rubabel 0.1.0 → 0.1.1

data/README.rdoc

@@ -16,9 +16,19 @@ interface attempts to be a ruby-ish analogue of
 
 == Installing
 
-=== Install openbabel
+First, many thanks to Andreas Maunz for packaging openbabel as a gem which makes this install quite painless.
 
-First, make sure you have the ruby openbabel bindings properly installed.  You can do this by {properly installing the gem][https://github.com/amaunz/openbabel-gem].  Alternatively, you can following these instructions to build from source:
+=== Quick Install
+
+On a POSIX system, make sure you have openbabel (including header files), cmake, curl, tar, sed and make {see openbabel instructions}[https://github.com/amaunz/openbabel-gem].  On ubuntu/debian:
+
+    sudo apt-get install openbabel libopenbabel-dev cmake make curl
+
+Then install the gem (which should install the openbabel gem, too):
+
+    gem install rubabel
+
+=== Building from Source
 
 1. download openbabel 
 2. swap out Init_OpenBabel for Init_openbabel in scripts/ruby/openbabel-ruby.cpp (see here[http://forums.openbabel.org/Ruby-Open-Babel-in-2-1-1-td957640.html]).  Some versions have this fixed already, apparently.
@@ -39,13 +49,7 @@ Here's a complete example of compiling for a single user on Ubuntu 11.10 and pro
     cmake ../openbabel-2.3.1 -DRUBY_BINDINGS=ON -DCMAKE_INSTALL_PREFIX=~/tools/openbabel-rvmruby1.9.3
     make && make install
 
-=== Install the gem
-
-    gem install rubabel
-
-Assuming you have the {dependencies for the openbabel gem}[https://github.com/amaunz/openbabel-gem], you could install in one go like this:
-
-    gem install openbabel rubabel
+[I still need to make directions to install the gem on top of a build from source]
  
 == Copyright
 

data/Rakefile

@@ -14,12 +14,20 @@ Jeweler::Tasks.new do |gem|
 interface attempts to be a ruby-ish analogue of pybel.}
   gem.email = "jtprince@gmail.com"
   gem.authors = ["John T. Prince"]
+  [
+    ["openbabel", "~> 2.3.1.2"],
+    ["commander", "~> 4.1.2"],
+    ["andand", "~> 1.3.3"]
+  ].each do |args|
+    gem.add_dependency(*args)
+  end
+
   [
     ["rspec", "~> 2.8.0"], 
     ["rdoc", "~> 3.12"], 
     ["jeweler", "~> 1.8.3"]
-  ].each do |name, version_string|
-    gem.add_development_dependency(name, version_string)
+  ].each do |args|
+    gem.add_development_dependency(*args)
   end
 end
 Jeweler::RubygemsDotOrgTasks.new

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/bin/rubabel

@@ -0,0 +1,229 @@
+#!/usr/bin/env ruby
+
+require 'rubygems'
+require 'commander/import'
+require 'rubabel'
+
+program :version, Rubabel::VERSION
+program :description, 'tools for manipulating molecules with rubabel'
+
+=begin
+    filename = filename.first unless options[:string_format]
+    mol_iter = 
+      if str_f=options[:string_format]
+        # assumes you aren't passing massive numbers of molecules as strings
+        # on the commandline
+        filename.map {|str| Rubabel.read_string(str, str_f.to_sym) }.each
+      else
+        Rubabel.foreach(ARGV.first)
+      end
+    mol_iter.each do |mol|
+      mol.add_h! unless mol.ob.has_hydrogens_added
+      mol.ob.get_title || 
+
+    end
+=end
+
+def mol_iterator(args, strings)
+  
+end
+
+
+command :babel do |c|
+  c.syntax = 'rubabel babel [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Babel
+  end
+end
+
+command :obabel do |c|
+  c.syntax = 'rubabel obabel [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Obabel
+  end
+end
+
+command :chiral do |c|
+  c.syntax = 'rubabel chiral [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Chiral
+  end
+end
+
+command :conformer do |c|
+  c.syntax = 'rubabel conformer [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Conformer
+  end
+end
+
+command :energy do |c|
+  c.syntax = 'rubabel energy [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Energy
+  end
+end
+
+command :fit do |c|
+  c.syntax = 'rubabel fit [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Fit
+  end
+end
+
+command :gen do |c|
+  c.syntax = 'rubabel gen [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Gen
+  end
+end
+
+command :grep do |c|
+  c.syntax = 'rubabel grep [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Grep
+  end
+end
+
+command :gui do |c|
+  c.syntax = 'rubabel gui [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Gui
+  end
+end
+
+command :minimize do |c|
+  c.syntax = 'rubabel minimize [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Minimize
+  end
+end
+
+command :probe do |c|
+  c.syntax = 'rubabel probe [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Probe
+  end
+end
+
+command :prop do |c|
+  c.syntax = 'rubabel prop [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Prop
+  end
+end
+
+command :probe do |c|
+  c.syntax = 'rubabel probe [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Probe
+  end
+end
+
+command :prop do |c|
+  c.syntax = 'rubabel prop [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Prop
+  end
+end
+
+command :rotamer do |c|
+  c.syntax = 'rubabel rotamer [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Rotamer
+  end
+end
+
+command :rotate do |c|
+  c.syntax = 'rubabel rotate [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Rotate
+  end
+end
+
+command :spectrophore do |c|
+  c.syntax = 'rubabel spectrophore [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Spectrophore
+  end
+end
+
+command :roundtrip do |c|
+  c.syntax = 'rubabel roundtrip [options]'
+  c.summary = ''
+  c.description = ''
+  c.example 'description', 'command example'
+  c.option '--some-switch', 'Some switch that does something'
+  c.action do |args, options|
+    # Do something or c.when_called Rubabel::Commands::Roundtrip
+  end
+end
+

