Mercurial > repos > deepakjadmin > mayatool3_test2

diff bin/SDFilesToHTML.pl @ 0:4816e4a8ae95 draft default tip
Uploaded
author: deepakjadmin
date: Wed, 20 Jan 2016 09:23:18 -0500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/SDFilesToHTML.pl	Wed Jan 20 09:23:18 2016 -0500
@@ -0,0 +1,2480 @@
+#!/usr/bin/perl -w
+#
+# $RCSfile: SDFilesToHTML.pl,v $
+# $Date: 2015/02/28 20:46:20 $
+# $Revision: 1.50 $
+#
+# Author: Manish Sud <msud@san.rr.com>
+#
+# Copyright (C) 2015 Manish Sud. All rights reserved.
+#
+# This file is part of MayaChemTools.
+#
+# MayaChemTools is free software; you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the Free
+# Software Foundation; either version 3 of the License, or (at your option) any
+# later version.
+#
+# MayaChemTools is distributed in the hope that it will be useful, but without
+# any warranty; without even the implied warranty of merchantability of 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 MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
+# write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
+# Boston, MA, 02111-1307, USA.
+#
+
+use strict;
+use FindBin; use lib "$FindBin::Bin/../lib";
+use Getopt::Long;
+use File::Basename;
+use File::Spec;
+use Text::ParseWords;
+use Benchmark;
+use Cwd;
+use FileUtil;
+use SDFileUtil;
+use TextUtil;
+use HTMLUtil;
+
+my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
+
+# Autoflush STDOUT
+$| = 1;
+
+# Starting message...
+$ScriptName = basename($0);
+print "\n$ScriptName: Starting...\n\n";
+$StartTime = new Benchmark;
+
+# Get the options and setup script...
+SetupScriptUsage();
+if ($Options{help} || @ARGV < 1) {
+  die GetUsageFromPod("$FindBin::Bin/$ScriptName");
+}
+
+my(@SDFilesList);
+@SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
+
+#Make sure appropriate mode specific option values are specified...
+print "Processing options...\n";
+my(%OptionsInfo);
+ProcessOptions();
+
+# Collect information about SD files...
+print "Checking input SD file(s)...\n";
+my(%SDFilesInfo);
+RetrieveSDFilesInfo();
+SetupMultipleTablesAndMiscInfo();
+
+# Generate output files...
+my($FileIndex);
+if (@SDFilesList > 1) {
+  print "\nProcessing SD files...\n";
+}
+for $FileIndex (0 .. $#SDFilesList) {
+  if ($SDFilesInfo{FileOkay}[$FileIndex]) {
+    print "\nProcessing file $SDFilesList[$FileIndex]...\n";
+    GenerateHTMLTable($FileIndex);
+  }
+}
+print "\n$ScriptName:Done...\n\n";
+
+$EndTime = new Benchmark;
+$TotalTime = timediff ($EndTime, $StartTime);
+print "Total time: ", timestr($TotalTime), "\n";
+
+###############################################################################
+
+# Generate HTML table(s)...
+sub GenerateHTMLTable {
+  my($Index) = @_;
+
+  if ($SDFilesInfo{MultipleHTMLTables}[$Index]) {
+    GenerateMultipleHTMLTables($Index);
+  }
+  else {
+    GenerateOneHTMLTable($Index);
+  }
+}
+
+# Generate one HTML table...
+sub GenerateOneHTMLTable {
+  my($Index) = @_;
+  my($SDFile, $TopHTMLDir, $HTMLFile, $StartCmpdNum, $EndCmpdNum, $CSSFile, $CSSRef, $CSSFilePath, $TableNum);
+
+  $HTMLFile = $SDFilesInfo{HTMLRoot}[$Index] . ".html";
+  $SDFile = $SDFilesList[$Index];
+
+  # Setup data directories...
+  ($TopHTMLDir) = SetupDataDirs($Index);
+
+  # Setup stylesheet file...
+  $CSSRef = "";
+  if ($Options{stylesheet} =~ /^new$/i) {
+    $CSSFile = $SDFilesInfo{HTMLRoot}[$Index] . ".css"; $CSSRef = ".\/" . "$CSSFile";
+    $CSSFilePath = "$TopHTMLDir" . "\/" . $CSSFile;
+    GenerateStyleSheetFile($CSSFilePath);
+  }
+  elsif ($Options{stylesheet} =~ /^old$/i) {
+    $CSSRef = $Options{stylesheetname};
+  }
+
+  # Set HTML file location...
+  $HTMLFile = "$TopHTMLDir" . "\/" . $HTMLFile;
+
+  print "Generating HTML file $HTMLFile...\n";
+  open HTMLFILE, ">$HTMLFile" or die "Error: Can't open $HTMLFile: $! \n";
+  open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n";
+
+  # Write out HTML page header...
+  print HTMLFILE SetupHTMLPageHeader($SDFilesInfo{HTMLTitle}[$Index], $CSSRef, $OptionsInfo{TopHTMLDirStrViewerJSFileRef});
+
+  if ($OptionsInfo{StrViewerJSFileRef}) {
+    print HTMLFILE SetupStrViewerJSInitCmd($OptionsInfo{StrViewerType}, $OptionsInfo{TopHTMLDirStrViewerCodeBase});
+  }
+
+  # Setup page title...
+  if ($OptionsInfo{TitleDisplay}) {
+    print HTMLFILE SetupHTMLPageTitle($SDFilesInfo{HTMLTitle}[$Index]);
+  }
+  else {
+    print HTMLFILE SetupHTMLEmptyLines(1);
+  }
+
+  # Start the table...
+  print HTMLFILE SetupHTMLAlignmentBegin("center");
+  print HTMLFILE SetupHTMLTableHeader($OptionsInfo{TableBorder}, $OptionsInfo{TableCellPadding}, $OptionsInfo{TableCellSpacing});
+
+  # Generate table rows...
+  $StartCmpdNum = 1;
+  $EndCmpdNum = $SDFilesInfo{CmpdCount}[$Index];
+  $TableNum = 1;
+  GenerateTableRows($Index, $TableNum, $StartCmpdNum, $EndCmpdNum, \*SDFILE, \*HTMLFILE);
+
+  # Finish up the table...
+  print HTMLFILE SetupHTMLTableEnd();
+  print HTMLFILE SetupHTMLAlignmentEnd("center");
+
+  # Write out HTML page end...
+  print HTMLFILE SetupHTMLPageEnd($OptionsInfo{FooterMsg});
+
+  close HTMLFILE;
+  close SDFILE;
+}
+
+# Generate multiple tables...
+sub GenerateMultipleHTMLTables {
+  my($Index) = @_;
+  my($TopHTMLDir, $SubHTMLDir, $SDFile, $HTMLFile, $TableNum, $TableCount, $TableIndex, $TableStartCmpdNum, $TableEndCmpdNum, $PrintMsg, $CSSFile, $CSSRef, $CSSFilePath, $NewStyleSheet, $StrViewerCodeBase, $StrViewerJSFileRef);
+
+  # Open SD file...
+  $SDFile = $SDFilesList[$Index];
+  open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n";
+
+  # Set up data directories to hold various html files...
+  ($TopHTMLDir, $SubHTMLDir) = SetupDataDirs($Index);
+
+  # Create stylesheet file...
+  $CSSRef = "";
+  $NewStyleSheet = 0;
+  if ($Options{stylesheet} =~ /^new$/i) {
+    $NewStyleSheet = 1;
+    $CSSFile = $SDFilesInfo{HTMLRoot}[$Index] . ".css";
+    $CSSFilePath = "$TopHTMLDir" . "\/" . $CSSFile;
+    GenerateStyleSheetFile($CSSFilePath);
+  }
+  elsif ($Options{stylesheet} =~ /^old$/i) {
+    $CSSRef = $Options{stylesheetname};
+  }
+
+  $PrintMsg = 1;
+  # Generate HTML files for all the tables...
+  $TableCount = $SDFilesInfo{TableCount}[$Index];
+  for $TableNum (1 .. $TableCount) {
+    $TableIndex = $TableNum - 1;
+    $HTMLFile = ${$SDFilesInfo{TableHTMLFiles}[$Index]}[$TableIndex];
+    $TableStartCmpdNum = ${$SDFilesInfo{TableStartCmpdNum}[$Index]}[$TableIndex];
+    $TableEndCmpdNum = ${$SDFilesInfo{TableEndCmpdNum}[$Index]}[$TableIndex];
+
+    # Setup file name...
+    if ($TableNum == 1) {
+      $HTMLFile = "$TopHTMLDir" . "\/" . $HTMLFile;
+      print "Generating HTML file $HTMLFile...\n";
+    }
+    else {
+      $HTMLFile = "$SubHTMLDir" . "\/" . $HTMLFile;
+      if ($PrintMsg) {
+	$PrintMsg = 0;
+	if ($TableCount == 2) {
+	  print "Generating HTML file $HTMLFile...\n";
+	}
+	else {
+	  print "Generating ", ($TableCount - 1), " other HTML files: $SubHTMLDir\/$SDFilesInfo{HTMLRoot}[$Index]\*.html...\n";
+	}
+      }
+    }
+    # Setup stylesheet reference...
+    if ($NewStyleSheet) {
+      $CSSRef = ($TableNum == 1) ? ".\/" : "..\/";
+      $CSSRef .= $CSSFile;
+    }
+
+    open HTMLFILE, ">$HTMLFile" or die "Error: Can't open $HTMLFile: $! \n";
+    # Write out HTML page header...
+    $StrViewerJSFileRef = ($TableNum == 1) ? $OptionsInfo{TopHTMLDirStrViewerJSFileRef} : $OptionsInfo{SubHTMLDirStrViewerJSFileRef};
+    print HTMLFILE SetupHTMLPageHeader($SDFilesInfo{HTMLTitle}[$Index], $CSSRef, $StrViewerJSFileRef);
+
+    if ($OptionsInfo{StrViewerJSFileRef}) {
+      $StrViewerCodeBase = ($TableNum == 1) ? $OptionsInfo{TopHTMLDirStrViewerCodeBase} : $OptionsInfo{SubHTMLDirStrViewerCodeBase};
+      print HTMLFILE SetupStrViewerJSInitCmd($OptionsInfo{StrViewerType}, $StrViewerCodeBase);
+    }
+
+    # Set up the navigation links for this table...
+    if ($OptionsInfo{NavLinksAtTop}) {
+      WriteNavigationLinks($Index, $TableNum, \*HTMLFILE);
+    }
+    # Setup page title...
+    if ($OptionsInfo{TitleDisplay}) {
+      print HTMLFILE SetupHTMLPageTitle($SDFilesInfo{HTMLTitle}[$Index]);
+    }
+    else {
+      print HTMLFILE SetupHTMLEmptyLines(1);
+    }
+
+    # Start the table...
+    print HTMLFILE SetupHTMLAlignmentBegin("center");
+    print HTMLFILE SetupHTMLTableHeader($OptionsInfo{TableBorder}, $OptionsInfo{TableCellPadding}, $OptionsInfo{TableCellSpacing});
+
+    # Generate table content...
+    GenerateTableRows($Index, $TableNum, $TableStartCmpdNum, $TableEndCmpdNum, \*SDFILE, \*HTMLFILE);
+
+    # Finish up the table...
+    print HTMLFILE SetupHTMLTableEnd();
+    print HTMLFILE SetupHTMLAlignmentEnd("center");
+
+    # Set up the navigation links for this table...
+    if ($OptionsInfo{NavLinksAtBottom}) {
+      print HTMLFILE SetupHTMLEmptyLines(1);
+      WriteNavigationLinks($Index, $TableNum, \*HTMLFILE);
+    }
+
+    # Write out HTML page end...
+    print HTMLFILE SetupHTMLPageEnd($OptionsInfo{FooterMsg});
+    close HTMLFILE;
+  }
+  close SDFILE;
+
+}
+
+# Generate table content...
+sub GenerateTableRows {
+  my($Index, $TableNum, $StartCmpdNum, $EndCmpdNum, $SDFileRef, $HTMLFileRef) = @_;
+
+  if ($OptionsInfo{StructuresOnlyMode}) {
+    WriteRowStructures($Index, $TableNum, $StartCmpdNum, $EndCmpdNum, $SDFileRef, $HTMLFileRef);
+  }
+  else {
+    WriteColLabels($Index, $SDFileRef, $HTMLFileRef);
+    WriteRowValues($Index, $TableNum, $StartCmpdNum, $EndCmpdNum, $SDFileRef, $HTMLFileRef);
+  }
+}
+
+# Create stylesheet file...
+sub GenerateStyleSheetFile {
+  my($CSSFile) = @_;
+    print "Generating stylesheet file $CSSFile...\n";
+    open CSSFILE, ">$CSSFile" or die "Error: Can't open $CSSFile: $! \n";
+    print CSSFILE SetupHTMLStyleSheetTags();
+    close CSSFILE;
+}
+
+# Write out table header using column labels...
+sub WriteColLabels {
+  my($Index, $SDFileRef, $HTMLFileRef) = @_;
+
+  my(@ColLabels, $Label);
+  print $HTMLFileRef $SDFilesInfo{TableRowHeaderTags};
+
+  # Write out structure label...
+  $Label = "Structure";
+  print $HTMLFileRef SetupHTMLTableRowHeaderValue($Label);
+
+  # Write out field values..
+  @ColLabels = @{$SDFilesInfo{SpecifiedDataFieldLabels}[$Index]};
+  for $Label (@ColLabels) {
+    print $HTMLFileRef SetupHTMLTableRowHeaderValue($Label);
+  }
+  print $HTMLFileRef $SDFilesInfo{RowEndTags};
+}
+
+# Write out the rows value...
+sub WriteRowValues {
+  my($Index, $TableNum, $StartCmpdNum, $EndCmpdNum, $SDFileRef, $HTMLFileRef) = @_;
+  my($BackgroundColor, $FontColor, $RowNum, $CmpdNum, $CmpdString, @CmpdLines, $Label, %DataFieldValues, $Value);
+
+  $RowNum = 0;
+  for $CmpdNum ($StartCmpdNum .. $EndCmpdNum) {
+    $RowNum++;
+    $CmpdString = ReadCmpdString($SDFileRef);
+    if ($OptionsInfo{ShadeRowsStatus}) {
+      print $HTMLFileRef ($RowNum % 2) ? $SDFilesInfo{BgFilledOddRowHeaderTags} : $SDFilesInfo{BgFilledEvenRowHeaderTags};
+    }
+    else {
+      print $HTMLFileRef $SDFilesInfo{RowHeaderTags};
+    }
+    @CmpdLines = split "\n", $CmpdString;
+    %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
+
+    # Setup structure column...
+    SetupStructureColumn($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef);
+    # Write out field values..
+    for $Label (@{$SDFilesInfo{SpecifiedDataFieldLabels}[$Index]}) {
+      $Value = (IsNotEmpty($DataFieldValues{$Label})) ? $DataFieldValues{$Label} : "";
+      $BackgroundColor = ""; $FontColor = "";
+      if ($OptionsInfo{HighlightStatus}) {
+	if (exists($OptionsInfo{SpecifiedHighlightDataFieldLabelsMap}{$Label})) {
+	  ($BackgroundColor, $FontColor) = GetValueHighlightColors($Label, $Value);
+	}
+      }
+      print $HTMLFileRef SetupHTMLTableRowDataValue($Value, $BackgroundColor, $FontColor);
+    }
+    print $HTMLFileRef $SDFilesInfo{RowEndTags};
+  }
+}
+
+# Write only structures...
