mddb 0.0.1

data/.gitignore

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+*.gem
+.bundle
+Gemfile.lock
+pkg/*

data/Gemfile

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+source "http://rubygems.org"
+
+# Specify your gem's dependencies in mddb.gemspec
+gemspec

data/Rakefile

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+require "bundler/gem_tasks"

data/bin/mddb

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+#! /usr/bin/env ruby
+
+if File.exists?(File.join(File.expand_path('../..', __FILE__), 'lib'))
+  mddb_path = File.expand_path('../../lib', __FILE__)
+  $:.unshift(mddb_path)
+end
+
+require 'mddb'
+require "mddb/cli"
+
+Mddb::CLI.run

data/config.yml

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+# Example config
+#
+# database:
+#   host: localhost
+#   port: 12345
+#   name: 'sim1' 
+#
+#
+# If host or port are not defined, localhost and 27017
+# MongoDB's default port, will be used.
+#
+# Only the database name must be strictly defined. It is important
+# that you choose a database name that does not already exist, if 
+# you not want to mess up an older database.
+
+database:
+  host: 
+  port:
+  name: 'mddb'
+
+simulation:
+  file:  'quick.xyz'
+  frames: 5
+  dimensions: 24.8522, 24.8522, 24.8522
+  count: 1538 # total number of objects per frame
+  objects:
+    water: 
+      count: 512
+      start: 1
+      atom:
+        - oxygen
+        - hydrogen
+        - hydrogen
+    chain: 
+      count: 1
+      start: 1537
+      atom:
+        - phobe
+        - phobe

data/lib/mddb.rb

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+require "mddb/version"
+require "mddb/calculations"
+require "mddb/cli"
+require "mongo_mapper"
+require "mddb/config"
+require "mddb/parser"
+
+if File.exists? "config.yml"
+  Mddb::Config.config = "config.yml"
+  require "mddb/point"
+  require "mddb/vector"
+  require "mddb/atom"
+  require "mddb/frame"
+  require "mddb/molecule"
+  require "require_all"
+  require_all 'models' unless Dir.glob('models/**/*.rb').size == 0
+end
+
+module Mddb
+  TEMPLATES = File.expand_path('../mddb/templates', __FILE__)
+end

data/lib/mddb/atom.rb

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+require 'mddb/calculations'
+require 'mddb/point'
+require 'mongo_mapper'
+module Mddb
+  class Atom
+    include MongoMapper::EmbeddedDocument
+    include Mddb::Calculations
+    key :position, Point
+    key :fid, Integer
+
+    def distance_to a
+      if a.is_a? Point
+        self.position.distance_to a
+      elsif a.is_a? Mddb::Atom
+        self.position.distance_to a.position
+      end
+    end
+
+    def vector_to a
+      if a.is_a? Point
+        self.position.vector_to a
+      elsif a.is_a? Mddb::Atom
+        self.position.vector_to a.position
+      end
+    end
+
+  end
+end

data/lib/mddb/calculations.rb

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+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
+      end
+    end
+    
+    def self.included(base)
+      base.extend(ClassMethods)
+    end
+
+    module ClassMethods
+      @@calculations = []
+      
+      def get_calculations
+        @@calculations
+      end
+
+      def calculations *args
+        args.each do |arg|
+          @@calculations.push "calc_#{arg}"
+        end
+      end
+
+      def list_calculations
+        return @@calculations
+      end
+    end
+  end
+end

data/lib/mddb/cli.rb

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+require 'mddb/version'
+ module Mddb
+  class CLI
+    def self.run
+      if ARGV.empty? 
+        puts "Using MDDB v." + Mddb::VERSION
+        puts "Options:"
+        puts "  new                 Creates a new project"
+        puts "  generate <model>    Creates a new model." 
+        puts "                      Leave blank for list of available "
+        puts "                      models"
+        puts "  console             Starts an interactice MDDB console"
+      elsif %w{-v --version --v}.include? ARGV.first
+        puts Mddb::VERSION
+      elsif ARGV.first == 'new'
+        ARGV.shift
+        require 'mddb/commands/new'
+      elsif ARGV.first == 'console'
+        require 'mddb/commands/console'
+      elsif ARGV.first == 'load'
+        require 'mddb/commands/load'
+      elsif  %w{g generate}.include? ARGV.first
+        ARGV.shift
+        require 'mddb/generators'
+      end
+    end
+  end
+end

data/lib/mddb/commands/console.rb

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+#!/usr/bin/env ruby
+
+def start_console
+  require 'irb'
+  require 'irb/completion'
+  require 'require_all'
+  require 'hirb'
+  Hirb.enable
+  # Require all our models
+  require_all 'models' unless Dir.glob('models/**/*.rb').size == 0
+  ARGV.clear
+  puts "Wecome to Mddb!"
+  IRB.start
+end
+
+if File.exists? 'config.yml'
+  start_console
+else
+  puts "Your not in the project root directory"
+end

