class Chem::Structure

• Chem::Structure
• Reference
• Object

Overview

Gather, check and annotate types registering a format

Defined in:

Constant Summary

MAX_CHAINS = 62

MIN_RING_ANGLE = 50

Constructors

• .build(*args, **options, &) : self
• .from_chgcar(io : IO) : self
• .from_chgcar(path : Path | String) : self
• .from_cube(io : IO) : self
• .from_cube(path : Path | String) : self
• .from_gen(io : IO, guess_bonds : Bool = false, guess_names : Bool = false) : self
• .from_gen(path : Path | String, guess_bonds : Bool = false, guess_names : Bool = false) : self
• .from_jdftx(io : IO, guess_bonds : Bool = false, guess_names : Bool = false) : self
• .from_jdftx(path : Path | String, guess_bonds : Bool = false, guess_names : Bool = false) : self
• .from_locpot(io : IO) : self
• .from_locpot(path : Path | String) : self
• .from_mol(io : IO) : self
• .from_mol(path : Path | String) : self
• .from_mol2(io : IO) : self
• .from_mol2(path : Path | String) : self
• .from_pdb(io : IO, info : PDB::Info | Nil = nil, alt_loc : Char | Nil = nil, chains : Enumerable(Char) | String | Nil = nil, guess_bonds : Bool = false, het : Bool = true) : self
• .from_pdb(path : Path | String, info : PDB::Info | Nil = nil, alt_loc : Char | Nil = nil, chains : Enumerable(Char) | String | Nil = nil, guess_bonds : Bool = false, het : Bool = true) : self
• .from_poscar(io : IO, guess_bonds : Bool = false, guess_names : Bool = false) : self
• .from_poscar(path : Path | String, guess_bonds : Bool = false, guess_names : Bool = false) : self
• .from_psf(io : IO) : self
• .from_psf(path : Path | String) : self
• .from_sdf(io : IO) : self
• .from_sdf(path : Path | String) : self
• .from_xyz(io : IO, guess_bonds : Bool = false, guess_names : Bool = false) : self
• .from_xyz(path : Path | String, guess_bonds : Bool = false, guess_names : Bool = false) : self
• .new(source_file : Path | String | Nil = nil)
• .read(input : IO | Path | String, format : Chem::Cube.class) : self
• .read(input : IO | Path | String, format : Chem::Gen.class) : self
• .read(input : IO | Path | String, format : Chem::JDFTx.class) : self
• .read(input : IO | Path | String, format : Chem::Mol.class) : self
• .read(input : IO | Path | String, format : Chem::Mol2.class) : self
• .read(input : IO | Path | String, format : Chem::PDB.class) : self
• .read(input : IO | Path | String, format : Chem::PSF.class) : self
• .read(input : IO | Path | String, format : Chem::SDF.class) : self
• .read(input : IO | Path | String, format : Chem::XYZ.class) : self
• .read(input : IO | Path | String, format : Chem::VASP::Chgcar.class) : self
• .read(input : IO | Path | String, format : Chem::VASP::Locpot.class) : self
• .read(input : IO | Path | String, format : Chem::VASP::Poscar.class) : self
• .read(input : IO | Path | String, format) : self

  FIXME Make it compile time error.

• .read(path : IO | Path | String) : self

Class Method Summary

• .guess_element(atom_name : String) : Element

  Returns the element of an atom based on its name.

• .guess_element?(atom_name : String) : Element | Nil

  Returns the element of an atom based on its name if possible, else nil.

Instance Method Summary

• #[](chain_id : Char) : Chain
• #[]?(chain_id : Char) : Chain | Nil
• #angles : Array::View(Angle)

  Returns the angles in the topology.

• #angles=(angles : Array(Chem::Angle))

  Angles in the topology.

• #apply_templates : Nil

  Assign bonds, formal charges, and residue's type from known residue types.

• #atoms : AtomView
• #biases : Array(Chem::Bias)
• #bonds : Array(Bond)

  Returns the bonds between all atoms.

• #cell : Spatial::Parallelepiped

  Returns the unit cell.

• #cell=(cell : Spatial::Parallelepiped | Nil)
• #cell? : Spatial::Parallelepiped | Nil | Nil
• #chains : ChainView
• #clear : self
• #clone : self

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

• #delete(ch : Chain) : Chain | Nil
• #dig(id : Char) : Chain
• #dig(id : Char, *subindexes)
• #dig?(id : Char) : Chain | Nil
• #dig?(id : Char, *subindexes)
• #dihedrals : Array::View(Dihedral)

  Returns the dihedral angles in the topology.

• #dihedrals=(dihedrals : Array(Chem::Dihedral))

  Dihedral angles in the topology.

• #experiment : Structure::Experiment | Nil
• #experiment=(experiment : Structure::Experiment | Nil)
• #extract(copy_properties : Bool = true, & : Atom -> Bool) : self

  Returns a new structure containing the selected atoms by the given block.

• #formal_charge : Int32

  TODO implement compound accessors in a global module

• #guess_angles : Nil

  Determines the angles based on connectivity.

• #guess_bonds(perceive_order : Bool = true) : Nil

  Determines the bonds from connectivity and geometry.

• #guess_dihedrals : Nil

  Determines the dihedral angles based on connectivity.

• #guess_formal_charges : Nil

  Sets the formal charges based on the existing bonds.

• #guess_impropers : Nil

  Determines the improper dihedral angles based on connectivity.

• #guess_names(registry : Templates::Registry = Templates::Registry.default) : Nil

  Detects and assigns topology names from known residue templates based on bond information.

• #guess_unknown_residue_types : Nil

  Determines the type of unknown residues based on their neighbors.

• #impropers : Array::View(Improper)

  Returns the improper dihedral angles in the topology.

