PLearn 0.1
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00001 // -*- C++ -*- 00002 00003 // MoleculeTemplate.h 00004 // 00005 // Copyright (C) 2006 Pascal Lamblin 00006 // 00007 // Redistribution and use in source and binary forms, with or without 00008 // modification, are permitted provided that the following conditions are met: 00009 // 00010 // 1. Redistributions of source code must retain the above copyright 00011 // notice, this list of conditions and the following disclaimer. 00012 // 00013 // 2. Redistributions in binary form must reproduce the above copyright 00014 // notice, this list of conditions and the following disclaimer in the 00015 // documentation and/or other materials provided with the distribution. 00016 // 00017 // 3. The name of the authors may not be used to endorse or promote 00018 // products derived from this software without specific prior written 00019 // permission. 00020 // 00021 // THIS SOFTWARE IS PROVIDED BY THE AUTHORS ``AS IS'' AND ANY EXPRESS OR 00022 // IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES 00023 // OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN 00024 // NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 00025 // SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED 00026 // TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR 00027 // PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF 00028 // LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING 00029 // NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 00030 // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 00031 // 00032 // This file is part of the PLearn library. For more information on the PLearn 00033 // library, go to the PLearn Web site at www.plearn.org 00034 00035 // Authors: Pascal Lamblin 00036 00040 #ifndef MoleculeTemplate_INC 00041 #define MoleculeTemplate_INC 00042 00043 #include "Molecule.h" 00044 00045 namespace PLearn { 00046 using namespace std; 00047 00048 class MoleculeTemplate; 00049 typedef PP<MoleculeTemplate> MolTemplate; 00050 00059 class MoleculeTemplate : public Molecule 00060 { 00061 typedef Molecule inherited; 00062 00063 public: 00064 //##### Public Build Options ############################################ 00065 00067 00069 Vec geom_dev; 00070 00072 Mat feat_dev; 00073 00075 int class_label; 00076 00077 00078 public: 00079 //##### Public Member Functions ######################################### 00080 00082 MoleculeTemplate( int the_class_label = -1 ); 00083 00085 MoleculeTemplate( const PPath& filename, int the_class_label = -1 ); 00086 00088 MoleculeTemplate( const Molecule& molecule, 00089 const Vec& the_geom_dev = Vec(), 00090 const Mat& the_feat_dev = Mat(), 00091 int the_class_label = -1 ); 00092 00093 //##### PLearn::Object Protocol ######################################### 00094 00095 // Declares other standard object methods. 00096 // ### If your class is not instantiatable (it has pure virtual methods) 00097 // ### you should replace this by PLEARN_DECLARE_ABSTRACT_OBJECT 00098 PLEARN_DECLARE_OBJECT(MoleculeTemplate); 00099 00100 // Simply calls inherited::build() then build_() 00101 virtual void build(); 00102 00104 // (PLEASE IMPLEMENT IN .cc) 00105 virtual void makeDeepCopyFromShallowCopy(CopiesMap& copies); 00106 00107 protected: 00108 //##### Protected Options ############################################### 00109 00110 // ### Declare protected option fields (such as learned parameters) here 00111 // ... 00112 00113 protected: 00114 //##### Protected Member Functions ###################################### 00116 virtual void readFromAMATFile( const PPath& filename ); 00117 00119 virtual void writeToAMATFile( const PPath& filename ); 00120 00122 // (PLEASE IMPLEMENT IN .cc) 00123 static void declareOptions(OptionList& ol); 00124 00125 private: 00126 //##### Private Member Functions ######################################## 00127 00129 // (PLEASE IMPLEMENT IN .cc) 00130 void build_(); 00131 00132 private: 00133 //##### Private Data Members ############################################ 00134 00135 // The rest of the private stuff goes here 00136 }; 00137 00138 // Declares a few other classes and functions related to this class 00139 DECLARE_OBJECT_PTR(MoleculeTemplate); 00140 00141 } // end of namespace PLearn 00142 00143 #endif 00144 00145 00146 /* 00147 Local Variables: 00148 mode:c++ 00149 c-basic-offset:4 00150 c-file-style:"stroustrup" 00151 c-file-offsets:((innamespace . 0)(inline-open . 0)) 00152 indent-tabs-mode:nil 00153 fill-column:79 00154 End: 00155 */ 00156 // vim: filetype=cpp:expandtab:shiftwidth=4:tabstop=8:softtabstop=4:encoding=utf-8:textwidth=79 :