assembly.hpp File Reference

Generating biological assemblies by applying operations from struct Assembly to a Model. Includes chain (re)naming utilities. More...

#include "model.hpp"
#include "util.hpp"
#include "logger.hpp"

Go to the source code of this file.

Classes
struct	gemmi::ChainNameGenerator

Namespaces
namespace	gemmi

Enumerations
enum class	gemmi::HowToNameCopiedChain { gemmi::Short , gemmi::AddNumber , gemmi::Dup }

Functions
void	gemmi::ensure_unique_chain_name (const Model &model, Chain &chain)
GEMMI_DLL Model	gemmi::make_assembly (const Assembly &assembly, const Model &model, HowToNameCopiedChain how, const Logger &logging)
Assembly	gemmi::pseudo_assembly_for_unit_cell (const UnitCell &cell)
GEMMI_DLL void	gemmi::transform_to_assembly (Structure &st, const std::string &assembly_name, HowToNameCopiedChain how, const Logger &logging, bool keep_spacegroup=false, double merge_dist=0.2)
	If called with assembly_name="unit_cell" changes structure to unit cell (P1).
GEMMI_DLL Model	gemmi::expand_ncs_model (const Model &model, const std::vector< NcsOp > &ncs, HowToNameCopiedChain how)
GEMMI_DLL void	gemmi::merge_atoms_in_expanded_model (Model &model, const UnitCell &cell, double max_dist=0.2, bool compare_serial=true)
	Searches and merges overlapping equivalent atoms from different chains.
GEMMI_DLL void	gemmi::shorten_chain_names (Structure &st)
GEMMI_DLL void	gemmi::expand_ncs (Structure &st, HowToNameCopiedChain how, double merge_dist=0.2)
GEMMI_DLL void	gemmi::split_chains_by_segments (Model &model, HowToNameCopiedChain how)
	HowToNameCopiedChain::Dup adds segment name to chain name.

Detailed Description

Generating biological assemblies by applying operations from struct Assembly to a Model. Includes chain (re)naming utilities.

Definition in file assembly.hpp.