mddb 0.0.1 → 0.0.3

data/lib/mddb/atom.rb

@@ -23,6 +23,21 @@ module Mddb
         self.position.vector_to a.position
       end
     end
+    
+    def mass
+      begin
+        self.class::MASS
+      rescue
+        raise "Please define a MASS constant in #{self.class} class"
+     end
+    end
 
+    def charge
+      begin
+        self.class::CHARGE
+      rescue
+        raise "Please define a CHARGE constant in #{self.class} class"
+      end
+    end
   end
 end

data/lib/mddb/calculations.rb

@@ -1,35 +1,31 @@
 module Mddb
   module Calculations
-    # This module provides a simple way
-    # of ordering calculation methods in a 
-    # Mddb Model
-      
-    # Run the calculations on an instance
-    def run_calculations
-      self.get_calculations.each do |calc|
-        self.send calc
+    def run
+      begin
+       get_calculations.each do |c|
+          self.send(c)
+        end
+      rescue
+        raise "You haven't added any calculations to the calculations macro"
       end
     end
-    
-    def self.included(base)
-      base.extend(ClassMethods)
-    end
 
-    module ClassMethods
-      @@calculations = []
-      
-      def get_calculations
-        @@calculations
+    def list_calculations
+      begin
+        get_calculations
+      rescue
+        raise "You haven't added any calculations to the calculations macro"
       end
+    end
 
-      def calculations *args
-        args.each do |arg|
-          @@calculations.push "calc_#{arg}"
-        end
-      end
+    def self.included(klass)
+      klass.extend ClassMethods
+    end
 
-      def list_calculations
-        return @@calculations
+    module ClassMethods
+      def calculations *args
+        a = args.map {|a| "calc_#{a}"}
+        define_method :get_calculations, lambda {a} 
       end
     end
   end

data/lib/mddb/commands/load.rb

@@ -6,6 +6,11 @@ def start_console
   require 'irb'
   require 'irb/completion'
   ARGV.clear
+  begin
+    last_frame = Frame.sort(:fid.desc).first.fid
+  rescue
+    last_frame = 0
+  end
   puts "loading xyz"
   c = YAML.load File.open('config.yml').read
   sim = c['simulation']
@@ -21,7 +26,7 @@ def start_console
     end
   end
   p = Mddb::Parser::Parser.new
-  fid = 1
+  fid = 1 + last_frame
   p.each_frame do |f|
     puts "Frame: #{fid}"
     frame = Frame.new :fid => fid

data/lib/mddb/frame.rb

@@ -1,5 +1,5 @@
 module Mddb
-  class Frame
+  class FrameBase
     include MongoMapper::Document
     include Mddb::Calculations
     key :fid, Integer

data/lib/mddb/generators/molecule.rb

@@ -9,8 +9,11 @@ module Mddb::Generators
       File.expand_path('../../templates', __FILE__)
     end
 
-    def atom
+    def molecule
       template "molecule.rb.tt", "models/molecules/#{name}.rb"
+      inject_into_class "models/frame.rb", Frame do 
+        "  many :#{name.pluralize}, :class_name => '#{name.capitalize}'\n"
+      end
       template "spec/molecule_spec.rb.tt", "spec/molecules/#{name}_spec.rb"
     end
   end

data/lib/mddb/molecule.rb

@@ -5,9 +5,58 @@ module Mddb
     include Mddb::Calculations
     key :fid, Integer
     key :mid, Integer
+    key :rg, Float
+    key :sasa, Float
     belongs_to :frame, :class_name => 'Mddb::Frame'
     many :atoms, :class_name => 'Mddb::Atom'
 
+    def calc_rg
+      sum_ij = 0
+      self.atoms.each do |i|
+        self.atoms.each do |j|
+          sum_ij += (i.position.distance_to j.position)**2
+        end
+      end
+
+      rg2 = sum_ij / (2*(32**2))
+      rg = rg2**0.5
+
+      self.rg = rg/0.529
+      self.save
+    end
+
+    def calc_sasa 
+      nodes=GsdSphere.new(1000).nodes
+      r_oxygen = 1.58
+      r_monomer = 1.58
+      surface = 0
+      origin = Point[0,0,0]
+      self.atoms.each do |atom|
+        nodes.each do |node|
+          pos_tranformation = origin.vector_to atom.position
+          
+          point = node + pos_tranformation
+
+          v_radius = atom.position.vector_to point
+
+          test_point = atom.position + (v_radius * (r_oxygen + r_monomer))
+          other_atoms =  self.atoms - [atom]
+
+          inside = false
+
+          other_atoms.each do |other|
+            if (test_point.distance_to other.position) < (r_oxygen + r_monomer)
+              inside = true
+            end
+          end
+
+          surface += 1 if inside == false
+        end
+      end
+      self.sasa = surface.to_f/(self.atoms.count*nodes.count)
+      self.save
+    end
+
     def timeline
       self.class.where(:mid => self.mid).all
     end
@@ -19,5 +68,13 @@ module Mddb
         raise "Bad timestep. No frame exists or out of range"
       end
     end
+
+    def mass
+      mass = 0
+      self.atoms.each do |a|
+        mass += a.mass
+      end
+      mass
+    end
   end
 end

data/lib/mddb/parser.rb

@@ -7,18 +7,26 @@ module Mddb
         @objects = Mddb::Config.simulation['count']
       end
 
