Class: Bio::PDB::ChemicalComponent
- Defined in:
- lib/bio/db/pdb/chemicalcomponent.rb
Overview
Bio::PDB::ChemicalComponet is a parser for a entry of the PDB Chemical Component Dictionary.
The PDB Chemical Component Dictionary is available in deposit.pdb.org/het_dictionary.txt
Defined Under Namespace
Classes: Record
Constant Summary collapse
- DELIMITER =
delimiter for reading via Bio::FlatFile
RS = "\n\n"
Instance Attribute Summary collapse
-
#data ⇒ Object
readonly
all records in this entry as an array.
-
#hash ⇒ Object
readonly
all records in this entry as an hash accessed by record names.
Instance Method Summary collapse
-
#conect ⇒ Object
Returns an hash of bindings of atoms.
-
#entry_id ⇒ Object
Identifier written in the first line “RESIDUE” record.
-
#formul ⇒ Object
The chemical formula of the chemical component.
-
#hetnam ⇒ Object
The name of the chemical component.
-
#hetsyn ⇒ Object
Synonyms for the comical component.
-
#initialize(str) ⇒ ChemicalComponent
constructor
Creates a new object.
-
#record(name = nil) ⇒ Object
Gets all records whose record type is name.
Constructor Details
#initialize(str) ⇒ ChemicalComponent
Creates a new object.
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# File 'lib/bio/db/pdb/chemicalcomponent.rb', line 123 def initialize(str) @data = str.split(/[\r\n]+/) @hash = {} #Flag to say whether the current line is part of a continuation cont = false #Goes through each line and replace that line with a PDB::Record @data.collect! do |line| #Go to next if the previous line was contiunation able, and #add_continuation returns true. Line is added by add_continuation next if cont and cont = cont.add_continuation(line) #Make the new record f = Record.get_record_class(line).new.initialize_from_string(line) #p f #Set cont cont = f if f.continue? #Set the hash to point to this record either by adding to an #array, or on it's own key = f.record_name if a = @hash[key] then a << f else @hash[key] = [ f ] end f end #each #At the end we need to add the final model @data.compact! end |
Instance Attribute Details
#data ⇒ Object (readonly)
all records in this entry as an array.
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# File 'lib/bio/db/pdb/chemicalcomponent.rb', line 156 def data @data end |
#hash ⇒ Object (readonly)
all records in this entry as an hash accessed by record names.
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# File 'lib/bio/db/pdb/chemicalcomponent.rb', line 159 def hash @hash end |
Instance Method Details
#conect ⇒ Object
Returns an hash of bindings of atoms. Note that each white spaces are stripped for atom symbols.
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# File 'lib/bio/db/pdb/chemicalcomponent.rb', line 192 def conect unless defined? @conect c = {} @hash["CONECT"].each do |e| key = e.name.to_s.strip unless key.empty? val = e.other_atoms.collect { |x| x.strip } #warn "Warning: #{key}: atom name conflict?" if c[key] c[key] = val end end @conect = c end @conect end |
#entry_id ⇒ Object
Identifier written in the first line “RESIDUE” record. (e.g. CMP)
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# File 'lib/bio/db/pdb/chemicalcomponent.rb', line 162 def entry_id @data[0].hetID end |
#formul ⇒ Object
The chemical formula of the chemical component. Returns a string (or nil, if the entry is something wrong).
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# File 'lib/bio/db/pdb/chemicalcomponent.rb', line 186 def formul @hash["FORMUL"][0].text end |
#hetnam ⇒ Object
The name of the chemical component. Returns a string (or nil, if the entry is something wrong).
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# File 'lib/bio/db/pdb/chemicalcomponent.rb', line 180 def hetnam @hash["HETNAM"][0].text end |
#hetsyn ⇒ Object
Synonyms for the comical component. Returns an array of strings.
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# File 'lib/bio/db/pdb/chemicalcomponent.rb', line 167 def hetsyn unless defined? @hetsyn if r = @hash["HETSYN"] @hetsyn = r[0].hetSynonyms.to_s.split(/\;\s*/) else return [] end end @hetsyn end |
#record(name = nil) ⇒ Object
Gets all records whose record type is name. Returns an array of Bio::PDB::Record::*
objects.
if name is nil, returns hash storing all record data.
Example: p pdb.record(‘CONECT’) p pdb.record
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# File 'lib/bio/db/pdb/chemicalcomponent.rb', line 217 def record(name = nil) name ? @hash[name] : @hash end |