Rosetta 3.4
Functions
protocols::enzdes::enzutil Namespace Reference

Functions

static basic::Tracer tr ("protocols.enzdes.enzdes_util")
bool 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
utility::vector1< core::Sizecatalytic_res (core::pose::Pose const &pose)
core::Real 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
void 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
void make_continuous_true_regions_in_bool_vector (utility::vector1< bool > &the_vector, core::Size const min_number_continuous_trues)
core::pack::task::PackerTaskOP recreate_task (core::pose::Pose const &pose, core::pack::task::PackerTask const &orig_task)
toolbox::match_enzdes_util::EnzConstraintIOCOP 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
void remove_remark_header_for_geomcst (core::pose::Pose &pose, core::Size geomcst)
void create_remark_headers_from_cstcache (core::pose::Pose &pose)
 function to write proper remark headers from whatever is found in the pose cstcache
std::string get_pdb_code_from_pose_tag (core::pose::Pose const &pose)
bool is_digit (char *cha)
 delete and use cctype functions
bool is_uppercase_letter (char *cha)
 delete and use cctype functions
bool is_lowercase_letter (char *cha)
 delete and use cctype functions
void disable_constraint_scoreterms (core::scoring::ScoreFunctionOP scorefxn)
void enable_constraint_scoreterms (core::scoring::ScoreFunctionOP scorefxn)
bool is_scofx_cstfied (core::scoring::ScoreFunctionCOP scorefxn)
void scorefxn_update_from_options (core::scoring::ScoreFunctionOP scorefxn)
void remove_all_enzdes_constraints (core::pose::Pose &pose)
void get_resnum_from_cstid_list (std::string const &cstidlist, core::pose::Pose const &pose, utility::vector1< core::Size > &resnums)
core::Size 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.

Function Documentation

utility::vector1< core::Size > protocols::enzdes::enzutil::catalytic_res ( core::pose::Pose const &  pose)
void protocols::enzdes::enzutil::create_remark_headers_from_cstcache ( core::pose::Pose pose)
void protocols::enzdes::enzutil::disable_constraint_scoreterms ( core::scoring::ScoreFunctionOP  scorefxn)
void protocols::enzdes::enzutil::enable_constraint_scoreterms ( core::scoring::ScoreFunctionOP  scorefxn)
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

References protocols::toolbox::match_enzdes_util::get_enzdes_observer().

Referenced by protocols::enzdes::SecondaryMatchProtocol::do_matching(), and protocols::enzdes::EnzdesBaseProtocol::enzdes_pack().

std::string protocols::enzdes::enzutil::get_pdb_code_from_pose_tag ( core::pose::Pose const &  pose)

function not implemented very slick at the moment, need to find way to compile boost regex library :(( to extract the pdb code from the pose tag without a regular expression module, some explicit functions have been written below

References core::pose::Pose::data(), is_digit(), is_lowercase_letter(), is_uppercase_letter(), and protocols::kinmatch::str().

Referenced by protocols::enzdes::DesignVsNativeComparison::compare_to_native().

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.

  • see enzdes style REMARKs format used to specify match type constraint between two residues (template A and template B)

References protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and core::pose::Pose::total_residue().

Referenced by protocols::enzdes::EnzScoreFilter::compute(), and get_resnum_from_cstid_list().

void protocols::enzdes::enzutil::get_resnum_from_cstid_list ( std::string const &  cstidlist,
core::pose::Pose const &  pose,
utility::vector1< core::Size > &  resnums 
)
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

References protocols::toolbox::match_enzdes_util::get_enzdes_observer().

Referenced by protocols::enzdes::DetectProteinLigandInterface::apply(), protocols::enzdes::EnzdesBaseProtocol::design_targets(), and protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position().

bool protocols::enzdes::enzutil::is_digit ( char *  cha)

delete and use cctype functions

Referenced by get_pdb_code_from_pose_tag().

bool protocols::enzdes::enzutil::is_lowercase_letter ( char *  cha)

delete and use cctype functions

Referenced by get_pdb_code_from_pose_tag().

bool protocols::enzdes::enzutil::is_scofx_cstfied ( core::scoring::ScoreFunctionCOP  scorefxn)
bool protocols::enzdes::enzutil::is_uppercase_letter ( char *  cha)

delete and use cctype functions

Referenced by get_pdb_code_from_pose_tag().

void protocols::enzdes::enzutil::make_continuous_true_regions_in_bool_vector ( utility::vector1< bool > &  the_vector,
core::Size const  min_number_continuous_trues 
)
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

References protocols::enzdes::GenerateStoredRBConfs::apply(), protocols::toolbox::match_enzdes_util::get_enzdes_observer(), and core::import_pose::pose_from_pdb().

Referenced by protocols::enzdes::EnzdesJobInputter::pose_from_job().

core::pack::task::PackerTaskOP protocols::enzdes::enzutil::recreate_task ( core::pose::Pose const &  pose,
core::pack::task::PackerTask const &  orig_task 
)
void protocols::enzdes::enzutil::remove_all_enzdes_constraints ( core::pose::Pose pose)
void protocols::enzdes::enzutil::remove_remark_header_for_geomcst ( core::pose::Pose pose,
core::Size  geomcst 
)
void protocols::enzdes::enzutil::scorefxn_update_from_options ( core::scoring::ScoreFunctionOP  scorefxn)
core::Real protocols::enzdes::enzutil::sum_constraint_scoreterms ( core::pose::Pose const &  pose,
int  which_res 
)
static basic::Tracer protocols::enzdes::enzutil::tr ( "protocols.enzdes.enzdes_util"  ) [static]
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