+      def new_frame? lineno
+        lineno == 3
+      end
+
+      def end_of_frame? lineno
+        lineno == @objects + 2 
+      end
+
       def each_frame
-        frame = nil
+        frame = []
+        lineno = 0 
         @file.each do |line|
-          if line == "#{@objects}\n"
-            yield(frame) if frame != nil
+          lineno += 1
+          raw = line.split
+          point = Point[raw[1].to_f, raw[2].to_f, raw[3].to_f]
+          frame.push point
+          if end_of_frame? lineno
+            lineno = 0
+            yield(frame[2..(frame.count - 1)]) if frame != nil
             frame = []
-          else
-            if line.split.count == 4
-              raw = line.split
-              point = Point[raw[1].to_f, raw[2].to_f, raw[3].to_f]
-              frame.push point
-            end
           end
         end
       end

data/lib/mddb/templates/frame.rb.tt

@@ -1,4 +1,4 @@
-class Frame < Mddb::Frame
+class Frame < Mddb::FrameBase
   # Relationships here
   # 
   # Eg.

data/lib/mddb/version.rb

@@ -1,3 +1,3 @@
 module Mddb
-  VERSION = "0.0.1"
+  VERSION = "0.0.3"
 end

data/lib/mddb.rb

@@ -9,8 +9,8 @@ if File.exists? "config.yml"
   Mddb::Config.config = "config.yml"
   require "mddb/point"
   require "mddb/vector"
-  require "mddb/atom"
   require "mddb/frame"
+  require "mddb/atom"
   require "mddb/molecule"
   require "require_all"
   require_all 'models' unless Dir.glob('models/**/*.rb').size == 0
@@ -18,4 +18,34 @@ end
 
 module Mddb
   TEMPLATES = File.expand_path('../mddb/templates', __FILE__)
+
+  def Mddb.run  opts = {}
+    if opts[:all]
+      frames = Frame.all
+    else
+      frames = Frame.where(:fid.gte => opts[:from], :fid.lte => opts[:to]).all 
+    end
+    if frames.empty?
+      puts "There were no frames in in this range"
+    else 
+      klasses = Frame.associations.keys.map {|k| k.to_s.classify}
+      if klasses.empty?
+        puts "There are no objects associated with frame"
+      else
+        puts "#{klasses.count} models found"
+        frames.each do |f|
+          klasses.each do |k|
+            begin
+              puts "attempting to run #{k}"
+              m = Object.const_get(k).where(:fid => f.fid).all
+              m.each {|m| m.run}
+            rescue
+              puts "couldn't run calculation on #{k}"
+            end
+          end
+          f.run
+        end
+      end
+    end
+  end
 end

data/spec/oxygen_spec.rb

@@ -1,12 +1,46 @@
 require 'spec_helper'
 
 describe "Atoms"  do
-  class Oxygen < Mddb::Atom
-#    include Mddb::Calculations
-    calculations :fun, :bad, :ok
+  describe "OxygenWithContants" do
+    class OxygenWithConstants < Mddb::Atom
+      include Mddb::Calculations
+      MASS = 1.23
+      CHARGE = -4.23
+      calculations   :fun, :bad, :ok
+    end
+
+    it "should have 3 calculations" do
+      OxygenWithConstants.new.list_calculations.should == %W(calc_fun calc_bad calc_ok)
+    end
+
+    it "should have a charge method" do
+      OxygenWithConstants.new.charge.should == -4.23
+    end
+
+    it "should have a mass method" do
+      OxygenWithConstants.new.mass.should == 1.23
+    end
   end
 
-  it "should have 3 calculations" do
-    Oxygen.list_calculations.should == %W(calc_fun calc_bad calc_ok)
+  describe "OxygenWithoutContants" do
+    class OxygenWithoutConstants < Mddb::Atom
+      include Mddb::Calculations
+    end
+
+    it "should raise an error on charge method" do
+      lambda {OxygenWithoutConstants.new.charge }.should raise_error(RuntimeError, "Please define a CHARGE constant in OxygenWithoutConstants class") 
+    end
+
+    it "should raise an error on mass method" do
+      lambda {OxygenWithoutConstants.new.mass}.should raise_error RuntimeError
+    end
+
+    it "should raise an error on list_calculations" do
+      lambda {OxygenWithoutConstants.new.list_calculations}.should raise_error RuntimeError
+    end
+
+    it "should raise an error on run" do
+      lambda {OxygenWithoutConstants.new.run}.should raise_error RuntimeError
+    end
   end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mddb
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.3
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-01-11 00:00:00.000000000Z
+date: 2012-02-15 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70196309243000 !ruby/object:Gem::Requirement
+  requirement: &70212474145840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70196309243000
+  version_requirements: *70212474145840
 - !ruby/object:Gem::Dependency
   name: mongo_mapper
-  requirement: &70196309242480 !ruby/object:Gem::Requirement
+  requirement: &70212474145420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70196309242480
+  version_requirements: *70212474145420
 - !ruby/object:Gem::Dependency
   name: hirb
-  requirement: &70196309241960 !ruby/object:Gem::Requirement
+  requirement: &70212474145000 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70196309241960
+  version_requirements: *70212474145000
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &70196309241300 !ruby/object:Gem::Requirement
+  requirement: &70212474144540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,7 +54,7 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70196309241300
+  version_requirements: *70212474144540
 description: MDDB makes analysing molecular dynamics simulations easy
 email:
 - thom.mulvaney@gmail.com