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import_pose.hh File Reference

various functions to construct Pose object(s) from PDB(s) More...

#include <core/import_pose/import_pose_options.fwd.hh>
#include <iosfwd>
#include <basic/Tracer.fwd.hh>
#include <core/types.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/id/AtomID_Mask.fwd.hh>
#include <core/io/StructFileRep.fwd.hh>
#include <core/io/StructFileReaderOptions.fwd.hh>
#include <core/pose/full_model_info/FullModelParameters.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <utility/options/OptionCollection.fwd.hh>
#include <core/import_pose/FullModelPoseBuilder.fwd.hh>
#include <utility/vector1.fwd.hh>
#include <map>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::import_pose
 

Typedefs

typedef
utility::pointer::shared_ptr
< CifFile > 
CifFileOP
 
typedef
utility::pointer::shared_ptr
< CifParser > 
CifParserOP
 
typedef std::string core::import_pose::String
 

Enumerations

enum  core::import_pose::FileType {
  core::import_pose::PDB_file =1, core::import_pose::CIF_file, core::import_pose::MMTF_file, core::import_pose::SRLZ_file,
  core::import_pose::end_of_filetype_list, core::import_pose::Unknown_file = end_of_filetype_list
}
 Enum for the file type. More...
 

Functions

std::ostream & core::import_pose::operator<< (std::ostream &stream, FileType type)
 
std::string core::import_pose::extension_from_filetype (FileType const filetype)
 Given a filetype, return the string for the extension. More...
 
void core::import_pose::read_all_poses (utility::vector1< std::string > const &filenames, utility::vector1< core::pose::PoseOP > &poses)
 
void core::import_pose::read_additional_pdb_data (std::string const &s, pose::Pose &pose, io::StructFileRepCOP, bool read_fold_tree)
 
void core::import_pose::read_additional_pdb_data (std::string const &s, pose::Pose &pose, ImportPoseOptions const &options, bool read_fold_tree)
 
pose::PoseOP core::import_pose::pose_from_file (std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Returns a PoseOP object from the Pose created from input PDB <filename> More...
 
pose::PoseOP core::import_pose::pose_from_file (std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
 Returns a PoseOP object from the Pose created from input PDB <filename>, taking a set of custom ImportPoseOptions parameters. More...
 
pose::PoseOP core::import_pose::pose_from_file (chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Returns a PoseOP object from the Pose created by reading the input PDB <filename>, this constructor allows for a non-default ResidueTypeSet <residue_set> More...
 
FileType core::import_pose::determine_file_type (std::string const &contents_of_file)
 Determine what file type is passed to function there should only be one function that calls this, pose_from_file and only calls it when the filetype is unknown. More...
 
void core::import_pose::pose_from_file (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType file_type)
 
void core::import_pose::pose_from_file (pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Reads in data from input PDB <filename> and stores it in the Pose <pose>, this constructor allows for a non-default ResidueTypeSet <residue_set> More...
 
void core::import_pose::pose_from_file (pose::Pose &pose, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Reads in data from input PDB <filename> and stores it in the Pose <pose>, uses the FA_STANDARD ResidueTypeSet (fullatom) by default. More...
 
void core::import_pose::pose_from_file (pose::Pose &pose, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
 
void core::import_pose::pose_from_file (utility::vector1< pose::Pose > &poses, chemical::ResidueTypeSet const &residue_set, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Reads data from an input PDB containing multiple models named <filename> and stores it in a vector of Pose objects named <poses> using ResidueTypeSet <residue_set> More...
 
