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/********************************************************************** |
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patty.cpp - Programmable atom typer. |
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|
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Copyright (C) 1998-2001 by OpenEye Scientific Software, Inc. |
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Some portions Copyright (C) 2001-2005 by Geoffrey R. Hutchison |
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|
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This file is part of the Open Babel project. |
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For more information, see <http://openbabel.sourceforge.net/> |
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|
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the GNU General Public License as published by |
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the Free Software Foundation version 2 of the License. |
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|
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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GNU General Public License for more details. |
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***********************************************************************/ |
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|
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#include "mol.hpp" |
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#include "obutil.hpp" |
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#include "parsmart.hpp" |
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#include "patty.hpp" |
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|
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// Simple programmable atom typer |
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// WPW - 070199 |
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// Usage is in sample main below |
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|
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using namespace std; |
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|
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namespace OpenBabel |
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{ |
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|
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/*! \class patty |
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\brief Programmable Atom Typer |
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|
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Patty stands for programmable atom typer. The patty class was kindly |
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donated by W. Patrick Walters. The patty class provides a more |
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flexible means for atom typing than the OBAtomTyper. The behavior of |
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patty is similar to the OBAtomTyper in that rules apply only to the |
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first atom in the SMARTS pattern. The patty class can read any free |
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format ASCII file which contains SMARTS patterns associated with user |
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defined atom type. The following is an example of a valid patty rule |
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\code |
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O=C hbacceptor |
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\endcode |
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The following is a code sample that demonstrates the use of patty |
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class: |
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\code |
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OBMol mol; |
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|
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string rulefile = "rules.txt"; |
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patty p; |
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p.read_rules(p); |
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vector<string> type; |
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p.assign_types(mol,type); |
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for (int i = 1;i <= mol.NumAtoms();i++) |
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cout << "atom number " << i << " was given a type " << type[i] << endl; |
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\endcode |
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The array indices in the vector<string> into which the result values |
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are placed match the corresponding atom numbers. Since atoms are |
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numbered beginning from one, the first element in the vector<string> |
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is empty, and the values are placed in [1...mol.NumAtoms()]. |
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*/ |
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void patty::read_rules(const string &infile) |
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{ |
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ifstream ifs, ifs1, *ifsP; |
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vector<string> vs; |
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char buffer[BUFF_SIZE]; |
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char tmp_str[BUFF_SIZE]; |
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char patty_dir[BUFF_SIZE]; |
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OBSmartsPattern *sp; |
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|
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ifs.open(infile.c_str()); |
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ifsP= &ifs; |
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if (!ifs) |
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{ |
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if (getenv("FORCE_PARAM_PATH") == NULL) |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
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#else |
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strstream errorMsg; |
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#endif |
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errorMsg << "The FORCE_PARAM_PATH environment variable is not defined" << endl; |
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errorMsg << "Please define it so the program can find " << infile << endl; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obWarning); |
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// exit(0); |
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} |
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else |
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strcpy(patty_dir,getenv("FORCE_PARAM_PATH")); |
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strcat(patty_dir,FILE_SEP_CHAR); |
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strcat(patty_dir,infile.c_str()); |
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ifs1.open(patty_dir); |
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ifsP= &ifs1; |
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// if (!ifs1) |
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// { |
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// cerr << "Could not open " << patty_dir << endl; |
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// exit(0); |
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// } |
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} |
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|
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if (!ifsP) |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
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#else |
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strstream errorMsg; |
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#endif |
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errorMsg << "Could not open " << patty_dir << endl; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obWarning); |
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// exit(0); |
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} |
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while (ifsP->getline(buffer,BUFF_SIZE)) |
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{ |
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if (buffer[0] != '#') |
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{ |
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tokenize(vs,buffer," \t\n"); |
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if (vs.size() >= 2) |
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{ |
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strcpy(tmp_str,vs[0].c_str()); |
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sp = new OBSmartsPattern; |
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sp->Init(tmp_str); |
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_sp.push_back(sp); |
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smarts.push_back(vs[0]); |
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typ.push_back(vs[1]); |
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} |
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} |
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} |
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} |
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|
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void patty::assign_rules(std::vector<std::string> &rules) |
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{ |
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vector<string> vs; |
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char buffer[BUFF_SIZE]; |
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char tmp_str[BUFF_SIZE]; |
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unsigned int i; |
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OBSmartsPattern *sp; |
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|
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for ( i = 0 ; i < rules.size() ; i++ ) |
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{ |
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strncpy(buffer, rules[i].c_str(), BUFF_SIZE); |
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if (buffer[0] != '#') |
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{ |
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tokenize(vs,buffer," \t\n"); |
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if (vs.size() >= 2) |
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{ |
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strcpy(tmp_str,vs[0].c_str()); |
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sp = new OBSmartsPattern; |
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sp->Init(tmp_str); |
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_sp.push_back(sp); |
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smarts.push_back(vs[0]); |
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typ.push_back(vs[1]); |
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} |
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} |
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} |
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} |
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|
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|
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void patty::assign_types(OBMol &mol, std::vector<std::string> &atm_typ) |
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{ |
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atm_typ.resize(mol.NumAtoms()+1); |
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|
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obErrorLog.ThrowError(__func__, |
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"Ran OpenBabel::PATTY::AssignTypes", obAuditMsg); |
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|
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for (unsigned int i = 0; i < _sp.size(); i++) |
