# File lib/bio/db/pdb/chain.rb, line 40
40:       def initialize(id = nil, model = nil)
41:         
42:         @chain_id  = id
43:         
44:         @model    = model
45:         
46:         @residues   = []
47:         @residues_hash = {}
48:         @heterogens = []
49:         @heterogens_hash = {}
50:       end

     # File lib/bio/db/pdb/chain.rb, line 166
166:       def <=>(other)
167:         return @chain_id <=> other.chain_id
168:       end

    # File lib/bio/db/pdb/chain.rb, line 77
77:       def [](key)
78:         get_residue_by_id(key)
79:       end

     # File lib/bio/db/pdb/chain.rb, line 182
182:       def aaseq
183:         unless defined? @aaseq
184:           string = ""
185:           last_residue_num = nil
186:           @residues.each do |residue|
187:             if last_residue_num and 
188:                 (x = (residue.resSeq.to_i - last_residue_num).abs) > 1 then
189:               x.times { string << 'X' }
190:             end
191:             tlc = residue.resName.capitalize
192:             olc = (begin
193:                      Bio::AminoAcid.three2one(tlc)
194:                    rescue ArgumentError
195:                      nil
196:                    end || 'X')
197:             string << olc
198:           end
199:           @aaseq = Bio::Sequence::AA.new(string)
200:         end
201:         @aaseq
202:       end

     # File lib/bio/db/pdb/chain.rb, line 100
100:       def addLigand(ligand)
101:         raise "Expecting a Bio::PDB::Residue" unless ligand.is_a? Bio::PDB::Residue
102:         @heterogens.push(ligand)
103:         if @heterogens_hash[ligand.residue_id] then
104:           $stderr.puts "Warning: heterogen_id (residue_id) #{ligand.residue_id.inspect} is already used" if $VERBOSE
105:         else
106:           @heterogens_hash[ligand.residue_id] = ligand
107:         end
108:         self
109:       end

    # File lib/bio/db/pdb/chain.rb, line 88
88:       def addResidue(residue)
89:         raise "Expecting a Bio::PDB::Residue" unless residue.is_a? Bio::PDB::Residue
90:         @residues.push(residue)
91:         if @residues_hash[residue.residue_id] then
92:           $stderr.puts "Warning: residue_id #{residue.residue_id.inspect} is already used" if $VERBOSE
93:         else
94:           @residues_hash[residue.residue_id] = residue
95:         end
96:         self
97:       end

     # File lib/bio/db/pdb/chain.rb, line 154
154:       def each(&x) #:yields: residue
155:         @residues.each(&x)
156:       end

     # File lib/bio/db/pdb/chain.rb, line 161
161:       def each_heterogen(&x) #:yields: heterogen
162:         @heterogens.each(&x)
163:       end

    # File lib/bio/db/pdb/chain.rb, line 82
82:       def get_heterogen_by_id(key)
83:         #@heterogens.find { |r| r.residue_id == key }
84:         @heterogens_hash[key]
85:       end

    # File lib/bio/db/pdb/chain.rb, line 67
67:       def get_residue_by_id(key)
68:         #@residues.find { |r| r.residue_id == key }
69:         @residues_hash[key]
70:       end

     # File lib/bio/db/pdb/chain.rb, line 177
177:       def inspect
178:         "#<#{self.class.to_s} id=#{chain_id.inspect} model.serial=#{(model ? model.serial : nil).inspect} residues.size=#{residues.size} heterogens.size=#{heterogens.size} aaseq=#{aaseq.inspect}>"
179:       end

     # File lib/bio/db/pdb/chain.rb, line 148
148:       def rehash
149:         rehash_residues
150:         rehash_heterogens
151:       end

     # File lib/bio/db/pdb/chain.rb, line 130
130:       def rehash_heterogens
131:         begin
132:           heterogens_bak = @heterogens
133:           heterogens_hash_bak = @heterogens_hash
134:           @heterogens = []
135:           @heterogens_hash = {}
136:           heterogens_bak.each do |heterogen|
137:             self.addLigand(heterogen)
138:           end
139:         rescue RuntimeError
140:           @heterogens = heterogens_bak
141:           @heterogens_hash = heterogens_hash_bak
142:           raise
143:         end
144:         self
145:       end

     # File lib/bio/db/pdb/chain.rb, line 112
112:       def rehash_residues
113:         begin
114:           residues_bak = @residues
115:           residues_hash_bak = @residues_hash
116:           @residues = []
117:           @residues_hash = {}
118:           residues_bak.each do |residue|
119:             self.addResidue(residue)
120:           end
121:         rescue RuntimeError
122:           @residues = residues_bak
123:           @residues_hash = residues_hash_bak
124:           raise
125:         end
126:         self
127:       end

     # File lib/bio/db/pdb/chain.rb, line 171
171:       def to_s
172:         @residues.join('') + "TER\n" + @heterogens.join('')
173:       end