::pose::Pose::residue_type().

Referenced by figure_out_working_interface_res().

StepWisePackerOP protocols::stepwise::modeler::packer::get_packer	(	core::scoring::ScoreFunctionCOP	pack_scorefxn,
		utility::vector1< core::Size > const &	moving_res_list,
		protocols::stepwise::modeler::options::StepWiseModelerOptionsCOP	options
	)

Referenced by protocols::stepwise::modeler::packer::StepWiseMasterPacker::initialize_packer(), and protocols::stepwise::legacy::modeler::protein::StepWiseProteinConnectionSampler::initialize_poses_and_checkers().