rino 0.1.0

data/ext/src/util.h

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+/*
+ * International Union of Pure and Applied Chemistry (IUPAC)
+ * International Chemical Identifier (InChI)
+ * Version 1
+ * Software version 1.00
+ * April 13, 2005
+ * Developed at NIST
+ */
+
+#ifndef __UTIL_H__
+#define __UTIL_H__
+
+#include "inpdef.h"
+
+/* BILLY 8/6/04 */
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+extern "C" {
+#endif
+#endif
+
+int get_atw(const char *elname);
+int get_atw_from_elnum( int nAtNum );
+int get_num_H (const char* elname, int inp_num_H, S_CHAR num_iso_H[], int charge, int radical,
+              int chem_bonds_valence, int atom_input_valence, int bAliased, int bDoNotAddH, int bHasMetalNeighbor );
+int extract_ChargeRadical( char *elname, int *pnRadical, int *pnCharge );
+int extract_H_atoms( char *elname, S_CHAR num_iso_H[] );
+int normalize_name( char* name );
+
+int mystrncpy(char *target,const char *source,unsigned maxlen);
+char* LtrimRtrim( char *p, int* nLen );
+char* fgets_up_to_lf( char* line, int line_len, FILE* inp );
+void remove_trailing_spaces( char* p );
+void remove_one_lf( char* p);
+void mystrrev( char *p );
+#ifndef INCHI_LIBRARY
+int my_fgets( char *szLine, int len, FILE *f, int *bTooLongLine );
+int my_fgetsTab( char *szLine, int len, FILE *f, int *bTooLongLine );
+int my_fgetsTab1( char *szLine, int len, FILE *f, int *bTooLongLine );
+#endif
+int my_fgetsUpToLfOrTab( char *szLine, int len, FILE *f );
+
+
+AT_NUMB *is_in_the_list( AT_NUMB *pathAtom, AT_NUMB nNextAtom, int nPathLen );
+int get_periodic_table_number( const char* elname );
+int is_el_a_metal( int nPeriodicNum );
+int get_el_valence( int nPeriodicNum, int charge, int val_num );
+int get_unusual_el_valence( int nPeriodicNum, int charge, int radical, int bonds_valence, int num_H, int num_bonds );
+int detect_unusual_el_valence( int nPeriodicNum, int charge, int radical, int bonds_valence, int num_H, int num_bonds );
+int needed_unusual_el_valence( int nPeriodicNum, int charge, int radical, int bonds_valence, int num_H, int num_bonds );
+int get_el_type( int nPeriodicNum );
+int get_el_number( const char* elname );
+int do_not_add_H( int nPeriodicNum );
+int GetElementFormulaFromAtNum(int nAtNum, char *szElement );
+int MakeRemovedProtonsString( int nNumRemovedProtons, NUM_H *nNumExchgIsotopicH, NUM_H *nNumRemovedProtonsIsotopic,
+                              int bIsotopic, char *szRemovedProtons, int *num_removed_iso_H );
+
+/* ion pairs and fixing bonds */
+int num_of_H( inp_ATOM *at, int iat );
+int has_other_ion_neigh( inp_ATOM *at, int iat, int iat_ion_neigh, const char *el, int el_len );
+int has_other_ion_in_sphere_2(inp_ATOM *at, int iat, int iat_ion_neigh, const char *el, int el_len );
+int nNoMetalNumBonds( inp_ATOM *at, int at_no );
+int nNoMetalBondsValence( inp_ATOM *at, int at_no );
+int nNoMetalNeighIndex( inp_ATOM *at, int at_no );
+int nNoMetalOtherNeighIndex( inp_ATOM *at, int at_no, int cur_neigh );
+int nNoMetalOtherNeighIndex2( inp_ATOM *at, int at_no, int cur_neigh, int cur_neigh2 );
+
+
+/* IChICan2.c */
+int SetBitFree( void );
+
+void WriteCoord( char *str, double x );
+
+
+extern int ERR_ELEM;
+
+/* BILLY 8/6/04 */
+#ifndef INCHI_ALL_CPP
+#ifdef __cplusplus
+}
+#endif
+#endif
+
+#endif /* __UTIL_H__*/
+

