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enzdes_util.hh File Reference

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

#include <core/conformation/Residue.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <protocols/toolbox/match_enzdes_util/EnzConstraintIO.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/vector1.hh>

Namespaces

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

Functions

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::Sizeprotocols::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_file (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)
 
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 Expects cstid string to be of format [0-9]+[A-Z], where the number is constraint number and trailing letter is temlplate id i.e. either A or B. 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