class Chem::Chain
- Chem::Chain
- Reference
- Object
Included Modules
Defined in:
chem/core/chain.crConstructors
Instance Method Summary
-
#<=>(rhs : self) : Int32
The comparison operator.
- #[](number : Int32, insertion_code : Char | Nil = nil) : Residue
- #[]?(number : Int32, insertion_code : Char | Nil = nil) : Residue | Nil
- #clear : self
- #delete(residue : Residue) : Residue | Nil
- #dig(number : Int32, insertion_code : Char | Nil) : Residue
- #dig(number : Int32, insertion_code : Char | Nil, *subindexes)
- #dig(number : Int32) : Residue
- #dig(number : Int32, *subindexes)
- #dig?(number : Int32, insertion_code : Char | Nil) : Residue | Nil
- #dig?(number : Int32, insertion_code : Char | Nil, *subindexes)
- #dig?(number : Int32) : Residue | Nil
- #dig?(number : Int32, *subindexes)
- #each_atom : Iterator(Atom)
- #each_atom(&block : Atom -> )
- #each_residue : Iterator(Residue)
- #each_residue(&block : Residue -> )
- #id : Char
- #n_atoms : Int32
- #n_residues : Int32
- #polymer? : Bool
-
#renumber_residues_by(& : Residue -> _) : Nil
Renumber residues based on the order by the output value of the block.
-
#renumber_residues_by_connectivity : Nil
Renumber residues based on bond information.
- #reset_cache : Nil
-
#spec(io : IO) : Nil
Writes the chain specification to the given IO.
-
#spec : String
Returns the chain specification.
- #structure(*args, **options)
- #structure(*args, **options, &)
-
#to_s(io : IO)
Appends a short String representation of this object which includes its class name and its object address.
- #top : Topology
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::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
Constructor Detail
Instance Method Detail
The comparison operator.
Returns -1, 0 or 1 depending on whether self precedes
rhs, equals to rhs or comes after rhs. The comparison is
done based on chain identifier.
chains = Structure.read("peptide.pdb").chains
chains[0] <=> chains[1] # => -1
chains[1] <=> chains[1] # => 0
chains[2] <=> chains[1] # => 1Renumber residues based on the order by the output value of the block.
Renumber residues based on bond information. Residue ordering is computed based on the link bond if available.
Writes the chain specification to the given IO.
Chain specification is a short string representation encoding chain information including the id.
Returns the chain specification.
Chain specification is a short string representation encoding chain information including the id.
Appends a short String representation of this object which includes its class name and its object address.
class Person
def initialize(@name : String, @age : Int32)
end
end
Person.new("John", 32).to_s # => #<Person:0x10a199f20>