--- trunk/src/applications/atom2md/atom2md.cpp	2006/08/02 18:06:18	1020
+++ trunk/src/applications/atom2md/atom2md.cpp	2010/05/10 17:28:26	1442
@@ -1,12 +1,14 @@
 /**********************************************************************
-main.cpp - Main conversion program, command-line handling.
+atom2md.cpp - OpenBabel-based conversion program to OpenMD file, 
+              command-line handling.
 
 Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
-Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
-Some portions Copyright (C) 2004-2005 by Chris Morley
+Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
+Some portions Copyright (C) 2004-2006 by Chris Morley
+Some portions Copyright (C) 2008-2009 by J. Daniel Gezelter
 
-This file is part of the Open Babel project.
-For more information, see <http://openbabel.sourceforge.net/>
+This file is part of both the OpenMD and Open Babel projects.
+For more information, see <http://openmd.net> and <http://openbabel.sourceforge.net/>
 
 This program is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -19,22 +21,18 @@ GNU General Public License for more details.
 ***********************************************************************/
 
 #include "config.h"
-#if HAVE_IOSTREAM
-	#include <iostream>
-#elif HAVE_IOSTREAM_H
-	#include <iostream.h>
+
+// used to set import/export for Cygwin DLLs
+#ifdef WIN32
+#define USING_OBDLL
 #endif
-#if HAVE_FSTREAM
-	#include <fstream>
-#elif HAVE_FSTREAM_H
-	#include <fstream.h>
-#endif
-#if HAVE_SSTREAM
-	#include <sstream>
-#elif
-	#include <sstream.h>
-#endif
 
+#include <openbabel/babelconfig.h>
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+
 #include <string>
 #include <map>
 #if HAVE_CONIO_H
@@ -45,14 +43,16 @@ extern "C" int strncasecmp(const char *s1, const char 
 extern "C" int strncasecmp(const char *s1, const char *s2, size_t n);
 #endif
 
-#include "openbabel/obconversion.hpp"
-#include "brains/Register.hpp"
+#include <openbabel/obconversion.h>
+#include <openbabel/plugin.h>
+#include <cstdlib>
+#include <cstring>
 
 using namespace std;
 using namespace OpenBabel;
-using namespace oopse;
-void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, 
-							int& arg, int argc, char *argv[]); 
+
+void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ,
+	      int& arg, int argc, char *argv[]); 
 void usage();
 void help();
 
@@ -61,28 +61,27 @@ int main(int argc,char *argv[])
 
 int main(int argc,char *argv[])
 {
-  registerOBFormats();	
   OBConversion Conv(&cin, &cout); //default input and output are console 
 
-//  string GenOptions;
   OBFormat* pInFormat = NULL;
   OBFormat* pOutFormat = NULL;
   vector<string> FileList, OutputFileList;
   string OutputFileName;
-//  obMessageLevel filterLevel = obWarning; // 2 out of 5
 
   // Parse commandline
   bool gotInType = false, gotOutType = false;
-  bool UseSavedOptions = false;
+  bool SplitOrBatch=false;
 
-  char *oext;
-  char *iext;
+  char *oext = NULL;
+  char *iext = NULL;
+
+  // for use with command name to type conversion
   string inputExt;
   string outputExt;
 
   //Save name of program without its path (and .exe)
   string pn(argv[0]);
-  unsigned int pos;
+  string::size_type pos;
 #ifdef _WIN32
   pos = pn.find(".exe");
   if(pos!=string::npos)
@@ -94,193 +93,313 @@ int main(int argc,char *argv[])
   else
     program_name=argv[0]+pos+1;
 
-	const char* p;
-	int arg;
-	for (arg = 1; arg < argc; arg++)
-	{
-		if (argv[arg])
-		{
-			if (argv[arg][0] == '-')
-			{
-				switch (argv[arg][1])
-				{
+  const char* p;
+  int arg;
+  for (arg = 1; arg < argc; ++arg)
+    {
+      if (argv[arg])
+        {
+          if (argv[arg][0] == '-')
+            {
+              switch (argv[arg][1])
+                {
 
-				case 'V':
-				{
-					cout << "Open Babel " << BABEL_VERSION << " -- " 
-				       << __DATE__ << " -- " << __TIME__ << endl;
-					exit(0);
-				}
+                case 'V':
+                  {
+                    cout << program_name << ": part of OpenMD " << 
+                      OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << 
+                      "." << OPENMD_VERSION_TINY << 
+                      " and Open Babel " << BABEL_VERSION << " -- " 
+                         << __DATE__ << " -- " << __TIME__ << endl;
+                    exit(0);
+                  }
 
