class

Chem::Structure

Inherits Chem::ResidueCollection / Chem::ChainCollection / Chem::AtomCollection / Reference / Object

Constructors

build(*args, **options, &) : self

from_chgcar(input : IO | Path | String) : self

Returns the structure encoded in input using the Chem::VASP::Chgcar file format. Arguments are forwarded to Chem::VASP::Chgcar::Reader.open.

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from_cube(input : IO | Path | String) : self

Returns the structure encoded in input using the Chem::Cube file format. Arguments are forwarded to Chem::Cube::Reader.open.

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from_gen(input : IO | Path | String, guess_bonds : Bool = false, guess_names : Bool = false) : self

Returns the structure encoded in input using the Chem::Gen file format. Arguments are forwarded to Chem::Gen::Reader.open.

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from_locpot(input : IO | Path | String) : self

Returns the structure encoded in input using the Chem::VASP::Locpot file format. Arguments are forwarded to Chem::VASP::Locpot::Reader.open.

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from_mol(input : IO | Path | String) : self

Returns the structure encoded in input using the Chem::Mol file format. Arguments are forwarded to Chem::Mol::Reader.open.

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from_mol2(input : IO | Path | String) : self

Returns the structure encoded in input using the Chem::Mol2 file format. Arguments are forwarded to Chem::Mol2::Reader.open.

If input contains multiple entries, this method returns the first one only. Use Array#from_mol2 or Chem::Mol2::Reader#each to get multiple entries instead.

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Returns the structure encoded in input using the Chem::PDB file format. Arguments are forwarded to Chem::PDB::Reader.open.

If input contains multiple entries, this method returns the first one only. Use Array#from_pdb or Chem::PDB::Reader#each to get multiple entries instead.

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from_poscar(input : IO | Path | String, guess_bonds : Bool = false, guess_names : Bool = false) : self

Returns the structure encoded in input using the Chem::VASP::Poscar file format. Arguments are forwarded to Chem::VASP::Poscar::Reader.open.

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from_psf(input : IO | Path | String) : self

Returns the structure encoded in input using the Chem::PSF file format. Arguments are forwarded to Chem::PSF::Reader.open.

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from_sdf(input : IO | Path | String) : self

Returns the structure encoded in input using the Chem::SDF file format. Arguments are forwarded to Chem::SDF::Reader.open.

If input contains multiple entries, this method returns the first one only. Use Array#from_sdf or Chem::SDF::Reader#each to get multiple entries instead.

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from_xyz(input : IO | Path | String, guess_bonds : Bool = false, guess_names : Bool = false) : self

Returns the structure encoded in input using the Chem::XYZ file format. Arguments are forwarded to Chem::XYZ::Reader.open.

If input contains multiple entries, this method returns the first one only. Use Array#from_xyz or Chem::XYZ::Reader#each to get multiple entries instead.

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new(topology : Topology = Topology.new, source_file : Path | String | Nil = nil)

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read(input : IO | Path | String, format : Chem::Format | String) : self

Returns the structure encoded in the specified file using format. Raises ArgumentError if format has required arguments or cannot read Chem::Structure.

If input contains multiple entries, this method returns the first one only. Use Array.read or Chem::FormatReader::MultiEntry#each (reader can be obtained via Chem::Format.reader) to get multiple entries instead.

The supported file formats are Chem::Cube, Chem::Gen, Chem::Mol2, Chem::Mol, Chem::PDB, Chem::PSF, Chem::SDF, Chem::VASP::Chgcar, Chem::VASP::Locpot, Chem::VASP::Poscar, Chem::XYZ. Use the .from_* methods to customize how the object is decoded in the corresponding file format if possible.

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read(path : Path | String) : self

Returns the structure encoded in the specified file. The file format is chosen based on the filename (see Chem::Format#from_filename). Raises ArgumentError if the file format cannot be determined.

If the file contains multiple entries, this method returns the first one only. Use Array.read to get multiple entries instead.

