Instance methods inherited from module Chem::ResidueCollection

each_residue : Iterator(Residue)
each_residue(&block : Residue -> ) each_residue, each_residue_fragment(& : ResidueView -> ) : Nil each_residue_fragment, each_secondary_structure(reuse : Bool | Array(Residue) = false, strict : Bool = true, handedness : Bool = true) : Iterator(ResidueView)
each_secondary_structure(reuse : Bool | Array(Residue) = false, strict : Bool = true, handedness : Bool = true, & : ResidueView, Protein::SecondaryStructure -> ) : Nil each_secondary_structure, link_bond : Templates::Bond | Nil link_bond, n_residues : Int32 n_residues, reset_secondary_structure : self reset_secondary_structure, residue_fragments : Array(ResidueView) residue_fragments, residues : ResidueView residues, sec=(seclist : Array(Protein::SecondaryStructure)) : Array(Protein::SecondaryStructure)
sec=(sec : Protein::SecondaryStructure) : Protein::SecondaryStructure sec=, secondary_structures(strict : Bool = true, handedness : Bool = true) : Array(ResidueView) secondary_structures

Instance methods inherited from module Chem::ChainCollection

chains : ChainView chains, each_chain : Iterator(Chain)
each_chain(&block : Chain -> ) each_chain, n_chains : Int32 n_chains

Instance methods inherited from module Chem::AtomCollection

atoms : AtomView atoms, bonds : Array(Bond) bonds, coords : Spatial::CoordinatesProxy coords, coords=(coords : Enumerable(Spatial::Vec3)) : Enumerable(Spatial::Vec3) coords=, each_atom : Iterator(Atom)
each_atom(&block : Atom -> ) each_atom, each_fragment(& : AtomView -> ) : Nil each_fragment, formal_charge : Int32 formal_charge, formal_charges : Array(Int32) formal_charges, fragments : Array(AtomView) fragments, has_hydrogens? : Bool has_hydrogens?, n_atoms : Int32 n_atoms, to_gen(fractional : Bool = false) : String
to_gen(output : IO | Path | String, fractional : Bool = false) : Nil to_gen, to_mol2(output : IO | Path | String) : Nil
to_mol2 : String to_mol2, to_pdb(bonds : Chem::PDB::Writer::BondOptions = Chem::PDB::Writer::BondOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false) : String
to_pdb(output : IO | Path | String, bonds : Chem::PDB::Writer::BondOptions = Chem::PDB::Writer::BondOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false) : Nil to_pdb, to_xyz(extended : Bool = false, fields : Array(String) = [] of String) : String
to_xyz(output : IO | Path | String, extended : Bool = false, fields : Array(String) = [] of String) : Nil to_xyz, write(output : IO | Path | String, format : Chem::Format | String) : Nil
write(path : Path | String) : Nil write

Instance methods inherited from module Indexable(Chem::Atom)

sentence(io : IO, separator : String = ", ", *, pair_separator : String = " and ", tail_separator : String = ", and ", & : T, IO -> ) : Nil
sentence(io : IO, separator : String = ", ", *, pair_separator : String = " and ", tail_separator : String = ", and ") : Nil
sentence(separator : String = ", ", *, pair_separator : String = " and ", tail_separator : String = ", and ", & : T -> ) : String
sentence(separator : String = ", ", *, pair_separator : String = " and ", tail_separator : String = ", and ") : String sentence

Instance methods inherited from module Enumerable(Chem::Atom)

average(weights : Indexable(Number))
average(weights : Indexable(Number), & : T -> _) average, mean
mean(& : T -> _) mean