struct Chem::ChainView

Included Modules

Defined in:

chem/core/chain_view.cr
chem/register_format.cr

Instance Method Summary

Instance methods inherited from module Indexable(Chem::Chain)

[](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::Chain)

===(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

def atoms : AtomView #

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def residues : ResidueView #

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def to_gen(fractional : Bool = false) : String #

Returns a string representation of the chain view using the Chem::Gen file format. Arguments are forwarded to Chem::Gen::Writer.open.


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

Writes the chain view to output using the Chem::Gen file format. Arguments are forwarded to Chem::Gen::Writer.open.


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def to_mol(variant : Chem::Mol::Variant = :v2000) : String #

Returns a string representation of the chain view using the Chem::Mol file format. Arguments are forwarded to Chem::Mol::Writer.open.


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def to_mol(output : IO | Path | String, variant : Chem::Mol::Variant = :v2000) : Nil #

Writes the chain view to output using the Chem::Mol file format. Arguments are forwarded to Chem::Mol::Writer.open.


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

Writes the chain view to output using the Chem::Mol2 file format. Arguments are forwarded to Chem::Mol2::Writer.open.


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def to_mol2 : String #

Returns a string representation of the chain view using the Chem::Mol2 file format. Arguments are forwarded to Chem::Mol2::Writer.open.


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def 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 chain view using the Chem::PDB file format. Arguments are forwarded to Chem::PDB::Writer.open.


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def 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 chain view to output using the Chem::PDB file format. Arguments are forwarded to Chem::PDB::Writer.open.


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

Returns a string representation of the chain view using the Chem::XYZ file format. Arguments are forwarded to Chem::XYZ::Writer.open.


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

Writes the chain view to output using the Chem::XYZ file format. Arguments are forwarded to Chem::XYZ::Writer.open.


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

Writes the chain view to output using format. Raises ArgumentError if format has required arguments or cannot write Chem::ChainView.

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.


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def write(path : Path | String) : Nil #

Writes the chain 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:

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


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