class Chem::Structure

• Chem::Structure
• Reference
• Object

Included Modules

• Chem::AtomCollection
• Chem::ChainCollection
• Chem::ResidueCollection

Defined in:

Constructors

• .build(guess_topology : Bool = true, &) : self
• .from_gen(input : ::IO | Path | String, *args, **options) : self
• .from_mol2(input : ::IO | Path | String, *args, **options) : self
• .from_pdb(input : ::IO | Path | String, *args, **options) : self
• .from_poscar(input : ::IO | Path | String, *args, **options) : self
• .from_xyz(input : ::IO | Path | String, *args, **options) : self
• .read(path : Path | String, guess_topology : Bool = true) : self
• .read(input : ::IO | Path | String, format : IO::FileFormat | String, guess_topology : Bool = true) : self

Instance Method Summary

• #[](*args, **options)
• #[](*args, **options, &)
• #[]?(*args, **options)
• #[]?(*args, **options, &)
• #biases : Array(Chem::Bias)
• #clear : self
• #clone : self

  Returns a deep copy of self, that is, every chain/residue/atom is copied.

• #coords : Spatial::CoordinatesProxy
• #delete(ch : Chain) : Chain | Nil
• #dig(id : Char) : Chain
• #dig(id : Char, *subindexes)
• #dig?(id : Char) : Chain | Nil
• #dig?(id : Char, *subindexes)
• #each_atom : Iterator(Atom)
• #each_atom(&block : Atom -> )
• #each_chain : Iterator(Chain)
• #each_chain(&block : Chain -> )
• #each_residue : Iterator(Residue)
• #each_residue(&block : Residue -> )
• #empty?
• #experiment : Structure::Experiment | Nil
• #experiment=(experiment : Structure::Experiment | Nil)
• #inspect(io : ::IO)
• #lattice : Lattice | Nil
• #lattice=(lattice : Lattice | Nil)
• #n_atoms : Int32
• #n_chains : Int32
• #n_residues : Int32
• #periodic? : Bool
• #renumber_by_connectivity(split_chains : Bool = true) : Nil

  Renumber chain and residues based on bond information.

• #sequence : Protein::Sequence | Nil
• #sequence=(sequence : Protein::Sequence | Nil)
• #title : String
• #title=(title : String)
• #to_pymol(output : ::IO | Path | String, *args, **options) : Nil
• #to_pymol(*args, **options) : String
• #to_s(io : ::IO)
• #to_stride(output : ::IO | Path | String, *args, **options) : Nil
• #to_stride(*args, **options) : String
• #to_vmd(output : ::IO | Path | String, *args, **options) : Nil
• #to_vmd(*args, **options) : String
• #unwrap : self
• #write(output : ::IO | Path | String, format : IO::FileFormat | String) : Nil
• #write(path : Path | String) : Nil

Constructor Detail

Instance Method Detail

structure = Structure.new "/path/to/file.pdb"
other = structure.clone
other == structure     # => true
other.same?(structure) # => false

structure.dig('A', 23, "OG").partial_charge         # => 0.0
other.dig('A', 23, "OG").partial_charge             # => 0.0
structure.dig('A', 23, "OG").partial_charge = 0.635 # => 0.635
other.dig('A', 23, "OG").partial_charge             # => 0.0