Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2020 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #include "core/ActionShortcut.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "mapping/Path.h"
      25             : 
      26             : //+PLUMEDOC DIMRED SKETCHMAP_PROJECTION
      27             : /*
      28             : Read in a sketch-map projection
      29             : 
      30             : \par Examples
      31             : 
      32             : */
      33             : //+ENDPLUMEDOC
      34             : 
      35             : namespace PLMD {
      36             : namespace dimred {
      37             : 
      38             : class SketchMapProjection : public ActionShortcut {
      39             : public:
      40             :   static void registerKeywords( Keywords& keys );
      41             :   explicit SketchMapProjection( const ActionOptions& ao );
      42             : };
      43             : 
      44             : PLUMED_REGISTER_ACTION(SketchMapProjection,"SKETCHMAP_PROJECTION")
      45             : 
      46           4 : void SketchMapProjection::registerKeywords( Keywords& keys ) {
      47           4 :   ActionShortcut::registerKeywords( keys );
      48           4 :   mapping::Path::registerInputFileKeywords( keys );
      49           4 :   keys.add("compulsory","PROPERTY","the property to be used in the index. This should be in the REMARK of the reference");
      50           4 :   keys.add("compulsory","WEIGHT","the weight of each individual landmark in the stress fucntion that is to be optimised");
      51           4 :   keys.add("compulsory","HIGH_DIM_FUNCTION","the parameters of the switching function in the high dimensional space");
      52           4 :   keys.add("compulsory","LOW_DIM_FUNCTION","the parameters of the switching function in the low dimensional space");
      53           4 :   keys.add("compulsory","CGTOL","1E-6","The tolerance for the conjugate gradient minimization that finds the out of sample projections");
      54           8 :   keys.setValueDescription("scalar/vector","the out-of-sample projections of the input arguments using the input sketch-map projection");
      55           4 :   keys.needsAction("RMSD");
      56           4 :   keys.needsAction("PDB2CONSTANT");
      57           4 :   keys.needsAction("CONSTANT");
      58           4 :   keys.needsAction("CUSTOM");
      59           4 :   keys.needsAction("EUCLIDEAN_DISTANCE");
      60           4 :   keys.needsAction("NORMALIZED_EUCLIDEAN_DISTANCE");
      61           4 :   keys.needsAction("SUM");
      62           4 :   keys.needsAction("MORE_THAN");
      63           4 :   keys.needsAction("PROJECT_POINTS");
      64           4 : }
      65             : 
      66           1 : SketchMapProjection::SketchMapProjection( const ActionOptions& ao):
      67             :   Action(ao),
      68           1 :   ActionShortcut(ao) {
      69             :   // Use path to read in the projections
      70             :   std::string refname, refactions, metric;
      71             :   std::vector<std::string> argnames;
      72           2 :   parseVector("ARG",argnames);
      73             :   std::string type, reference_data, reference;
      74           1 :   parse("REFERENCE",reference);
      75           1 :   parse("TYPE",type);
      76           1 :   mapping::Path::readInputFrames( reference, type, argnames, false, this, reference_data );
      77             :   // And read in the data that we want on the projections
      78             :   std::vector<std::string> pnames;
      79           2 :   parseVector("PROPERTY",pnames);
      80             :   std::string weights;
      81           1 :   parse("WEIGHT",weights);
      82           1 :   pnames.push_back( weights );
      83             :   // Now create fixed vectors using some sort of reference action
      84           1 :   mapping::Path::readPropertyInformation( pnames, getShortcutLabel(), reference, this );
      85             :   // Normalise the vector of weights
      86           2 :   readInputLine( getShortcutLabel() + "_wsum: SUM PERIODIC=NO ARG=" + weights + "_ref");
      87           2 :   readInputLine( getShortcutLabel() + "_weights: CUSTOM ARG=" + getShortcutLabel() + "_wsum," +  weights + "_ref FUNC=y/x PERIODIC=NO");
      88             :   // Transform the high dimensional distances
      89             :   std::string hdfunc;
      90           1 :   parse("HIGH_DIM_FUNCTION",hdfunc);
      91           2 :   readInputLine( getShortcutLabel() + "_targ: MORE_THAN ARG=" + getShortcutLabel() + "_data SQUARED SWITCH={" + hdfunc + "}");
      92             :   // Create the projection object
      93             :   std::string ldfunc, cgtol;
      94           1 :   parse("LOW_DIM_FUNCTION",ldfunc);
      95           2 :   parse("CGTOL",cgtol);
      96           1 :   std::string argstr="ARG=" + pnames[0] + "_ref";
      97           2 :   for(unsigned i=1; i<pnames.size()-1; ++i) {
      98           2 :     argstr += "," + pnames[i] + "_ref";
      99             :   }
     100           3 :   readInputLine( getShortcutLabel() + ": PROJECT_POINTS " + argstr + " TARGET1=" + getShortcutLabel() + "_targ " +
     101           3 :                  "FUNC1={" + ldfunc + "} WEIGHTS1=" + getShortcutLabel() + "_weights CGTOL=" + cgtol );
     102           3 : }
     103             : 
     104             : }
     105             : }