[BioRuby-cvs] bioruby/lib/bio/db/pdb pdb.rb, 1.10, 1.11 utils.rb, 1.3, 1.4

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory pub.open-bio.org:/tmp/cvs-serv15618

Modified Files:
	pdb.rb utils.rb 
Log Message:
* utils.rb
  * Changed Bio::PDB::Utils.to_xyz(obj) to convert_to_xyz(obj)
    (old to_xyz is still available for compatibility).
  * In Utils, distance, dihedral_angle, rad2reg, acos, calculatePlane are
    now module_function.
  * added RDoc.
  * added ChainFinder#chains, ResidueFinder#residues, AtomFinder#atoms,
    HetatmFinder#hetatms, and HeterogenFinder#heterogens.
* pdb.rb
  * modified some documents.


Index: utils.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/utils.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** utils.rb	4 Jan 2006 15:41:50 -0000	1.3
--- utils.rb	5 Jan 2006 11:10:10 -0000	1.4
***************
*** 26,51 ****
  module Bio; class PDB
  
    module Utils
-     #The methods in this mixin should be applicalbe to all PDB objects
      
!     #Returns the coordinates of the geometric centre (average co-ord)
!     #of any AtomFinder (or .atoms) implementing object
!     def geometricCentre()
!       
        x = y = z = count = 0
        
!       self.each_atom{ |atom|
          x += atom.x
          y += atom.y
          z += atom.z
          count += 1
!       }
!       
!       x = x / count
!       y = y / count
!       z = z / count
        
        Coordinate[x,y,z]
-       
      end
  
--- 26,54 ----
  module Bio; class PDB
  
+   # Utility methods for PDB data.
+   #
+   # The methods in this mixin should be applicalbe to all PDB objects.
    module Utils
      
!     # Returns the coordinates of the geometric centre (average co-ord)
!     # of any AtomFinder (or .atoms) implementing object
!     #
!     # If you want to get the geometric centre of hetatms,
!     # call geometricCentre(:each_hetatm).
!     def geometricCentre(method = :each_atom)
        x = y = z = count = 0
        
!       self.__send__(method) do |atom|
          x += atom.x
          y += atom.y
          z += atom.z
          count += 1
!       end
        
+       x = (x / count)
+       y = (y / count)
+       z = (z / count)
+      
        Coordinate[x,y,z]
      end
  
***************
*** 64,69 ****
      }
  
      def centreOfGravity()
-       
        x = y = z = total = 0
        
--- 67,72 ----
      }
  
+     # calculates centre of gravitiy
      def centreOfGravity()
        x = y = z = total = 0
        
***************
*** 82,98 ****
        
        Coordinate[x,y,z]
-       
      end
  
      #Perhaps distance and dihedral would be better off as class methods?
      #(rather) than instance methods
!     def self.distance(coord1,coord2)
!       coord1 = to_xyz(coord1)
!       coord2 = to_xyz(coord2)
        (coord1 - coord2).r
      end
  
!     def self.dihedral_angle(coord1,coord2,coord3,coord4)
!         
        (a1,b1,c1,d) = calculatePlane(coord1,coord2,coord3)
        (a2,b2,c2)   = calculatePlane(coord2,coord3,coord4)
--- 85,105 ----
        
        Coordinate[x,y,z]
      end
  
+     #--
      #Perhaps distance and dihedral would be better off as class methods?
      #(rather) than instance methods
!     #++
! 
!     # Calculates distance between _coord1_ and _coord2_.
!     def distance(coord1, coord2)
!       coord1 = convert_to_xyz(coord1)
!       coord2 = convert_to_xyz(coord2)
        (coord1 - coord2).r
      end
+     module_function :distance
  
!     # Calculates dihedral angle.
!     def dihedral_angle(coord1, coord2, coord3, coord4)
        (a1,b1,c1,d) = calculatePlane(coord1,coord2,coord3)
        (a2,b2,c2)   = calculatePlane(coord2,coord3,coord4)
***************
*** 106,112 ****
        end
      end
        
!     #Implicit conversion into Vector or Bio::PDB::Coordinate
!     def self.to_xyz(obj)
        unless obj.is_a?(Vector)
          begin
--- 113,120 ----
        end
      end
+     module_function :dihedral_angle
        
!     # Implicit conversion into Vector or Bio::PDB::Coordinate
!     def convert_to_xyz(obj)
        unless obj.is_a?(Vector)
          begin
***************
*** 118,133 ****
        obj
      end
  
      #Methods required for the dihedral angle calculations
      #perhaps these should go in some separate Math module
!     def self.rad2deg(r)
        (r/Math::PI)*180
      end
!     
!     def self.acos(x)
        Math.atan2(Math.sqrt(1 - x**2),x)
      end
!       
!     def self.calculatePlane(coord1,coord2,coord3)
        a = coord1.y * (coord2.z - coord3.z) +
            coord2.y * (coord3.z - coord1.z) + 
--- 126,155 ----
        obj
      end
+     module_function :convert_to_xyz
+ 
+     # (Deprecated) alias of convert_to_xyz(obj)
+     def self.to_xyz(obj)
+       convert_to_xyz(obj)
+     end
  
