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

Classes
class	SideChainCopier
class	StepWiseMasterPacker
class	StepWisePacker

Typedefs
typedef utility::pointer::shared_ptr< SideChainCopier >	SideChainCopierOP
typedef utility::pointer::shared_ptr< SideChainCopier const >	SideChainCopierCOP
typedef utility::pointer::shared_ptr< StepWiseMasterPacker >	StepWiseMasterPackerOP
typedef utility::pointer::shared_ptr< StepWiseMasterPacker const >	StepWiseMasterPackerCOP
typedef utility::pointer::shared_ptr< StepWisePacker >	StepWisePackerOP
typedef utility::pointer::shared_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, bool const pack_protein_side_chains)
utility::vector1< core::Size >	figure_out_working_interface_res (core::pose::Pose const &pose, utility::vector1< core::Size > const &working_moving_res_list, bool const pack_protein_side_chains)
bool	check_o2prime_contact (pose::Pose const &pose, core::Size const i, core::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, bool const pack_protein_side_chains)

Typedef Documentation

SideChainCopierCOP

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

SideChainCopierOP

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

StepWiseMasterPackerCOP

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

StepWiseMasterPackerOP

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

StepWisePackerCOP

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

StepWisePackerOP

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

Function Documentation

check_o2prime_contact()

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

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

Referenced by figure_out_working_interface_res().

figure_out_working_interface_res() [1/3]

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

References figure_out_working_interface_res().

Referenced by protocols::stepwise::monte_carlo::mover::ResampleMover::apply(), protocols::stepwise::monte_carlo::mover::DeleteMover::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().

figure_out_working_interface_res() [2/3]

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,
		bool const	pack_protein_side_chains
	)

References check_o2prime_contact(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), protocols::toolbox::rigid_body::figure_out_moving_partition_res(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), and core::chemical::VIRTUAL_RESIDUE_VARIANT.

Referenced by figure_out_working_interface_res().

figure_out_working_interface_res() [3/3]

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

References protocols::constel::at_interface(), figure_out_working_interface_res(), core::pose::Pose::size(), and core::pose::stepwise_addable_pose_residue().

get_packer()

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().