+sub WriteRowStructures {
+  my($Index, $TableNum, $StartCmpdNum, $EndCmpdNum, $SDFileRef, $HTMLFileRef) = @_;
+  my($CmpdNum, $CmpdString, $StartRowFlag, $ColNum, $RowNum, $RowBgColor, $RowStartTags, $ColumnHeaderTags, $ColumnEndTags, $CmpdDataFieldValue, $CmpdHTMLFileRef, $Value);
+
+  $StartRowFlag = 1; $ColNum = 0; $RowNum = 0;
+  $ColumnHeaderTags = SetupHTMLTableColumnHeader();
+  $ColumnEndTags = SetupHTMLTableColumnEnd();
+
+  if ($OptionsInfo{StructuresOnlyMode} && !$OptionsInfo{TableBorder} && ($OptionsInfo{OddRowsShadeColor} =~ /^(#ffffff|white)$/i)) {
+    print $HTMLFileRef SetupHTMLTableRowHeader($OptionsInfo{RowHAlignment}, $OptionsInfo{TableHeaderRowColor}, $OptionsInfo{RowVAlignment});
+    $Value = SetupHTMLTableRowDataValue("");
+    print $HTMLFileRef InsertHTMLTags($Value, "colspan", "$OptionsInfo{StrTableCols}");
+    print $HTMLFileRef $SDFilesInfo{RowEndTags};
+  }
+
+  for $CmpdNum ($StartCmpdNum .. $EndCmpdNum) {
+    $CmpdString = ReadCmpdString($SDFileRef);
+    if ($StartRowFlag) {
+      $StartRowFlag = 0;
+      $RowNum++;
+      if ($OptionsInfo{ShadeRowsStatus}) {
+	print $HTMLFileRef ($RowNum % 2) ? $SDFilesInfo{BgFilledOddRowHeaderTags} : $SDFilesInfo{BgFilledEvenRowHeaderTags};
+      }
+      else {
+	print $HTMLFileRef $SDFilesInfo{RowHeaderTags};
+      }
+    }
+    $ColNum++;
+
+    $CmpdDataFieldValue = "";
+    if ($OptionsInfo{CmpdDataField}) {
+      my($CmpdDataField, @CmpdLines, %DataFieldValues);
+      $CmpdDataField = $OptionsInfo{CmpdDataField};
+      @CmpdLines = split "\n", $CmpdString;
+      %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
+      if (exists($DataFieldValues{$CmpdDataField}) && length($DataFieldValues{$CmpdDataField})) {
+	$CmpdDataFieldValue = $DataFieldValues{$CmpdDataField};
+	if ($OptionsInfo{CmpdDataFieldLabel} =~ /^yes$/i) {
+	  $CmpdDataFieldValue = "${CmpdDataField}: ${CmpdDataFieldValue}";
+	}
+	# Make sure it's not to looong...
+	if (length($CmpdDataFieldValue) > 30) {
+	  $CmpdDataFieldValue = substr($CmpdDataFieldValue, 0, 30) . "...";
+	}
+      }
+    }
+    if ($CmpdDataFieldValue) {
+      $RowBgColor = "";
+      if ($OptionsInfo{ShadeRowsStatus}) {
+	$RowBgColor = ($RowNum % 2) ? $OptionsInfo{OddRowsShadeColor} : $OptionsInfo{EvenRowsShadeColor};
+      }
+      $RowStartTags = SetupHTMLTableRowHeader($OptionsInfo{CmpdDataFieldAlignment}, $RowBgColor, "middle");
+      # Start  a new table in current column...
+      print $HTMLFileRef $ColumnHeaderTags;
+      print $HTMLFileRef SetupHTMLAlignmentBegin("center");
+      print $HTMLFileRef SetupHTMLTableHeader(0, 0, 0);
+
+      if ($OptionsInfo{CmpdDataFieldPosition} =~ /^top$/i ) {
+	# Add an empty row...
+	print $HTMLFileRef $RowStartTags;
+	print $HTMLFileRef SetupHTMLTableRowDataValue("");
+	print $HTMLFileRef $SDFilesInfo{RowEndTags};
+
+	# Display the label value...
+	print $HTMLFileRef $RowStartTags;
+	$CmpdHTMLFileRef = SetupCompoundSummaryFileAndLink($Index, $TableNum, $CmpdString, $CmpdNum);
+	$Value = SetupHTMLHRef("$CmpdDataFieldValue", $CmpdHTMLFileRef, "Compound Summary");
+	print $HTMLFileRef SetupHTMLTableRowDataValue($Value);
+	print $HTMLFileRef $SDFilesInfo{RowEndTags};
+      }
+      # Display the structure...
+      print $HTMLFileRef SetupHTMLTableRowHeader("center", $RowBgColor, "middle");
+      SetupStructureDisplay($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef);
+      print $HTMLFileRef $SDFilesInfo{RowEndTags};
+
+      if ($OptionsInfo{CmpdDataFieldPosition} =~ /^bottom$/i ) {
+	# Display the label value...
+	print $HTMLFileRef $RowStartTags;
+	$CmpdHTMLFileRef = SetupCompoundSummaryFileAndLink($Index, $TableNum, $CmpdString, $CmpdNum);
+	$Value = SetupHTMLHRef("$CmpdDataFieldValue", $CmpdHTMLFileRef, "Compound Summary");
+	print $HTMLFileRef SetupHTMLTableRowDataValue($Value);
+	print $HTMLFileRef $SDFilesInfo{RowEndTags};
+
+	# Add an empty row...
+	print $HTMLFileRef $RowStartTags;
+	print $HTMLFileRef SetupHTMLTableRowDataValue("");
+	print $HTMLFileRef $SDFilesInfo{RowEndTags};
+      }
+
+      print $HTMLFileRef SetupHTMLTableEnd();
+      print $HTMLFileRef SetupHTMLAlignmentEnd("center");
+      print $HTMLFileRef $ColumnEndTags;
+    }
+    else {
+      SetupStructureDisplay($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef);
+    }
+
+    if ($ColNum == $OptionsInfo{StrTableCols}) {
+      # Finish up the current row and get ready for starting a new row...
+      print $HTMLFileRef $SDFilesInfo{RowEndTags};
+      $ColNum = 0;
+      $StartRowFlag = 1;
+    }
+  }
+  if (!$StartRowFlag) {
+    # Finish up an existing row...
+    my($ColIndex, $Value);
+    $Value = "";
+    for $ColIndex ($ColNum .. ($OptionsInfo{StrTableCols} - 1) ) {
+      print $HTMLFileRef SetupHTMLTableRowDataValue($Value);
+    }
+    print $HTMLFileRef $SDFilesInfo{RowEndTags};
+  }
+}
+
+# Setup structure column...
+sub SetupStructureColumn {
+  my($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef) = @_;
+
+  if ($OptionsInfo{DisplayStructure}) {
+    SetupStructureDisplay($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef);
+  }
+  else {
+    SetupStructureLink($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef);
+  }
+}
+
+# Setup structure display for compound summary page...
+sub SetupStructureDisplayForCmpdSummaryPage {
+  my($Index, $CmpdString, $CmpdNum, $HTMLFileRef) = @_;
+  my($TableNum, $RowNum);
+
+  # Use table num 0 to force usage of "../mol" prefix for all MOL file references. Row num
+  # doesn't matter...
+  $TableNum = 0;
+  $RowNum = 1;
+
+  $OptionsInfo{SettingUpCmpdSummaryPage} = 1;
+
+  # Setup size and bgcolor parameters for linking structures...
+  $OptionsInfo{StrViewerParams}{width} = $OptionsInfo{StrLinkWidth};
+  $OptionsInfo{StrViewerParams}{height} = $OptionsInfo{StrLinkHeight};
+  $OptionsInfo{StrViewerParams}{bgcolor} = $OptionsInfo{StrLinkBgColorSpecified};
+
+  SetupStructureDisplay($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef);
+
+  # Reset size and bgcolor parameters back to displaying structures in tables...
+  $OptionsInfo{StrViewerParams}{width} = $OptionsInfo{StrWidth};
+  $OptionsInfo{StrViewerParams}{height} = $OptionsInfo{StrHeight};
+  $OptionsInfo{StrViewerParams}{bgcolor} = $OptionsInfo{StrBgColorSpecified} ? $OptionsInfo{StrBgColorSpecified} : "";
+
+  $OptionsInfo{SettingUpCmpdSummaryPage} = 0;
+}
+
+
+# Setup structure column display...
+sub SetupStructureDisplay {
+  my($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef) = @_;
+  my($Nothing);
+
+ STRVIEWERTYPE: {
+    if ($OptionsInfo{StrViewerType} =~ /^JME$/i) { SetupJMEDisplay($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef); last STRVIEWERTYPE; }
+    if ($OptionsInfo{StrViewerType} =~ /^Jmol$/i) { SetupJmolDisplay($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef); last STRVIEWERTYPE; }
+    if ($OptionsInfo{StrViewerType} =~ /^Chime$/i) { SetupChimeDisplay($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef); last STRVIEWERTYPE; }
+    if ($OptionsInfo{StrViewerType} =~ /^(Chem3DActiveX|ChemDrawActiveX|ChemDrawPlugIn)$/i) { SetupCambridgeSoftDisplay($OptionsInfo{StrViewerType}, $Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef); last STRVIEWERTYPE; }
+    if ($OptionsInfo{StrViewerType} =~ /^MarvinView$/i) { SetupMarvinDisplay($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef); last STRVIEWERTYPE; }
+    if ($OptionsInfo{StrViewerType} =~ /^ViewerActiveX$/i) { SetupViewerAccelrysActiveXDisplay($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef); last STRVIEWERTYPE; }
+    $Nothing = 1;
+  }
+}
+
+# Setup JME display...
+sub SetupJMEDisplay {
+  my($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef) = @_;
+  my($MolString, $AppletBGColor, $Value, $ValueTag, $AppletName, $StrViewerCodeBase);
+
+  $Value = "";
+  ($MolString) = split "$SDFilesInfo{MolEndTag}", $CmpdString;
+  if (IsNotEmpty($MolString)) {
+    $AppletBGColor = SetupStructureBGColor($RowNum);
+    $MolString .= "$SDFilesInfo{MolEndTag}";
+
+    # JME viewer doesn't appear to support "bgcolor" param. So, always use white background for
+    # structure cell...
+    $AppletName = "JME" . $CmpdNum;
+    $OptionsInfo{StrViewerParams}{name} = $AppletName;
+    if (!$OptionsInfo{SettingUpCmpdSummaryPage}) {
+      if (!$OptionsInfo{StrBgColorSpecified}) {
+	$OptionsInfo{StrViewerParams}{bgcolor} = $AppletBGColor;
+      }
+    }
+    $StrViewerCodeBase = ($TableNum == 1) ? $OptionsInfo{TopHTMLDirStrViewerCodeBase} : $OptionsInfo{SubHTMLDirStrViewerCodeBase};
+    $Value = SetupStrViewerJMEApplet($MolString, $StrViewerCodeBase, \%{$OptionsInfo{StrViewerParams}});
+    $ValueTag = SetupHTMLTableRowDataValue($Value, $SDFilesInfo{White});
+  }
+  else {
+    $ValueTag = SetupHTMLTableRowDataValue($Value);
+  }
+  if ($OptionsInfo{SettingUpCmpdSummaryPage}) {
+    $ValueTag = InsertHTMLTags($ValueTag, ("class", "box"));
+  }
+  print $HTMLFileRef $ValueTag;
+}
+
+# Setup Marvin display...
+sub SetupMarvinDisplay {
+  my($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef) = @_;
+  my($MolString, $AppletBGColor, $Value, $ValueTag, $AppletName, $StrViewerCodeBase);
+
+  $Value = "";
+  ($MolString) = split "$SDFilesInfo{MolEndTag}", $CmpdString;
+  if (IsNotEmpty($MolString)) {
+    $AppletBGColor = SetupStructureBGColor($RowNum);
+    $MolString .= "$SDFilesInfo{MolEndTag}";
+
+    $AppletName = "MView" . $CmpdNum;
+    $OptionsInfo{StrViewerParams}{name} = $AppletName;
+    if (!$OptionsInfo{SettingUpCmpdSummaryPage}) {
+      if (!$OptionsInfo{StrBgColorSpecified}) {
+	$OptionsInfo{StrViewerParams}{bgcolor} = $AppletBGColor;
+      }
+    }
+    $StrViewerCodeBase = ($TableNum == 1) ? $OptionsInfo{TopHTMLDirStrViewerCodeBase} : $OptionsInfo{SubHTMLDirStrViewerCodeBase};
+    $Value = SetupStrViewerMarvinViewApplet($MolString, $StrViewerCodeBase, \%{$OptionsInfo{StrViewerParams}});
+    $ValueTag = SetupHTMLTableRowDataValue($Value);
+  }
+  else {
+    $ValueTag = SetupHTMLTableRowDataValue($Value);
+  }
+  if ($OptionsInfo{SettingUpCmpdSummaryPage}) {
+    $ValueTag = InsertHTMLTags($ValueTag, ("class", "box"));
+  }
+  print $HTMLFileRef $ValueTag;
+}
+
+# Setup Jmol display...
+sub SetupJmolDisplay {
+  my($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef) = @_;
+  my($MolString, $AppletBGColor, $Value, $ValueTag, $AppletName, $StrViewerCodeBase);
+
+  $Value = ""; $ValueTag = "";
+  ($MolString) = split "$SDFilesInfo{MolEndTag}", $CmpdString;
+  if (IsNotEmpty($MolString)) {
+    $AppletBGColor = SetupStructureBGColor($RowNum);
+    $MolString .= "$SDFilesInfo{MolEndTag}";
+
+    # Make sure MolName line is not empty; otherwise, JMol doesn't display structure...
+    my(@MolLines) = split "\n", $MolString;
+    if (IsEmpty($MolLines[0])) {
+      $MolLines[0] = "Cmpd${CmpdNum}";
+      $MolString = join "\n", @MolLines;
+    }
+
+    # Setup the applet...
+    $AppletName = "Jmol" . $CmpdNum;
+    $OptionsInfo{StrViewerParams}{name} = $AppletName;
+    if (!$OptionsInfo{SettingUpCmpdSummaryPage}) {
+      if (!$OptionsInfo{StrBgColorSpecified}) {
+	$OptionsInfo{StrViewerParams}{bgcolor} = $AppletBGColor;
+      }
+    }
+    $StrViewerCodeBase = ($TableNum == 1) ? $OptionsInfo{TopHTMLDirStrViewerCodeBase} : $OptionsInfo{SubHTMLDirStrViewerCodeBase};
+    $Value = SetupStrViewerJmolApplet($MolString, $StrViewerCodeBase, \%{$OptionsInfo{StrViewerParams}});
+    $ValueTag = SetupHTMLTableRowDataValue($Value);
+  }
+  else {
+    $ValueTag = SetupHTMLTableRowDataValue($Value);
+  }
+  if ($OptionsInfo{SettingUpCmpdSummaryPage}) {
+    $ValueTag = InsertHTMLTags($ValueTag, ("class", "box"));
+  }
+  print $HTMLFileRef $ValueTag;
+}
+
+# Setup Chime display...
+sub SetupChimeDisplay {
+  my($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef) = @_;
+  my($MolString, $BGColor, $Value, $ValueTag, $MolFileRef);
+
+  $Value = "";
+  ($MolString) = split "$SDFilesInfo{MolEndTag}", $CmpdString;
+  if (IsNotEmpty($MolString)) {
+    $BGColor = SetupStructureBGColor($RowNum);
+    $MolString .= "$SDFilesInfo{MolEndTag}";
+    # Write out MOL file...
+    $MolFileRef = SetupMOLFile($Index, $TableNum, $MolString, $CmpdNum);
+    # Setup the applet...
+    if (!$OptionsInfo{SettingUpCmpdSummaryPage}) {
+      if (!$OptionsInfo{StrBgColorSpecified}) {
+	$OptionsInfo{StrViewerParams}{bgcolor} = $BGColor;
+      }
+    }
+    $Value = SetupStrViewerChimePlugIn($MolFileRef, \%{$OptionsInfo{StrViewerParams}});
+    $ValueTag = SetupHTMLTableRowDataValue($Value);
+  }
+  else {
+    $ValueTag = SetupHTMLTableRowDataValue($Value);
+  }
+  if ($OptionsInfo{SettingUpCmpdSummaryPage}) {
+    $ValueTag = InsertHTMLTags($ValueTag, ("class", "box"));
+  }
+  print $HTMLFileRef $ValueTag;
+}
+
+# Setup displays for various viewers available from CambridgeSoft...
+sub SetupCambridgeSoftDisplay {
+  my($ViewerType, $Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef) = @_;
+  my($MolString, $BGColor, $Value, $ValueTag, $MolFileRef, $Name);
+
+  $Value = "";
+  ($MolString) = split "$SDFilesInfo{MolEndTag}", $CmpdString;
+  if (IsNotEmpty($MolString)) {
+    $BGColor = SetupStructureBGColor($RowNum);
+    $MolString .= "$SDFilesInfo{MolEndTag}";
+    # Write out MOL file...
+    $MolFileRef = SetupMOLFile($Index, $TableNum, $MolString, $CmpdNum);
+    # Setup the viewer...
+    $Name = "CS" . $CmpdNum;
+    if ($ViewerType =~ /^Chem3DActiveX$/) {
+      # Use white background for Chem3D and cell; otherwise, it doesn't look good:
+      # cell size is larger than Chem3D window size and different colors don't work
+      $BGColor = $SDFilesInfo{White};
+      $OptionsInfo{StrViewerParams}{name} = $Name;
+      if (!$OptionsInfo{SettingUpCmpdSummaryPage}) {
+	if (!$OptionsInfo{StrBgColorSpecified}) {
+	  $OptionsInfo{StrViewerParams}{bgcolor} = $BGColor;
+	}
+      }
+      $Value = SetupStrViewerChem3DActiveX($MolFileRef, \%{$OptionsInfo{StrViewerParams}});
+      $ValueTag = SetupHTMLTableRowDataValue($Value, $BGColor);
+    }
+    elsif ($ViewerType =~ /^ChemDrawActiveX$/i) {
+      # BGColor is not supported. So, make it all white...
