class

Chem::PDB::Reader

Inherits Chem::FormatReader::Headed / Chem::FormatReader::MultiEntry / Chem::FormatReader / IO::Wrapper / Reference / Object

Constants

HELIX_TYPES = {1 => Sec::RightHandedHelixAlpha, 3 => Sec::RightHandedHelixPi, 5 => Sec::RightHandedHelix3_10}

Constructors

new(io : IO, alt_loc : Char | Nil = nil, chains : Enumerable(Char) | String | Nil = nil, guess_bonds : Bool = false, het : Bool = true, sync_close : Bool = false)
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new(path : Path | String, alt_loc : Char | Nil = nil, chains : Enumerable(Char) | String | Nil = nil, guess_bonds : Bool = false, het : Bool = true) : self

Creates a new object from the given path. Positional and named arguments are forwarded to the designated constructor.

An IO object will be created and open from the given path, which will be closed when closing this object (sync_close = true). The file open mode is specified by the FILE_MODE constant.

Class methods

open(io : IO, alt_loc : Char | Nil = nil, chains : Enumerable(Char) | String | Nil = nil, guess_bonds : Bool = false, het : Bool = true, sync_close : Bool = false, & : self -> )

Creates a new object from the given io, yields it to the given block, and closes it at the end. Positional and named arguments are forwarded to the constructor.

open(path : Path | String, alt_loc : Char | Nil = nil, chains : Enumerable(Char) | String | Nil = nil, guess_bonds : Bool = false, het : Bool = true, & : self -> )

Creates a new object from the given path yields it to the given block, and closes it at the end. Positional and named arguments are forwarded to the constructor.

An IO object will be created and open from the given path, which will be closed when closing this object (sync_close = true). The file open mode is specified by the FILE_MODE constant.

Instance methods

next_entry

Returns the next entry in the IO, or nil if there are no more entries.

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read_header

Reads the header object from the IO. Raises IO::Error if the reader is closed or ParseException if the header cannot be decoded.

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skip_entry

Discards the next entry in the IO without fully parsing it.

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