void core::import_pose::pose_from_file (utility::vector1< pose::Pose > &poses, chemical::ResidueTypeSet const &residue_set, std::string const &filename, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
 
utility::vector1
< core::pose::PoseOP
core::import_pose::poseOPs_from_files (utility::vector1< std::string > const &filenames, bool read_fold_tree, FileType type)
 
utility::vector1
< core::pose::PoseOP
core::import_pose::poseOPs_from_files (utility::vector1< std::string > const &filenames, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
 
utility::vector1
< core::pose::PoseOP
core::import_pose::poseOPs_from_files (chemical::ResidueTypeSet const &residue_set, utility::vector1< std::string > const &filenames, ImportPoseOptions const &options, bool read_fold_tree, FileType type)
 
utility::vector1
< core::pose::Pose
core::import_pose::poses_from_files (utility::vector1< std::string > const &filenames, bool read_fold_tree, FileType type)
 
utility::vector1
< core::pose::Pose
core::import_pose::poses_from_files (chemical::ResidueTypeSet const &residue_set, utility::vector1< std::string > const &filenames, bool read_fold_tree, FileType type)
 
void core::import_pose::pose_from_file (utility::vector1< pose::Pose > &poses, std::string const &filename, bool read_fold_tree=false, FileType type=Unknown_file)
 Reads data from an input PDB containing multiple models named <filename> and stores it in a vector of Pose objects named <poses> using the FA_STANDARD ResidueTypeSet (fullatom) More...
 
void core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, std::string const &filename)
 
void core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, ImportPoseOptions const &options, std::string const &filename)
 
void core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, chemical::ResidueTypeSet const &residue_set, std::string const &filename)
 
void core::import_pose::pose_from_pdbstring (pose::Pose &pose, std::string const &pdbcontents, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options, std::string const &filename)
 
void core::import_pose::pose_from_pdb_stream (pose::Pose &pose, std::istream &pdb_stream, std::string const &filename, ImportPoseOptions const &options)
 
void core::import_pose::centroid_pose_from_pdb (pose::Pose &pose, std::string const &filename, bool read_fold_tree=false)
 Reads in data from input PDB <filename> and stores it in the Pose <pose> using the CENTROID ResidueTypeSet (centroid) More...
 
void core::import_pose::build_pose (io::StructFileRepOP fd,pose::Pose &pose, chemical::ResidueTypeSet const &residue_set)
 Create pose object, using given StructFileRep object. If PDB cleanin specified - it will be applied first. Constructs a ImportPoseOptions object from the command line. More...
 
void core::import_pose::build_pose (io::StructFileRepOP fd, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options)
 Build Rosetta 3 Pose object from StructFileRep. More...
 
void core::import_pose::build_pose_as_is (io::StructFileRepOP sfr, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, ImportPoseOptions const &options)
 Try to Build pose object from pdb 'as-is'. PDB file must be really clean. More...
 
void core::import_pose::build_pose_as_is2 (io::StructFileRepCOP, pose::Pose &pose, chemical::ResidueTypeSet const &residue_set, id::AtomID_Mask &missing, ImportPoseOptions const &options)
 
core::pose::PoseOP core::import_pose::get_pdb_with_full_model_info (std::string const &input_file, core::chemical::ResidueTypeSetCOP rsd_set)
 
core::pose::PoseOP core::import_pose::get_pdb_and_cleanup (std::string const &input_file)
 
core::pose::PoseOP core::import_pose::get_pdb_and_cleanup (std::string const &input_file, core::chemical::ResidueTypeSetCOP rsd_set)
 
void core::import_pose::get_other_poses (utility::vector1< core::pose::PoseOP > &other_poses, utility::vector1< std::string > const &other_files, core::chemical::ResidueTypeSetCOP rsd_set)
 
pose::PoseOP core::import_pose::initialize_pose_and_other_poses_from_command_line (core::chemical::ResidueTypeSetCOP rsd_set)
 
PoseOP core::import_pose::initialize_pose_and_other_poses_from_options (core::chemical::ResidueTypeSetCOP rsd_set, utility::options::OptionCollection const &options)
 