The supported file formats are the following:

Chem::Gen (.gen)
Chem::Mol (.mol)
Chem::Mol2 (.mol2)
Chem::PDB (.ent, .pdb)
Chem::PSF (.psf)
Chem::SDF (.sdf)
Chem::XYZ (.xyz)
Chem::VASP::Poscar (.poscar, POSCAR, CONTCAR)
Chem::Cube (.cube)
Chem::VASP::Chgcar (CHGCAR)
Chem::VASP::Locpot (LOCPOT)

Use the .from_* methods to customize how the object is decoded in the corresponding file format if possible.

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Instance methods

[](*args, **options)

TODO: remove this delegates... directly use the topology class

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[](*args, **options, &)

TODO: remove this delegates... directly use the topology class

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[]?(*args, **options)

TODO: remove this delegates... directly use the topology class

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[]?(*args, **options, &)

TODO: remove this delegates... directly use the topology class

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atoms(*args, **options)

TODO: remove this delegates... directly use the topology class

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atoms(*args, **options, &)

TODO: remove this delegates... directly use the topology class

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biases

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cell

Returns the unit cell. Raises Spatial::NotPeriodicError if cell is nil.

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cell=(cell : Spatial::Parallelepiped | Nil)

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cell?

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chains(*args, **options)

TODO: remove this delegates... directly use the topology class

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chains(*args, **options, &)

TODO: remove this delegates... directly use the topology class

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clear

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clone

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

Unlike array-like classes in the language, #dup (shallow copy) is not possible.

structure = Structure.new &quot;/path/to/file.pdb&quot;
other = structure.clone
other == structure     # =&gt; true
other.same?(structure) # =&gt; false

structure.dig('A', 23, &quot;OG&quot;).partial_charge         # =&gt; 0.0
other.dig('A', 23, &quot;OG&quot;).partial_charge             # =&gt; 0.0
structure.dig('A', 23, &quot;OG&quot;).partial_charge = 0.635 # =&gt; 0.635
other.dig('A', 23, &quot;OG&quot;).partial_charge             # =&gt; 0.0

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coords

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delete(*args, **options)

TODO: remove this delegates... directly use the topology class

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delete(*args, **options, &)

TODO: remove this delegates... directly use the topology class

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dig(*args, **options)

TODO: remove this delegates... directly use the topology class

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dig(*args, **options, &)

TODO: remove this delegates... directly use the topology class

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dig?(*args, **options)

TODO: remove this delegates... directly use the topology class

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dig?(*args, **options, &)

TODO: remove this delegates... directly use the topology class

each_atom

each_atom

each_chain

each_chain

each_residue

each_residue

experiment

experiment=(experiment : Structure::Experiment | Nil)

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extract(copy_properties : Bool = true, & : Atom -> Bool) : self

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

Structure properties such as biases, unit cell, title, etc. are copied only if copy_properties is true.

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metadata

Hash-like container that stores the structure's properties as key (string)-value pairs. A property's value can be any of the primitive types (string, integer, float, or bool), and so it's internally stored as Metadata::Any. Use the cast methods (#as_*) to convert to the desired type.

structure.metadata[&quot;foo&quot;] = 123
structure.metadata[&quot;foo&quot;]      # =&gt; Metadata::Any(123)
structure.metadata[&quot;foo&quot;].as_i # =&gt; 123
structure.metadata[&quot;foo&quot;].as_f # =&gt; 123.0
structure.metadata[&quot;foo&quot;].as_s # raises TypeCastError

n_atoms

n_chains

n_residues

periodic?

residues(*args, **options)

TODO: remove this delegates... directly use the topology class

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residues(*args, **options, &)

TODO: remove this delegates... directly use the topology class

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source_file

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title

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title=(title : String)

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to_gen(fractional : Bool = false) : String

Returns a string representation of the structure using the Chem::Gen file format. Arguments are fowarded to Chem::Gen::Writer.open.

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to_gen(output : IO | Path | String, fractional : Bool = false) : Nil

Writes the structure to output using the Chem::Gen file format. Arguments are fowarded to Chem::Gen::Writer.open.

