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/********************************************************************** |
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transform.cpp - Perform command-line requested transformations |
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Copyright (C) 2004-2005 by Chris Morley |
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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 <iostream> |
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|
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using namespace std; |
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namespace OpenBabel |
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{ |
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|
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OBBase* OBMol::DoTransformations(const std::map<std::string, std::string>* pOptions) |
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{ |
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// Perform any requested transformations |
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// on a OBMol |
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//The input map has option letters or name as the key and |
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//any associated text as the value. |
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//For normal(non-filter) transforms: |
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// returns a pointer to the OBMol (this) if ok or NULL if not. |
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//For filters returns a pointer to the OBMol (this) if there is a match, |
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//and NULL when not and in addition the OBMol object is deleted NULL. |
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|
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//This is now a virtual function. The OBBase version just returns the OBMol pointer. |
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//This is declared in mol.h |
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|
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//The filter options, s and v allow a obgrep facility. |
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//Used together they must both be true to allow a molecule through. |
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|
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//Parse GeneralOptions |
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if(pOptions->empty()) |
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return this; |
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|
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int ret=1; |
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bool smatch=true, vmatch=true; |
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|
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map<string,string>::const_iterator itr; |
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|
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if(pOptions->find("b")!=pOptions->end()) |
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ret=ConvertDativeBonds(); |
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|
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if(pOptions->find("d")!=pOptions->end()) |
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ret=DeleteHydrogens(); |
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|
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if(pOptions->find("h")!=pOptions->end()) |
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ret=AddHydrogens(false, false); |
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|
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if(pOptions->find("p")!=pOptions->end()) |
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ret=AddHydrogens(false, true); |
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|
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if(pOptions->find("c")!=pOptions->end()) |
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{ |
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Center(); |
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ret=1; |
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} |
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|
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itr = pOptions->find("addtotitle"); //Appends text to title |
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if(itr!=pOptions->end()) |
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{ |
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string title(GetTitle()); |
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title += itr->second; |
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SetTitle(title.c_str()); |
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ret=1; |
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} |
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|
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itr = pOptions->find("v"); |
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if(itr!=pOptions->end()) |
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{ |
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//inverse match quoted SMARTS string which follows |
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OBSmartsPattern sp; |
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sp.Init(itr->second); |
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vmatch = !sp.Match(*this); //(*pmol) ; |
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} |
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|
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itr = pOptions->find("s"); |
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if(itr!=pOptions->end()) |
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{ |
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//match quoted SMARTS string which follows |
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OBSmartsPattern sp; |
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sp.Init(itr->second.c_str()); |
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smatch = sp.Match(*this); //(*pmol) ; |
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} |
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|
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if(!smatch || !vmatch) |
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{ |
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//filter failed: delete OBMol and return NULL |
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delete this; |
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return NULL; |
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} |
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else |
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return ret ? this : NULL; |
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} |
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|
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/////////////////////////////////////////////////// |
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const char* OBMol::ClassDescription() |
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{ |
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return "For conversions of molecules\n \ |
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Additional options :\n \ |
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-d Delete Hydrogens\n \ |
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-h Add Hydrogens\n \ |
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-p Add Hydrogens appropriate for pH\n \ |
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-b Convert dative bonds e.g.[N+]([O-])=O to N(=O)=O\n \ |
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-c Center Coordinates\n \ |
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-j Join all input molecules into a single output molecule\n \ |
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-s\"smarts\" Convert only molecules matching SMARTS:\n \ |
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-v\"smarts\" Convert only molecules NOT matching SMARTS:\n\n" ; |
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} |
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|
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} //namespace OpenBabel |
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|
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//! \file transform.cpp |
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//! \brief Perform command-line requested transformations for OBMol |
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//! and SMARTS filtering |