data/lib/clean_tempfile.rb

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+# =================================
+# Rino - The InChI Toolkit for Ruby
+# =================================
+#
+# Project Info:  http://rino.rubyforge.org
+#
+# Copyright (C) 2006 Richard L. Apodaca
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License version 2.1 as published by the Free Software
+# Foundation.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free
+# Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor
+# Boston, MA 02111-1301, USA.
+#
+# This file originally appeared in the Ruby standard library
+# as 'tempfile.rb' and has been modified as documented.
+
+require 'delegate'
+require 'tmpdir'
+
+# A class for managing temporary files.  This library is written to be
+# thread safe.
+# CleanTempfile is a slightly modified version of Tempfile in the standard
+# Ruby library. Its open method opens the tempfile in write mode. This
+# clears the contents of the previously written molfile which would
+# otherwise be present in the standard Tempfile implementation.
+class CleanTempfile < DelegateClass(File)
+  MAX_TRY = 10
+  @@cleanlist = []
+
+  # Creates a temporary file of mode 0600 in the temporary directory
+  # whose name is basename.pid.n and opens with mode "w+".  A Tempfile
+  # object works just like a File object.
+  #
+  # If tmpdir is omitted, the temporary directory is determined by
+  # Dir::tmpdir provided by 'tmpdir.rb'.
+  # When $SAFE > 0 and the given tmpdir is tainted, it uses
+  # /tmp. (Note that ENV values are tainted by default)
+  def initialize(basename, tmpdir=Dir::tmpdir)
+    if $SAFE > 0 and tmpdir.tainted?
+      tmpdir = '/tmp'
+    end
+
+    lock = nil
+    n = failure = 0
+    
+    begin
+      Thread.critical = true
+
+      begin
+	tmpname = File.join(tmpdir, make_tmpname(basename, n))
+	lock = tmpname + '.lock'
+	n += 1
+      end while @@cleanlist.include?(tmpname) or
+	File.exist?(lock) or File.exist?(tmpname)
+
+      Dir.mkdir(lock)
+    rescue
+      failure += 1
+      retry if failure < MAX_TRY
+      raise "cannot generate tempfile `%s'" % tmpname
+    ensure
+      Thread.critical = false
+    end
+
+    @data = [tmpname]
+    @clean_proc = Tempfile.callback(@data)
+    ObjectSpace.define_finalizer(self, @clean_proc)
+
+    @tmpfile = File.open(tmpname, File::RDWR|File::CREAT|File::EXCL, 0600)
+    @tmpname = tmpname
+    @@cleanlist << @tmpname
+    @data[1] = @tmpfile
+    @data[2] = @@cleanlist
+
+    super(@tmpfile)
+
+    # Now we have all the File/IO methods defined, you must not
+    # carelessly put bare puts(), etc. after this.
+
+    Dir.rmdir(lock)
+  end
+
+  def make_tmpname(basename, n)
+    sprintf('%s%d.%d', basename, $$, n)
+  end
+  private :make_tmpname
+
+  # Opens or reopens the file with mode "w+", rather than
+  # "r+" as in tempfile.rb.
+  def open
+    @tmpfile.close if @tmpfile
+    
+    # uses 'w+' instead of 'r+' as used in tempfile.rb
+    @tmpfile = File.open(@tmpname, 'w+')
+    @data[1] = @tmpfile
+    __setobj__(@tmpfile)
+  end
+
+  def _close	# :nodoc:
+    @tmpfile.close if @tmpfile
+    @data[1] = @tmpfile = nil
+  end    
+  protected :_close
+
+  # Closes the file.  If the optional flag is true, unlinks the file
+  # after closing.
+  #
+  # If you don't explicitly unlink the temporary file, the removal
+  # will be delayed until the object is finalized.
+  def close(unlink_now=false)
+    if unlink_now
+      close!
+    else
+      _close
+    end
+  end
+
+  # Closes and unlinks the file.
+  def close!
+    _close
+    @clean_proc.call
+    ObjectSpace.undefine_finalizer(self)
+  end
+
+  # Unlinks the file.  On UNIX-like systems, it is often a good idea
+  # to unlink a temporary file immediately after creating and opening
+  # it, because it leaves other programs zero chance to access the
+  # file.
+  def unlink
+    # keep this order for thread safeness
+    begin
+      File.unlink(@tmpname) if File.exist?(@tmpname)
+      @@cleanlist.delete(@tmpname)
+      @data = @tmpname = nil
+      ObjectSpace.undefine_finalizer(self)
+    rescue Errno::EACCESS
+      # may not be able to unlink on Windows; just ignore
+    end
+  end
+  alias delete unlink
+
+  # Returns the full path name of the temporary file.
+  def path
+    @tmpname
+  end
+
+  # Returns the size of the temporary file.  As a side effect, the IO
+  # buffer is flushed before determining the size.
+  def size
+    if @tmpfile
+      @tmpfile.flush
+      @tmpfile.stat.size
+    else
+      0
+    end
+  end
+  alias length size
+
+  class << self
+    def callback(data)	# :nodoc:
+      pid = $$
+      lambda{
+	if pid == $$ 
+	  path, tmpfile, cleanlist = *data
+
+	  print "removing ", path, "..." if $DEBUG
+
+	  tmpfile.close if tmpfile
+
+	  # keep this order for thread safeness
+	  File.unlink(path) if File.exist?(path)
+	  cleanlist.delete(path) if cleanlist
+
+	  print "done\n" if $DEBUG
+	end
+      }
+    end
+
+    # If no block is given, this is a synonym for new().
+    #
+    # If a block is given, it will be passed tempfile as an argument,
+    # and the tempfile will automatically be closed when the block
+    # terminates.  In this case, open() returns nil.
+    def open(*args)
+      tempfile = new(*args)
+
+      if block_given?
+	begin
+	  yield(tempfile)
+	ensure
+	  tempfile.close
+	end
+
+	nil
+      else
+	tempfile
+      end
+    end
+  end
+end
+
+if __FILE__ == $0
+#  $DEBUG = true
+  f = Tempfile.new("foo")
+  f.print("foo\n")
+  f.close
+  f.open
+  p f.gets # => "foo\n"
+  f.close!
+end