+      $BGColor = $SDFilesInfo{White};
+      $OptionsInfo{StrViewerParams}{name} = $Name;
+      if (!$OptionsInfo{SettingUpCmpdSummaryPage}) {
+	if (!$OptionsInfo{StrBgColorSpecified}) {
+	  $OptionsInfo{StrViewerParams}{bgcolor} = $BGColor;
+	}
+      }
+      $Value = SetupStrViewerChemDrawActiveX($MolFileRef, \%{$OptionsInfo{StrViewerParams}});
+      $ValueTag = SetupHTMLTableRowDataValue($Value, $BGColor);
+    }
+    elsif ($ViewerType =~ /^ChemDrawPlugIn$/i) {
+      # BGColor is not supported. So, make it all white...
+      $BGColor = $SDFilesInfo{White};
+      if (!$OptionsInfo{SettingUpCmpdSummaryPage}) {
+	if (!$OptionsInfo{StrBgColorSpecified}) {
+	  $OptionsInfo{StrViewerParams}{bgcolor} = $BGColor;
+	}
+      }
+      $Value = SetupStrViewerChemDrawPlugIn($MolFileRef, \%{$OptionsInfo{StrViewerParams}});
+      $ValueTag = SetupHTMLTableRowDataValue($Value, $BGColor);
+    }
+  }
+  else {
+    $ValueTag = SetupHTMLTableRowDataValue($Value);
+  }
+  if ($OptionsInfo{SettingUpCmpdSummaryPage}) {
+    $ValueTag = InsertHTMLTags($ValueTag, ("class", "box"));
+  }
+  print $HTMLFileRef $ValueTag;
+}
+
+# Setup Accelrys Viewer ActiveX display...
+sub SetupViewerAccelrysActiveXDisplay {
+  my($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef) = @_;
+  my($MolString, $BGColor, $Value, $ValueTag, $Name, $MolFileRef);
+
+  $Value = "";
+  ($MolString) = split "$SDFilesInfo{MolEndTag}", $CmpdString;
+  if (IsNotEmpty($MolString)) {
+    $BGColor = SetupStructureBGColor($RowNum);
+    $MolString .= "$SDFilesInfo{MolEndTag}";
+    # Write out MOL file. Accelrys ActiveX viewer doesn't load mol files with relative path names.
+    # So, set up a complete path name for now; however, it may lead to issues during web
+    # deployment.
+    my($CompletePath) = 1;
+    $MolFileRef = SetupMOLFile($Index, $TableNum, $MolString, $CmpdNum, $CompletePath);
+    # Setup the viewer...
+    $Name = "ViewerActiveX" . $CmpdNum;
+    if (!$OptionsInfo{SettingUpCmpdSummaryPage}) {
+      if (!$OptionsInfo{StrBgColorSpecified}) {
+	$OptionsInfo{StrViewerParams}{bgcolor} = $BGColor;
+      }
+    }
+    $OptionsInfo{StrViewerParams}{name} = $Name;
+    $Value = SetupStrViewerAccelrysActiveX($MolFileRef, \%{$OptionsInfo{StrViewerParams}});
+    $ValueTag = SetupHTMLTableRowDataValue($Value);
+  }
+  else {
+    $ValueTag = SetupHTMLTableRowDataValue($Value);
+  }
+  if ($OptionsInfo{SettingUpCmpdSummaryPage}) {
+    $ValueTag = InsertHTMLTags($ValueTag, ("class", "box"));
+  }
+  print $HTMLFileRef $ValueTag;
+}
+
+
+# Setup structure background color...
+sub SetupStructureBGColor {
+  my($RowNum) = @_;
+  my($BGColor);
+
+  $BGColor = "";
+  if ($OptionsInfo{ShadeRowsStatus}) {
+    $BGColor =  ($RowNum % 2) ? $OptionsInfo{OddRowsShadeColor} : $OptionsInfo{EvenRowsShadeColor};
+  }
+  else {
+    $BGColor = $SDFilesInfo{White};
+  }
+  return $BGColor;
+}
+
+# Setup  MDL MOL file...
+sub SetupMOLFile {
+  my($Index, $TableNum, $MolString, $CmpdNum, $CompletePath);
+  my($SubMolDir, $MolFileName, $MolFile, $MolFileRef);
+
+  $CompletePath = "";
+  if (@_ == 5) {
+    ($Index, $TableNum, $MolString, $CmpdNum, $CompletePath) = @_;
+  }
+  else {
+    ($Index, $TableNum, $MolString, $CmpdNum) = @_;
+  }
+
+  $SubMolDir = $SDFilesInfo{SubMolDir}[$Index];
+  $MolFileName = $SDFilesInfo{HTMLRoot}[$Index] . "Cmpd" . $CmpdNum . ".mol";
+  $MolFile = $SubMolDir . "\/" . $MolFileName;
+
+  open MOLFILE, ">$MolFile" or die "Error: Can't open $MolFile: $! \n";
+  print MOLFILE "$MolString\n";
+  close MOLFILE;
+
+  if ($CompletePath) {
+    my($CWD, $NewCWD);
+    $CWD = cwd();
+    $NewCWD = ConvertCygwinPath($CWD);
+    $MolFileRef = $NewCWD . "\/" . $SDFilesInfo{TopHTMLDir}[$Index] .  "\/mol\/$MolFileName" ;
+  }
+  else {
+    $MolFileRef = ($TableNum == 1) ? ".\/mol\/$MolFileName" : "..\/mol\/$MolFileName";
+  }
+
+  return $MolFileRef;
+}
+
+# Setup a link to structure and other available information...
+sub SetupStructureLink {
+  my($Index, $TableNum, $RowNum, $CmpdString, $CmpdNum, $HTMLFileRef) = @_;
+  my($CmpdHTMLFileRef, $Value);
+
+  $CmpdHTMLFileRef = SetupCompoundSummaryFileAndLink($Index, $TableNum, $CmpdString, $CmpdNum);
+
+  if ($Options{strlinktype} =~ /^button$/i) {
+    $Value = SetupHTMLButtonRef("View", $CmpdHTMLFileRef);
+  }
+  else {
+    $Value = SetupHTMLHRef("View", $CmpdHTMLFileRef);
+  }
+  print $HTMLFileRef SetupHTMLTableRowDataValue($Value);
+}
+
+# Setup HTML compound summary file and link...
+sub SetupCompoundSummaryFileAndLink {
+  my($Index, $TableNum, $CmpdString, $CmpdNum) = @_;
+  my($CmpdHTMLFile, $CmpdHTMLFileName, $CmpdHTMLFileRef, $CSSRef, @CmpdLines, $Label, @DataFieldLabels, %DataFieldValues, $Value, $Tag);
+
+  # Setup compound file names...
+  $CmpdHTMLFileName = $SDFilesInfo{HTMLRoot}[$Index] . "Cmpd" . $CmpdNum . ".html";
+  $CmpdHTMLFile = $SDFilesInfo{SubHTMLDir}[$Index] . "\/" . $CmpdHTMLFileName;
+
+  # Setup stylesheet reference....
+  $CSSRef = "";
+  if ($Options{stylesheet} =~ /^old$/i) {
+    $CSSRef = $Options{stylesheetname};
+  }
+  else {
+    $CSSRef = "..\/" . $SDFilesInfo{HTMLRoot}[$Index] . ".css";
+  }
+
+  # Write out compound data in a new HTML file. For summary page, usage of even and odd row shade color
+  # is reversed: it causes structure background to be white by default...
+  open CMPDHTMLFILE, ">$CmpdHTMLFile" or die "Error: Can't open $CmpdHTMLFile: $! \n";
+  print CMPDHTMLFILE SetupHTMLPageHeader($OptionsInfo{StrLinkTitle}, $CSSRef, $OptionsInfo{SubHTMLDirStrViewerJSFileRef});
+
+  if ($OptionsInfo{StrViewerJSFileRef}) {
+    print CMPDHTMLFILE SetupStrViewerJSInitCmd($OptionsInfo{StrViewerType}, $OptionsInfo{SubHTMLDirStrViewerCodeBase});
+  }
+
+  if ($OptionsInfo{StrLinkTitleDisplay}) {
+    print CMPDHTMLFILE SetupHTMLPageTitle($OptionsInfo{StrLinkTitle}, "center");
+  }
+  else {
+    print CMPDHTMLFILE SetupHTMLEmptyLines(1);
+  }
+  print CMPDHTMLFILE SetupHTMLAlignmentBegin("center");
+
+  # Setup structure display ...
+  print CMPDHTMLFILE SetupHTMLTableHeader(0, 5, 2);
+
+  print CMPDHTMLFILE SetupHTMLTableRowHeader("center", "#ffffff", "middle");
+
+  SetupStructureDisplayForCmpdSummaryPage($Index, $CmpdString, $CmpdNum, \*CMPDHTMLFILE);
+  print CMPDHTMLFILE $SDFilesInfo{RowEndTags};
+
+  if ($Options{strlinkmode} =~ /^plain$/i) {
+    print CMPDHTMLFILE SetupHTMLTableRowHeader("center", $OptionsInfo{StrLinkShadeColor});
+    $Tag = SetupHTMLTableRowDataValue("");
+    print CMPDHTMLFILE $Tag;
+    print CMPDHTMLFILE $SDFilesInfo{RowEndTags};
+  }
+
+  print CMPDHTMLFILE SetupHTMLTableRowHeader("left", "", "middle");
+  # Start a new table with two columns, one each for data field labels and values, in
+  # current column...
+  print CMPDHTMLFILE SetupHTMLTableColumnHeader();
+  print CMPDHTMLFILE SetupHTMLAlignmentBegin("left");
+  print CMPDHTMLFILE SetupHTMLTableHeader(0, 5, 2);
+
+  # Setup table for other available data...
+  my($CmpdRowHeaderTags);
+  $CmpdRowHeaderTags = SetupHTMLTableRowHeader("left", "", "middle");
+
+  @CmpdLines = split "\n", $CmpdString;
+
+  @DataFieldLabels = GetCmpdDataHeaderLabels(\@CmpdLines);
+  %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
+
+  my($LabelWrapLength, $ValueWrapLength, $LabelColWidth);
+  $LabelWrapLength = 30; $ValueWrapLength = 60; $LabelColWidth = 40;
+
+  for $Label (@DataFieldLabels) {
+    $Value =  $DataFieldValues{$Label};
+    $Label .= ":";
+    if ($Label && (length($Label) > $LabelWrapLength)) {
+      $Label = WrapText($Label,  $LabelWrapLength, "<br>");
+    }
+    print CMPDHTMLFILE $CmpdRowHeaderTags;
+    if ($Options{strlinkmode} =~ /^plain$/i) {
+      $Tag = SetupHTMLTableRowDataValue($Label, "", "", 1);
+    }
+    else {
+      $Tag = SetupHTMLTableRowDataValue($Label, $OptionsInfo{StrLinkShadeColor});
+    }
+    $Tag = InsertHTMLTags($Tag, "width", "$LabelColWidth");
+    print CMPDHTMLFILE $Tag;
+
+    if ($Value && (length($Value) >=$ValueWrapLength) && $Value !~ /a href/i) {
+      $Value =~ s/(\r\n)|(\r)|\n//g;
+      $Value = WrapText($Value,  $ValueWrapLength, "<br>");
+    }
+    $Tag = SetupHTMLTableRowDataValue($Value);
+    print CMPDHTMLFILE $Tag;
+    print CMPDHTMLFILE $SDFilesInfo{RowEndTags};
+  }
+
+  # Finish up table holding numerical data...
+  print CMPDHTMLFILE SetupHTMLTableEnd();
+  print CMPDHTMLFILE SetupHTMLAlignmentEnd("left");
+  print CMPDHTMLFILE SetupHTMLTableColumnEnd();
+  print CMPDHTMLFILE $SDFilesInfo{RowEndTags};
+
+  # Finish up main table...
+  print CMPDHTMLFILE SetupHTMLTableEnd();
+  print CMPDHTMLFILE SetupHTMLAlignmentEnd("center");
+
+  if ($OptionsInfo{StrLinkNavigation} && ($SDFilesInfo{CmpdCount}[$Index] > 1) ) {
+    print CMPDHTMLFILE SetupHTMLEmptyLines(1);
+    WriteCompoundSummaryNavigationLinks($Index, $TableNum, $CmpdNum, \*CMPDHTMLFILE);
+  }
+
+  print CMPDHTMLFILE SetupHTMLPageEnd($OptionsInfo{FooterMsg});
+  close CMPDHTMLFILE;
+
+  # Add a link to compound's HTML file in table cell...
+  $CmpdHTMLFileRef = ($TableNum == 1) ? ".\/html\/" : ".\/";
+  $CmpdHTMLFileRef .= $CmpdHTMLFileName;
+
+  return $CmpdHTMLFileRef;
+}
+
+# Write navigation link information for compound summary page...
+sub WriteCompoundSummaryNavigationLinks {
+  my($Index, $CurTableNum, $CurCmpdNum, $CmpdHTMLFileRef) = @_;
+  my($FirstTableNum, $CurTableIndex, $FirstCmpdNum, $LastCmpdNum, $PreviousCmpdNum, $NextCmpdNum, $HTMLFile, $HTMLRefFile, $HTMLRefValue);
+
+  $FirstTableNum = 1;
+  $FirstCmpdNum = 1;
+
+  $CurTableIndex = $CurTableNum - 1;
+
+  if ($SDFilesInfo{MultipleHTMLTables}[$Index]) {
+    my($FirstTableIndex, $LastTableNum, $LastTableIndex);
+    $FirstTableIndex = $FirstTableNum - 1;
+    $LastTableNum = $SDFilesInfo{TableCount}[$Index]; $LastTableIndex = $LastTableNum - 1;
+    $LastCmpdNum = ${$SDFilesInfo{TableEndCmpdNum}[$Index]}[$LastTableIndex];
+  }
+  else {
+    $LastCmpdNum = $SDFilesInfo{CmpdCount}[$Index];
+  }
+
+  $PreviousCmpdNum = ($CurCmpdNum == $FirstCmpdNum) ? 0 : ($CurCmpdNum - 1);
+  $NextCmpdNum = ($CurCmpdNum == $LastCmpdNum) ? 0 : ($CurCmpdNum + 1);
+
+  my($InactiveLinkNumColor, $InactiveLinkFontBold) = ("#8e2323", "1");
+  my($LinkTextColor, $LinkBGColor, $LinkFontBold) = ("", "", "0");
+  my($BorderWidth, $CellPadding, $CellSpacing) = (0, 2, 2);
+
+  # Start link table...
+  print $CmpdHTMLFileRef SetupHTMLAlignmentBegin("center");
+  print $CmpdHTMLFileRef SetupHTMLDivBegin("tablenav");
+  print $CmpdHTMLFileRef  SetupHTMLTableHeader($BorderWidth, $CellPadding, $CellSpacing);
+  print $CmpdHTMLFileRef $SDFilesInfo{RowHeaderTags};
+
+  print $CmpdHTMLFileRef SetupHTMLTableRowDataValue("Compounds: ");
+
+  # Setup a link to first compound...
+  if ($CurCmpdNum != $FirstCmpdNum) {
+    $HTMLFile = $SDFilesInfo{HTMLRoot}[$Index] . "Cmpd" . $FirstCmpdNum . ".html";
+    $HTMLRefFile = "./${HTMLFile}";
+    $HTMLRefValue = SetupHTMLHRef("First", $HTMLRefFile, "First Compound");
+    print $CmpdHTMLFileRef SetupHTMLTableRowDataValue($HTMLRefValue, $LinkBGColor, $LinkTextColor, $LinkFontBold);
+  }
+
+  # Setup a link to previous compund
+  if ($PreviousCmpdNum) {
+    $HTMLFile = $SDFilesInfo{HTMLRoot}[$Index] . "Cmpd" . $PreviousCmpdNum . ".html";
+    $HTMLRefFile = "./${HTMLFile}";
+    $HTMLRefValue = SetupHTMLHRef("Previous", $HTMLRefFile, "Previous Compound");
+    print $CmpdHTMLFileRef SetupHTMLTableRowDataValue($HTMLRefValue, $LinkBGColor, $LinkTextColor, $LinkFontBold);
+  }
+
+  # Setup a link to compound table...
+  if ($SDFilesInfo{MultipleHTMLTables}[$Index]) {
+    $HTMLFile = ${$SDFilesInfo{TableHTMLFiles}[$Index]}[$CurTableIndex];
+  }
+  else {
+    $HTMLFile = $SDFilesInfo{HTMLRoot}[$Index] . ".html";
+  }
+  $HTMLRefFile = (($CurTableNum == $FirstTableNum) ? "../" : "./") . $HTMLFile;
+  $HTMLRefValue = SetupHTMLHRef("Table", $HTMLRefFile, "Table With This Compound");
+  print $CmpdHTMLFileRef SetupHTMLTableRowDataValue($HTMLRefValue, $LinkBGColor, $LinkTextColor, $LinkFontBold);
+
+  # Setup a link to next compound...
