struct Chem::AtomView
- Chem::AtomView
- Struct
- Value
- Object
Included Modules
- Array::Wrapper(Chem::Atom)
Defined in:
chem/core/atom_view.crchem/register_format.cr
Instance Method Summary
- #bonds : Array(Bond)
- #chains : ChainView
- #each_fragment(& : self -> ) : Nil
- #fragments : Array(self)
- #pos : Spatial::Positions3Proxy
-
#pos=(pos : Enumerable(Spatial::Vec3)) : Enumerable(Spatial::Vec3)
Sets the atom coordinates.
- #residues : ResidueView
-
#to_gen(fractional : Bool = false) : String
Returns a string representation of the atom view using the
Chem::Genfile format. -
#to_gen(output : IO | Path | String, fractional : Bool = false) : Nil
Writes the atom view to output using the
Chem::Genfile format. -
#to_mol(variant : Chem::Mol::Variant = :v2000) : String
Returns a string representation of the atom view using the
Chem::Molfile format. -
#to_mol(output : IO | Path | String, variant : Chem::Mol::Variant = :v2000) : Nil
Writes the atom view to output using the
Chem::Molfile format. -
#to_mol2(output : IO | Path | String) : Nil
Writes the atom view to output using the
Chem::Mol2file format. -
#to_mol2 : String
Returns a string representation of the atom view using the
Chem::Mol2file format. -
#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 atom view using the
Chem::PDBfile format. -
#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 atom view to output using the
Chem::PDBfile format. -
#to_xyz(extended : Bool = false, fields : Array(String) = [] of String) : String
Returns a string representation of the atom view using the
Chem::XYZfile format. -
#to_xyz(output : IO | Path | String, extended : Bool = false, fields : Array(String) = [] of String) : Nil
Writes the atom view to output using the
Chem::XYZfile format. -
#write(output : IO | Path | String, format : Chem::Format | String) : Nil
Writes the atom view to output using format.
-
#write(path : Path | String) : Nil
Writes the atom view to the specified file.
Instance methods inherited from module Indexable(Chem::Atom)
[](idxs : Tuple) : Tuple[](idxs : Enumerable(Int)) : Array(T)
[](*idxs : Int) : Tuple [], 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)
===(atom : Chem::Atom) : Bool===(chain : Chem::Chain) : Bool
===(residue : Chem::Residue) : Bool ===, average(weights : Indexable(Number))
average(weights : Indexable(Number), & : T -> _) average, find(pattern, if_none default = nil) find, find!(pattern) find!, mean
mean(& : T -> _) mean
Instance Method Detail
Sets the atom coordinates.
Returns a string representation of the atom view using
the Chem::Gen file format. Arguments are forwarded to
Chem::Gen::Writer.open.
Writes the atom view to output using the Chem::Gen
file format. Arguments are forwarded to Chem::Gen::Writer.open.
Returns a string representation of the atom view using
the Chem::Mol file format. Arguments are forwarded to
Chem::Mol::Writer.open.
Writes the atom view to output using the Chem::Mol
file format. Arguments are forwarded to Chem::Mol::Writer.open.
Writes the atom view to output using the Chem::Mol2
file format. Arguments are forwarded to Chem::Mol2::Writer.open.
Returns a string representation of the atom view using
the Chem::Mol2 file format. Arguments are forwarded to
Chem::Mol2::Writer.open.
Returns a string representation of the atom view using
the Chem::PDB file format. Arguments are forwarded to
Chem::PDB::Writer.open.
Writes the atom view to output using the Chem::PDB
file format. Arguments are forwarded to Chem::PDB::Writer.open.
Returns a string representation of the atom view using
the Chem::XYZ file format. Arguments are forwarded to
Chem::XYZ::Writer.open.
Writes the atom view to output using the Chem::XYZ
file format. Arguments are forwarded to Chem::XYZ::Writer.open.
Writes the atom view to output using format. Raises
ArgumentError if format has required arguments or cannot
write Chem::AtomView.
The supported file formats are Chem::Gen, Chem::Mol2, Chem::Mol, Chem::PDB, Chem::XYZ. Use the
#to_* methods to customize how the object is written in the
corresponding file format if possible.
Writes the atom view 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::Mol(.mol)Chem::Mol2(.mol2)Chem::PDB(.ent, .pdb)Chem::XYZ(.xyz)
Use the #to_* methods to customize how the object is written
in the corresponding file format if possible.