struct
Chem::Spatial::Positions3
- Chem::Spatial::Positions3
- Struct
- Value
- Object
Overview
Gather, check and annotate types registering a format
Included Modules
Defined in:
chem/register_format.crchem/spatial/positions3.cr
Constructors
- .from_dcd(io : IO, info : Info, index : Int) : self
- .from_dcd(io : IO, info : Info) : self
- .new(pos : Slice(Vec3), cell : Parallelepiped | Nil = nil)
- .read(input : IO | Path | String, format : Chem::DCD.class) : self
-
.read(input : IO | Path | String, format) : self
FIXME Make it compile time error.
- .read(path : IO | Path | String) : self
Instance Method Summary
- #cell : Parallelepiped | Nil
- #cell? : Parallelepiped | Nil | Nil
- #size(*args, **options)
- #size(*args, **options, &)
- #to_dcd(io : IO, buffer : Slice(Float32) = Slice(Float32).new(frame.size)) : Nil
- #to_dcd(buffer : Slice(Float32) = Slice(Float32).new(frame.size)) : String
-
#to_slice : Slice(Vec3)
Returns a read-only slice of the positions.
- #unsafe_fetch(*args, **options)
- #unsafe_fetch(*args, **options, &)
- #write(output : IO | Path | String, format : Chem::DCD.class) : Nil
-
#write(output : IO | Path | String, format) : Nil
FIXME Make it compile time error.
- #write(path : IO | Path | String) : Nil
Instance methods inherited from module Indexable(Chem::Spatial::Vec3)
[](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, to_dcd(io : IO, title : String | Nil = nil) : Nil
to_dcd(title : String | Nil = nil) : String
to_dcd(path : Path | String, title : String | Nil = nil) : Nil to_dcd
Instance methods inherited from module Enumerable(Chem::Spatial::Vec3)
===(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, to_dcd(io : IO, title : String | Nil = nil) : Nil
to_dcd(title : String | Nil = nil) : String
to_dcd(path : Path | String, title : String | Nil = nil) : Nil to_dcd, to_mol2(io : IO) : Nil
to_mol2(path : Path | String) : Nil
to_mol2 : String to_mol2, to_pdb(io : IO, conect conect_options : PDB::ConectOptions = PDB::ConectOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false) : Nil
to_pdb(conect conect_options : PDB::ConectOptions = PDB::ConectOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false) : String
to_pdb(path : Path | String, conect conect_options : PDB::ConectOptions = PDB::ConectOptions.flags(Het, Disulfide), renumber : Bool = true, ter_on_fragment : Bool = false) : Nil to_pdb, to_sdf(io : IO, variant : Mol::Variant = :v2000) : Nil
to_sdf(path : Path | String, variant : Mol::Variant = :v2000) : Nil
to_sdf(variant : Mol::Variant = :v2000) : String to_sdf, 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 to_xyz
Constructor Detail
FIXME Make it compile time error. Should raise if format is not registered or format is incompatible with open_type. Better create an override with the other formats, and leave this as a fallback.
Instance Method Detail
FIXME Make it compile time error. Should raise if format is not registered or format is incompatible with open_type. Better create an override with the other formats, and leave this as a fallback.