+  if ($NextCmpdNum) {
+    $HTMLFile = $SDFilesInfo{HTMLRoot}[$Index] . "Cmpd" . $NextCmpdNum . ".html";
+    $HTMLRefFile = "./${HTMLFile}";
+    $HTMLRefValue = SetupHTMLHRef("Next", $HTMLRefFile, "Next Compound");
+    print $CmpdHTMLFileRef SetupHTMLTableRowDataValue($HTMLRefValue, $LinkBGColor, $LinkTextColor, $LinkFontBold);
+  }
+
+  # Setup a link to last compund
+  if ($CurCmpdNum != $LastCmpdNum) {
+    $HTMLFile = $SDFilesInfo{HTMLRoot}[$Index] . "Cmpd" . $LastCmpdNum . ".html";
+    $HTMLRefFile = "./${HTMLFile}";
+    $HTMLRefValue = SetupHTMLHRef("Last", $HTMLRefFile, "Last Compound");
+    print $CmpdHTMLFileRef SetupHTMLTableRowDataValue($HTMLRefValue, $LinkBGColor, $LinkTextColor, $LinkFontBold);
+  }
+
+  # Setup current table info text....
+  print $CmpdHTMLFileRef SetupHTMLTableRowDataValue("&nbsp");
+  print $CmpdHTMLFileRef SetupHTMLTableRowDataValue("&nbsp");
+  print $CmpdHTMLFileRef SetupHTMLTableRowDataValue("Showing $CurCmpdNum of $LastCmpdNum");
+
+  print $CmpdHTMLFileRef $SDFilesInfo{RowEndTags};
+
+  # End link table...
+  print $CmpdHTMLFileRef SetupHTMLTableEnd();
+  print $CmpdHTMLFileRef SetupHTMLDivEnd();
+  print $CmpdHTMLFileRef SetupHTMLAlignmentEnd("center");
+}
+
+# Setup navigation link information for each table.
+#
+# All table sets besides first and last have these links: FirstTable, Previous, Current-1,Current,Current+1,  Next, and LastTable
+# First set: Current, Next, and LastTable
+# Last set: FirstTable, Previous and Current.
+#
+sub WriteNavigationLinks {
+  my($Index, $CurTableNum, $HTMLFileRef) = @_;
+  my($TableNum, $StartTableNum, $EndTableNum, $TableIndex, $BorderWidth, $CellPadding, $CellSpacing,$HTMLFile, $HTMLRefFile, $RelativeFileDir, $HTMLRefValue, $FirstTableNum, $FirstTableIndex, $LastTableNum, $LastTableIndex, $TableStartCmpdNum, $TableEndCmpdNum, $LastCmpdNum, $BGColor, $LinksOffSet);
+
+  $LinksOffSet = 10;
+
+  $FirstTableNum = 1; $FirstTableIndex = $FirstTableNum - 1;
+  $LastTableNum = $SDFilesInfo{TableCount}[$Index]; $LastTableIndex = $LastTableNum - 1;
+  $LastCmpdNum = ${$SDFilesInfo{TableEndCmpdNum}[$Index]}[$LastTableIndex];
+
+  # Figure out which links to display for a particular table...
+  $StartTableNum = $CurTableNum - $LinksOffSet + 1;
+  $StartTableNum = ($StartTableNum < $FirstTableNum) ? $FirstTableNum : $StartTableNum;
+  if ($CurTableNum < $LinksOffSet) {
+    $EndTableNum = $LinksOffSet;
+  }
+  else {
+    $EndTableNum = $CurTableNum + $LinksOffSet - 1;
+  }
+  $EndTableNum = ($EndTableNum > $LastTableNum) ? $LastTableNum : $EndTableNum;
+
+  my($InactiveLinkNumColor, $InactiveLinkFontBold) = ("#8e2323", "1");
+  my($LinkTextColor, $LinkBGColor, $LinkFontBold) = ("", "", "1");
+
+  # Start link table...
+  $BorderWidth = 0; $CellPadding = 2; $CellSpacing = 2;
+  print $HTMLFileRef SetupHTMLAlignmentBegin("center");
+  print $HTMLFileRef SetupHTMLDivBegin("tablenav");
+  print $HTMLFileRef  SetupHTMLTableHeader($BorderWidth, $CellPadding, $CellSpacing);
+  print $HTMLFileRef $SDFilesInfo{RowHeaderTags};
+
+  if ($OptionsInfo{NavLinksTableInfo} && $OptionsInfo{NavLinksCmpdInfo}) {
+    print $HTMLFileRef SetupHTMLTableRowDataValue("Showing table $CurTableNum of $LastTableNum");
+    print $HTMLFileRef SetupHTMLTableRowDataValue("&nbsp");
+    print $HTMLFileRef SetupHTMLTableRowDataValue("&nbsp");
+  }
+
+  print $HTMLFileRef SetupHTMLTableRowDataValue("Tables: ");
+  # Setup a link to first table...
+  if ($StartTableNum != $FirstTableNum) {
+    $HTMLFile = ${$SDFilesInfo{TableHTMLFiles}[$Index]}[$FirstTableIndex];
+    $HTMLRefFile = GetRelativeFileDir($CurTableNum, $FirstTableNum, $FirstTableNum) . $HTMLFile;
+    $TableStartCmpdNum = ${$SDFilesInfo{TableStartCmpdNum}[$Index]}[$FirstTableIndex];
+    $TableEndCmpdNum = ${$SDFilesInfo{TableEndCmpdNum}[$Index]}[$FirstTableIndex];
+    $HTMLRefValue = SetupHTMLHRef("First", $HTMLRefFile, "First Table Containing Compounds $TableStartCmpdNum To $TableEndCmpdNum");
+    print $HTMLFileRef SetupHTMLTableRowDataValue($HTMLRefValue, $LinkBGColor, $LinkTextColor, $LinkFontBold);
+  }
+
+  # Setup link to previous table...
+  if ($CurTableNum != $FirstTableNum) {
+    my($PreviousTableNum, $PreviousTableIndex);
+    $PreviousTableNum = $CurTableNum - 1; $PreviousTableIndex = $PreviousTableNum - 1;
+    $HTMLFile = ${$SDFilesInfo{TableHTMLFiles}[$Index]}[$PreviousTableIndex];
+    $HTMLRefFile = GetRelativeFileDir($CurTableNum, $PreviousTableNum, $FirstTableNum) . $HTMLFile;
+    $TableStartCmpdNum = ${$SDFilesInfo{TableStartCmpdNum}[$Index]}[$PreviousTableIndex];
+    $TableEndCmpdNum = ${$SDFilesInfo{TableEndCmpdNum}[$Index]}[$PreviousTableIndex];
+    $HTMLRefValue = SetupHTMLHRef("Previous", $HTMLRefFile, "Previous Table Containing Compounds $TableStartCmpdNum To $TableEndCmpdNum");
+    print $HTMLFileRef SetupHTMLTableRowDataValue($HTMLRefValue, $LinkBGColor, $LinkTextColor, $LinkFontBold);
+  }
+
+  for $TableNum ($StartTableNum .. $EndTableNum) {
+    $TableIndex = $TableNum - 1;
+    $HTMLFile = ${$SDFilesInfo{TableHTMLFiles}[$Index]}[$TableIndex];
+    if ($TableNum == $CurTableNum) {
+      print $HTMLFileRef SetupHTMLTableRowDataValue($TableNum, $LinkBGColor, $InactiveLinkNumColor, $InactiveLinkFontBold);
+    }
+    else {
+      # Setup the link...
+      my($RefTitle);
+      $TableStartCmpdNum = ${$SDFilesInfo{TableStartCmpdNum}[$Index]}[$TableIndex];
+      $TableEndCmpdNum = ${$SDFilesInfo{TableEndCmpdNum}[$Index]}[$TableIndex];
+      $RefTitle = AddNumberSuffix($TableNum) . " Table Containing Compounds $TableStartCmpdNum To $TableEndCmpdNum";
+      $HTMLRefFile = GetRelativeFileDir($CurTableNum, $TableNum, $FirstTableNum) . $HTMLFile;
+      $HTMLRefValue = SetupHTMLHRef($TableNum, $HTMLRefFile, $RefTitle);
+      print $HTMLFileRef SetupHTMLTableRowDataValue($HTMLRefValue);
+    }
+  }
+
+  # Setup link to next table...
+  if ($CurTableNum != $LastTableNum) {
+    my($NextTableNum, $NextTableIndex);
+    $NextTableNum = $CurTableNum + 1; $NextTableIndex = $NextTableNum - 1;
+    $HTMLFile = ${$SDFilesInfo{TableHTMLFiles}[$Index]}[$NextTableIndex];
+    $HTMLRefFile = GetRelativeFileDir($CurTableNum, $NextTableNum, $FirstTableNum) . $HTMLFile;
+    $TableStartCmpdNum = ${$SDFilesInfo{TableStartCmpdNum}[$Index]}[$NextTableIndex];
+    $TableEndCmpdNum = ${$SDFilesInfo{TableEndCmpdNum}[$Index]}[$NextTableIndex];
+    $HTMLRefValue = SetupHTMLHRef("Next", $HTMLRefFile, "Next Table Containing Compounds $TableStartCmpdNum To $TableEndCmpdNum");
+    print $HTMLFileRef SetupHTMLTableRowDataValue($HTMLRefValue, $LinkBGColor, $LinkTextColor, $LinkFontBold);
+  }
+
+  # Setup link to last table...
+  if ($EndTableNum != $LastTableNum) {
+    $HTMLFile = ${$SDFilesInfo{TableHTMLFiles}[$Index]}[$LastTableIndex];
+    $HTMLRefFile = GetRelativeFileDir($CurTableNum, $LastTableNum, $FirstTableNum) . $HTMLFile;
+    $TableStartCmpdNum = ${$SDFilesInfo{TableStartCmpdNum}[$Index]}[$LastTableIndex];
+    $TableEndCmpdNum = ${$SDFilesInfo{TableEndCmpdNum}[$Index]}[$LastTableIndex];
+    $HTMLRefValue = SetupHTMLHRef("Last", $HTMLRefFile, "Last Table Containing Compounds $TableStartCmpdNum To $TableEndCmpdNum");
+    print $HTMLFileRef SetupHTMLTableRowDataValue($HTMLRefValue, $LinkBGColor, $LinkTextColor, $LinkFontBold);
+  }
+  # Setup current table info text....
+  print $HTMLFileRef SetupHTMLTableRowDataValue("&nbsp");
+  print $HTMLFileRef SetupHTMLTableRowDataValue("&nbsp");
+  $TableStartCmpdNum = ${$SDFilesInfo{TableStartCmpdNum}[$Index]}[$CurTableNum - 1];
+  $TableEndCmpdNum = ${$SDFilesInfo{TableEndCmpdNum}[$Index]}[$CurTableNum - 1];
+  if ($OptionsInfo{NavLinksCmpdInfo}) {
+    print $HTMLFileRef SetupHTMLTableRowDataValue("Showing compounds $TableStartCmpdNum to $TableEndCmpdNum of $LastCmpdNum");
+  }
+  else {
+    print $HTMLFileRef SetupHTMLTableRowDataValue("Showing table $CurTableNum of $LastTableNum");
+  }
+
+  print $HTMLFileRef $SDFilesInfo{RowEndTags};
+  # End link table...
+  print $HTMLFileRef SetupHTMLTableEnd();
+  print $HTMLFileRef SetupHTMLDivEnd();
+  print $HTMLFileRef SetupHTMLAlignmentEnd("center");
+}
+
+# Generate relative directory path...
+sub GetRelativeFileDir {
+  my($FromTableNum, $ToTableNum, $FirstTableNum) = @_;
+  my($RelativeFileDir) = "";
+
+  if ($FromTableNum == $FirstTableNum) {
+    $RelativeFileDir = ($ToTableNum == $FirstTableNum) ? ".\/" : ".\/html\/";
+  }
+  else {
+    $RelativeFileDir = ($ToTableNum == $FirstTableNum) ? "..\/" : ".\/";
+  }
+  return $RelativeFileDir;
+}
+
+# Based on hightlight stype, return appropriate colors for background or text...
+sub GetValueHighlightColors {
+  my($Label, $Value) = @_;
+  my($DataType, $Criterion, $CriterionValue, $BgColor, $FontColor, $ValueOk, $Nothing);
+
+  $BgColor = ""; $FontColor = "";
+  $DataType = $OptionsInfo{SpecifiedHighlightDataFieldTypesMap}{$Label};
+  $Criterion = $OptionsInfo{SpecifiedHighlightDataFieldCriteriaMap}{$Label};
+  $CriterionValue = $OptionsInfo{SpecifiedHighlightDataFieldValueMap}{$Label};
+
+  $ValueOk = 0;
+  if ($DataType =~ /^numeric$/i) {
+  NUMSWITCH: {
+      if ($Criterion =~ /^ge$/i) { $ValueOk = ($Value >= $CriterionValue) ? 1 : 0; last NUMSWITCH; }
+      if ($Criterion =~ /^le$/i) { $ValueOk = ($Value <= $CriterionValue) ? 1 : 0; last NUMSWITCH; }
+      if ($Criterion =~ /^eq$/i) { $ValueOk = ($Value == $CriterionValue) ? 1 : 0; last NUMSWITCH; }
+      $Nothing = 1;
+    }
+  }
+  else {
+  TEXTSWITCH: {
+      if ($Criterion =~ /^ge$/i) { $ValueOk = ($Value ge $CriterionValue) ? 1 : 0; last TEXTSWITCH; }
+      if ($Criterion =~ /^le$/i) { $ValueOk = ($Value le $CriterionValue) ? 1 : 0; last TEXTSWITCH; }
+      if ($Criterion =~ /^eq$/i) { $ValueOk = ($Value eq $CriterionValue) ? 1 : 0; last TEXTSWITCH; }
+      $Nothing = 1;
+    }
+  }
+  $BgColor = $ValueOk ? $OptionsInfo{ValueOkColor} : $OptionsInfo{ValueNotOkColor};
+  if ($Options{highlightstyle} =~ /^text$/i) {
+    $BgColor = "";
+    $FontColor = $ValueOk ? $OptionsInfo{ValueOkColor} : $OptionsInfo{ValueNotOkColor};
+  }
+  return ($BgColor, $FontColor);
+}
+
+#Make sure appropriate mode specific option values are specified...
