polyheur.hpp File Reference

Heuristic methods for working with chains and polymers. Also includes a few well-defined functions, such as removal of waters. More...

#include <vector>
#include "model.hpp"
#include "util.hpp"

Go to the source code of this file.

Classes
struct	gemmi::AtomNameElement

Namespaces
namespace	gemmi

Functions
GEMMI_DLL PolymerType	gemmi::check_polymer_type (const ConstResidueSpan &span, bool ignore_entity_type=false)
PolymerType	gemmi::get_or_check_polymer_type (const Entity *ent, const ConstResidueSpan &polymer)
std::vector< AtomNameElement >	gemmi::get_mainchain_atoms (PolymerType ptype)
bool	gemmi::in_peptide_bond_distance (const Atom *a1, const Atom *a2)
	distance-based check for peptide bond
bool	gemmi::have_peptide_bond (const Residue &r1, const Residue &r2)
bool	gemmi::in_nucleotide_bond_distance (const Atom *a1, const Atom *a2)
	distance-based check for phosphodiester bond between nucleotide
bool	gemmi::have_nucleotide_bond (const Residue &r1, const Residue &r2)
bool	gemmi::are_connected (const Residue &r1, const Residue &r2, PolymerType ptype)
	check C-N or O3'-P distance
bool	gemmi::are_connected2 (const Residue &r1, const Residue &r2, PolymerType ptype)
	are_connected2() is less exact, but requires only CA (or P) atoms.
bool	gemmi::are_connected3 (const Residue &r1, const Residue &r2, PolymerType ptype)
	are_connected3() = are_connected() + fallback to are_connected2()
GEMMI_DLL std::string	gemmi::make_one_letter_sequence (const ConstResidueSpan &polymer)
GEMMI_DLL void	gemmi::add_entity_types (Chain &chain, bool overwrite)
	Assigns entity_type=Polymer|NonPolymer|Water for each Residue (only for residues with entity_type==Unknown, unless overwrite=true).
GEMMI_DLL void	gemmi::add_entity_types (Structure &st, bool overwrite)
GEMMI_DLL void	gemmi::remove_entity_types (Structure &st)
	Assigns entity_type=Unknown for all residues.
GEMMI_DLL void	gemmi::add_entity_ids (Structure &st, bool overwrite)
	Assigns Residue::entity_id based on Residue::subchain and Entity::subchains.
GEMMI_DLL void	gemmi::assign_subchain_names (Chain &chain, int &nonpolymer_counter)
	The subchain field in the residue is where we store_atom_site.label_asym_id from mmCIF files.
GEMMI_DLL void	gemmi::assign_subchains (Structure &st, bool force, bool fail_if_unknown=true)
GEMMI_DLL void	gemmi::ensure_entities (Structure &st)
GEMMI_DLL void	gemmi::deduplicate_entities (Structure &st)
void	gemmi::setup_entities (Structure &st)
GEMMI_DLL char	gemmi::recommended_het_flag (const Residue &res)
	Determine ATOM/HETATM record type, based on Residue::entity_type.
template<class T >
void	gemmi::assign_het_flags (T &obj, char flag='R')
	R = recommended_het_flag(), other valid values are A, H and '\0'.
template<>
void	gemmi::assign_het_flags (Residue &res, char flag)
template<class T >
void	gemmi::remove_waters (T &obj)
template<>
void	gemmi::remove_waters (Chain &ch)
template<class T >
void	gemmi::remove_ligands_and_waters (T &obj)
template<>
void	gemmi::remove_ligands_and_waters (Chain &ch)
GEMMI_DLL bool	gemmi::trim_to_alanine (Residue &res)
void	gemmi::trim_to_alanine (Chain &chain)
GEMMI_DLL void	gemmi::shorten_ccd_codes (Structure &st)
GEMMI_DLL void	gemmi::restore_full_ccd_codes (Structure &st)
GEMMI_DLL void	gemmi::add_microhetero_to_sequences (Structure &st, bool overwrite=false)
	Modifies Entity::full_sequence. Uses only the first chain for each Entity.
GEMMI_DLL void	gemmi::add_tls_group_ids (Structure &st)

Detailed Description

Heuristic methods for working with chains and polymers. Also includes a few well-defined functions, such as removal of waters.

Definition in file polyheur.hpp.