PoseOP core::import_pose::initialize_pose_and_other_poses_from_options_and_input_poses (core::chemical::ResidueTypeSetCOP rsd_set, utility::options::OptionCollection const &options, utility::vector1< pose::PoseOP > &input_poses)
 
void core::import_pose::cleanup (pose::Pose &pose, bool const force_cut_at_rna_chainbreak)
 
core::pose::full_model_info::FullModelParametersOP core::import_pose::get_sequence_information (std::string const &fasta_file, utility::vector1< core::Size > &cutpoint_open_in_full_model, bool const add_virt=false)
 
void core::import_pose::setup_for_density_scoring (core::pose::Pose &pose)
 
void core::import_pose::get_extra_cutpoints_from_names (core::Size const nres, utility::vector1< core::Size > &cutpoints, std::map< core::Size, std::string > const &non_standard_residue_map)
 
void core::import_pose::setup_fold_trees (utility::vector1< core::pose::Pose * > &pose_pointers, utility::vector1< core::Size > &cutpoint_open_in_full_model, utility::vector1< core::Size > &fixed_domain_map, utility::vector1< core::Size > const &cutpoint_closed, utility::vector1< core::Size > const &extra_minimize_res, utility::vector1< core::Size > const &extra_minimize_jump_res, utility::vector1< core::Size > const &sample_res, utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &jump_res, utility::vector1< core::Size > const &preferred_root_res, utility::vector1< core::Size > const &virtual_sugar_res, core::pose::full_model_info::FullModelParameters const &full_model_parameters, utility::vector1< utility::vector1< core::Size > > const &pose_res_lists)
 
void core::import_pose::update_pose_fold_tree (core::pose::Pose &pose, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &extra_min_res, utility::vector1< core::Size > const &sample_res, utility::vector1< core::Size > const &jump_res, core::pose::full_model_info::FullModelParameters const &full_model_parameters)
 
void core::import_pose::define_chains (core::pose::Pose const &pose, utility::vector1< utility::vector1< core::Size > > &all_res_in_chain, utility::vector1< utility::vector1< core::Size > > &all_fixed_res_in_chain, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &extra_min_res)
 
void core::import_pose::setup_user_defined_jumps (utility::vector1< core::Size > const &jump_res, utility::vector1< core::Size > &jump_partners1, utility::vector1< core::Size > &jump_partners2, utility::vector1< std::pair< core::Size, core::Size > > &chain_connections, utility::vector1< core::Size > const &res_list, utility::vector1< utility::vector1< core::Size > > const &all_res_in_chain)
 
core::Size core::import_pose::get_chain (core::Size const i, utility::vector1< utility::vector1< core::Size > > const &all_res_in_chain)
 
void core::import_pose::setup_jumps (core::pose::Pose const &pose, utility::vector1< core::Size > &jump_partners1, utility::vector1< core::Size > &jump_partners2, utility::vector1< std::pair< core::Size, core::Size > > &chain_connections, utility::vector1< utility::vector1< core::Size > > const &all_res_in_chain, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &resnum_and_chain_and_segid_in_pose)
 
core::kinematics::FoldTree core::import_pose::get_tree (core::pose::Pose const &pose, utility::vector1< core::Size > const &cuts, utility::vector1< core::Size > const &jump_partners1, utility::vector1< core::Size > const &jump_partners2)
 
core::kinematics::FoldTree core::import_pose::get_tree (core::Size const nres, utility::vector1< core::Size > const &cuts, utility::vector1< core::Size > const &jump_partners1, utility::vector1< core::Size > const &jump_partners2, utility::vector1< std::string > const &jump_atoms1, utility::vector1< std::string > const &jump_atoms2)
 
void core::import_pose::update_fixed_domain_from_extra_minimize_jump_res (utility::vector1< core::Size > &fixed_domain, core::pose::Pose const &pose, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &extra_minimize_jump_res)
 
void core::import_pose::add_cutpoint_closed (core::pose::Pose &pose, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &cutpoint_closed)
 
void core::import_pose::put_in_cutpoint (pose::Pose &pose, Size const i)
 
void core::import_pose::add_virtual_sugar_res (core::pose::Pose &pose, utility::vector1< core::Size > const &res_list, utility::vector1< core::Size > const &virtual_sugar_res)
 