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{ |
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_sp[i]->Match(mol); |
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vector<vector<int> > match = _sp[i]->GetMapList(); |
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//vector<vector<int> >& match = _sp[i]->GetMapList(); |
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if (match.size()) |
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{ |
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if (debug) |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
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#else |
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strstream errorMsg; |
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#endif |
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errorMsg << typ[i] << " " << smarts[i] << " matched "; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug); |
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} |
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|
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for (unsigned int j = 0; j < match.size(); j++) |
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{ |
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if (debug) |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
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#else |
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strstream errorMsg; |
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#endif |
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errorMsg << match[j][0] << " "; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug); |
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} |
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atm_typ[match[j][0]] = typ[i]; |
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} |
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} |
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} |
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} |
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|
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void patty::assign_types(OBMol &mol,vector<int> &atm_typ) |
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{ |
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atm_typ.resize(mol.NumAtoms()+1); |
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|
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obErrorLog.ThrowError(__func__, |
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"Ran OpenBabel::PATTY::AssignTypes", obAuditMsg); |
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|
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for (unsigned int i = 0; i < _sp.size(); i++) |
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{ |
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_sp[i]->Match(mol); |
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vector<vector<int> > match = _sp[i]->GetMapList(); |
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//vector<vector<int> >& match = _sp[i]->GetMapList(); |
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if (match.size()) |
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{ |
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if (debug) |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
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#else |
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strstream errorMsg; |
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#endif |
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errorMsg << typ[i] << " " << smarts[i] << " matched " ; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug); |
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} |
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|
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for (unsigned int j = 0; j < match.size(); j++) |
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{ |
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if (debug) |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
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#else |
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strstream errorMsg; |
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#endif |
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errorMsg << match[j][0] << " "; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obDebug); |
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} |
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atm_typ[match[j][0]] = type_to_int(typ[i]); |
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} |
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} |
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} |
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} |
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|
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|
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int patty::type_to_int(const string &type, bool failOnUndefined) |
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{ |
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int result; |
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|
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switch(toupper(type.c_str()[0])) |
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{ |
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case 'C' : // CAT - CATION |
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result = PT_CATION; |
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break; |
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case 'A' : |
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if (toupper(type.c_str()[1]) == 'N') // ANI - ANION |
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result = PT_ANION; |
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else |
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result = PT_ACCEPTOR; |
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break; |
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case 'P' : // POL - POLAR |
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result = PT_POLAR; |
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break; |
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case 'D' : // DON - DONOR |
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result = PT_DONOR; |
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break; |
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case 'H' : // HYD - HYDROPHOBIC |
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result = PT_HYDROPHOBIC; |
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break; |
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case 'M' : // Metal |
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result = PT_METAL; |
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break; |
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case 'O' : // OTH - OTHER |
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result = PT_OTHER; |
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break; |
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default : |
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// This was added by Brian, |
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// Behavior will fail if type is undefined |
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if (failOnUndefined) |
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{ |
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#ifdef HAVE_SSTREAM |
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stringstream errorMsg; |
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#else |
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strstream errorMsg; |
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#endif |
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errorMsg << "Unable to find type of feature passed in " << endl; |
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errorMsg << "Feature passed in is " << type << endl; |
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obErrorLog.ThrowError(__func__, errorMsg.str(), obInfo); |
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// exit(-1); |
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} |
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else |
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{ |
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result = 7; |
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} |
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} |
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return(result); |
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} |
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|
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//! return null if the type does not exist, the type position otherwise |
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//! the first position start at 1 |
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int patty::Istype(const std::string &type) |
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{ |
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for(unsigned int pos=0; pos < typ.size(); pos++) |
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{ |
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if(typ[pos] == type) |
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return (pos + 1); |
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} |
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|
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return (0); |
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} |
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|
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} |
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|
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#ifdef COMPILE_PATTY_MAIN |
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// This was written for OB-1.x and would need updating for OB-2.0 if needed |
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// Consider it deprecated. |
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|
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int main(int argc, char *argv[]) |
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{ |
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OBMol mol(SDF,SDF); |
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vector<string> types; |
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|
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ifstream ifs(argv[1]); |
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if (!ifs) |
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{ |
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cerr << "Could not open supplied file " << endl; |
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// exit(0); |
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} |
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|
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patty p("simple.txt"); |
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for (;;) |
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{ |
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ifs >> mol; |
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if (!mol.NumAtoms()) |
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break; |
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p.assign_types(mol,types); |
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mol.Clear(); |
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} |
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|
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for (int i = 1; i < types.size(); i++) |
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{ |
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cout << i << " " << types[i] << endl; |
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} |
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} |
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|
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#endif |
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|
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//! \file patty.cpp |
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//! \brief Programmable atom typer. |
