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| template<class T > |
| void | gemmi::remove_alternative_conformations (T &obj) |
| | Remove alternative conformations.
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| |
| template<> |
| void | gemmi::remove_alternative_conformations (Chain &chain) |
| |
| template<class T > |
| void | gemmi::remove_hydrogens (T &obj) |
| | Remove hydrogens.
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| |
| 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).
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| |
| 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) |
| |
| void | gemmi::rename_chain (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.
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| |
| void | gemmi::standardize_crystal_frame (Structure &st) |
| | Convert coordinates to the standard coordinate system for the unit cell.
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| |