+sub ProcessOptions {
+
+  %OptionsInfo = ();
+
+  $OptionsInfo{TitleDisplay} = ($Options{titledisplay} =~ /^yes$/i) ? 1 : 0;
+
+  $OptionsInfo{RowHAlignment} = "left"; $OptionsInfo{RowVAlignment} = "middle";
+  if (exists($Options{align})) {
+    my (@AlignValues) = split ",", $Options{align};
+    if (@AlignValues == 2) {
+      $OptionsInfo{RowHAlignment} = $AlignValues[0];
+      $OptionsInfo{RowVAlignment} = $AlignValues[1];
+    }
+    elsif (@AlignValues == 1) {
+      $OptionsInfo{RowHAlignment} = $AlignValues[0];
+    }
+    else {
+      die "Error: Invalid number of values, ", scalar(@AlignValues) , ", specified by \"-a --align\" option.\nIt must contain only one or two values.\n";
+    }
+    if ($OptionsInfo{RowHAlignment} !~ /^(left|center|right)$/i) {
+      die "Error: The horizontal alignment value specified, $Options{align}, for option \"-a --align\" is not valid. Allowed values: left, center, or right\n";
+    }
+    if ($OptionsInfo{RowVAlignment} !~ /^(top|middle|bottom)$/i) {
+      die "Error: The horizontal alignment value specified, $Options{align}, for option \"-a --align\" is not valid. Allowed values: top, middle, or bottom\n";
+    }
+  }
+
+  $OptionsInfo{TableHeaderRowHAlignment} = "center"; $OptionsInfo{TableHeaderRowVAlignment} = "middle";
+  if (exists($Options{headeralign})) {
+    my (@AlignValues) = split ",", $Options{headeralign};
+    if (@AlignValues == 2) {
+      $OptionsInfo{TableHeaderRowHAlignment} = $AlignValues[0];
+      $OptionsInfo{TableHeaderRowVAlignment} = $AlignValues[1];
+    }
+    elsif (@AlignValues == 1) {
+      $OptionsInfo{TableHeaderRowHAlignment} = $AlignValues[0];
+    }
+    else {
+      die "Error: Invalid number of values, ", scalar(@AlignValues) , ", specified by \"--headeralign\" option.\nIt must contain only one or two value.\n";
+    }
+    if ($OptionsInfo{TableHeaderRowHAlignment} !~ /^(left|center|right)$/i) {
+      die "Error: The horizontal alignment value specified, $Options{headeralign}, for option \"--headeralign\" is not valid. Allowed values: left, center, or right\n";
+    }
+    if ($OptionsInfo{TableHeaderRowVAlignment} !~ /^(top|middle|bottom)$/i) {
+      die "Error: The horizontal alignment value specified, $Options{headeralign}, for option \"-a --headeralign\" is not valid. Allowed values: top, middle, or bottom\n";
+    }
+  }
+
+  if (exists($Options{border})) {
+    $OptionsInfo{TableBorder} = $Options{border};
+  }
+  else {
+    $OptionsInfo{TableBorder} = ($Options{mode} =~ /^(plain|highlight)$/i) || $Options{mode} =~ /^structuresonly$/i ? 1 : 0;
+  }
+  $OptionsInfo{TableCellPadding} = $Options{cellpadding};
+  $OptionsInfo{TableCellSpacing} = $Options{cellspacing};
+  $OptionsInfo{FooterMsg} = $Options{footer} ? $Options{footer} : "";
+
+  if ($Options{headercolor}) {
+    $OptionsInfo{TableHeaderRowColor} = $Options{headercolor};
+  }
+  else {
+    $OptionsInfo{TableHeaderRowColor} = ($Options{mode} =~ /^plain$/i) ? "" : "#e0e9eb";
+  }
+
+  $OptionsInfo{NavLinksAtBottom} = 1; $OptionsInfo{NavLinksAtTop} = 0;
+  if ($Options{displaylinks} =~ /^(both|top)$/i) {
+    $OptionsInfo{NavLinksAtTop} = 1;
+  }
+  $OptionsInfo{NavLinksTableInfo} = 1; $OptionsInfo{NavLinksCmpdInfo} = 0;
+  if ($Options{displaylinksinfo} =~ /^both$/i) {
+    $OptionsInfo{NavLinksCmpdInfo} = 1;
+    $OptionsInfo{NavLinksTableInfo} = 1;
+  }
+  elsif ($Options{displaylinksinfo} =~ /^compound$/i) {
+    $OptionsInfo{NavLinksCmpdInfo} = 1;
+    $OptionsInfo{NavLinksTableInfo} = 0;
+  }
+
+  if ($Options{stylesheet} =~ /^old$/i ) {
+    if (!$Options{stylesheetname}) {
+      die "Error: No stylesheet name specified using \"--stylesheetname\" option: It is required for \"old\" value of \"-s --stylesheet\" option. \n";
+    }
+  }
+
+  my(@ColorValues);
+  $OptionsInfo{ShadeRowsStatus} = 0;
+  $OptionsInfo{OddRowsShadeColor} = "#ffffff";
+  $OptionsInfo{EvenRowsShadeColor} = "#e0e9eb";
+  if ($Options{shadecolor}) {
+    # Make sure only one value is specified...
+    @ColorValues = split ",", $Options{shadecolor};
+    if (@ColorValues == 2) {
+      $OptionsInfo{OddRowsShadeColor} = $ColorValues[0];
+      $OptionsInfo{EvenRowsShadeColor} = $ColorValues[1];
+    }
+    else {
+      die "Error: Invalid number of values, ", scalar(@ColorValues) , ", specified by \"--shadecolor\" option.\nIt must contain only two value.\n";
+    }
+  }
+  if ($Options{mode} =~ /^(shade|shadedhighlight|shadedstructuresonly)$/i) {
+    $OptionsInfo{ShadeRowsStatus} = 1;
+  }
+
+  $OptionsInfo{SettingUpCmpdSummaryPage} = 0;
+  $OptionsInfo{StrLinkShadeColor} = (exists $Options{strlinkshadecolor}) ? $Options{strlinkshadecolor} : "#e0e9eb";
+  $OptionsInfo{DisplayStructure} = ($Options{structure} =~ /^display$/i) ? 1 : 0;
+  $OptionsInfo{StrViewerType} = $Options{strviewertype};
+  $OptionsInfo{StrLinkNavigation} = ($Options{strlinknavigation} =~ /^yes$/i) ? 1 : 0;
+  $OptionsInfo{StrLinkTitleDisplay} = ($Options{strlinktitledisplay} =~ /^yes$/i) ? 1 : 0;
+  $OptionsInfo{StrLinkTitle} = (exists($Options{strlinktitle}) && length($Options{strlinktitle})) ? "$Options{strlinktitle}" : "Compound Summary";
+
+  my($StrViewerEmbedUsingJS) = (($Options{strviewerembed} =~ /^javascript$/i) && ($OptionsInfo{StrViewerType} =~ /^(Jmol|MarvinView|ChemDrawPlugIn|ChemDrawActiveX|Chem3DActiveX)$/i )) ? 1 : 0;
+
+  $OptionsInfo{StrTableRows} = 6; $OptionsInfo{StrTableCols} = 4;
+  if ($Options{strtablesize}) {
+    my(@StrTableSizeValues) = split ",", $Options{strtablesize};
+    if (@StrTableSizeValues == 2) {
+      $OptionsInfo{StrTableRows} = $StrTableSizeValues[0];
+      $OptionsInfo{StrTableCols} = $StrTableSizeValues[1];
+      if (!IsPositiveInteger($OptionsInfo{StrTableRows})) {
+	die "Error: The first value specified, $OptionsInfo{StrTableRows},  for option \"--strtablesize\" is not valid: Allowed integer values: > 0.\n";
+      }
+      if (!IsPositiveInteger($OptionsInfo{StrTableCols})) {
+	die "Error: The first value specified, $OptionsInfo{StrTableCols},  for option \"--strtablesize\" is not valid: Allowed integer values: > 0.\n";
+      }
+    }
+    else {
+      die "Error: Invalid number of values, ", scalar(@StrTableSizeValues), ", specified by \"--strtablesize\" option.\nIt must contain only two value for structuresonly \"-m --mode\" option.\n";
+    }
+  }
+
+  # Setup applet information...
+  $OptionsInfo{StrViewerCodeBase} = GetMayaChemToolsLibDirName() . "/Jmol";
+  $OptionsInfo{TopHTMLDirStrViewerCodeBase} = $OptionsInfo{StrViewerCodeBase};
+  $OptionsInfo{SubHTMLDirStrViewerCodeBase} = $OptionsInfo{StrViewerCodeBase};
+
+  my($StrViewerAppletArchive, $StrViewerAppletCode) = SetupDefaultAppletArchiveAndCode($OptionsInfo{StrViewerType});
+  if ($Options{strviewerconfig}) {
+    my(@StrViewerConfigParts) = split ",", $Options{strviewerconfig};
+    if (@StrViewerConfigParts >=1 && @StrViewerConfigParts <= 3) {
+      if (@StrViewerConfigParts == 3) {
+	$OptionsInfo{StrViewerCodeBase} = $StrViewerConfigParts[0];
+	$StrViewerAppletArchive = $StrViewerConfigParts[1];
+	$StrViewerAppletCode = $StrViewerConfigParts[2];
+      }
+      elsif (@StrViewerConfigParts == 2) {
+	$OptionsInfo{StrViewerCodeBase} = $StrViewerConfigParts[0];
+	$StrViewerAppletArchive = $StrViewerConfigParts[1];
+	my($AppletArchive, $AppletCode) = SetupDefaultAppletArchiveAndCode($OptionsInfo{StrViewerType});
+	$StrViewerAppletCode = $AppletCode;
+      }
+      else {
+	$OptionsInfo{StrViewerCodeBase} = $StrViewerConfigParts[0];
+	($StrViewerAppletArchive, $StrViewerAppletCode) = SetupDefaultAppletArchiveAndCode($OptionsInfo{StrViewerType});
+      }
+    }
+    else {
+      die "Error: Invalid number of values, ", scalar(@StrViewerConfigParts), ", specified by \"--strviewerconfig\" option.\nNumver of allowed values:1 to 3 \n";
+    }
+  }
+  else {
+    if ($OptionsInfo{StrViewerType} =~ /^(JME|MarvinView)$/i ) {
+      die "Error: No codebase specified using \"--strviewerconfig\" option for $OptionsInfo{StrViewerType} structure viewer\n";
+    }
+    if ($StrViewerEmbedUsingJS && $OptionsInfo{StrViewerType} !~ /^Jmol$/i) {
+      die "Error: No codebase specified using \"--strviewerconfig\" option for javascript value of \"--strviewerembed\" option for $OptionsInfo{StrViewerType} structure viewer \n";
+    }
+  }
+
+  if (-d $OptionsInfo{StrViewerCodeBase}) {
+    # Change local code base direcrory name to a relative directory name based on the
+    # current directory containing SD file; otherwise, Java applets and JavaScripts don't
+    # get loaded into Firefox and Chrome browsers.
+    #
+    # For top and sub HTML directories, add prefix "../" and "../../" to relative path...
+    $OptionsInfo{StrViewerCodeBase} = File::Spec->abs2rel($OptionsInfo{StrViewerCodeBase}, Cwd::cwd());
+
+    $OptionsInfo{TopHTMLDirStrViewerCodeBase} = "../" . $OptionsInfo{StrViewerCodeBase};
+    $OptionsInfo{SubHTMLDirStrViewerCodeBase} = "../../" . $OptionsInfo{StrViewerCodeBase};
+  }
+
+  # Setup structure viewer parameter information...
+  %{$OptionsInfo{StrViewerParams}} = ();
+  if ($Options{strviewerparams}) {
+    my(@ParamsSplit, @ParamPairSplit, $ParamPair);
+    #@ParamsSplit = split " ", $Options{strviewerparams};
+    @ParamsSplit = quotewords(" ", 0, $Options{strviewerparams});
+    for $ParamPair (@ParamsSplit) {
+      @ParamPairSplit = split "=", $ParamPair;
+      if (@ParamPairSplit == 2) {
+	$OptionsInfo{StrViewerParams}{$ParamPairSplit[0]} = $ParamPairSplit[1];
+      }
+      else {
+	die "Error: Invalid value, $ParamPair, specified by \"--strviewerparams\" option.\nValid values: name=value\n";
+      }
+    }
+  }
+
+  if ($OptionsInfo{StrViewerType} =~ /^(JME|Jmol|MarvinView)$/i ) {
+    $OptionsInfo{StrViewerParams}{name} = $StrViewerAppletCode;
+    $OptionsInfo{StrViewerParams}{archive} = $StrViewerAppletArchive;
+    $OptionsInfo{StrViewerParams}{code} = $StrViewerAppletCode;
+  }
+  $OptionsInfo{StrWidth} = exists($OptionsInfo{StrViewerParams}{width}) ? $OptionsInfo{StrViewerParams}{width} : 250;
+  $OptionsInfo{StrViewerParams}{width} = $OptionsInfo{StrWidth};
+  $OptionsInfo{StrHeight} = exists($OptionsInfo{StrViewerParams}{height}) ? $OptionsInfo{StrViewerParams}{height} : 170;
+  $OptionsInfo{StrViewerParams}{height} = $OptionsInfo{StrHeight};
+
+  $OptionsInfo{StrLinkWidth} = 500;
+  if (exists($OptionsInfo{StrViewerParams}{strlinkwidth})) {
+    $OptionsInfo{StrLinkWidth} = $OptionsInfo{StrViewerParams}{strlinkwidth};
+    $OptionsInfo{StrViewerParams}{strlinkwidth} = "";
+  }
+  $OptionsInfo{StrLinkHeight} = 295;
+  if (exists($OptionsInfo{StrViewerParams}{strlinkheight})) {
+    $OptionsInfo{StrLinkHeight} = $OptionsInfo{StrViewerParams}{strlinkheight};
+    $OptionsInfo{StrViewerParams}{strlinkheight} = "";
+  }
+
+  $OptionsInfo{StrBgColorSpecified} = "";
+  if (exists($OptionsInfo{StrViewerParams}{bgcolor})) {
+    $OptionsInfo{StrBgColorSpecified} = $OptionsInfo{StrViewerParams}{bgcolor};
+  }
+
+  $OptionsInfo{StrLinkBgColorSpecified} = "#ffffff";
+  if (exists($OptionsInfo{StrViewerParams}{strlinkbgcolor})) {
+    $OptionsInfo{StrLinkBgColorSpecified} = $OptionsInfo{StrViewerParams}{strlinkbgcolor};
+    $OptionsInfo{StrViewerParams}{strlinkbgcolor} = "";
+  }
+
+  # Setup Java Script usage...
+  $OptionsInfo{StrViewerJSFileRef} = "";
+  $OptionsInfo{TopHTMLDirStrViewerJSFileRef} = "";
+  $OptionsInfo{SubHTMLDirStrViewerJSFileRef} = "";
+
+  if ($StrViewerEmbedUsingJS) {
+    my ($StrViewerJSFileName) = "";
+    if ($Options{strviewerjsfile}) {
+      $StrViewerJSFileName = $Options{strviewerjsfile};
+    }
+    else {
+      if ($OptionsInfo{StrViewerType} =~ /^Jmol$/i) {
+	$StrViewerJSFileName = "Jmol.js";
+      }
+      elsif ($OptionsInfo{StrViewerType} =~ /^MarvinView$/i) {
+	$StrViewerJSFileName = "marvin.js";
+      }
+      elsif ($OptionsInfo{StrViewerType} =~ /^(ChemDrawPlugIn|ChemDrawActiveX)$/i) {
+	$StrViewerJSFileName = "chemdraw.js";
+      }
+      elsif ($OptionsInfo{StrViewerType} =~ /^Chem3DActiveX$/i) {
+	$StrViewerJSFileName = "chem3d.js";
+      }
+    }
+    if ($StrViewerJSFileName) {
+      $OptionsInfo{StrViewerParams}{usejavascript} = $StrViewerJSFileName;
+      $OptionsInfo{StrViewerJSFileRef} = "$OptionsInfo{StrViewerCodeBase}" . "\/" . "$StrViewerJSFileName";
+      $OptionsInfo{TopHTMLDirStrViewerJSFileRef} = "$OptionsInfo{TopHTMLDirStrViewerCodeBase}" . "\/" . "$StrViewerJSFileName";
+      $OptionsInfo{SubHTMLDirStrViewerJSFileRef} = "$OptionsInfo{SubHTMLDirStrViewerCodeBase}" . "\/" . "$StrViewerJSFileName";
+    }
+  }
+
+  # Check any other user specified parametrs applicable to all structure viewers...
+
+  $OptionsInfo{StructuresOnlyMode} = 0;
+  $OptionsInfo{MaxCmpdsPerTable} = ($Options{structure} =~ /^display$/i) ? 15 : 50;
+  if (exists $Options{numcmpds}) {
+    $OptionsInfo{MaxCmpdsPerTable} = $Options{numcmpds};
+  }
+  if ($Options{mode} =~ /^(structuresonly|shadedstructuresonly)$/i) {
+    $OptionsInfo{MaxCmpdsPerTable} = ($OptionsInfo{MaxCmpdsPerTable} > 0) ? ($OptionsInfo{StrTableRows} * $OptionsInfo{StrTableCols}) : 0;
+    $OptionsInfo{StructuresOnlyMode} = 1;
+  }
+  $OptionsInfo{CmpdDataField} = "";
+  $OptionsInfo{CmpdDataFieldLabel} = "no";
+  $OptionsInfo{CmpdDataFieldPosition} = "bottom";
+  $OptionsInfo{CmpdDataFieldAlignment} = "center";
+  if (exists($Options{cmpddatafield}) && length($Options{cmpddatafield})) {
+    my (@CmpdDataFieldValues) = split ",", $Options{cmpddatafield};
+    if (@CmpdDataFieldValues == 1) {
+      $OptionsInfo{CmpdDataField} = $CmpdDataFieldValues[0];
+    }
+    elsif (@CmpdDataFieldValues == 2) {
+      $OptionsInfo{CmpdDataField} = $CmpdDataFieldValues[0];
+      $OptionsInfo{CmpdDataFieldLabel} = $CmpdDataFieldValues[1];
+    }
+    elsif (@CmpdDataFieldValues == 3) {
+      $OptionsInfo{CmpdDataField} = $CmpdDataFieldValues[0];
+      $OptionsInfo{CmpdDataFieldLabel} = $CmpdDataFieldValues[1];
+      $OptionsInfo{CmpdDataFieldPosition} = $CmpdDataFieldValues[2];
+    }
+    elsif (@CmpdDataFieldValues == 4) {
+      $OptionsInfo{CmpdDataField}  = $CmpdDataFieldValues[0];
+      $OptionsInfo{CmpdDataFieldLabel} = $CmpdDataFieldValues[1];
+      $OptionsInfo{CmpdDataFieldPosition} = $CmpdDataFieldValues[2];
+      $OptionsInfo{CmpdDataFieldAlignment} = $CmpdDataFieldValues[3];
+    }
+    else {
+      die "Error: Invalid number of values, ", scalar(@CmpdDataFieldValues) , ", specified by \"--cmpddatafield\" option.\nIt must contain only one, two, three, or four values.\n";
+    }
+    if ($OptionsInfo{CmpdDataFieldLabel} !~ /^(yes|no)$/ ) {
+      die "Error: The label value specified, $Options{cmpddatafield}, for option \"--cmpddatafield\" is not valid. Allowed values: yes or no\n";
+    }
+    if ($OptionsInfo{CmpdDataFieldPosition} !~ /^(top|bottom)$/ ) {
+      die "Error: The position value specified, $Options{cmpddatafield}, for option \"--cmpddatafield\" is not valid. Allowed values: top or bottom\n";
+    }
+    if ($OptionsInfo{CmpdDataFieldAlignment} !~ /^(left|center|right)$/ ) {
+      die "Error: The alignment value specified, $Options{cmpddatafield}, for option \"--cmpddatafield\" is not valid. Allowed values: left, center, or right\n";
+    }
+  }
+
+  # Process data fields to be displayed in tables...