data/lib/rubabel.rb

@@ -1,10 +1,21 @@
 require 'openbabel'
+require 'rubabel/molecule'
 
 %w(atom molecule fingerprint smarts molecule_data).each do |klass|
   require "rubabel/#{klass}"
 end
 
 module Rubabel
+  # the mass of an electron
+  MASS_E = 0.0005486
+  # www.mikeblaber.org/oldwine/chm1045/notes/Atoms/.../Atoms03.htm
+
+  # available force-fields (would like to generate this with introspection)
+  AVAILABLE_FORCEFIELDS = [:mmff94, :ghemical, :mm2, :uff] 
+  DEFAULT_FORCEFIELD = AVAILABLE_FORCEFIELDS.first
+
+  BUILDER = OpenBabel::OBBuilder.new
+
   # the command to execute the utility.  They are initialized to be eponymous.
   CMD = {
     babel: 'babel',
@@ -13,6 +24,14 @@ module Rubabel
 
   class << self
 
+    def [](string, type=Rubabel::Molecule::DEFAULT_IN_TYPE)
+      Rubabel::Molecule.from_string(string, type)
+    end
+
+    def force_field(type=DEFAULT_FORCEFIELD)
+      OpenBabel::OBForceField.find_force_field(type.to_s)
+    end
+
     # returns a hash keyed by type (Symbol) pointing to a description of the
     # format
     def in_formats
@@ -25,13 +44,29 @@ module Rubabel
       @out_formats ||= formats_to_hash(OpenBabel::OBConversion.new.get_supported_output_format)
     end
 
+    # returns the format Symbol that can be used for conversion, or nil if
+    # the extension is not recognized.
+    def format_from_ext(filename)
+      obformat = OpenBabel::OBConversion.format_from_ext(filename)
+      obformat.get_id.to_sym if obformat
+    end
+
+    alias_method :filetype, :format_from_ext
+
+    # returns a format Symbol that can be used for conversion, or nil if the
+    # mime-type is not recognized
+    def format_from_mime(mime_type)
+      obformat = OpenBabel::OBConversion.format_from_mime(mime_type)
+      obformat.get_id.to_sym if obformat
+    end
+
     # determines the extension from filename if type is nil
     def foreach(filename, type=nil, &block)
       block or return enum_for(__method__, filename, type)
       (obmol, obconv, not_at_end) = read_first_obmol(filename, type)
       # the obmol is not valid if we are already at the end!
       while not_at_end
-        block.call Rubabel::Molecule.new(obmol)
+        block.call Rubabel::Molecule.new(obmol, obconv)
         obmol = OpenBabel::OBMol.new
         not_at_end = obconv.read(obmol)
       end
@@ -40,24 +75,18 @@ module Rubabel
     # returns a Rubabel::Molecule (the first in the file if there are
     # multiples).  See ::foreach for accessing all molecules in a file
     # determines the type from the extension if type is nil.
-    def read_file(filename, type=nil)
-      obmol = read_first_obmol(filename, type).first
-      Rubabel::Molecule.new(obmol)
+    def molecule_from_file(filename, type=nil)
+      (obmol, obconv, not_at_end) = read_first_obmol(filename, type).first
+      Rubabel::Molecule.new(obmol, obconv)
     end
 
     # reads one molecule from the string
-    def read_string(string, type=:smi)
+    def molecule_from_string(string, type=:smi)
       obmol = OpenBabel::OBMol.new
       obconv = OpenBabel::OBConversion.new
       obconv.set_in_format(type.to_s) || raise(ArgumentError, "invalid format #{type}")
-      success = obconv.read_string(obmol, string)
-      Rubabel::Molecule.new(obmol)
-    end
-
-    # returns a filetype symbol based on the extension
-    def filetype(filename)
-      # should use the openbabel method in the future
-      File.extname(filename)[1..-1].to_sym
+      obconv.read_string(obmol, string) || raise(ArgumentError, "invalid string" )
+      Rubabel::Molecule.new(obmol, obconv)
     end
 
     private
@@ -66,7 +95,7 @@ module Rubabel
     # but is necessary based on discrepancies between accessing the first
     # molecule and subsequent molecules.
     def read_first_obmol(filename, type=nil)
-      type ||= filetype(filename)
+      type ||= format_from_ext(filename)
       obconv = OpenBabel::OBConversion.new
       obconv.set_in_format(type.to_s) || raise(ArgumentError, "invalid format #{type}")
       obmol = OpenBabel::OBMol.new
@@ -97,6 +126,9 @@ module Rubabel
 