data/lib/mddb/commands/load.rb

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+#!/usr/bin/env ruby
+
+def start_console
+  require 'mddb'
+  require 'mddb/point'
+  require 'irb'
+  require 'irb/completion'
+  ARGV.clear
+  puts "loading xyz"
+  c = YAML.load File.open('config.yml').read
+  sim = c['simulation']
+  objects = sim['objects']
+  objects.keys.each do |key|
+    unless Object.const_defined?(key.capitalize)
+      puts "No model for #{key}! Please create one!" 
+    end
+    objects[key]['atom'].each do |a|
+      unless Object.const_defined?(a.capitalize)
+        puts "No model for #{a}! Please create one!" 
+      end
+    end
+  end
+  p = Mddb::Parser::Parser.new
+  fid = 1
+  p.each_frame do |f|
+    puts "Frame: #{fid}"
+    frame = Frame.new :fid => fid
+    objects.keys.each do |mol|
+      (objects[mol]['start']..(objects[mol]['start']+objects[mol]['count']) - 1).to_a.each do |i|
+        m = Object.const_get(mol.capitalize).new :mid => i, :fid => fid
+        objects[mol]['atom'].each_with_index do |a,z|
+          line = z*objects[mol]['count'] + i
+          a = Object.const_get(a.capitalize).new :aid => (z+1), :position => f[line-1], :fid => fid
+          m.atoms << a
+        end
+        m.save
+        frame.send(mol.pluralize) << m
+      end
+    end
+    frame.save
+    fid +=1
+  end
+
+end
+
+if File.exists? 'config.yml'
+  start_console
+else
+  puts "Your not in the project root directory"
+end

data/lib/mddb/commands/new.rb

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+require 'thor'
+require 'thor/group'
+class New < Thor::Group
+  include Thor::Actions
+  argument :name
+  
+  def self.source_root
+    File.expand_path('../../templates', __FILE__)
+  end
+
+  def README
+    template "README.tt", "#{name}/README"
+  end
+
+  def config
+    template "config.yml.tt", "#{name}/config.yml"
+  end
+
+  def models
+    empty_directory "#{name}/models"
+  end
+
+  def frame
+    template "frame.rb.tt", "#{name}/models/frame.rb"
+  end
+
+  def spec
+    empty_directory "#{name}/spec"
+  end
+
+end 
+
+New.start

data/lib/mddb/config.rb

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+module Mddb
+  module Config
+    def self.database
+     @@config['database'] ||= {}
+    end
+
+    def self.simulation
+      @@config['simulation']
+    end
+
+    def self.config=(file)
+      config = YAML.load_file(file)
+      config['database']['host'] = 'localhost' if config['database']['host'].nil?
+      config['database']['port'] = 27017 if config['database']['port'].nil?
+      raise "bad config file: database name needs to be defined" if config['database']['name'].nil?
+      config['simulation']['dimensions'] = config['simulation']['dimensions'].split(',').collect {|a| a.to_f}
+      @@config = config
+      self.connect
+    end
+
+
+    # The ranges of atoms in the config file are described as strings, we need
+    # to make them into ruby strings. 
+    def self.connect
+      host = Mddb::Config.database['host']
+      database = Mddb::Config.database['name'] 
+      MongoMapper.connection = Mongo::Connection.new(host)
+      MongoMapper.database = database
+    end
+  end
+end

data/lib/mddb/frame.rb

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+module Mddb
+  class Frame
+    include MongoMapper::Document
+    include Mddb::Calculations
+    key :fid, Integer
+  end
+end

data/lib/mddb/generators.rb

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+require 'mddb/generators/atom'
+require 'mddb/generators/molecule'
+module Mddb
+  module Generators
+    def Generators.list
+      gens = Mddb::Generators.constants.map {|x| x.to_s.downcase}
+      gens - ['run']
+    end
+
+    class Run
+      def self.start
+        if ARGV.empty?
+          puts "try one of the following"
+          Mddb::Generators.list.each do |g|
+            puts "  #{g} <name>"
+          end
+        elsif Mddb::Generators.list.include? ARGV.first
+          gen = ARGV.first
+          ARGV.shift
+          if ARGV.empty?
+            puts "supply a name"
+          else
+            eval("Mddb::Generators::" + gen.capitalize + ".start")
+          end
+        end
+          
+      end
+    end
+  end
+end
+
+Mddb::Generators::Run.start

data/lib/mddb/generators/atom.rb

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+require 'thor'
+require 'thor/group'
+module Mddb::Generators
+  class Atom < Thor::Group
+    argument :name
+    include Thor::Actions
+
+    def self.source_root
+      File.expand_path('../../templates', __FILE__)
+    end
+
+    def atom
+      template "atom.rb.tt", "models/atoms/#{name}.rb"
+      template "spec/atom_spec.rb.tt", "spec/atoms/#{name}_spec.rb"
+    end
+  end
+end
+

data/lib/mddb/generators/molecule.rb

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+require 'thor'
+require 'thor/group'
+module Mddb::Generators
+  class Molecule < Thor::Group
+    argument :name
+    include Thor::Actions
+
+    def self.source_root
+      File.expand_path('../../templates', __FILE__)
+    end
+
+    def atom
+      template "molecule.rb.tt", "models/molecules/#{name}.rb"
+      template "spec/molecule_spec.rb.tt", "spec/molecules/#{name}_spec.rb"
+    end
+  end
+end
+

data/lib/mddb/molecule.rb

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+require 'mddb/calculations'
+module Mddb
+  class Molecule
+    include MongoMapper::Document
+    include Mddb::Calculations
+    key :fid, Integer
+    key :mid, Integer
+    belongs_to :frame, :class_name => 'Mddb::Frame'
+    many :atoms, :class_name => 'Mddb::Atom'
+
+    def timeline
+      self.class.where(:mid => self.mid).all
+    end
+
+    def timestep n=0
+      if self.fid + n <= Frame.count and self.fid + n > 0
+        self.class.where(:mid => self.mid, :fid => (self.fid+n)).all
+      else
+        raise "Bad timestep. No frame exists or out of range"
+      end
+    end
+  end
+end

data/lib/mddb/parser.rb

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+module Mddb
+  module Parser
+
+    class Parser
+      def initialize
+        @file = File.open(Mddb::Config.simulation['file']).readlines
+        @objects = Mddb::Config.simulation['count']
+      end
+
+      def each_frame
+        frame = nil
+        @file.each do |line|
+          if line == "#{@objects}\n"
+            yield(frame) 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
+
+    end
+  end
+end