+  $OptionsInfo{SpecifiedDataFields} = exists($Options{datafields}) ? $Options{datafields} : "All";
+
+  $OptionsInfo{ValueOkColor} = ""; $OptionsInfo{ValueNotOkColor} = ""; $OptionsInfo{HighlightStatus} = 0;
+  if ($Options{mode} =~ /^(highlight|shadedhighlight)$/i) {
+    my($HighlightMode, $HighlightBy);
+    $HighlightMode = $Options{mode}; $HighlightBy = $Options{highlightby};
+
+    $OptionsInfo{HighlightStatus} = 1;
+    $OptionsInfo{ValueOkColor} = "#0fff0f";
+    $OptionsInfo{ValueNotOkColor} = "#ff0f0f";
+    if ($Options{highlightstyle} =~ /^text$/i) {
+      $OptionsInfo{ValueOkColor} = "#0fbb0f";
+      $OptionsInfo{ValueNotOkColor} = "#ff0f0f";
+    }
+    if ($Options{highlightcolor}) {
+      # Make sure two values are specified...
+      @ColorValues = split ",", $Options{highlightcolor};
+      if (@ColorValues == 2) {
+	$OptionsInfo{ValueOkColor} = $ColorValues[0];
+	$OptionsInfo{ValueNotOkColor} = $ColorValues[1];
+      }
+      else {
+	die "Error: Invalid number of values, ", scalar(@ColorValues), ", specified by \"--highlightcolor\" option.\nIt must contain only two value for $HighlightMode value specified using \"-m --mode\" option.\n";
+      }
+    }
+    if (!$Options{highlight}) {
+      die "Error: Specify columns to be highlighted using \"--hightlight\" option\n";
+    }
+    # Retrieve quartet values from "hightlight" option...
+    my(@HighlightValueQuartets);
+
+    @HighlightValueQuartets = ();
+    @HighlightValueQuartets = split ",", $Options{highlight};
+    if ((@HighlightValueQuartets % 4)) {
+      die "Error: Quartets not found in values specified using \"--highlight\" option for $HighlightMode \"-m --mode\"\n";
+    }
+    # Process quartets...
+    my($Index, $Label, $DataType, $Criterion, $Value);
+
+    @{$OptionsInfo{SpecifiedHighlightDataFieldLabels}} = ();
+    %{$OptionsInfo{SpecifiedHighlightDataFieldLabelsMap}} = ();
+    %{$OptionsInfo{SpecifiedHighlightDataFieldTypesMap}} = ();
+    %{$OptionsInfo{SpecifiedHighlightDataFieldCriteriaMap}} = ();
+    %{$OptionsInfo{SpecifiedHighlightDataFieldValueMap}} = ();
+
+    for ($Index = 0; $Index < @HighlightValueQuartets; $Index = $Index + 4) {
+      $Label = $HighlightValueQuartets[$Index];
+      $DataType = $HighlightValueQuartets[$Index + 1];
+      $Criterion = $HighlightValueQuartets[$Index + 2];
+      $Value = $HighlightValueQuartets[$Index + 3];
+      if ($DataType !~ /^(numeric|text)$/i) {
+	die "Error: Invalid column data type, $DataType, specified in quartet, \"$Label,$DataType,$Criterion,$Value\", using \"--hightlight\" option: Valid values: numeric or text\n";
+      }
+      if ($Criterion !~ /^(eq|le|ge)$/i) {
+	die "Error: Invalid criterion value, $Criterion, specified in quartet, \"$Label,$DataType,$Criterion,$Value\", using \"--hightlight\" option: Valid values: le, ge, or eq\n";
+      }
+      if ($DataType =~ /^numeric$/i) {
+	if (!IsFloat($Value)) {
+	  die "Error: Invalid criterion value, $Value, specified in quartet, \"$Label,$DataType,$Criterion,$Value\", using \"--hightlight\" option: Numeric value required for numeric data type\n";
+	}
+      }
+      if (exists($OptionsInfo{SpecifiedHighlightDataFieldLabelsMap}{$Label})) {
+	die "Error: Invalid field label value, $Label, in quartet, \"$Label,$DataType,$Criterion,$Value\", using \"--hightlight\" option: Multiple occurences of label.  \n";
+      }
+      push @{$OptionsInfo{SpecifiedHighlightDataFieldLabels}}, $Label;
+      $OptionsInfo{SpecifiedHighlightDataFieldLabelsMap}{$Label} = $Label;
+      $OptionsInfo{SpecifiedHighlightDataFieldTypesMap}{$Label} = $DataType;
+      $OptionsInfo{SpecifiedHighlightDataFieldCriteriaMap}{$Label} = $Criterion;
+      $OptionsInfo{SpecifiedHighlightDataFieldValueMap}{$Label} = $Value;
+    }
+  }
+}
+
+# Set up default archive and code values for a specific applet...
+sub SetupDefaultAppletArchiveAndCode {
+  my($ViewerType) = @_;
+  my($Archive, $Code, $Nothing);
+
+ STRVIEWERTYPE: {
+    if ($OptionsInfo{StrViewerType} =~ /^JME$/i) { $Archive = "JME.jar"; $Code = "JME"; last STRVIEWERTYPE; }
+    if ($OptionsInfo{StrViewerType} =~ /^Jmol$/i) {$Archive = "JmolApplet.jar"; $Code = "JmolApplet";  last STRVIEWERTYPE; }
+    if ($OptionsInfo{StrViewerType} =~ /^MarvinView$/i) { $Archive = "marvin.jar"; $Code = "MView"; last STRVIEWERTYPE; }
+    $Nothing = 1;
+  }
+  return ($Archive, $Code);
+}
+
+# Retrieve information about input SD files...
+sub RetrieveSDFilesInfo {
+  my($SDFile, $FileDir, $FileName, $HTMLFile, $CSSFile, $HTMLRoot, $HTMLTitle, $FileExt, $Index, $TopHTMLDir);
+
+  %SDFilesInfo = ();
+
+  @{$SDFilesInfo{FileOkay}} = ();
+  @{$SDFilesInfo{CmpdCount}} = ();
+  @{$SDFilesInfo{SpecifiedDataFieldLabels}} = ();
+
+  @{$SDFilesInfo{HTMLRoot}} = ();
+  @{$SDFilesInfo{HTMLTitle}} = ();
+  @{$SDFilesInfo{MultipleHTMLTables}} = ();
+
+  @{$SDFilesInfo{TopHTMLDir}} = ();
+  @{$SDFilesInfo{SubHTMLDir}} = ();
+  @{$SDFilesInfo{SubMolDir}} = ();
+
+
+  FILELIST: for $Index (0 .. $#SDFilesList) {
+    $SDFile = $SDFilesList[$Index];
+
+    $SDFilesInfo{FileOkay}[$Index] = 0;
+    $SDFilesInfo{CmpdCount}[$Index] = 0;
+    $SDFilesInfo{HTMLRoot}[$Index] = "";
+    $SDFilesInfo{HTMLTitle}[$Index] = "";
+    $SDFilesInfo{MultipleHTMLTables}[$Index] = 0;
+    $SDFilesInfo{TopHTMLDir}[$Index] = "";
+    $SDFilesInfo{SubHTMLDir}[$Index] = "";
+    $SDFilesInfo{SubMolDir}[$Index] = "";
+
+    @{$SDFilesInfo{SpecifiedDataFieldLabels}[$Index]} = ();
+
+    if (!(-e $SDFile)) {
+      warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
+      next FILELIST;
+    }
+    if (!CheckFileType($SDFile, "sd sdf")) {
+      warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
+      next FILELIST;
+    }
+    ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
+
+    if (!open SDFILE, "$SDFile") {
+      warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
+      next FILELIST;
+    }
+    # Count number of compounds and collect all possible data field labels...
+    my($CmpdCount, $CmpdString, @DataFieldLabels, @CommonDataFieldLabels);
+    $CmpdCount = 0;
+    @DataFieldLabels = ();
+    @CommonDataFieldLabels = ();
+    if ($OptionsInfo{SpecifiedDataFields} =~ /^(All|Common)$/i ) {
+      my($DataFieldLabelsRef, $CommonDataFieldLabelsRef);
+      ($CmpdCount, $DataFieldLabelsRef, $CommonDataFieldLabelsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
+      push @DataFieldLabels, @{$DataFieldLabelsRef};
+      push @CommonDataFieldLabels, @{$CommonDataFieldLabelsRef};
+    }
+    else {
+      while ($CmpdString = ReadCmpdString(\*SDFILE)) {
+	$CmpdCount++;
+      }
+    }
+    close SDFILE;
+
+    $FileDir = ""; $FileName = ""; $FileExt = "";
+    ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
+    $HTMLRoot = $FileName;
+    if ($Options{root} && (@SDFilesList == 1)) {
+      my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
+      if ($RootFileName && $RootFileExt) {
+	$HTMLRoot = $RootFileName;
+      }
+      else {
+	$HTMLRoot = $Options{root};
+      }
+    }
+    $HTMLTitle = $HTMLRoot;
+    if ($Options{title} && (@SDFilesList == 1)) {
+      $HTMLTitle = $Options{title};
+    }
+    $HTMLFile = lc($HTMLRoot) . "-html";
+    if (!$Options{overwrite}) {
+      if (-d $HTMLFile) {
+	warn "Warning: Ignoring file $SDFile: The directory $HTMLFile already exists\n";
+	next FILELIST;
+      }
+    }
+    $SDFilesInfo{FileOkay}[$Index] = 1;
+    $SDFilesInfo{CmpdCount}[$Index] = $CmpdCount;
+    $SDFilesInfo{HTMLRoot}[$Index] = "$HTMLRoot";
+    $SDFilesInfo{HTMLTitle}[$Index] = "$HTMLTitle";
+    if ($OptionsInfo{MaxCmpdsPerTable} == 0 || $CmpdCount <= $OptionsInfo{MaxCmpdsPerTable}) {
+      $SDFilesInfo{MultipleHTMLTables}[$Index] = 0;
+    }
+    else {
+      $SDFilesInfo{MultipleHTMLTables}[$Index] = 1;
+    }
+    if ($OptionsInfo{SpecifiedDataFields} =~ /^All$/i ) {
+      push @{$SDFilesInfo{SpecifiedDataFieldLabels}[$Index]}, @DataFieldLabels;
+    }
+    elsif ($OptionsInfo{SpecifiedDataFields} =~ /^Common$/i) {
+      push @{$SDFilesInfo{SpecifiedDataFieldLabels}[$Index]}, @CommonDataFieldLabels;
+    }
+    else {
+      push @{$SDFilesInfo{SpecifiedDataFieldLabels}[$Index]}, split(",", $OptionsInfo{SpecifiedDataFields});
+    }
+
+    # Setup HTML data directories paths...
+    $TopHTMLDir = lc($SDFilesInfo{HTMLRoot}[$Index]) . "-html";
+    $SDFilesInfo{TopHTMLDir}[$Index] = "$TopHTMLDir";
+    $SDFilesInfo{SubHTMLDir}[$Index] = "$TopHTMLDir\/html";
+    $SDFilesInfo{SubMolDir}[$Index] = "$TopHTMLDir\/mol";
+  }
+}
+
+# Setup information...
+sub SetupMultipleTablesAndMiscInfo {
+  SetupMultipleTablesInfo();
+  SetupMiscInfo();
+}
+
+# Setup navigation link information for multiple tables...
+sub SetupMultipleTablesInfo {
+  my($Index, $LinesPerTable);
+
+  $LinesPerTable = $OptionsInfo{MaxCmpdsPerTable};
+
+  @{$SDFilesInfo{TableCount}} = ();
+  @{$SDFilesInfo{TableHTMLFiles}} = ();
+  @{$SDFilesInfo{TableStartCmpdNum}} = ();
+  @{$SDFilesInfo{TableEndCmpdNum}} = ();
+
+  for $Index (0 .. $#SDFilesList) {
+    $SDFilesInfo{TableCount}[$Index] = 1;
+    @{$SDFilesInfo{TableHTMLFiles}[$Index]} = ();
+    @{$SDFilesInfo{TableStartCmpdNum}[$Index]} = ();
+    @{$SDFilesInfo{TableEndCmpdNum}[$Index]} = ();
+
+    if ($SDFilesInfo{FileOkay}[$Index]) {
+      if ($SDFilesInfo{MultipleHTMLTables}[$Index]) {
+	my($TableIndex, $TotalLines, $TableCount, $TableStartLineNum, $TableEndLineNum, $Name);
+
+	$TotalLines = $SDFilesInfo{CmpdCount}[$Index];
+	$TableCount = ($TotalLines % $LinesPerTable) ? (int($TotalLines/$LinesPerTable) + 1) : ($TotalLines/$LinesPerTable);
+	$SDFilesInfo{TableCount}[$Index] = $TableCount;
+	for $TableIndex (1 .. $TableCount) {
+	  $TableStartLineNum = ($TableIndex - 1) * $LinesPerTable + 1;
+	  $TableEndLineNum = ($TableIndex == $TableCount) ? $TotalLines : ($TableIndex * $LinesPerTable);
+	  push @{$SDFilesInfo{TableStartCmpdNum}[$Index]}, $TableStartLineNum;
+	  push @{$SDFilesInfo{TableEndCmpdNum}[$Index]}, $TableEndLineNum;
+
+	  # Setup HTML file names for all the tables...
+	  $Name = "Cmpd" . "$TableStartLineNum" . "To" . "$TableEndLineNum";
+	  if ($TableIndex == 1) {
+	    $Name = "";
+	  }
+	  $Name = $SDFilesInfo{HTMLRoot}[$Index] . $Name . ".html";
+	  push @{$SDFilesInfo{TableHTMLFiles}[$Index]}, $Name;
+	}
+	#print "$SDFilesList[$Index]: $TableCount -  @{$SDFilesInfo{TableStartCmpdNum}[$Index]} - @{$SDFilesInfo{TableEndCmpdNum}[$Index]} -  @{$SDFilesInfo{TableHTMLFiles}[$Index]}\n";
+      }
+    }
+  }
+}
+
+# Setup HTML tags and other information...
+sub SetupMiscInfo {
+  $SDFilesInfo{RowHeaderTags} = "";
+  $SDFilesInfo{RowEndTags} = "";
+  $SDFilesInfo{BgFilledOddRowHeaderTags} = "";
+  $SDFilesInfo{BgFilledEvenRowHeaderTags} = "";
+  $SDFilesInfo{TableRowHeaderTags} = "";
+
+  $SDFilesInfo{RowHeaderTags} = SetupHTMLTableRowHeader($OptionsInfo{RowHAlignment}, "", $OptionsInfo{RowVAlignment});
+  $SDFilesInfo{RowEndTags} = SetupHTMLTableRowEnd();
+
+  if ($OptionsInfo{ShadeRowsStatus}) {
+    $SDFilesInfo{BgFilledOddRowHeaderTags} = SetupHTMLTableRowHeader($OptionsInfo{RowHAlignment}, $OptionsInfo{OddRowsShadeColor}, $OptionsInfo{RowVAlignment});
+    $SDFilesInfo{BgFilledEvenRowHeaderTags} = SetupHTMLTableRowHeader($OptionsInfo{RowHAlignment}, $OptionsInfo{EvenRowsShadeColor}, $OptionsInfo{RowVAlignment});
+  }
+
+  $SDFilesInfo{TableRowHeaderTags} = SetupHTMLTableRowHeader($OptionsInfo{TableHeaderRowHAlignment}, $OptionsInfo{TableHeaderRowColor}, $OptionsInfo{TableHeaderRowVAlignment});
+
+  $SDFilesInfo{MolEndTag} = "M  END";
+  $SDFilesInfo{White} = qq(#ffffff);
+}
+
+# Setup various data directories to hold HTML and other related files...