-				case 'i':
-					gotInType = true;
-					iext = argv[arg] + 2;
-					if(!*iext)
-						iext = argv[++arg]; //space left after -i: use next argument
+                case 'i':
+                  gotInType = true;
+                  iext = argv[arg] + 2;
+                  if(!*iext)
+                    iext = argv[++arg]; //space left after -i: use next argument
 
-					if (strncasecmp(iext, "MIME", 4) == 0)
-					{
-						// get the MIME type from the next argument
-						iext = argv[++arg];
-						pInFormat = Conv.FormatFromMIME(iext);
-					}
-					else
-					{
-						//The ID provided by the OBFormat class is used as the identifying file extension
-						pInFormat = Conv.FindFormat(iext);
-					}
-					if(pInFormat==NULL)
-					{
-						cerr << program_name << ": cannot read input format!" << endl;
-						usage();
-					}
-                                inputExt = iext;
-					break;
+                  if (strncasecmp(iext, "MIME", 4) == 0)
+                    {
+                      // get the MIME type from the next argument
+                      iext = argv[++arg];
+                      pInFormat = Conv.FormatFromMIME(iext);
+                    }
+                  else
+                    {
+                      //The ID provided by the OBFormat class is used as the identifying file extension
+                      pInFormat = Conv.FindFormat(iext);
+                    }
+                  if(pInFormat==NULL)
+                    {
+                      cerr << program_name << ": cannot read input format!" << endl;
+                      usage();
+                    }
+                  break;
+                  
+                case 'o':
+                  gotOutType = true;
+                  oext = argv[arg] + 2;
+                  if(!*oext)
+                    oext = argv[++arg]; //space left after -i: use next argument
 					
-				case 'o':
-					gotOutType = true;
-					oext = argv[arg] + 2;
-					if(!*oext)
-						oext = argv[++arg]; //space left after -i: use next argument
-					
-					if (strncasecmp(oext, "MIME", 4) == 0)
-					{
-						// get the MIME type from the next argument
-						oext = argv[++arg];
-						pOutFormat = Conv.FormatFromMIME(oext);
-					}
-					else
-						pOutFormat = Conv.FindFormat(oext);
+                  if (strncasecmp(oext, "MIME", 4) == 0)
+                    {
+                      // get the MIME type from the next argument
+                      oext = argv[++arg];
+                      pOutFormat = Conv.FormatFromMIME(oext);
+                    }
+                  else
+                    pOutFormat = Conv.FindFormat(oext);
 
-					if(pOutFormat==NULL)
-					{
-						cerr << program_name << ": cannot write output format!" << endl;
-						usage();
-					}
-                                outputExt = oext;
-					break;				
-				
-				case '?':
-				case 'H':
-					if(isalnum(argv[arg][2]))
-					{
-						if(strncasecmp(argv[arg]+2,"all",3))
-						{
-							OBFormat* pFormat = Conv.FindFormat(argv[arg]+2);
-							if(pFormat)
-								{
-									cout << argv[arg]+2 << "  " << pFormat->Description() << endl;
-									if(strlen(pFormat->SpecificationURL()))
-							cout << "Specification at: " << pFormat->SpecificationURL() << endl;
-								}
-							else
-								cout << "Format type: " << argv[arg]+2 << " was not recognized" <<endl;
-						}
-						else
-						{
-							Formatpos pos;
-							OBFormat* pFormat;
-							const char* str=NULL;
-							while(OBConversion::GetNextFormat(pos,str,pFormat))
-								{
-									if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE))
-										continue;
-									cout << str << endl;
-									const char* p = strchr(pFormat->Description(),'\n');
-									cout << p+1; //second line of description
-									if(strlen(pFormat->SpecificationURL()))
-							cout << "Specification at: " << pFormat->SpecificationURL();
-									cout << endl << endl;
-								}
-						}
-					}
-					else
-						help();
-						exit(0);					
+                  if(pOutFormat==NULL)
+                    {
+                      cerr << program_name << ": cannot write output format!" << endl;
+                      usage();
+                    }
+                  break;
+
+                /*case 'F':
+                  if(!Conv.SetOutFormat("fpt"))
+                    cout << "FingerprintFormat needs to be loaded" << endl;
+                  else
+                    {
+                      Conv.AddOption("F",OBConversion::OUTOPTIONS);
+                      Conv.Write(NULL);
+                    }
+                  return 0;
+                  */
+                case 'L': //display a list of plugin type or classes
+                  {
+                    const char* param=NULL;
+                    if(argc>arg+1)
+                      param = argv[arg+2];
+                    OBPlugin::List(argv[arg+1], param);
+                    return 0;
+                  }
+                case '?':
+                case 'H':
+                  if(isalnum(argv[arg][2]) || arg==argc-2)
+                    {
+                      if(strncasecmp(argv[arg]+2,"all",3))
+                        {
+                          const char* pID= (arg==argc-2) ? argv[arg+1] : argv[arg]+2;
+                          OBFormat* pFormat = Conv.FindFormat(pID);
+                          if(pFormat)
+                            {
+                              cout << pID << "  " << pFormat->Description() << endl;
+                              if(pFormat->Flags() & NOTWRITABLE)
+                                cout << " This format is Read-only" << endl;
+                              if(pFormat->Flags() & NOTREADABLE)
+                                cout << " This format is Write-only" << endl;
+
+                              if(strlen(pFormat->SpecificationURL()))
+                                cout << "Specification at: " << pFormat->SpecificationURL() << endl;
+                            }
+                          else
+                            cout << "Format type: " << pID << " was not recognized" <<endl;
+                        }
+                      else
+                        {
+                          OBPlugin::List("formats","verbose");
+                        }
+                    }
+                  else
+                    help();
+                  return 0;
 					
