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| GEMMI_DLL PolymerType | gemmi::check_polymer_type (const ConstResidueSpan &span, bool ignore_entity_type=false) |
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| PolymerType | gemmi::get_or_check_polymer_type (const Entity *ent, const ConstResidueSpan &polymer) |
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| std::vector< AtomNameElement > | gemmi::get_mainchain_atoms (PolymerType ptype) |
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| bool | gemmi::in_peptide_bond_distance (const Atom *a1, const Atom *a2) |
| | distance-based check for peptide bond
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| bool | gemmi::have_peptide_bond (const Residue &r1, const Residue &r2) |
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| bool | gemmi::in_nucleotide_bond_distance (const Atom *a1, const Atom *a2) |
| | distance-based check for phosphodiester bond between nucleotide
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| bool | gemmi::have_nucleotide_bond (const Residue &r1, const Residue &r2) |
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| bool | gemmi::are_connected (const Residue &r1, const Residue &r2, PolymerType ptype) |
| | check C-N or O3'-P distance
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| bool | gemmi::are_connected2 (const Residue &r1, const Residue &r2, PolymerType ptype) |
| | are_connected2() is less exact, but requires only CA (or P) atoms.
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| bool | gemmi::are_connected3 (const Residue &r1, const Residue &r2, PolymerType ptype) |
| | are_connected3() = are_connected() + fallback to are_connected2()
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| std::string | gemmi::make_one_letter_sequence (const ConstResidueSpan &polymer) |
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| 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).
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| GEMMI_DLL void | gemmi::add_entity_types (Structure &st, bool overwrite) |
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| GEMMI_DLL void | gemmi::remove_entity_types (Structure &st) |
| | Assigns entity_type=Unknown for all residues.
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| GEMMI_DLL void | gemmi::add_entity_ids (Structure &st, bool overwrite) |
| | Assigns Residue::entity_id based on Residue::subchain and Entity::subchains.
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| 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.
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| GEMMI_DLL void | gemmi::assign_subchains (Structure &st, bool force, bool fail_if_unknown=true) |
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| GEMMI_DLL void | gemmi::ensure_entities (Structure &st) |
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| GEMMI_DLL void | gemmi::deduplicate_entities (Structure &st) |
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| void | gemmi::setup_entities (Structure &st) |
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| template<class T > |
| void | gemmi::remove_waters (T &obj) |
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| template<> |
| void | gemmi::remove_waters (Chain &ch) |
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| template<class T > |
| void | gemmi::remove_ligands_and_waters (T &obj) |
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| template<> |
| void | gemmi::remove_ligands_and_waters (Chain &ch) |
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| bool | gemmi::trim_to_alanine (Residue &res) |
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| void | gemmi::trim_to_alanine (Chain &chain) |
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| GEMMI_DLL void | gemmi::change_ccd_code (Structure &st, const std::string &old, const std::string &new_) |
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| GEMMI_DLL void | gemmi::shorten_ccd_codes (Structure &st) |
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| void | gemmi::restore_full_ccd_codes (Structure &st) |
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