+sub SetupDataDirs {
+  my($Index) = @_;
+  my($TopHTMLDir, $SubHTMLDir, $SubMolDir, $CreateTopHTMLDir, $CreateSubHTMLDir, $CreateSubMolDir);
+
+  $TopHTMLDir = $SDFilesInfo{TopHTMLDir}[$Index];
+  $SubHTMLDir = $SDFilesInfo{SubHTMLDir}[$Index];
+  $SubMolDir = $SDFilesInfo{SubMolDir}[$Index];
+
+  # Clean up existing directories...
+  if (-d $TopHTMLDir) {
+    unlink "<$TopHTMLDir/*.html>";
+    unlink "<$TopHTMLDir/*.css>";
+  }
+  if (-d $SubHTMLDir) {
+    unlink "<$SubHTMLDir/*.html>";
+  }
+  if (-d $SubMolDir) {
+    unlink "<$SubMolDir/*.mol>";
+  }
+
+  # What directories need to be created...
+  $CreateTopHTMLDir = (-d $TopHTMLDir) ? 0 : 1;
+  $CreateSubHTMLDir = (-d $SubHTMLDir) ? 0 : 1;
+  $CreateSubMolDir = 0;
+  if ($OptionsInfo{StrViewerType} =~ /^(Jmol|Chime|Chem3DActiveX|ChemDrawActiveX|ChemDrawPlugIn|ViewerActiveX)$/i) {
+    $CreateSubMolDir = (-d $SubMolDir) ? 0 : 1;
+  }
+
+  # Create appropriate directories...
+  if ($CreateTopHTMLDir) {
+    mkdir $TopHTMLDir or die "Couldn't mkdir $TopHTMLDir: $! \n";
+  }
+  if ($CreateSubHTMLDir) {
+    mkdir $SubHTMLDir or die "Error: Couldn't mkdir $SubHTMLDir: $! \n";
+  }
+  else {
+    unlink <$SubHTMLDir/*.html>;
+  }
+  if ($CreateSubMolDir) {
+    mkdir $SubMolDir or die "Error: Couldn't mkdir $SubMolDir: $! \n";
+  }
+  return ($TopHTMLDir, $SubHTMLDir, $SubMolDir);
+}
+
+# Setup script usage  and retrieve command line arguments specified using various options...
+sub SetupScriptUsage {
+
+  # Retrieve all the options...
+  %Options = ();
+
+  $Options{mode} = "shade";
+  $Options{highlightstyle} = "background";
+
+  $Options{cellpadding} = 2;
+  $Options{cellspacing} = 1;
+
+  $Options{displaylinks} = "both";
+  $Options{displaylinksinfo} = "both";
+  $Options{stylesheet} = "new";
+
+  $Options{structure} = "display";
+  $Options{strlinktype} = "href";
+  $Options{strlinkmode} = "plain";
+  $Options{strlinknavigation} = "yes";
+  $Options{strlinktitledisplay} = "no";
+
+  $Options{strviewertype} = "Jmol";
+  $Options{strviewerembed} = "direct";
+
+  $Options{titledisplay} = "yes";
+
+  if (!GetOptions(\%Options, "align|a=s", "border|b=i", "cellpadding=i", "cellspacing=i", "cmpddatafield|c=s", "datafields=s", "footer=s", "displaylinks|d=s", "displaylinksinfo=s", "help|h", "headeralign=s", "headercolor=s", "highlight=s", "highlightcolor=s", "highlightstyle=s", "mode|m=s", "numcmpds|n=i", "overwrite|o", "root|r=s", "shadecolor=s", "stylesheet=s", "stylesheetname=s", "structure|s=s", "strlinkmode=s", "strlinknavigation=s", "strlinkshadecolor=s", "strlinktitle=s", "strlinktitledisplay=s", "strlinktype=s", "strviewertype=s", "strviewerconfig=s", "strviewerparams=s", "strviewerembed=s",  "strviewerjsfile=s", "strtablesize=s", "title|t=s", "titledisplay=s", "workingdir|w=s")) {
+    die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
+  }
+
+  if ($Options{workingdir}) {
+    if (! -d $Options{workingdir}) {
+      die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
+    }
+    chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
+  }
+  if ($Options{displaylinks} !~ /^(top|bottom|both)$/i) {
+    die "Error: The value specified, $Options{displaylinks}, for option \"-d --displaylinks\" is not valid. Allowed values: top, bottom, or both\n";
+  }
+  if ($Options{displaylinksinfo} !~ /^(compound|table|both)$/i) {
+    die "Error: The value specified, $Options{displaylinksinfo}, for option \"--displaylinksinfo\" is not valid. Allowed values: compound, table, or both\n";
+  }
+  if ($Options{highlightstyle} !~ /^(background|text)$/i) {
+    die "Error: The value specified, $Options{highlightstyle}, for option \"--highlightstyle\" is not valid. Allowed values: background or text\n";
+  }
+  if ($Options{mode} !~ /^(plain|shade|highlight|shadedhighlight|structuresonly|shadedstructuresonly)$/i) {
+    die "Error: The value specified, $Options{mode}, for option \"-m --mode\" is not valid. Allowed values: plain, shade, hightlight, shadedhighlight, structuresonly, or shadedstructuresonly\n";
+  }
+  if ($Options{stylesheet} !~ /^(old|new|none)$/i) {
+    die "Error: The value specified, $Options{stylesheet}, for option \"-s --stylesheet\" is not valid. Allowed values: old, new, or none\n";
+  }
+  if ($Options{structure} !~ /^(display|link)$/i) {
+    die "Error: The value specified, $Options{structure}, for option \"-s --structure\" is not valid. Allowed values: display or link\n";
+  }
+  if ($Options{strlinkmode} !~ /^(plain|shade)$/i) {
+    die "Error: The value specified, $Options{strlinkmode}, for option \"--strlinkmode\" is not valid. Allowed values: plain or shade\n";
+  }
+  if ($Options{strlinktype} !~ /^(href|button)$/i) {
+    die "Error: The value specified, $Options{strlinktype}, for option \"--strlinktype\" is not valid. Allowed values: href or button\n";
+  }
+  if ($Options{strlinknavigation} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{strlinknavigation}, for option \"--strlinknavigation\" is not valid. Allowed values: yes or no\n";
+  }
+  if ($Options{strlinktitledisplay} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{strlinktitledisplay}, for option \"--strlinktitledisplay\" is not valid. Allowed values: yes or no\n";
+  }
+  if ($Options{strviewertype} !~ /^(JME|Jmol|Chime|MarvinView|ChemDrawPlugIn|Chem3DActiveX|ChemDrawActiveX|ViewerActiveX)$/i) {
+    die "Error: The value specified, $Options{strviewertype}, for option \"--strviewertype\" is not valid. Allowed values: Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn, Chime, JME, Jmol, MarvinView, or ViewerActiveX.\n";
+  }
+  if ($Options{strviewerembed} !~ /^(direct|javascript)$/i) {
+    die "Error: The value specified, $Options{strviewerembed},  for option \"--strviewerembed\" is not valid. Allowed values: direct or javascript \n";
+  }
+  if (exists $Options{numcmpds} && $Options{numcmpds} < 0) {
+    die "Error: The value specified, $Options{numcmpds},  for option \"-n --numcmpds\" is not valid. Allowed values: >= 0 \n";
+  }
+  if ($Options{titledisplay} !~ /^(yes|no)$/i) {
+    die "Error: The value specified, $Options{titledisplay}, for option \"--titledisplay\" is not valid. Allowed values: yes or no\n";
+  }
+  if (exists($Options{border})) {
+    if ($Options{border} < 0) {
+      die "Error: The value specified, $Options{border},  for option \"--border\" is not valid. Allowed values: >= 0 \n";
+    }
+  }
+  if ($Options{cellpadding} < 0) {
+    die "Error: The value specified, $Options{cellpadding},  for option \"--cellpadding\" is not valid. Allowed values: >= 0 \n";
+  }
+  if ($Options{cellspacing} < 0) {
+    die "Error: The value specified, $Options{cellspacing},  for option \"--cellspacing\" is not valid. Allowed values: >= 0 \n";
+  }
+}
+
+__END__
+
+=head1 NAME
+
+SDFilesToHTML.pl - Generate HTML table file(s) from SDFile(s)
+
+=head1 SYNOPSIS
+
+SDFilesToHTML.pl  SDFiles(s)...
+
+SDFilesToHTML.pl [B<-a, --align> left | center | right,[top | middle | bottom]] [B<-b, --border> borderwidth] [B<--cellpadding> padding]
+[B<--cellspacing> spacing] [B<--cmpddatafield> "fieldlabel,[label,position,alignment]"] [B<--datafields> "fieldlabel,[fieldlabel]..." | Common | All]
+[B<--footer> string] [B<-d, --displaylinks> top | bottom | both] [B<--displaylinksinfo> compound | table | both] [B<-h, --help>]
+[B<--headeralign> left | center | right,[top | middle | bottom]] [B<--headercolor> "#RRGGBB"]
+[B<--highlight> "fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]"]
+[B<--highlightcolor> "#RRGGBB,#RRGGBB"] [B<--highlightstyle> text | background]
+[B<-m, --mode> plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly]
+[B<-n, --numcmpds> number] [B<-o, --overwrite>] [B<-r, --root> rootname] [B<-s, --structure> display | link]
+[B<--strlinkmode> plain | shaded] [B<--strlinknavigation> yes | no]
+[B<--strlinkshadecolor> "#RRGGBB"] [B<--strlinktitle> string] [B<--strlinktitledisplay> yes | no] [B<--strlinktype> href | button]
+[B<--strviewertype> Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | JME | Jmol | MarvinView | ViewerActiveX]
+[B<--strviewerconfig> codebase[,archive,code]] [B<--strviewerparams> "name=value [name=value ...]"]
+[B<--strviewerembed> direct | javascript] [B<--strviewerjsfile> javascriptfilename]
+[B<--strtablesize> "numrows,numcols"] [B<--stylesheet> old | new | none]
+[B<--stylesheetname> filename] [B<--shadecolor> "#RRGGBB,#RRGGBB"] [B<-t, --title> string] [B<--titledisplay> yes | no]
+[B<-w, --workingdir> dirname] SDFiles(s)...
+
+=head1 DESCRIPTION
+
+Generate HTML file(s) from I<SDFile(s)>. The HTML file(s) contain data tables
+and appropriate navigational links to view other tables; navigational links are also
+provided on compound HTML pages. These files can be generated for local viewing or
+deployment on a web server. A variety of options are provided to control style and
+appearance of tables. And for viewing structures, options are available to use any one of
+these viewers: Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn, Chime, Jmol, JME,
+MarvinView, or ViewerActiveX. Jmol is the default structure viewer and it is also distributed
+along with this package; however, to use any other supported viewers, make sure it's available
+in your environment.
+
+Multiple I<SDFile(s)> names are separated by space. The valid file extensions are
+I<.sdf> and I<.sd>. All other file names are ignored. All the SD files in a current directory can
+be specified either by I<*.sdf> or the current directory name.
+
+=head1 OPTIONS
+
+=over 4
+
+=item B<-a, --align> I<left | center | right,[top | middle | bottom]>
+
+Horizontal and vertical alignment for table rows except for header row which is specified
+using B<--headeralign> option. Possible horizontal alignment values: I<left, center, or right>.
+Possible vertical alignment values: I<top, middle, or bottom>.
+
+Default values: I<left,middle>
+
+=item B<-b, --border> I<borderwidth>
+
+Table border width. Default value: 1 for I<plain> and I<highlight> mode; 0 for I<shade>
+and I<shadedhightlight> mode. Zero indicates no border.
+
+=item B<--cellpadding> I<padding>
+
+Table cell padding. Default value: I<2>.
+
+=item B<--cellspacing> I<spacing>
+
+Table cell spacing. Default value: I<1>.
+
+=item B<--cmpddatafield> I<fieldlabel,[label,position,alignment]>
+
+This value is mode specific. It indicates data field value to be displayed with the structure along
+with its label, position and alignment during  I<structuresonly | shadedstructuresonly> value of B<-m, --mode>
+option. Possible values: feldlabel - valid data field label; label - yes or no; position - I<top or bottom>; alignment
+- I<left, center, or right>. Default: I<none,no,bottom,center>. Example:
+
+    MolWt,no,bottom,middle
+
+B<--cmpddatafield> option value is also linked to compound summary page.
+
+=item B<--datafields> I<"fieldlabel,[fieldlabel]..." | Common | All>
+
+Data fields to display in HTML table(s). Possible values: list of comma separated data field
+labels, data fields common to all records, or all data fields. Default value: I<All>.
+Examples:
+
+    ALogP,MolWeight,EC50
+    "MolWeight,PSA"
+
+=item B<--footer> I<string>
+
+Text string to be included at bottom of each HTML file. Default: none.
+
+=item B<-d --displaylinks> I<top | bottom | both>
+
+Specify where to display navigation links in each HTML file for accessing all other HTML
+files. Possible values: I<top, bottom, or both>. Default: I<both>. This option is
+only valid during multiple HTML files generation for an input file.
+
+=item B<--displaylinksinfo> I<compound | table | both>
+
+Control display of additional information along with navigational links: Showing compound
+n of m is displyed for compound and showing table n of m for table. Possible values: I<compound
+| table | both>. Default: I<both>. This option is only valid  during multiple HTML files generation.
+
+=item B<-h, --help>
+
+Print this help message.
+
+=item B<--headeralign> I<left | center | right,[top | middle | bottom>
+
+Horizontal and vertical alignment for table header rows. Possible horizontal alignment
+values: I<left, center, or right>. Possible vertical alignment values: I<top, middle, or bottom>.
+
+Default values: I<center,middle>
+
+=item B<--headercolor> I<#RRGGBB>
+
+Color used to fill background of table header row containing column labels
+represented as a hexadecimal string. Default value: None for B<-m, --mode> option
+value of I<plain> and I<#ccccff>, light blue, for others.
+
+=item B<--highlight> I<"fieldlabel,datatype,criterion,value,[fieldlabel,datatype,criterion,value,...]">
+
+Highlighting methodology used to highlight various SDFile(s) data field values in
+HTML file(s). Same set of quartets values are applied to all SDFile(s).
+
+Input text contains these quartets: I<fieldlabel,datatype,criterion,value,...>.
+Possible datatype values: I<numeric or text>. Possible criterion values: I<le, ge, or eq>.
+Examples:
+
+    "MolWt,numeric,le,450"
+    "MolWt,numeric,le,450,LogP,numeric,le,5"
+    Name,text,eq,Aspirin
+
+=item B<--highlightcolor> I<"#RRGGBB,#RRGGBB">
+
+Colors used to highlight column values during I<highlight> and I<shadedhightlight>
+mode represented as hexadecimal strings.
+
+For B<--highlighstyle> option values of I<text> and I<background>, these colors represent
+text or background colors respectively. For a specific column, first color string is used for
+values which meet criterion indicated by B<--highlight> option; the second color is used for
+ rest of the values.
+
+Default values for I<background> B<--highlightstyle>: I<"#0fff0f,#ff0f0f">. And default values for
+I<text> B<--highlightstyle>: I<"#0fbb0f,#ff0f0f">. Hexadecimal strings for both B<--highlightstyle>
+colors correspond to I<reddish> and I<greenish>.
+
+=item B<--highlightstyle> I<text | background>
+
+This value is mode specific. It indicates highlight style used to differentiate column
+values which meet a specified criterion in B<--highlight> option. Possible values: I<text or
+background>. Default: I<background>.
+
+=item B<-m, --mode> I<plain | shade | highlight | shadedhighlight | structuresonly | shadedstructuresonly>
+
+Specify how to generate HTML table(s): plain tables with line borders, background of
+alternate rows filled with a specified color, column values highlighted using a specified
+criteria, combination of previous two styles,  tables containing only structures, or tables
+containing only structures with filled background of alternate rows.
+
+Possible values: I<plain, shade, highlight, shadedhighlight, structuresonly, or
+shadedstructuresonly>. Default: I<shade>.
+
+=item B<-n, --numcmpds> I<number>
+
+Maximum number of compounds per table. Default value: I<15> for tables with structures and
+I<50> for tables with links to structures. Use 0 to put all compounds into one table. For SDFile(s)
+with more than maximum number of specified compounds, multiple HTML tables, with appropriate
+navigation links, are created.
+
+=item B<-o, --overwrite>
+
+Overwrite existing files.
+
+=item B<-r, --root> I<rootname>
+
+New file or directory name is generated using the root: <root>.html or <root>-html.
+Default new file name: <InitialSDFileName>.html. Default directory name:
+<InitialSDFileName>-html.
+
+For SDFile(s) with more than maximum number of specified compounds per table,
+this directory tree is generated using <Name> where <Name> corresponds to <root>
+or <InitialSDFileName>: Top dir - <Name>-html; Sub dirs - html and mols. <Top dir> contains
+<Name>.html and <Name>.css files and <sub dir> html conatins various
+<Name>Lines<Start>To<End>.html files; <sub dir> mols is created as needed and contains
+MOL files.