   # atomic number to lowercase symbol abbreviation
   NUM_TO_EL = Hash[ ELEMENTS.each_with_index.map {|el,i| [i+1,el.downcase.to_sym] } ]
+
+  EL_TO_NUM = NUM_TO_EL.invert
+  ELEMENT_TO_NUM = NUM_TO_ELEMENT.invert
 end
 
 =begin

data/lib/rubabel/atom.rb

@@ -1,4 +1,5 @@
 require 'matrix'
+require 'andand'
 
 require 'rubabel/bond'
 
@@ -12,6 +13,21 @@ module Rubabel
   class Atom
     include Enumerable
 
+    class << self
+      # takes an element symbol and creates that atom
+      def [](el_sym=:h, id=0)
+        ob_atom = OpenBabel::OBAtom.new
+        ob_atom.set_id(id)
+        ob_atom.set_atomic_num(Rubabel::EL_TO_NUM[el_sym])
+        self.new(ob_atom)
+      end
+    end
+
+    # returns the molecule that is parent of this atom
+    def mol
+      @ob.get_parent.andand.upcast
+    end
+
     # the OpenBabel::OBAtom object
     attr_accessor :ob
 
@@ -42,6 +58,16 @@ module Rubabel
       NUM_TO_ELEMENT[atomic_num]
     end
 
+    # creates a bond and adds it to both atoms
+    def add_atom!(other)
+      obbond = OpenBabel::OBBond.new
+      obbond.set_begin(self.ob)
+      obbond.set_end(other.ob)
+      @ob.add_bond(obbond)
+      other.ob.add_bond(obbond)
+      self
+    end
+
     def each_bond(&block)
       block or return enum_for(__method__)
       iter = @ob.begin_bonds
@@ -54,6 +80,11 @@ module Rubabel
 
     alias_method :each, :each_bond
 
+    # retrieves the bond 
+    def get_bond(atom)
+      @ob.get_bond(atom.ob).andand.upcast
+    end
+
     # returns the bonds.  Consider using each_bond.
     def bonds
       each_bond.map.to_a
@@ -92,6 +123,11 @@ module Rubabel
     end
     alias_method :charge, :formal_charge
 
+    def formal_charge=(val)
+      @ob.set_formal_charge(val)
+    end
+    alias_method :charge=, :formal_charge=
+
     def heavy_valence
       @ob.get_heavy_valence
     end
@@ -132,6 +168,48 @@ module Rubabel
       @ob.get_vector
     end
 
+    def hydrogen?() @ob.is_hydrogen end
+    def carbon?() @ob.is_carbon end
+    def nitrogen?() @ob.is_nitrogen end
+    def oxygen?() @ob.is_oxygen end
+    def sulfur?() @ob.is_sulfur end
+    def phosphorus?() @ob.is_phosphorus end
+    def aromatic?() @ob.is_aromatic end
+    def in_ring?() @ob.is_in_ring end
+    def in_ring_size?() @ob.is_in_ring_size end
+    def heteroatom?() @ob.is_heteroatom end
+    def not_c_or_h?() @ob.is_not_cor_h end
+    def connected?() @ob.is_connected end
+    def one_three?() @ob.is_one_three end
+    def one_four?() @ob.is_one_four end
+    def carboxyl_oxygen?() @ob.is_carboxyl_oxygen end
+    def phosphate_oxygen?() @ob.is_phosphate_oxygen end
+    def sulfate_oxygen?() @ob.is_sulfate_oxygen end
+    def nitro_oxygen?() @ob.is_nitro_oxygen end
+    def amide_nitrogen?() @ob.is_amide_nitrogen end
+    def polar_hydrogen?() @ob.is_polar_hydrogen end
+    def non_polar_hydrogen?() @ob.is_non_polar_hydrogen end
+    def aromatic_noxide?() @ob.is_aromatic_noxide end
+    def chiral?() @ob.is_chiral end
+    def axial?() @ob.is_axial end
+    def clockwise?() @ob.is_clockwise end
+    def anti_clockwise?() @ob.is_anti_clockwise end
+    def positive_stereo?() @ob.is_positive_stereo end
+    def negative_stereo?() @ob.is_negative_stereo end
+    def chirality_specified?() @ob.has_chirality_specified end
+    def chiral_volume?() @ob.has_chiral_volume end
+    def hbond_acceptor?() @ob.is_hbond_acceptor end
+    def hbond_donor?() @ob.is_hbond_donor end
+    def hbond_donor_h?() @ob.is_hbond_donor_h end
+
+    def carboxyl_carbon?
+      atoms.any?(&:carboxyl_oxygen?)
+    end
+
+#    # does this carbon hold a primary alcohol
+#    def primary_alcohol_carbon?
+#    end
+
     def coords
       Vector[@ob.x, @ob.y, @ob.z]
     end