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Rosetta
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Helper functions for nub initio. More...
#include <protocols/fold_from_loops/utils/utils.hh>#include <protocols/fold_from_loops/selectors/CutpointResidueSelector.hh>#include <protocols/fold_from_loops/selectors/ConstraintResidueSelector.hh>#include <core/pose/Pose.hh>#include <core/pose/PDBInfo.hh>#include <core/pose/variant_util.hh>#include <core/pose/subpose_manipulation_util.hh>#include <core/id/SequenceMapping.hh>#include <core/sequence/Sequence.hh>#include <core/sequence/SequenceAlignment.hh>#include <core/conformation/Conformation.hh>#include <core/conformation/ResidueFactory.hh>#include <core/conformation/Residue.hh>#include <core/kinematics/FoldTree.hh>#include <core/select/residue_selector/ResidueSelector.hh>#include <core/select/residue_selector/ResidueRanges.hh>#include <core/select/residue_selector/util.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/types.hh>#include <basic/Tracer.hh>#include <utility/vector1.hh>#include <utility/stream_util.hh>#include <iterator>#include <algorithm>#include <iomanip>#include <core/kinematics/MoveMap.hh>Namespaces | |
| protocols | |
| The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP. | |
| protocols::fold_from_loops | |
| protocols::fold_from_loops::utils | |
Functions | |
| static basic::Tracer | protocols::fold_from_loops::utils::TR ("protocols.fold_from_loops.utils", basic::t_trace) |
| core::select::residue_selector::ResidueRanges | protocols::fold_from_loops::utils::split_mid_ranges (std::string structure, core::select::residue_selector::ResidueRanges const &ranges) |
It will take each range that is not the first or the last one and split it into two, following the logic of find_cutpoint_from_secondary_structure Input Ranges are not modified, a new ResidueRanges is returned. WARNING1: When splitting a range of 1 residue, it splits into 1 range of 1 and another from 0 to 0, so that it is easy to filter afterwards ( for the purpose of NubInitio, this means adding and empty pose to the vector, for example ). WARNING2: If the first ResidueRange does not start with 1, an empty_range (0,0) is set at the begining too. WARNING3: If the final number of ranges is odds, we will assume that the last insertion is C-terminal and add a final empty range at the end. More... | |
| core::Size | protocols::fold_from_loops::utils::find_cutpoint_from_secondary_structure (std::string structure) |
| Given a Secondary Structure definition as a string, it finds what it considers the optimal cutpoint. This means that, if there is no loop 'L' segment it will return the middle point as a residue; otherwise it will try to split the larger loop 'L' region. More... | |
| void | protocols::fold_from_loops::utils::attach_n_and_c_unfolded_poses_to_pose (core::pose::Pose const &n_insert, core::pose::Pose &scaffold, core::pose::Pose const &c_insert) |
| To a given scaffold it attaches a unfolded version of a pose to the N-terminal and another to the C-terminal Generates a FoldTree that goes from the middle of 'scaffold' towards both directions. More... | |
| void | protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term (core::pose::Pose const &insert, core::pose::Pose &scaffold, core::chemical::ResidueTypeSetCOP rsd_set) |
| adds the 'insert' unfolded pose to the N-terminal of the provided pose More... | |
| void | protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term (core::pose::Pose const &insert, core::pose::Pose &scaffold, core::chemical::ResidueTypeSetCOP rsd_set) |
| adds the 'insert' unfolded pose to the C-terminal of the provided pose More... | |
| void | protocols::fold_from_loops::utils::append_pose_to_pose_keep_fold_tree (core::pose::Pose &scaffold, core::pose::Pose const &insert, bool new_chain) |
| Basically works as 'core::pose::append_pose_to_pose' but the FoldTree is build by joining by jump the root of 'insert' FoldTree to that of 'scaffold' FoldTree. More... | |
| core::id::SequenceMapping | protocols::fold_from_loops::utils::map_by_residue_subsets (core::pose::Pose const &p1, core::select::residue_selector::ResidueSubset const &r1, core::pose::Pose const &p2, core::select::residue_selector::ResidueSubset const &r2) |
| Creates a sequence mapping between two proteins assuming that the False selections on a ResidueSubset marks the residues that are the same for both of them. Assumes the same number of non-selected patches for each pose. More... | |
| void | protocols::fold_from_loops::utils::report_unfolded (core::pose::Pose const &pose, core::kinematics::MoveMapOP movemap) |
| @ brief reports the conditions of the pose More... | |
Helper functions for nub initio.
1.9.1