+     #--
      #Methods required for the dihedral angle calculations
      #perhaps these should go in some separate Math module
!     #++
! 
!     # radian to degree
!     def rad2deg(r)
        (r/Math::PI)*180
      end
!     module_function :rad2deg
! 
!     # acos
!     def acos(x)
        Math.atan2(Math.sqrt(1 - x**2),x)
      end
!     module_function :acos
! 
!     # calculates plane
!     def calculatePlane(coord1, coord2, coord3)
        a = coord1.y * (coord2.z - coord3.z) +
            coord2.y * (coord3.z - coord1.z) + 
***************
*** 147,157 ****
  
        return [a,b,c,d]
-         
      end
  
!     #Every class in the heirarchy implements finder, this takes 
!     #a class which determines which type of object to find, the associated
!     #block is then run in classic .find style
!     def finder(findtype,&block)
        if findtype == Bio::PDB::Atom
          return self.find_atom(&block)
--- 169,182 ----
  
        return [a,b,c,d]
      end
+     module_function :calculatePlane
  
!     # Every class in the heirarchy implements finder, this takes 
!     # a class which determines which type of object to find, the associated
!     # block is then run in classic .find style.
!     # 
!     # The method might be deprecated.
!     # You'd better using find_XXX  directly.
!     def finder(findtype, &block) #:yields: obj
        if findtype == Bio::PDB::Atom
          return self.find_atom(&block)
***************
*** 167,236 ****
      end
    end #module Utils
!   
    #The *Finder modules implement a find_* method which returns
    #an array of anything for which the block evals true
    #(suppose Enumerable#find_all method).
    #The each_* style methods act as classic iterators.
    module ModelFinder
!     def find_model()
        array = []
!       self.each_model{ |model|
          array.push(model) if yield(model)
!       }
        return array
      end
!   end
    
    #The heirarchical nature of the objects allow us to re-use the
    #methods from the previous level - e.g. A PDB object can use the .models
    #method defined in ModuleFinder to iterate through the models to find the
    #chains
    module ChainFinder
!     def find_chain()
        array = []
!       self.each_chain{ |chain|
          array.push(chain) if yield(chain)
!       }
        return array
      end
!     def each_chain()
!       self.each_model{ |model|
!         model.each{ |chain| yield chain }
!       }
      end
!   end
    
    module ResidueFinder
!     def find_residue()
        array = []
!       self.each_residue{ |residue|
          array.push(residue) if yield(residue)
!       }
        return array
      end
!     def each_residue()
!       self.each_chain{ |chain|
!         chain.each{ |residue| yield residue }
!       }
      end
!   end
    
    module AtomFinder
!     def find_atom()
        array = []
!       self.each_atom{ |atom|
          array.push(atom) if yield(atom)
!       }
        return array
      end
!     def each_atom()
!       self.each_residue{ |residue|
!         residue.each{ |atom| yield atom }
!       }
      end
-   end
  
    module HetatmFinder
!     def find_hetatm()
        array = []
        self.each_hetatm do |hetatm|
--- 192,315 ----
      end
    end #module Utils
! 
!   #--
    #The *Finder modules implement a find_* method which returns
    #an array of anything for which the block evals true
    #(suppose Enumerable#find_all method).
    #The each_* style methods act as classic iterators.
+   #++
+ 
+   # methods to access models
+   #
+   # XXX#each_model must be defined.
    module ModelFinder
!     # returns an array containing all chains for which given block
!     # is not +false+ (similar to Enumerable#find_all).
!     def find_model
        array = []
!       self.each_model do |model|
          array.push(model) if yield(model)
!       end
        return array
      end
!   end #module ModelFinder
    
+   #--
    #The heirarchical nature of the objects allow us to re-use the
    #methods from the previous level - e.g. A PDB object can use the .models
    #method defined in ModuleFinder to iterate through the models to find the
    #chains
+   #++
+ 
+   # methods to access chains
+   #
+   # XXX#each_model must be defined.
    module ChainFinder
! 
!     # returns an array containing all chains for which given block
!     # is not +false+ (similar to Enumerable#find_all).
!     def find_chain
        array = []
!       self.each_chain do |chain|
          array.push(chain) if yield(chain)
!       end
        return array
      end
! 
!     # iterates over each chain
!     def each_chain(&x) #:yields: chain
!       self.each_model { |model| model.each(&x) }
      end
! 
!     # returns all chains
!     def chains
!       array = []
!       self.each_model { |model| array.concat(model.chains) }
!       return array
!     end
!   end #module ChainFinder
    
+   # methods to access residues
+   #
+   # XXX#each_chain must be defined.
    module ResidueFinder
! 
!     # returns an array containing all residues for which given block
!     # is not +false+ (similar to Enumerable#find_all).
!     def find_residue
        array = []
!       self.each_residue do |residue|
          array.push(residue) if yield(residue)
!       end
        return array
      end
! 
!     # iterates over each residue
!     def each_residue(&x) #:yields: residue
!       self.each_chain { |chain| chain.each(&x) }
      end
! 
!     # returns all residues
!     def residues
!       array = []
!       self.each_chain { |chain| array.concat(chain.residues) }
!       return array
!     end
!   end #module ResidueFinder
    
