mddb 0.0.25 → 0.0.26

data/lib/mddb/commands/load.rb

@@ -1,57 +1,72 @@
 #!/usr/bin/env ruby
+require 'trollop'
+
+
 catch :shit_user do
 def start_console
+  opts = Trollop::options do
+    opt :pid, "Choose a PID", :type => :int
+    opt :file, "Choose a file", :type => String
+    opt :output, "Enable output"
+  end
   require 'mddb'
   require 'mddb/point'
   require 'irb'
   require 'irb/completion'
-  ARGV.shift
-  file = ARGV.shift
-  if ARGV.empty?
-    puts "Hey i need a pid"
-    throw :shit_user
-  else
-    pid = ARGV.shift.to_i
-  end
-  begin
-    last_frame = Frame.where(:pid => pid).sort(:fid.desc).first.fid
-  rescue
-    last_frame = 0
+  if opts[:pid].nil?
+    $stderr.puts "please specify a PID. see --help"
+    abort
+  elsif opts[:file].nil?
+    $stderr.puts "please specify a file. see --help"
+    abort
   end
-  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!" 
+  pid = opts[:pid]
+  if File.exists? opts[:file]
+    begin
+      last_frame = Frame.where(:pid => pid).sort(:fid.desc).first.fid
+    rescue
+      last_frame = 0
     end
-    objects[key]['atom'].each do |a|
-      unless Object.const_defined?(a.capitalize)
-        puts "No model for #{a}! Please create one!" 
+    $stderr.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)
+        $stderr.puts "No model for #{key}! Please create one!" 
+      end
+      objects[key]['atom'].each do |a|
+        unless Object.const_defined?(a.capitalize)
+          $stderr.puts "No model for #{a}! Please create one!" 
+        end
       end
     end
-  end
-  puts "parsing"
-  p = Mddb::Parser::Parser.new file
-  fid = 1 + last_frame
-  p.each_frame do |f|
-    puts "Frame: #{fid}"
-    frame = Frame.new :fid => fid, :pid => pid
-    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, :pid => pid
-        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, :pid => pid
-          m.atoms << a
+    $stderr.puts "parsing"
+    p = Mddb::Parser::Parser.new opts[:file]
+    fid = 1 + last_frame
+    p.each_frame do |f|
+      $stderr.puts "Frame: #{fid}"
+      frame = Frame.new :fid => fid, :pid => pid
+      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, :pid => pid
+          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, :pid => pid
+            m.atoms << a
+          end
+          m.save
+          frame.send(mol.pluralize) << m
         end
-        m.save
-        frame.send(mol.pluralize) << m
       end
+      frame.save
+      fid +=1
+    end
+    if opts[:output]
+      puts "#{opts[:pid]}"
+      puts "#{last_frame + 1}"
+      puts "#{fid - 1}"
     end
-    frame.save
-    fid +=1
   end
 
 end
@@ -59,5 +74,5 @@ end
 if File.exists? 'config.yml'
   start_console
 else
-  puts "Your not in the project root directory"
+  $stderr.puts "Your not in the project root directory"
 end

data/lib/mddb/version.rb

@@ -1,3 +1,3 @@
 module Mddb
-  VERSION = "0.0.25"
+  VERSION = "0.0.26"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mddb
 version: !ruby/object:Gem::Version
-  version: 0.0.25
+  version: 0.0.26
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-22 00:00:00.000000000Z
+date: 2012-03-23 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &70265779694900 !ruby/object:Gem::Requirement
+  requirement: &70215825876300 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,10 +21,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *70265779694900
+  version_requirements: *70215825876300
 - !ruby/object:Gem::Dependency
   name: mongo_mapper
-  requirement: &70265779694480 !ruby/object:Gem::Requirement
+  requirement: &70215825875880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -32,10 +32,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70265779694480
+  version_requirements: *70215825875880
 - !ruby/object:Gem::Dependency
   name: hirb
-  requirement: &70265779694060 !ruby/object:Gem::Requirement
+  requirement: &70215825875460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -43,10 +43,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70265779694060
+  version_requirements: *70215825875460
 - !ruby/object:Gem::Dependency
   name: thor
-  requirement: &70265779693640 !ruby/object:Gem::Requirement
+  requirement: &70215825875040 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,10 +54,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70265779693640
+  version_requirements: *70215825875040
 - !ruby/object:Gem::Dependency
   name: micro-optparse
-  requirement: &70265779724180 !ruby/object:Gem::Requirement
+  requirement: &70215825874620 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -65,10 +65,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70265779724180
+  version_requirements: *70215825874620
 - !ruby/object:Gem::Dependency
   name: resque
-  requirement: &70265779723760 !ruby/object:Gem::Requirement
+  requirement: &70215825874200 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -76,10 +76,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70265779723760
+  version_requirements: *70215825874200
 - !ruby/object:Gem::Dependency
   name: bson_ext
-  requirement: &70265779723340 !ruby/object:Gem::Requirement
+  requirement: &70215825873780 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -87,10 +87,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70265779723340
+  version_requirements: *70215825873780
 - !ruby/object:Gem::Dependency
   name: require_all
-  requirement: &70265779722920 !ruby/object:Gem::Requirement
+  requirement: &70215825873360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -98,7 +98,7 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *70265779722920
+  version_requirements: *70215825873360
 description: MDDB makes analysing molecular dynamics simulations easy
 email:
 - thom.mulvaney@gmail.com