+                case '-': //long option --name text
+                  {
+                    //Do nothing if name is empty
+                    //Option's text is the next arg provided it doesn't start with -
+                    char* nam = argv[arg]+2;
+                    if(*nam != '\0')
+                      {
+                        string txt;
+                        int i;
+                        for(i=0; i<Conv.GetOptionParams(nam, OBConversion::GENOPTIONS)
+                              && arg<argc-1 && argv[arg+1];++i) //removed  && *argv[arg+1]!='-'
+                          {
+                            if(!txt.empty()) txt+=' ';
+                            txt += argv[++arg];
+                          }
+                        if(*nam=='-')
+                          {
+                            // Is a API directive, e.g.---errorlevel
+                            //Send to the pseudoformat "obapi" (without any leading -)
+                            OBConversion apiConv;
+                            OBFormat* pAPI= OBConversion::FindFormat("obapi");
+                            if(pAPI)
+                              {
+                                apiConv.SetOutFormat(pAPI);
+                                apiConv.AddOption(nam+1, OBConversion::GENOPTIONS, txt.c_str());
+                                apiConv.Write(NULL, &std::cout);
+                              }
+                          }
+                        else
+                          // Is a long option name, e.g --addtotitle
+                          Conv.AddOption(nam,OBConversion::GENOPTIONS,txt.c_str());
+                      }
+                  }
+                  break;
 					
-				default: //single character general option
-					p = argv[arg]+1;
-					DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv);
-					break;
-				}
-			}
-			else 
-			{
-				//filenames
-				if(!gotOutType)
-					FileList.push_back(argv[arg]);
-				else
-					OutputFileName = argv[arg];
-			}
-		}
-	}
-    
-  //user didn't specify input and output format in commandline option
-  //try to parse it from program name (pdb2mdin means input format is pdb, output format is mdin)
+                case 'm': //multiple output files
+                  SplitOrBatch=true;
+                  break;
+					
+                case 'a': //single character input option
+                  p = argv[arg]+2;
+                  DoOption(p,Conv,OBConversion::INOPTIONS,arg,argc,argv);
+                  break;
+
+                case 'x': //single character output option
+                  p = argv[arg]+2;
+                  DoOption(p,Conv,OBConversion::OUTOPTIONS,arg,argc,argv);
+                  break;
+					
+                default: //single character general option
+                  p = argv[arg]+1;
+                  DoOption(p,Conv,OBConversion::GENOPTIONS,arg,argc,argv);
+                  break;
+                }
+            }
+          else 
+            {
+              //filenames
+              if(!gotOutType)
+                FileList.push_back(argv[arg]);
+              else
+                OutputFileName = argv[arg];
+            }
+        }
+    }
+  
+  // user didn't specify input and output format in commandline option
+  // try to parse it from program name (pdb2md means input format is pdb, 
+  // output format is md)
+
   string formatName(program_name);
   pos = formatName.find_first_of("2");
   if(pos!=string::npos) {
     if (!gotInType)
-    {
+      {
         string tmpExt = formatName.substr(0, pos);
         pInFormat = Conv.FindFormat(tmpExt.c_str());
- 	 if(pInFormat==NULL)
- 	 {
- 		cerr << program_name << ": cannot read input format!" << endl;
- 		usage();
- 	 } else 
-        {
+        if(pInFormat==NULL)
+          {
+            cerr << program_name << ": cannot read input format!" << endl;
+            usage();
+          } else 
+          {
             gotInType = true;
             inputExt = tmpExt;
- 	 }
-    }
+          }
+      }
 