+   # methods to access atoms
+   #
+   # XXX#each_residue must be defined.
    module AtomFinder
!     # returns an array containing all atoms for which given block
!     # is not +false+ (similar to Enumerable#find_all).
!     def find_atom
        array = []
!       self.each_atom do |atom|
          array.push(atom) if yield(atom)
!       end
        return array
      end
! 
!     # iterates over each atom
!     def each_atom(&x) #:yields: atom
!       self.each_residue { |residue| residue.each(&x) }
      end
  
+     # returns all atoms
+     def atoms
+       array = []
+       self.each_residue { |residue| array.concat(residue.atoms) }
+       return array
+     end
+   end #module AtomFinder
+ 
+   # methods to access HETATMs
+   #
+   # XXX#each_heterogen must be defined.
    module HetatmFinder
!     # returns an array containing all HETATMs for which given block
!     # is not +false+ (similar to Enumerable#find_all).
!     def find_hetatm
        array = []
        self.each_hetatm do |hetatm|
***************
*** 239,249 ****
        return array
      end
      def each_hetatm(&x) #:yields: hetatm
        self.each_heterogen { |heterogen| heterogen.each(&x) }
      end
-   end
  
    module HeterogenFinder
!     def find_heterogen()
        array = []
        self.each_heterogen do |heterogen|
--- 318,342 ----
        return array
      end
+ 
+     # iterates over each HETATM
      def each_hetatm(&x) #:yields: hetatm
        self.each_heterogen { |heterogen| heterogen.each(&x) }
      end
  
+     # returns all HETATMs
+     def hetatms
+       array = []
+       self.each_heterogen { |heterogen| array.concat(heterogen.hetatms) }
+       return array
+     end
+   end #module HetatmFinder
+ 
+   # methods to access heterogens (compounds or ligands)
+   #
+   # XXX#each_chain must be defined.
    module HeterogenFinder
!     # returns an array containing all heterogens for which given block
!     # is not +false+ (similar to Enumerable#find_all).
!     def find_heterogen
        array = []
        self.each_heterogen do |heterogen|
***************
*** 252,259 ****
        return array
      end
      def each_heterogen(&x) #:yields: heterogen
        self.each_chain { |chain| chain.each_heterogen(&x) }
      end
!   end
  
  end; end #module Bio; class PDB
--- 345,361 ----
        return array
      end
+ 
+     # iterates over each heterogens
      def each_heterogen(&x) #:yields: heterogen
        self.each_chain { |chain| chain.each_heterogen(&x) }
      end
! 
!     # returns all heterogens
!     def heterogens
!       array = []
!       self.each_chain { |chain| array.concat(chain.heterogens) }
!       return array
!     end
!   end #module HeterogenFinder
  
  end; end #module Bio; class PDB

Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** pdb.rb	5 Jan 2006 09:24:54 -0000	1.10
--- pdb.rb	5 Jan 2006 11:10:10 -0000	1.11
***************
*** 31,36 ****
  module Bio
  
!   #This is the main PDB class which takes care of parsing, annotations
!   #and is the entry way to the co-ordinate data held in models
    class PDB #< DB
  
--- 31,37 ----
  module Bio
  
!   # This is the main PDB class which takes care of parsing, annotations
!   # and is the entry way to the co-ordinate data held in models.
!   # 
    class PDB #< DB
  
***************
*** 48,52 ****
      DELIMITER = RS = nil # 1 file 1 entry
  
!     #Modules required by the field definitions
      module DataType
  
--- 49,53 ----
      DELIMITER = RS = nil # 1 file 1 entry
  
!     # Modules required by the field definitions
      module DataType
  
***************
*** 1369,1375 ****
      attr_reader :hash
  
      attr_reader :models
  
!     #Adds a Bio::Model to the current strucutre
      def addModel(model)
        raise "Expecting a Bio::PDB::Model" if not model.is_a? Bio::PDB::Model
--- 1370,1377 ----
      attr_reader :hash
  
+     # models in this PDB entry
      attr_reader :models
  
!     # Adds a Bio::Model object to the current strucutre
      def addModel(model)
        raise "Expecting a Bio::PDB::Model" if not model.is_a? Bio::PDB::Model
***************
*** 1378,1386 ****
      end
      
!     #Iterates over the models
      def each
        @models.each{ |model| yield model }
      end
!     #Alias needed for Bio::PDB::ModelFinder
      alias each_model each
      
--- 1380,1388 ----
      end
      
!     # Iterates over each model
      def each
        @models.each{ |model| yield model }
      end
!     # Alias needed for Bio::PDB::ModelFinder
      alias each_model each
      
***************
*** 1390,1394 ****
        @models.find{ |model| key == model.model_serial }
      end
!     
      #Stringifies to a list of atom records - we could add the annotation
      #as well if needed
--- 1392,1396 ----
        @models.find{ |model| key == model.model_serial }
      end
! 
      #Stringifies to a list of atom records - we could add the annotation
      #as well if needed