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/**********************************************************************
Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc.
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
the Free Software Foundation version 2 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
***********************************************************************/
#include "mol.h"
#include "obutil.h"
#include "parsmart.h"
#include "patty.h"
// Simple programmable atom typer
// WPW - 070199
// Usage is in sample main below
namespace OpenBabel {
void patty::read_rules(const string &infile)
{
ifstream ifs, ifs1, *ifsP;
vector<string> vs;
char buffer[BUFF_SIZE];
char tmp_str[BUFF_SIZE];
char patty_dir[BUFF_SIZE];
_sp.resize(1000);
ifs.open(infile.c_str());
ifsP= &ifs;
if (!ifs)
{
if (getenv("BABEL_DATADIR") == NULL)
{
cerr << "The BABEL_DATADIR environment variable is not defined" << endl;
cerr << "Please define it so the program can find " << infile << endl;
exit(0);
}
else
strcpy(patty_dir,getenv("BABEL_DATADIR"));
strcat(patty_dir,FILE_SEP_CHAR);
strcat(patty_dir,infile.c_str());
ifs1.open(patty_dir);
ifsP= &ifs1;
// if (!ifs1)
// {
// cerr << "Could not open " << patty_dir << endl;
// exit(0);
// }
}
int i = 0;
if (!ifsP){
cerr << "Could not open " << patty_dir << endl;
exit(0);
}
while (ifsP->getline(buffer,BUFF_SIZE))
{
if (buffer[0] != '#')
{
tokenize(vs,buffer," \t\n");
if (vs.size() >= 2)
{
strcpy(tmp_str,vs[0].c_str());
_sp[i]->Init(tmp_str);
smarts.push_back(vs[0]);
typ.push_back(vs[1]);
i++;
}
}
}
_sp.resize(i);
}
void patty::assign_rules(vector<string> &rules)
{
vector<string> vs;
char buffer[BUFF_SIZE];
char tmp_str[BUFF_SIZE];
unsigned int i;
_sp.resize(1000);
for ( i = 0 ; i < rules.size() ; i++ )
{
strncpy(buffer, rules[i].c_str(), BUFF_SIZE);
if (buffer[0] != '#')
{
tokenize(vs,buffer," \t\n");
if (vs.size() >= 2)
{
strcpy(tmp_str,vs[0].c_str());
_sp[i]->Init(tmp_str);
smarts.push_back(vs[0]);
typ.push_back(vs[1]);
}
else
i--;
}
else
i--;
}
_sp.resize(i);
}
void patty::assign_types(OBMol &mol,vector<string> &atm_typ)
{
atm_typ.resize(mol.NumAtoms()+1);
for (unsigned int i = 0; i < _sp.size(); i++)
{
_sp[i]->Match(mol);
vector<vector<int> > match = _sp[i]->GetMapList();
//vector<vector<int> >& match = _sp[i]->GetMapList();
if (match.size())
{
if (debug)
cout << typ[i] << " " << smarts[i] << " matched " ;
for (unsigned int j = 0; j < match.size(); j++)
{
if (debug)
cout << match[j][0] << " ";
atm_typ[match[j][0]] = typ[i];
}
if (debug)
cout << endl;
}
}
}
void patty::assign_types(OBMol &mol,vector<int> &atm_typ)
{
atm_typ.resize(mol.NumAtoms()+1);
for (unsigned int i = 0; i < _sp.size(); i++)
{
_sp[i]->Match(mol);
vector<vector<int> > match = _sp[i]->GetMapList();
//vector<vector<int> >& match = _sp[i]->GetMapList();
if (match.size())
{
if (debug)
cout << typ[i] << " " << smarts[i] << " matched " ;
for (unsigned int j = 0; j < match.size(); j++)
{
if (debug)
cout << match[j][0] << " ";
atm_typ[match[j][0]] = type_to_int(typ[i]);
}
if (debug)
cout << endl;
}
}
}
int patty::type_to_int(const string &type, bool failOnUndefined)
{
int result;
switch(toupper(type.c_str()[0]))
{
case 'C' : // CAT - CATION
result = PT_CATION;
break;
case 'A' :
if (toupper(type.c_str()[1]) == 'N') // ANI - ANION
result = PT_ANION;
else
result = PT_ACCEPTOR;
break;
case 'P' : // POL - POLAR
result = PT_POLAR;
break;
case 'D' : // DON - DONOR
result = PT_DONOR;
break;
case 'H' : // HYD - HYDROPHOBIC
result = PT_HYDROPHOBIC;
break;
case 'M' : // Metal
result = PT_METAL;
break;
case 'O' : // OTH - OTHER
result = PT_OTHER;
break;
default :
// This was added by Brian,
// Behavior will fail if type is undefined
if (failOnUndefined){
cerr << "Unable to find type of feature passed in " << endl;
cerr << "Feature passed in is " << type << endl;
exit(-1);
}else{
result = 7;
}
}
return(result);
}
}
#ifdef I_EVER_BUY_A_MICHAEL_BOLTON_ALBUM
int main(int argc, char *argv[])
{
OBMol mol(SDF,SDF);
vector<string> types;
ifstream ifs(argv[1]);
if (!ifs)
{
cerr << "Could not open argv[1] " << endl;
exit(0);
}
patty p("simple.txt");
for (;;)
{
ifs >> mol;
if (!mol.NumAtoms()) break;
p.assign_types(mol,types);
mol.Clear();
}
for (int i = 1; i < types.size(); i++)
{
cout << i << " " << types[i] << endl;
}
}
#endif
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