modify.hpp File Reference

Modify various properties of the model. More...

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

Go to the source code of this file.

Namespaces
namespace	gemmi

Functions
template<class T >
void	gemmi::remove_alternative_conformations (T &obj)
	Remove alternative conformations.
template<>
void	gemmi::remove_alternative_conformations (Chain &chain)
template<class T >
void	gemmi::remove_hydrogens (T &obj)
	Remove hydrogens.
template<>
void	gemmi::remove_hydrogens (Residue &res)
template<class T >
void	gemmi::assign_b_iso (T &obj, float b_min, float b_max)
	Set isotropic ADP to the range (b_min, b_max).
template<>
void	gemmi::assign_b_iso (Atom &atom, float b_min, float b_max)
template<class T >
void	gemmi::remove_anisou (T &obj)
	Remove anisotropic ADP.
template<>
void	gemmi::remove_anisou (Atom &atom)
template<class T >
void	gemmi::ensure_anisou (T &obj)
	Set absent ANISOU to value from B_iso.
template<>
void	gemmi::ensure_anisou (Atom &atom)
template<class T >
void	gemmi::transform_pos_and_adp (T &obj, const Transform &tr)
	apply Transform to both atom's position and ADP
template<>
void	gemmi::transform_pos_and_adp (Atom &atom, const Transform &tr)
void	gemmi::assign_serial_numbers (Model &model, bool numbered_ter=false)
	set atom site serial numbers to 1, 2, ..., optionally leaving gaps for TERs
void	gemmi::assign_serial_numbers (Structure &st, bool numbered_ter=false)
template<typename Func >
void	gemmi::process_addresses (Structure &st, Func func)
	Helper function for processing (usually: changing) names and numbers in AtomAddress instances in metadata: Connection, CisPep, Helix, Sheet::Strand.
template<typename Func >
void	gemmi::process_sequence_ids (Structure &st, Func func)
	Takes func(const std::string& chain_name, gemmi::SeqId& seqid).
void	gemmi::rename_chain (Structure &st, const std::string &old_name, const std::string &new_name)
void	gemmi::rename_residues (Structure &st, const std::string &old_name, const std::string &new_name)
void	gemmi::rename_atom_names (Structure &st, const std::string &res_name, const std::map< std::string, std::string > &old_new)
void	gemmi::replace_d_fraction_with_altlocs (Residue &res)
bool	gemmi::replace_deuterium_with_fraction (Residue &res)
void	gemmi::store_deuterium_as_fraction (Structure &st, bool store_fraction)
	Hydrogens modelled as H/D mixture (altlocs H and D with the same position and ADP, but with refined fraction of D), it can be stored in mmCIF either as two atoms (H and D) or, using CCP4/Refmac extension, as H atoms with the ccp4_deuterium_fraction parameter.
void	gemmi::standardize_crystal_frame (Structure &st)
	Convert coordinates to the standard coordinate system for the unit cell.

Detailed Description

Modify various properties of the model.

Definition in file modify.hpp.