• #impropers=(impropers : Array(Chem::Improper))

  Improper dihedral angles in the topology.

• #inspect(io : IO) : Nil

  Appends a String representation of this object which includes its class name, its object address and the values of all instance variables.

• #metadata : Chem::Metadata

  Hash-like container that stores the structure's properties as key (string)-value pairs.

• #periodic? : Bool
• #pos : Spatial::Positions3Proxy
• #pos=(pos : Spatial::Positions3) : Spatial::Positions3

  Sets the atom coordinates and cell.

• #pos=(pos : Enumerable(Spatial::Vec3)) : Enumerable(Spatial::Vec3)

  Sets the atom coordinates.

• #renumber_residues_by(& : Residue -> _) : Nil

  Renumber residues per chain based on the order by the output value of the block.

• #renumber_residues_by_connectivity(split_chains : Bool = true) : Nil

  Renumber chain and residues based on bond information.

• #reset_connectivity : Nil

  Deletes all bonds and resets formal charges to zero.

• #residues : ResidueView
• #source_file : Path | Nil
• #title : String
• #title=(title : String)
• #to_gen(io : IO, fractional : Bool = false) : Nil
• #to_gen(fractional : Bool = false) : String
• #to_gen(path : Path | String, fractional : Bool = false) : Nil
• #to_jdftx(io : IO, fractional : Bool = false, wrap : Bool = false, single_file : Bool = true) : Nil
• #to_jdftx(fractional : Bool = false, wrap : Bool = false, single_file : Bool = true) : String
• #to_jdftx(path : Path | String, fractional : Bool = false, wrap : Bool = false, single_file : Bool = true) : Nil
• #to_mol(io : IO, variant : Mol::Variant = :v2000) : Nil
• #to_mol(variant : Mol::Variant = :v2000) : String
• #to_mol(path : Path | String, variant : Mol::Variant = :v2000) : Nil
• #to_mol2(io : IO) : Nil
• #to_mol2(path : Path | String) : Nil
• #to_mol2 : String
• #to_pdb(io : IO, conect conect_options : PDB::ConectOptions = PDB::ConectOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false, include_header : Bool = true, include_end : Bool = true) : Nil
• #to_pdb(conect conect_options : PDB::ConectOptions = PDB::ConectOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false, include_header : Bool = true, include_end : Bool = true) : String
• #to_pdb(path : Path | String, conect conect_options : PDB::ConectOptions = PDB::ConectOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false, include_header : Bool = true, include_end : Bool = true) : Nil
• #to_poscar(io : IO, order : Array(Element) | Array(String) | Nil = nil, fractional : Bool = false, wrap : Bool = false) : Nil
• #to_poscar(order : Array(Element) | Array(String) | Nil = nil, fractional : Bool = false, wrap : Bool = false) : String
• #to_poscar(path : Path | String, order : Array(Element) | Array(String) | Nil = nil, fractional : Bool = false, wrap : Bool = false) : Nil
• #to_poscar(order : Array(Element) | Array(String) | Nil = nil, fractional : Bool = false, wrap : Bool = false) : String
• #to_pymol(io : IO) : Nil
• #to_pymol(path : Path | String) : Nil
• #to_pymol : String
• #to_s(io : IO)

  Appends a short String representation of this object which includes its class name and its object address.

• #to_sdf(io : IO, variant : Mol::Variant = :v2000) : Nil
• #to_sdf(variant : Mol::Variant = :v2000) : String
• #to_sdf(path : Path | String, variant : Mol::Variant = :v2000) : Nil
• #to_stride(io : IO) : Nil
• #to_stride(path : Path | String) : Nil
• #to_stride : String
• #to_vmd(io : IO) : Nil
• #to_vmd(path : Path | String) : Nil
• #to_vmd : String
• #to_xyz(io : IO, extended : Bool = false, fields : Array(String) = [] of String) : Nil
• #to_xyz(extended : Bool = false, fields : Array(String) = [] of String) : String
• #to_xyz(path : Path | String, extended : Bool = false, fields : Array(String) = [] of String) : Nil
• #write(output : IO | Path | String, format : Chem::Gen.class) : Nil
• #write(output : IO | Path | String, format : Chem::JDFTx.class) : Nil
• #write(output : IO | Path | String, format : Chem::Mol.class) : Nil
• #write(output : IO | Path | String, format : Chem::Mol2.class) : Nil
• #write(output : IO | Path | String, format : Chem::PDB.class) : Nil
• #write(output : IO | Path | String, format : Chem::PyMOL.class) : Nil
• #write(output : IO | Path | String, format : Chem::SDF.class) : Nil
• #write(output : IO | Path | String, format : Chem::VMD.class) : Nil
• #write(output : IO | Path | String, format : Chem::XYZ.class) : Nil
• #write(output : IO | Path | String, format : Chem::Protein::Stride.class) : Nil
• #write(output : IO | Path | String, format : Chem::VASP::Poscar.class) : Nil
• #write(output : IO | Path | String, format) : Nil

  FIXME Make it compile time error.

• #write(path : IO | Path | String) : Nil

Constructor Detail

Class Method 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

Nele - Tele + V

class Person
  def initialize(@name : String, @age : Int32)
  end
end

Person.new("John", 32).inspect # => #<Person:0x10fd31f20 @name="John", @age=32>

structure.metadata["foo"] = 123
structure.metadata["foo"]      # => Metadata::Any(123)
structure.metadata["foo"].as_i # => 123
structure.metadata["foo"].as_f # => 123.0
structure.metadata["foo"].as_s # raises TypeCastError

class Person
  def initialize(@name : String, @age : Int32)
  end
end

Person.new("John", 32).to_s # => #<Person:0x10a199f20>