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Rosetta
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utility functions for making poses from sequences More...
#include <core/pose/annotated_sequence.hh>#include <core/conformation/Conformation.hh>#include <core/pose/Pose.hh>#include <core/pose/PDBInfo.hh>#include <core/pose/carbohydrates/util.hh>#include <core/types.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/ResidueTypeFinder.hh>#include <core/chemical/ResidueType.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/carbohydrates/CarbohydrateInfo.hh>#include <core/chemical/carbohydrates/CarbohydrateInfoManager.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueFactory.hh>#include <core/io/carbohydrates/pose_io.hh>#include <basic/Tracer.hh>#include <utility/vector1.hh>#include <utility/string_util.hh>#include <list>#include <sstream>Namespaces | |
| core | |
| A class for reading in the atom type properties. | |
| core::pose | |
Functions | |
| static basic::Tracer | core::pose::TR ("core.pose") |
| void | core::pose::parse_sequence (std::string const &sequence_in, utility::vector1< std::string > &fullname_list, std::vector< Size > &oneletter_to_fullname_index, std::string &one_letter_sequence) |
| parse the annotated sequence. More... | |
| Size | core::pose::get_sequence_len (std::string const &sequence_in) |
| Get the length of the annotated sequence. More... | |
| chemical::ResidueTypeCOPs | core::pose::residue_types_from_sequence (std::string const &sequence_in, chemical::ResidueTypeSet const &residue_set, bool const auto_termini=true, bool const metapatches=true) |
| return a list of ResidueTypes corresponding to an annotated protein sequence More... | |
| chemical::ResidueTypeCOPs | core::pose::residue_types_from_saccharide_sequence_recursive (std::string const &sequence, chemical::ResidueTypeSet const &residue_set) |
| Internal implementation detail of residue_types_from_saccharide_sequence() Returns the reorganized (but not reversed) set of residuetypes. More... | |
| chemical::ResidueTypeCOPs | core::pose::residue_types_from_saccharide_sequence (std::string const &sequence, chemical::ResidueTypeSet const &residue_set) |
| Return a list of carbohydrate ResidueTypes corresponding to an annotated, linear, IUPAC polysaccharide sequence. More... | |
| void | core::pose::append_pose_with_glycan_residues (pose::Pose &pose, chemical::ResidueTypeCOPs residue_types, core::uint resnum_to_be_appended=0) |
| Append an empty or current Pose with saccharide residues, building branches as necessary. More... | |
| void | core::pose::make_pose_from_sequence (pose::Pose &pose, chemical::ResidueTypeCOPs requested_types, bool const auto_termini=true) |
| Creates a Pose from the annotated protein sequence <sequence> with ResidueTypeSet <residue_set> and stores it in <pose> More... | |
| void | core::pose::make_pose_from_sequence (pose::Pose &pose, std::string const &sequence_in, chemical::ResidueTypeSet const &residue_set, bool const auto_termini, bool const metapatches) |
| void | core::pose::make_pose_from_sequence (pose::Pose &pose, std::string const &sequence_in, chemical::ResidueTypeSetCOP residue_set, bool const auto_termini, bool const metapatches) |
| void | core::pose::make_pose_from_sequence (pose::Pose &pose, std::string const &sequence, std::string const &type_set_name, bool const auto_termini=true, bool const metapatches=true) |
| Creates a Pose from the annotated protein sequence <sequence> with the desired <type_set_name> and stores it in <pose> More... | |
| void | core::pose::make_pose_from_saccharide_sequence (pose::Pose &pose, std::string const &sequence, chemical::ResidueTypeSet const &residue_set, bool const auto_termini=true, bool const idealize_linkages=true) |
| Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with ResidueTypeSet <residue_set> and store it in <pose>. More... | |
| void | core::pose::make_pose_from_saccharide_sequence (pose::Pose &pose, std::string const &sequence, std::string const &type_set_name="fa_standard", bool const auto_termini=true, bool const idealize_linkages=true) |
| Create a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with residue type set name <type_set_name> and store it in <pose>. More... | |
| pose::PoseOP | core::pose::pose_from_saccharide_sequence (std::string const &sequence, std::string const &type_set_name="fa_standard", bool const auto_termini=true, bool const idealize_linkages=true) |
| Return a Pose from an annotated, linear, IUPAC polysaccharide sequence <sequence> with residue type set name <type_set_name>. More... | |
| std::string | core::pose::annotated_to_oneletter_sequence (std::string const &annotated_seq) |
| Returns the oneletter_sequence that corresponds to the given annotated sequence. More... | |
| chemical::ResidueTypeCOP | core::pose::get_rsd_type_from_aa (chemical::ResidueTypeSet const &residue_set, core::chemical::AA const &my_aa, bool const &is_lower_terminus, bool const &is_upper_terminus, bool const metapatches=true) |
| use efficient residue type finder to find simplest residue type with this AA & requested termini. More... | |
utility functions for making poses from sequences
1.9.1