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root/OpenMD/trunk/src/openbabel/patty.cpp
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Comparing trunk/src/openbabel/patty.cpp (file contents):
Revision 819 by tim, Fri Dec 16 21:52:50 2005 UTC vs.
Revision 1081 by gezelter, Thu Oct 19 20:49:05 2006 UTC

# Line 2 | Line 2 | Copyright (C) 1998-2001 by OpenEye Scientific Software
2   patty.cpp - Programmable atom typer.
3  
4   Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
5 < Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison
5 > Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison
6  
7   This file is part of the Open Babel project.
8   For more information, see <http://openbabel.sourceforge.net/>
# Line 68 | Line 68 | void patty::read_rules(const string &infile)
68      vector<string> vs;
69      char buffer[BUFF_SIZE];
70      char tmp_str[BUFF_SIZE];
71 <    char patty_dir[BUFF_SIZE];
71 >    string patty_dir;
72      OBSmartsPattern *sp;
73  
74      ifs.open(infile.c_str());
75      ifsP= &ifs;
76      if (!ifs)
77      {
78 <        if (getenv("FORCE_PARAM_PATH") == NULL)
78 >        if (getenv("BABEL_DATADIR") == NULL)
79          {
80   #ifdef HAVE_SSTREAM
81            stringstream errorMsg;
82   #else
83            strstream errorMsg;
84   #endif
85 <          errorMsg << "The FORCE_PARAM_PATH environment variable is not defined" << endl;
85 >          errorMsg << "The BABEL_DATADIR environment variable is not defined" << endl;
86            errorMsg << "Please define it so the program can find " << infile << endl;
87            obErrorLog.ThrowError(__func__, errorMsg.str(), obWarning);
88              //            exit(0);
89          }
90          else
91 <            strcpy(patty_dir,getenv("FORCE_PARAM_PATH"));
92 <        strcat(patty_dir,FILE_SEP_CHAR);
93 <        strcat(patty_dir,infile.c_str());
94 <        ifs1.open(patty_dir);
91 >            patty_dir = getenv("BABEL_DATADIR");
92 >        patty_dir += FILE_SEP_CHAR;
93 >        patty_dir += infile;
94 >        ifs1.open(patty_dir.c_str());
95          ifsP= &ifs1;
96          //     if (!ifs1)
97          //    {
# Line 118 | Line 118 | void patty::read_rules(const string &infile)
118              tokenize(vs,buffer," \t\n");
119              if (vs.size() >= 2)
120              {
121 <                strcpy(tmp_str,vs[0].c_str());
121 >                strncpy(tmp_str,vs[0].c_str(), sizeof(tmp_str) - 1);
122 >                tmp_str[sizeof(tmp_str) - 1] = '\0';
123                  sp = new OBSmartsPattern;
124                  sp->Init(tmp_str);
125                  _sp.push_back(sp);
# Line 145 | Line 146 | void patty::assign_rules(std::vector<std::string> &rul
146              tokenize(vs,buffer," \t\n");
147              if (vs.size() >= 2)
148              {
149 <                strcpy(tmp_str,vs[0].c_str());
149 >                strncpy(tmp_str,vs[0].c_str(), sizeof(tmp_str) - 1);
150 >                tmp_str[sizeof(tmp_str) - 1] = '\0';
151                  sp = new OBSmartsPattern;
152                  sp->Init(tmp_str);
153                  _sp.push_back(sp);

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