class Chem::PDB::Reader

Included Modules

Defined in:

chem/formats/pdb.cr

Constant Summary

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

Constructors

Class Method Summary

Instance Method Summary

Instance methods inherited from module Chem::FormatReader::Headed(Chem::Structure::Experiment)

read_header : T read_header

Instance methods inherited from module Chem::FormatReader::MultiEntry(Chem::Structure)

each(indexes : Enumerable(Int), & : T -> )
each(& : T -> ) : Nil each, next_entry : T | Nil next_entry, read_entry : T read_entry, skip_entry : Nil skip_entry

Instance methods inherited from module Chem::FormatReader(Chem::Structure)

read? : Bool read?, read_entry : T read_entry

Instance methods inherited from module IO::Wrapper

close close, closed? : Bool closed?, sync_close : Bool sync_close, sync_close=(sync_close : Bool) sync_close=

Constructor Detail

def self.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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def self.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 Method Detail

def self.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.


def self.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 Method Detail

def next_entry : Structure | Nil #
Description copied from module Chem::FormatReader::MultiEntry(Chem::Structure)

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


[View source]
def read_header : Structure::Experiment #
Description copied from module Chem::FormatReader::Headed(Chem::Structure::Experiment)

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


[View source]
def skip_entry : Nil #
Description copied from module Chem::FormatReader::MultiEntry(Chem::Structure)

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


[View source]