+
+This option is ignored for multiple input files.
+
+=item B<-s, --structure> I<display | link>
+
+Structure display control: display structures in a table column or set up a link for each
+structure which opens up a new HTML page containing structure and other appropriate
+information. Possible values: I<display or link>. Default value: I<display>
+
+=item B<--strlinkmode> I<plain | shaded>
+
+Specify how to display compound HTML page: plain or background of data field
+field labels is filled with a specified color. Possible values: I<plain or shad>.
+Default value: I<plane>.
+
+Structure viewer background color is white. Use B<--strviewerparams> option to change
+default behavior of structure viewers.
+
+=item B<--strlinknavigation> I<yes | no>
+
+Display navigation links to other compounds in compound HTML page. Possible values:
+I<yes or no>. Default value: I<yes>.
+
+=item B<--strlinkshadecolor> I<"#RRGGBB">
+
+This value is B<--strlinkmode> specific. For I<shade> value of B<--strlinkmode> option, it
+represents colors used to fill background of data field labels.
+
+Default value: I<"#e0e9eb"> - it's a very light blue color.
+
+=item B<--strlinktitle> I<string>
+
+Title for compound HTML page. Default value: I<Compound Summary>.
+
+=item B<--strlinktitledisplay> I<yes | no>
+
+Display title for compound HTML page. Possible values: I<yes or no>. Default value: I<no>.
+
+=item B<--strlinktype> I<href | button>
+
+Type of structure link. Possible values: I<href or button>. Default: I<href>.
+
+=item B<--strviewertype> I<Chem3DActiveX | ChemDrawActiveX | ChemDrawPlugIn | Chime | JME | Jmol | MarvinView | ViewerActiveX>
+
+Structure viewer supported for viewing structures. Possible values: I<Chem3DActiveX,
+ChemDrawActiveX, ChemDrawPlugIn, Chime, JME, Jmol, MarvinView, or ViewerActiveX>.
+Default value: I<Jmol>.
+
+Assuming you have access to one of these viewers on your machine, you are all set
+to use this script. Otherwise, visit one of these web sites to download and install
+your favorite viewer:
+
+    accelrys.com: Viewer ActiveX 5.0
+    cambridgesoft.com: Chem3DActiveX 8.0, ChemDrawActiveX 8.0,
+                       ChemDrawPlugIn
+    chemaxon.com: MarvinView applet
+    mdli.com: Chime plug-in
+    jmol.sourceforge.net: JmolApplet V10
+    molinspiration.com: JME applet
+
+The default viewer, JmolApplet V10, is distributed with MayaChemTools package.
+Earlier versions of JmolApplet are not supported: due to applet security issues related to
+reading files, this script uses in-line loading of MOL files and this option doesn't exist in
+earlier version of JmolApplet.
+
+=item B<--strviewerconfig> I<codebase[,archive,code]>
+
+Configuration information for structure viewers. This option is only valid for structure
+viewers which are applets: Jmol, JME and MarvinView. For other viewer types available via
+B<--strviewertype> option  - MDL Chime, ChemDrawActiveX, ChemDrawPlugIn, and
+Chem3DActiveX - this value is ignored.
+
+Input text format: I<codebase[,archive,code]>. For an applet viewer, I<codebase> must be
+specified; I<archive> and I<code> values are optional. Here are default I<archive> and
+I<codebase> values for various applets: Jmol - JmolApplet, JmolApplet.jar; JME - JME, JME.jar;
+ MarvinView: MView, marvin.jar
+
+For local deployment of HTML files, I<codebase> must correspond to a complete path to
+the local directory containing appropriate I<archive> file and the complete path is converted
+into appropriate relative path during generation of HTML files.
+
+By default, I<codebase> value of <this script dir>/../lib/Jmol is used for I<Jmol> applet viewer, and
+HTML file(s) are generated for local deployment; however, you can specify any supported
+applet viewer and generate HTML file(s) for deploying on a web server.
+
+For deploying the HTML file(s) on a web server, specify a valid I<codebase> directory name
+relative to <WWWRootDir>. Example when JME archive file, JME.jar, is available in
+I</jme> directory on the web server:
+
+    /jme
+
+For local deployment of HTML file(s), specify a complete I<codebase> directory name.
+Example when JmolApplet archive file, JmolApplet.jar, is present in <JMOLROOT> directory:
+
+    <JMOLROOT>
+
+In addition to I<codebase>, you can also specify I<archive> file name. Example for web
+deployment:
+
+    "/jme,JME.jar"
+    "/jme"
+
+Example for local deployment:
+
+    "<JMEROOT>,JME.jar"
+    "<JMEROOT>"
+
+=item B<--strviewerparams> I<"name=value [name=value ...]">
+
+Parameters name and value pairs for structure viewers. These name and value pairs
+are used to control the appearance and behavior of structure viewers in tables and
+compound HTML page during I<link> value for B<-s --structure> option.
+
+The parameter names, along with their values,  are just passed to each structure viewer
+in appropriate format without checking their validity. Check documentation of appropriate
+structure viewers to figure out valid parameter names.
+
+Input text format: I<name=value name=value ...> Example:
+
+    "width=250 height=170"
+
+Default for all structure viewers: I<width=250 height=170> for displaying structures in
+tables, and I<strlinkwidth=500 strlinkheight=295> for compound HTML page during I<link> value
+for B<-s --structure> option.
+
+Default background color for all structure viewers: same as B<--shadecolor> value for
+displaying structures in tables and I<strlinkbgcolor=#ffffff> for  compound HTML page;
+however, explicit specification of background color in this option overrides default value.
+To use black background for structures in tables and compound HTML page, specify I<bgcolor=#000000>
+and I<strlinkbgcolor=#000000> respectively.  Keep this in mind: Some structure viewers
+don't appear to support background color parameter.
+
+Additional structure viewer specific default values:
+
+    Chem3DActiveX: "displaytype=Ball&Stick rotationbars=false
+                    moviecontroller=false"
+    ChemDrawActiveX: "ViewOnly=1 ShrinkToFit=1 ShowToolsWhenVisible=1"
+    ChemDrawPlugIn: "type=chemical/x-mdl-molfile ViewOnly=1
+                     ShrinkToFit=1 ShowToolsWhenVisible=1"
+    Chime: "display2d=true"
+    JME: "options=depict"
+    Jmol: "progressbar=true progresscolor=#0000ff boxbgcolor=#000000
+           boxfgcolor=#ffffff script="select *; set frank off;
+           wireframe on; spacefill off""
+    MarvinView: "navmode=zoom"
+    ViewerActiveX:"Mouse=4 Convert2Dto3D=0"
+
+Try overriding default values or specify additional valid parameter/value pairs to get desired
+results. Example for using CPK rendering scheme with Jmol viewer:
+
+    "script="select *; set frank off; wireframe off; spacefill on""
+
+=item B<--strviewerembed> I<direct | javascript>
+
+Specify how to embed structure viewers in HTML pages. Possible values: I<direct> - use applet/object
+tags to emded structure viewer; I<javascript> - use vendor supplied java scripts. Default value:
+direct.
+
+This option only applies to these vieweres: I<Chem3DActiveX, ChemDrawActiveX, ChemDrawPlugIn,
+Jmol, and MarvinView>.
+
+For marvin.js to work correctly on your browser, you may need to set I<marvin_jvm=builtin> or
+I<marvin_jvm=plugin> using B<--strviewerparams> option. Additionally, MarvinView - at least
+in my hands - also has problems during usage of JavaScript for local deployment; however, it
+does work via web server.
+
+As far as I can tell, Jmol.js supplied with Jmol10 release has these issues: jmolSetAppletColor
+doesn't support background color; jmolInitialize disables relative specification of codebase
+directroy which works okay. So, use Jmol.js supplied with MayaChemTools.
+
+=item B<--strviewerjsfile> I<java script file name>
+
+Name of vendor supplied java script file. Default values: Chem3DActiveX: I<chem3d.js>; ChemDrawActiveX,
+and ChemDrawPlugIn: I<chemdraw.js>; Jmol: I<Jmol.js>, MarvinView: I<marvin.js>.
+
+Directory location for these files is specified via I<codebase> value of B<--strviewerconfig> option.
+
+=item B<--strtablesize> I<"numrows,numcols">
+
+This option is only valid for I<structuresonly> and I<shadedstructuresonly> modes. And it indicates
+maximum number of rows and columns per structure table. Default value:I<6,4>.
+
+=item B<--stylesheet> I<old | new | none>
+
+Controls usage of stylesheet for newly generated HTML file(s). Possible values: I<old,
+new, or none>. Default value: I<new>.
+
+Stylesheet file contains various properties which control appearance of HTML pages:
+type, size, and color of fonts; background color; and so on.
+
+For I<old> value, an existing stylesheet file specified by B<--stylesheetname> option is
+used for each HTML file; no new stylesheet file is created. This option is quite handy
+for deploying HTML file(s) on a web server: assuming you specify a valid stylesheet
+file location relative to your WWWRoot, a reference to this stylesheet is added to each
+HTML file. For local deployment of HTML file(s), a complete path to a local stylesheet
+is fine as well.
+
+For I<create> value, a new stylesheet is created and reference to this local stylesheet
+is added to each HTML file. Use option B<--stylesheetname> to specify name.
+
+For I<none> value, stylesheet usage is completely ignored.
+
+=item B<--stylesheetname> I<filename>
+
+Stylesheet file name to be used in conjunction with B<-s --stylesheet> option. It is only
+valid for I<old> value of B<-s --stylesheet> option. Specify a valid stylesheet file location
+relative to your WWWRoot and a reference to this stylesheet is added to each HTML
+file. Example: I<"/stylesheets/MyStyleSheet.css">. Or a complete path name to a local
+stylesheet file.
+
+For I<create> value of B<-s --stylesheet> option, a new stylesheet file is created using
+B<-r --root> option. And value of B<--stylesheetname> is simply ignored.
+
+=item B<--shadecolor> I<"#RRGGBB,#RRGGBB">
+
+Colors used to fill background of rows during I<shade> and I<shadedhightlight> mode
+represented as a pair of hexadecimal string; the first and second color values
+are used for odd and even number rows respectively.
+
+Default value: I<"#ffffff,#e0e9eb"> - it's white and very light blue for odd and even number rows.
+
+=item B<-t, --title> I<string>
+
+Title for HTML table(s). Default value: I<SDFileName>. This option is ignored for
+multiple input files. And B<-r --root> option is used to generate appropriate
+titles.
+
+=item B<--titledisplay> I<yes | no>
+
+Display title for HTML table(s). Possible values: I<yes or no>. Default value: I<yes>.
+
+=item B<-w, --workingdir> I<dirname>
+
+Location of working directory. Default: current directory.
+
+=back
+
+=head1 EXAMPLES
+
+HTML table file(s), containing structures, can be used in two different ways: browsing on a
+local machine or deployment via a web server. By default, HTML file(s) are created for viewing
+on a local machine using Jmol viewer through a browser; however, you can specify any
+supported applet viewer and  generate HTML file(s) for deploying on a web server.
+
+First two sets of examples show generation of HTML file(s) using different applet viewers
+and a variety of options for local browsing; last set deals with web deployment.
+
+B<Local deployment: Usage of default JMol viewer distributed with MayaChemTools:>
+
+To generate HTML tables with structure display using JMol viewer, rows background filled
+with white and light blue colors, navigation links on top and botton of each page, type:
+
+    % SDFilesToHTML.pl -o Sample1.sdf
+
+To generate HTML tables with structure display using JMol viewer, rows background filled
+with white and light blue colors, navigation links on top and botton of each page, and
+only containing MolWeight and Mol_ID SD data fields, type:
+
+    % SDFilesToHTML.pl --datafields "MolWeight,Mol_ID" -o Sample1.sdf
+
+To generate HTML tables with CPK structure display using JMol viewer, rows
+background filled with white and light blue colors, navigation links on top and botton of
+each page, type:
+
+    % SDFilesToHTML.pl --strviewerparams "script=\"select *; set frank off;
+      wireframe off; spacefill on\"" -o Sample1.sdf
+
+To generate HTML tables with structure display using JMol viewer and black background, rows
+background filled with light golden and greyish colors, navigation links on top and botton of
+each page, 10 rows in each table, greyish header row color, and cell spacing of 1, type:
+
+    % SDFilesToHTML.pl -o -n 10 --headeralign "center" --headercolor
+      "#a1a1a1" --shadecolor "#fafad2,#d1d1d1" --cellspacing 1
+      --strviewerparams "bgcolor=#000000" Sample1.sdf
+
+To highlight molecular weight values using specified highlight criteria and fill in default background
+colors, type:
+
+    % SDFilesToHTML.pl -n 10 --highlight "MolWeight,numeric,le,450"
+      --highlightstyle background -m shadedhighlight -o Sample1.sdf
+
+To highlight molecular weight values using specified highlight criteria, color the text using
+default colors, and add a footer message in every page, type:
+
+    % SDFilesToHTML.pl -n 4 --highlight "MolWeight,numeric,le,500"
+      --highlightstyle text -m shadedhighlight -o
+      --footer "Copyright (C) MayaChemTools" --cellspacing 1 Sample1.sdf
+
+To generate tables containing only structures, type:
+
+    % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4"
+      --cellspacing 1 -b 1 -o Sample1.sdf
+
+To generate tables containing only structures with molecular weight displayed above the
+structure, type:
+
+    % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4"
+      --cmpddatafield "MolWeight,no,top,center"  --cellspacing 1 -b 1
+      -o Sample1.sdf
+
+To generate tables containing links to structures and highlight molecular weight data field values
+using specified highlight criteria , type:
+
+    % SDFilesToHTML.pl -n 4 --footer "Copyright (C) MayaChemTools"
+      --highlight "MolWeight,numeric,le,450" --highlightstyle background
+      -d both -m shadedhighlight  -s link --strlinktype button
+      -o Sample1.sdf
+
+B<Local deployment: Usage of other structure viewers:>
+
+    % SDFilesToHTML.pl --strviewertype MarvinView --strviewerconfig
+      "<Marvin dir path>" -o Sample1.sdf
+
+    % SDFilesToHTML.pl -o -n 10 --headeralign "center" --headercolor
+      "#a1a1a1" --shadecolor "#fafad2,#d1d1d1" --cellspacing 1
+      --strviewerparams "bgcolor=#000000" --strviewertype Chime
+      Sample1.sdf
+
+    % SDFilesToHTML.pl -n 10 --highlight "MolWeight,numeric,le,450"
+      --highlightstyle background -m shadedhighlight --strviewertype
+      Chime -o Sample1.sdf
+
+    % SDFilesToHTML.pl -d both -m shadedstructuresonly --strtablesize "6,4"
+      --cellspacing 1 -b 1 -strviewertype JME -strviewerconfig "<JME dir
+      path>" -o Sample1.sdf
+
+B<Web deployment: Usage of different structure viewers and options:>
+
+For deploying HTML file(s) on a web server, specify a valid I<codebase> directory name
+relative to <WWWRootDir>. In addition to I<codebase>, you can also specify I<archive> file
+name.
+
+    % SDFilesToHTML.pl -m plain -s display --strviewertype Jmol
+      -strviewerconfig "/jmol" -n 5 -d both -r PlainTable -t "Example
+      using Jmol: Plain Table" -o Sample1.sdf
+
+    % SDFilesToHTML.pl -n 5 -m shade  -s display -strviewertype JME
+      -strviewerconfig "/jme,JME.jar" -r ShadeTable -t "Example using JME:
+      Shaded Table" -o Sample.sdf
+
+    % SDFilesToHTML.pl -n 5 --highlight "MolWeight,numeric,le,450"
+      --highlightstyle background  -d both -m shadedhighlight  -s display
+      -strviewertype MarvinView -strviewerconfig "/marvin" -r
+      ShadedHightlightTable -t "Example using MarvinView: Shaded and
+      Highlighted Table" -o Sample.sdf
+
+    % SDFilesToHTML.pl -n 4 --highlight "MolWeight,numeric,le,450" -s link
+      --strlinktype href --strviewertype ChemDrawPlugIn  --highlightstyle
+      background -m shadedhighlight -t "Example using ChemDrawPlugIn:
+      Shaded and Highlighted Table" -r ShadedHightlightTable -o Sample1.sdf
+
+=head1 AUTHOR
+
+Manish Sud <msud@san.rr.com>
+
+=head1 SEE ALSO
+
+FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, MergeTextFilesWithSD.pl
+
+=head1 COPYRIGHT
+
+Copyright (C) 2015 Manish Sud. All rights reserved.
+
+This file is part of MayaChemTools.
+
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.
+
+=cut
author	deepakjadmin
date	Wed, 20 Jan 2016 09:23:18 -0500
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