utility::vector1< core::Sizecore::import_pose::figure_out_working_res (utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &sample_res)
 
utility::vector1< core::Sizecore::import_pose::figure_out_sample_res (utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &working_res)
 
void core::import_pose::check_working_res (utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &sample_res)
 
void core::import_pose::check_extra_minimize_res_are_input (utility::vector1< core::Size > const &extra_minimize_res, utility::vector1< core::Size > const &input_domain_map)
 
void core::import_pose::figure_out_motif_mode (utility::vector1< core::Size > &extra_min_res, utility::vector1< core::Size > &terminal_res, utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &cutpoint_open_in_full_model)
 
void core::import_pose::add_block_stack_variants (utility::vector1< core::pose::Pose * > const &pose_pointers, utility::vector1< utility::vector1< core::Size > > const &pose_res_lists, utility::vector1< core::Size > const &block_stack_above_res, utility::vector1< core::Size > const &block_stack_below_res)
 
void core::import_pose::update_jump_res (utility::vector1< core::Size > &jump_res, utility::vector1< core::Size > const &extra_minimize_jump_res)
 
utility::vector1< core::Sizecore::import_pose::figure_out_fixed_domain_map (utility::vector1< core::Size > const &input_domain_map, utility::vector1< core::Size > const &extra_minimize_res)
 
utility::vector1< core::Sizecore::import_pose::figure_out_dock_domain_map (utility::vector1< core::Size > &cutpoint_open_in_full_model, utility::vector1< utility::vector1< core::Size > > const &pose_res_lists, utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &sample_res, core::Size const nres)
 
void core::import_pose::reorder_pose (core::pose::Pose &pose, utility::vector1< core::Size > &res_list)
 
bool core::import_pose::just_modeling_RNA (utility::vector1< std::string > const &fasta_files)
 
void core::import_pose::look_for_dna (utility::vector1< core::sequence::SequenceOP > &fasta_sequences)
 
void core::import_pose::setup_water_bank_for_magnesiums (std::map< Size, std::string > &non_standard_residue_map, utility::vector1< core::sequence::SequenceOP > &fasta_sequences)
 
utility::vector1< Size > core::import_pose::get_cutpoints (utility::vector1< core::sequence::SequenceCOP > const &fasta_sequences, std::map< Size, std::string > const &non_standard_residue_map, utility::vector1< char > const &conventional_chains, utility::vector1< int > const &conventional_numbering, utility::vector1< std::string > const &conventional_segids)
 
void core::import_pose::initialize_native_and_align_pose (PoseOP &native_pose, PoseOP &align_pose, core::chemical::ResidueTypeSetCOP rsd_set, PoseCOP start_pose)
 
void core::import_pose::process_input_file (std::string const &silent_file, utility::vector1< core::pose::PoseOP > &pose_list, bool is_pdb=false, bool coarse_rna=false)
 
std::string const core::import_pose::convert_based_on_match_type (std::string const &RNA_string, Size const type)
 
bool core::import_pose::compare_RNA_char (char const char1, char const char2)
 
bool core::import_pose::compare_RNA_secstruct (char const char1, char const char2)
 
Size core::import_pose::get_anchor_rsd (pose::Pose const &pose)
 
bool core::import_pose::involved_in_phosphate_torsion (std::string atomname)
 
void core::import_pose::remove_cutpoint_closed (pose::Pose &pose, Size const i)
 
void core::import_pose::remove_cutpoints_closed (pose::Pose &pose)
 
void core::import_pose::make_extended_coarse_pose (pose::Pose &coarse_pose, std::string const &full_sequence)
 
void core::import_pose::make_coarse_pose (pose::Pose const &pose, pose::Pose &coarse_pose)
 

Detailed Description

various functions to construct Pose object(s) from PDB(s)

Author
Sergey Lyskov

Typedef Documentation

typedef utility::pointer::shared_ptr< CifFile > CifFileOP
typedef utility::pointer::shared_ptr< CifParser > CifParserOP