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to_mol2(output : IO | Path | String) : Nil

Writes the structure to output using the Chem::Mol2 file format. Arguments are fowarded to Chem::Mol2::Writer.open.

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to_mol2

Returns a string representation of the structure using the Chem::Mol2 file format. Arguments are fowarded to Chem::Mol2::Writer.open.

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to_pdb(bonds : Chem::PDB::Writer::BondOptions = Chem::PDB::Writer::BondOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false) : String

Returns a string representation of the structure using the Chem::PDB file format. Arguments are fowarded to Chem::PDB::Writer.open.

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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

Writes the structure to output using the Chem::PDB file format. Arguments are fowarded to Chem::PDB::Writer.open.

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to_poscar(order : Array(Element) | Array(String) | Nil = nil, fractional : Bool = false, wrap : Bool = false) : String

Returns a string representation of the structure using the Chem::VASP::Poscar file format. Arguments are fowarded to Chem::VASP::Poscar::Writer.open.

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to_poscar(output : IO | Path | String, order : Array(Element) | Array(String) | Nil = nil, fractional : Bool = false, wrap : Bool = false) : Nil

Writes the structure to output using the Chem::VASP::Poscar file format. Arguments are fowarded to Chem::VASP::Poscar::Writer.open.

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to_pymol(output : IO | Path | String) : Nil

Writes the structure to output using the Chem::PyMOL file format. Arguments are fowarded to Chem::PyMOL::Writer.open.

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to_pymol

Returns a string representation of the structure using the Chem::PyMOL file format. Arguments are fowarded to Chem::PyMOL::Writer.open.

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to_s(io : IO)

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(&quot;John&quot;, 32).to_s # =&gt; #&lt;Person:0x10a199f20&gt;

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to_stride(output : IO | Path | String) : Nil

Writes the structure to output using the Chem::Protein::Stride file format. Arguments are fowarded to Chem::Protein::Stride::Writer.open.

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to_stride

Returns a string representation of the structure using the Chem::Protein::Stride file format. Arguments are fowarded to Chem::Protein::Stride::Writer.open.

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to_vmd(output : IO | Path | String) : Nil

Writes the structure to output using the Chem::VMD file format. Arguments are fowarded to Chem::VMD::Writer.open.

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to_vmd

Returns a string representation of the structure using the Chem::VMD file format. Arguments are fowarded to Chem::VMD::Writer.open.

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to_xyz(extended : Bool = false, fields : Array(String) = [] of String) : String

Returns a string representation of the structure using the Chem::XYZ file format. Arguments are fowarded to Chem::XYZ::Writer.open.

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to_xyz(output : IO | Path | String, extended : Bool = false, fields : Array(String) = [] of String) : Nil

Writes the structure to output using the Chem::XYZ file format. Arguments are fowarded to Chem::XYZ::Writer.open.

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topology

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write(output : IO | Path | String, format : Chem::Format | String) : Nil

Writes the structure to output using format. Raises ArgumentError if format has required arguments or cannot write Chem::Structure.

The supported file formats are Chem::Gen, Chem::Mol2, Chem::PDB, Chem::Protein::Stride, Chem::PyMOL, Chem::VASP::Poscar, Chem::VMD, Chem::XYZ. Use the #to_* methods to customize how the object is written in the corresponding file format if possible.

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write(path : Path | String) : Nil

Writes the structure to the specified file. The file format is chosen based on the filename (see Chem::Format#from_filename). Raises ArgumentError if the file format cannot be determined.

The supported file formats are the following:

Chem::Gen (.gen)
Chem::Mol2 (.mol2)
Chem::PDB (.ent, .pdb)
Chem::PyMOL (.pml)
Chem::VMD (.vmd)
Chem::XYZ (.xyz)
Chem::Protein::Stride (.stride)
Chem::VASP::Poscar (.poscar, POSCAR, CONTCAR)

Use the #to_* methods to customize how the object is written in the corresponding file format if possible.

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Constructors

Instance methods

Nested types