enzdes_util.cc File Reference

a bunch of utility functions used in enzdes More...

#include <protocols/enzdes/enzdes_util.hh>
#include <protocols/toolbox/match_enzdes_util/EnzdesCacheableObserver.hh>
#include <protocols/toolbox/match_enzdes_util/EnzdesCstCache.hh>
#include <protocols/toolbox/match_enzdes_util/EnzConstraintIO.hh>
#include <protocols/toolbox/match_enzdes_util/EnzConstraintParameters.hh>
#include <protocols/toolbox/match_enzdes_util/util_functions.hh>
#include <protocols/enzdes/ModifyStoredLigandRBConfsMovers.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/graph/Graph.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <basic/datacache/CacheableString.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/task/IGEdgeReweightContainer.hh>
#include <core/pack/rotamer_set/RotamerSetOperation.hh>
#include <core/pack/rotamer_set/RotamerSetFactory.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <basic/Tracer.hh>
#include <core/scoring/Energies.hh>
#include <basic/options/keys/enzdes.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <basic/options/keys/docking.OptionKeys.gen.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/string_util.hh>
#include <boost/foreach.hpp>
#include <core/import_pose/import_pose.hh>
#include <core/pose/util.hh>
#include <utility/vector1.hh>
#include <core/id/AtomID.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::enzdes
	protocols::enzdes::enzutil

Functions
static thread_local basic::Tracer	protocols::enzdes::enzutil::tr ("protocols.enzdes.enzdes_util")
bool	protocols::enzdes::enzutil::is_catalytic_seqpos (core::pose::Pose const &pose, core::Size const seqpos)
	queries whether a certain position is considered catalytic, i.e. if the residue is constrained according to the enzdes constraint file More...
utility::vector1< core::Size >	protocols::enzdes::enzutil::catalytic_res (core::pose::Pose const &pose)
core::Real	protocols::enzdes::enzutil::sum_constraint_scoreterms (core::pose::Pose const &pose, int which_res)
	sums up coordinate, atom_pair, angle, and dihedral constraint scores for the residue in question. in case which_res is -1, the scores for the whole pose will be taken More...
void	protocols::enzdes::enzutil::read_pose_from_pdb (core::pose::Pose &pose, std::string const &filename)
	convenience function to read in a pose for enzdes this function basically just calls pose_from_pdb, but it will create an enzdes cacheable observer in the pose, also, 1, if a multimodel pdb is requested, if there are different ligand positions, these will be saved in the enzdes cacheable observer and 2, if option additional_packing_ligand_rb_confs is active, random ligand rigid body confs will be generated and added to the cacheable observer More...
void	protocols::enzdes::enzutil::make_continuous_true_regions_in_bool_vector (utility::vector1< bool > &the_vector, core::Size const min_number_continuous_trues)
core::pack::task::PackerTaskOP	protocols::enzdes::enzutil::recreate_task (core::pose::Pose const &pose, core::pack::task::PackerTask const &orig_task)
toolbox::match_enzdes_util::EnzConstraintIOCOP	protocols::enzdes::enzutil::get_enzcst_io (core::pose::Pose const &pose)
	convenience function to get enzdes cst io out of cst cache. note: may return empty pointer in case cst cache wasn't set yet More...
void	protocols::enzdes::enzutil::remove_remark_header_for_geomcst (core::pose::Pose &pose, core::Size geomcst)
void	protocols::enzdes::enzutil::create_remark_headers_from_cstcache (core::pose::Pose &pose)
	function to write proper remark headers from whatever is found in the pose cstcache More...
std::string	protocols::enzdes::enzutil::get_pdb_code_from_pose_tag (core::pose::Pose const &pose)
bool	protocols::enzdes::enzutil::is_digit (char *cha)
	delete and use cctype functions More...
bool	protocols::enzdes::enzutil::is_uppercase_letter (char *cha)
	delete and use cctype functions More...
bool	protocols::enzdes::enzutil::is_lowercase_letter (char *cha)
	delete and use cctype functions More...
void	protocols::enzdes::enzutil::disable_constraint_scoreterms (core::scoring::ScoreFunctionOP scorefxn)
void	protocols::enzdes::enzutil::enable_constraint_scoreterms (core::scoring::ScoreFunctionOP scorefxn)
bool	protocols::enzdes::enzutil::is_scofx_cstfied (core::scoring::ScoreFunctionCOP scorefxn)
void	protocols::enzdes::enzutil::scorefxn_update_from_options (core::scoring::ScoreFunctionOP scorefxn)
void	protocols::enzdes::enzutil::remove_all_enzdes_constraints (core::pose::Pose &pose)
void	protocols::enzdes::enzutil::get_resnum_from_cstid_list (std::string const &cstidlist, core::pose::Pose const &pose, utility::vector1< core::Size > &resnums)
core::Size	protocols::enzdes::enzutil::get_resnum_from_cstid (std::string const &cstid, core::pose::Pose const &pose)
	Extracts residue number from cstid string. More...

Detailed Description

a bunch of utility functions used in enzdes

Author

Florian Richter, flori.nosp@m.c@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu