align.hpp File Reference

Sequence alignment, label_seq_id assignment, structure superposition. More...

#include "model.hpp"
#include "seqalign.hpp"
#include "qcp.hpp"
#include "polyheur.hpp"

Go to the source code of this file.

Namespaces
namespace	gemmi

Enumerations
enum class	gemmi::SupSelect { gemmi::CaP , gemmi::MainChain , gemmi::All }

Functions
std::vector< int >	gemmi::prepare_target_gapo (const ConstResidueSpan &polymer, PolymerType polymer_type, const AlignmentScoring *scoring=nullptr)
AlignmentResult	gemmi::align_sequence_to_polymer (const std::vector< std::string > &full_seq, const ConstResidueSpan &polymer, PolymerType polymer_type, const AlignmentScoring *scoring=nullptr)
bool	gemmi::seqid_matches_seqres (const ConstResidueSpan &polymer, const Entity &ent)
void	gemmi::clear_sequences (Structure &st)
GEMMI_DLL void	gemmi::assign_best_sequences (Structure &st, const std::vector< std::string > &fasta_sequences)
void	gemmi::assign_label_seq_to_polymer (ResidueSpan &polymer, const Entity *ent, bool force)
void	gemmi::clear_label_seq_id (Structure &st)
void	gemmi::assign_label_seq_id (Structure &st, bool force)
void	gemmi::prepare_positions_for_superposition (std::vector< Position > &pos1, std::vector< Position > &pos2, ConstResidueSpan fixed, ConstResidueSpan movable, PolymerType ptype, SupSelect sel, char altloc='\0', std::vector< int > *ca_offsets=nullptr)
SupResult	gemmi::calculate_current_rmsd (ConstResidueSpan fixed, ConstResidueSpan movable, PolymerType ptype, SupSelect sel, char altloc='\0')
SupResult	gemmi::calculate_superposition (ConstResidueSpan fixed, ConstResidueSpan movable, PolymerType ptype, SupSelect sel, int trim_cycles=0, double trim_cutoff=2.0, char altloc='\0')
std::vector< SupResult >	gemmi::calculate_superpositions_in_moving_window (ConstResidueSpan fixed, ConstResidueSpan movable, PolymerType ptype, double radius=10.0)

Detailed Description

Sequence alignment, label_seq_id assignment, structure superposition.

Definition in file align.hpp.