     if (!gotOutType)
-    {
+      {
         string tmpExt = formatName.substr(pos+1, string::npos);
         pOutFormat = Conv.FindFormat(tmpExt.c_str());
-   	 if(pOutFormat==NULL)
- 	 {
- 		cerr << program_name << ": cannot write output format!" << endl;
- 		usage();
- 	 }else {
-            gotOutType = true;
-            outputExt = tmpExt;
- 	 }
+        if(pOutFormat==NULL)
+          {
+            cerr << program_name << ": cannot write output format!" << endl;
+            usage();
+          }else {
+          gotOutType = true;
+          outputExt = tmpExt;
+        }
+      }
+  } 
+
+  if(!gotOutType) //the last file is the output
+    {
+      if(FileList.empty())
+        {
+          cerr << "No output file or format spec!" << endl;
+          usage();
+        }
+      OutputFileName = FileList.back();
+      FileList.pop_back();
     }
-  }
 
-    if(FileList.empty())
+#ifdef _WIN32
+  //Expand wildcards in input filenames and add to FileList
+  vector<string> tempFileList(FileList);
+  FileList.clear();
+  vector<string>::iterator itr;
+  for(itr=tempFileList.begin();itr!=tempFileList.end();++itr)
+    DLHandler::findFiles (FileList, *itr);
+#endif
+  
+  if (!gotInType)
     {
-    	cerr << "No input file or format spec!" <<endl;
-    	usage();
+      if(FileList.empty())
+        {
+          cerr << "No input file or format spec!" <<endl;
+          usage();
+        }
     }
 
-   if (OutputFileName.empty())
-   {
-        pos = FileList.front().rfind(".");
-        if(pos==string::npos)
-            OutputFileName = FileList.front()+ "." + outputExt;
-        else
-            OutputFileName = FileList.front().substr(0, pos) + "." + outputExt;            
+  if (!gotOutType)
+    {
+      pOutFormat = Conv.FormatFromExt(OutputFileName.c_str());
+      if(pOutFormat==NULL)
+        {
+          cerr << program_name << ": cannot write output format!" << endl;
+          usage();
+        }
     }
   
-  Conv.SetInAndOutFormats(pInFormat,pOutFormat);
+    if(!Conv.SetInFormat(pInFormat))
+    {
+      cerr << "Invalid input format" << endl;
+      usage();
+    }
+    if(!Conv.SetOutFormat(pOutFormat))
+    {
+      cerr << "Invalid output format" << endl;
+      usage();
+    }
 
+  if(SplitOrBatch)
+    {
+      //Put * into output file name before extension (or ext.gz)
+      if(OutputFileName.empty())
+        {
+          OutputFileName = "*.";
+          if (oext != NULL)
+            OutputFileName += oext;
+        }
+      else
+        {
+          string::size_type pos = OutputFileName.rfind(".gz");
+          if(pos==string::npos)
+            pos = OutputFileName.rfind('.');
+          else
+            pos = OutputFileName.rfind('.',pos-1);
+          if(pos==string::npos)
+            OutputFileName += '*';
+          else
+            OutputFileName.insert(pos,"*");
+        }
+    }
 
-  // send info message to clog -- don't mess up cerr or cout for user programs
   int count = Conv.FullConvert(FileList, OutputFileName, OutputFileList);
-  if ( count == 1 )
-    clog << count << " molecule converted" << endl;
-  else
-    clog << count << " molecules converted" << endl;
-  
+ 
+  Conv.ReportNumberConverted(count);
+
   if(OutputFileList.size()>1)
-  {
-    clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl;
-  }
+    {
+      clog << OutputFileList.size() << " files output. The first is " << OutputFileList[0] <<endl;
+    }
 
+  std::string messageSummary = obErrorLog.GetMessageSummary();
+  if (messageSummary.size())
+    {
+      clog << messageSummary << endl;
+    }
+
 #ifdef _DEBUG
   //CM keep window open
   cout << "Press any key to finish" <<endl;
@@ -290,57 +409,59 @@ int main(int argc,char *argv[])
   return 0;
 }
 