data/lib/rino.rb

@@ -0,0 +1,111 @@
+# =================================
+# Rino - The InChI Toolkit for Ruby
+# =================================
+#
+# Project Info:  http://rino.rubyforge.org
+#
+# Copyright (C) 2006 Richard L. Apodaca
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License version 2.1 as published by the Free Software
+# Foundation.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free
+# Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor
+# Boston, MA 02111-1301, USA.
+# 
+# Typical usage:
+# 
+#   reader = Rino::MolfileReader.new
+#   inchi = reader.read(IO.read('benzene.mol'))
+#
+#   puts inchi -> 'InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H'
+
+$:.unshift File.join(File.dirname(__FILE__), "..", "ext")
+
+require 'tempfile'
+require 'clean_tempfile'
+require 'ruby_inchi_main'
+
+module Rino
+  # Creates an InChI string from a molfile. This class coordinates the creation
+  # and deletion of temporary i/o files according to the rules used by Tempfile.
+  class MolfileReader
+  
+    # Accepts the same options as the InChI command line
+    # software. See: http://wwmm.ch.cam.ac.uk/inchifaq/ and the
+    # InChI Technical Manual for an explanation of these options.
+    #
+    # Example:
+    # 
+    # reader = Rino::MolfileReader.new
+    # 
+    # reader.options << "-Compress"
+    attr_reader :options
+    
+    def initialize
+      @in = CleanTempfile.new("inchi_input.mol")
+      @out = Tempfile.new("inchi_output.txt")
+      @log = Tempfile.new("inchi_log.txt")
+      @prob = Tempfile.new("inchi_problem.txt")
+      @main = Main.new
+      @options = Array.new
+    end
+    
+    #Reads the specified molfile encoded as a string, and returns the
+    #corresponding InChI identifier.
+    def read(molfile)
+      write_input(molfile)
+      
+      @main.run(create_argv)
+      
+      get_inchi
+    end
+    
+    private
+    
+    def write_input(molfile)
+      @in.open
+      @in << molfile
+      @in.close
+    end
+    
+    def create_argv
+      result = ["", @in.path, @out.path, @log.path, @prob.path]
+      
+      @options.each do |x|
+        result << x
+      end
+      
+      result;
+    end
+    
+    def get_inchi
+      result = ""
+      
+      @out.open
+      
+      2.times do |i|
+        begin
+          @out.readline
+          
+        rescue EOFError
+          raise "Unreadable molfile"
+        end
+      end
+      
+      result = @out.readline.rstrip!
+      
+      @out.close
+      
+      result
+    end
+  end
+end