-void DoOption(const char* p, OBConversion& Conv, OBConversion::Option_type typ, int& arg, int argc, char *argv[]) 
+void DoOption(const char* p, OBConversion& Conv,
+	      OBConversion::Option_type typ, int& arg, int argc, char *argv[]) 
 {
-	while(p && *p) //can have multiple single char options
-	{
-		char ch[2]="?";
-		*ch = *p++;
-		const char* txt=NULL;				
-		//Get the option text if needed
-		int nParams = Conv.GetOptionParams(ch, typ);
-		if(nParams)
-		{
-			if(*p)
-			{
-				txt = p; //use text immediately following the option letter
-				p=NULL; //no more single char options
-			}
-			else if(arg<argc-1)
-			{
-				txt = argv[++arg]; //use text from next arg
-				if(*txt=='-')
-				{
-					//...unless it is another option
-					cerr << "Option -" << ch << " takes a parameter" << endl;
-					exit(0);
-				}
-			}
-		}
-		Conv.AddOption(ch, typ, txt);
-	}
+  while(p && *p) //can have multiple single char options
+  {
+    char ch[2]="?";
+    *ch = *p++;
+    const char* txt=NULL;				
+    //Get the option text if needed
+    int nParams = Conv.GetOptionParams(ch, typ);
+    if(nParams)
+    {
+      if(*p)
+      {
+        txt = p; //use text immediately following the option letter
+        p=NULL; //no more single char options
+      }
+      else if(arg<argc-1)
+      {
+        txt = argv[++arg]; //use text from next arg
+        if(*txt=='-')
+        {
+          //...unless it is another option
+          cerr << "Option -" << ch << " takes a parameter" << endl;
+          exit(0);
+        }
+      }
+    }
+    Conv.AddOption(ch, typ, txt);
+  }
 }
 
 void usage()
 {
-  cout << "Open Babel " << BABEL_VERSION << " -- " << __DATE__ << " -- "
-       << __TIME__ << endl;
+  cout << program_name << ": part of OpenMD " << 
+    OPENMD_VERSION_MAJOR << "." << OPENMD_VERSION_MINOR << "." << 
+    OPENMD_VERSION_TINY << " and OpenBabel " << BABEL_VERSION << " -- " 
+       << __DATE__ << " -- " << __TIME__ << endl;
   cout << "Usage: " << program_name
        << " [-i<input-type>] <name> [-o<output-type>] <name>" << endl;
   cout << "Try  -H option for more information." << endl;
-/*  
+ 
 #ifdef _DEBUG
   //CM keep window open
   cout << "Press any key to finish" <<endl;
   getch();
 #endif
-*/  
   exit (0);
 }
 
 void help()
 {
-  cout << "Open Babel converts chemical structures from one file format to another"<< endl << endl;
+  cout << program_name << " converts chemical structures from one file format to another"<< endl << endl;
   cout << "Usage: " << program_name << " <input spec> <output spec> [Options]" << endl << endl;
   cout << "Each spec can be a file whose extension decides the format." << endl;
   cout << "Optionally the format can be specified by preceding the file by" << endl;
@@ -358,23 +479,23 @@ void help()
 
   
   OBFormat* pDefault = OBConversion::GetDefaultFormat();
-	if(pDefault)
-		cout << pDefault->TargetClassDescription();// some more options probably for OBMol
+  if(pDefault)
+    cout << pDefault->TargetClassDescription();// some more options probably for OBMol
   
-	OBFormat* pAPI= OBConversion::FindFormat("obapi");
-	if(pAPI)
-		cout << pAPI->Description();
-
-	cout << "The following file formats are recognized:" << endl;
+  OBFormat* pAPI= OBConversion::FindFormat("obapi");
+  if(pAPI)
+    cout << pAPI->Description();
+  
+  cout << "The following file formats are recognized:" << endl;
   Formatpos pos;
   OBFormat* pFormat;
   const char* str=NULL;
   while(OBConversion::GetNextFormat(pos,str,pFormat))
-  {
-		if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE))
-			continue;
-		cout << "  " << str << endl;
-	}
+    {
+      if((pFormat->Flags() & NOTWRITABLE) && (pFormat->Flags() & NOTREADABLE))
+	continue;
+      cout << "  " << str << endl;
+    }
   cout << "\nSee further specific info and options using -H<format-type>, e.g. -Hpdb" << endl;
 }