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             : This shortcut can be used to read in a projection of a trajectory that was generated using [SKETCHMAP](SKETCHMAP.md).
      31             : You can then use the coordinates that were read in to generate projections of other configurations.  Examples of how
      32             : this tool might be used are given in the last three papers cited below.  In these papers, a sketch-map projection is
      33             : computed from one particular set of data points.  This sketch-map projection that was output was then used to analyse
      34             : a second completely different data set.
      35             : 
      36             : An example input that illustrates how the sketch-map projection shortcut is used is shown below:
      37             : 
      38             : ```plumed
      39             : #SETTING INPUTFILES=regtest/dimred/rt-smap-read/smap.pdb
      40             : d1: DISTANCE ATOMS=1,2
      41             : d2: DISTANCE ATOMS=3,4
      42             : d3: DISTANCE ATOMS=5,6
      43             : 
      44             : smap: SKETCHMAP_PROJECTION ...
      45             :     ARG=d1,d2,d3 REFERENCE=regtest/dimred/rt-smap-read/smap.pdb
      46             :     PROPERTY=smap_coord-1,smap_coord-2 CGTOL=1E-3
      47             :     WEIGHT=WEIGHT HIGH_DIM_FUNCTION={SMAP R_0=4 A=3 B=2} LOW_DIM_FUNCTION={SMAP R_0=4 A=1 B=2}
      48             : ...
      49             : 
      50             : PRINT ARG=smap.* FILE=colvar
      51             : ```
      52             : 
      53             : Each frame in your input trajectory generates the three distances so one set of sketch-map coordinates are generated from each frame.
      54             : Notice that if you want to generate projections of multiple input points at once you need to use [PROJECT_POINTS](PROJECT_POINTS.md)
      55             : directly rather than this wrapper.
      56             : 
      57             : The configurations of the landmark points in your sketch-map input file can also be defined in terms of a set of atomic positions.
      58             : In this case the distance between the reference configurations and the instantaneous coordinates are calculated using [RMSD](RMSD.md).
      59             : An input for this type of calculation is as follows:
      60             : 
      61             : ```plumed
      62             : #SETTING INPUTFILES=regtest/dimred/rt-mds-rmsd/embed.pdb.reference
      63             : 
      64             : smap: SKETCHMAP_PROJECTION ...
      65             :    REFERENCE=regtest/dimred/rt-mds-rmsd/embed.pdb.reference
      66             :    PROPERTY=mds-1,mds-2 CGTOL=1E-3
      67             :    WEIGHT=weights HIGH_DIM_FUNCTION={SMAP R_0=4 A=3 B=2} LOW_DIM_FUNCTION={SMAP R_0=4 A=1 B=2}
      68             : ...
      69             : ```
      70             : 
      71             : */
      72             : //+ENDPLUMEDOC
      73             : 
      74             : namespace PLMD {
      75             : namespace dimred {
      76             : 
      77             : class SketchMapProjection : public ActionShortcut {
      78             : public:
      79             :   static void registerKeywords( Keywords& keys );
      80             :   explicit SketchMapProjection( const ActionOptions& ao );
      81             : };
      82             : 
      83             : PLUMED_REGISTER_ACTION(SketchMapProjection,"SKETCHMAP_PROJECTION")
      84             : 
      85           4 : void SketchMapProjection::registerKeywords( Keywords& keys ) {
      86           4 :   ActionShortcut::registerKeywords( keys );
      87           4 :   mapping::Path::registerInputFileKeywords( keys );
      88           4 :   keys.add("compulsory","PROPERTY","the property to be used in the index. This should be in the REMARK of the reference");
      89           4 :   keys.add("compulsory","WEIGHT","the weight of each individual landmark in the stress fucntion that is to be optimised");
      90           4 :   keys.add("compulsory","HIGH_DIM_FUNCTION","the parameters of the switching function in the high dimensional space");
      91           4 :   keys.add("compulsory","LOW_DIM_FUNCTION","the parameters of the switching function in the low dimensional space");
      92           4 :   keys.add("compulsory","CGTOL","1E-6","The tolerance for the conjugate gradient minimization that finds the out of sample projections");
      93           8 :   keys.setValueDescription("scalar/vector","the out-of-sample projections of the input arguments using the input sketch-map projection");
      94           4 :   keys.addDOI("10.1073/pnas.1108486108");
      95           4 :   keys.addDOI("10.1073/pnas.1201152109");
      96           4 :   keys.addDOI("10.1021/ct3010563");
      97           4 :   keys.addDOI("10.1021/ct500950z");
      98           4 :   keys.addDOI("10.1021/acs.jctc.5b00714");
      99           4 :   keys.needsAction("RMSD");
     100           4 :   keys.needsAction("PDB2CONSTANT");
     101           4 :   keys.needsAction("CONSTANT");
     102           4 :   keys.needsAction("CUSTOM");
     103           4 :   keys.needsAction("EUCLIDEAN_DISTANCE");
     104           4 :   keys.needsAction("NORMALIZED_EUCLIDEAN_DISTANCE");
     105           4 :   keys.needsAction("SUM");
     106           4 :   keys.needsAction("MORE_THAN");
     107           4 :   keys.needsAction("PROJECT_POINTS");
     108           4 : }
     109             : 
     110           1 : SketchMapProjection::SketchMapProjection( const ActionOptions& ao):
     111             :   Action(ao),
     112           1 :   ActionShortcut(ao) {
     113             :   // Use path to read in the projections
     114             :   std::string refname, refactions, metric;
     115             :   std::vector<std::string> argnames;
     116           2 :   parseVector("ARG",argnames);
     117             :   std::string type, reference_data, reference;
     118           1 :   parse("REFERENCE",reference);
     119           1 :   parse("TYPE",type);
     120           1 :   mapping::Path::readInputFrames( reference, type, argnames, false, this, reference_data );
     121             :   // And read in the data that we want on the projections
     122             :   std::vector<std::string> pnames;
     123           2 :   parseVector("PROPERTY",pnames);
     124             :   std::string weights;
     125           1 :   parse("WEIGHT",weights);
     126           1 :   pnames.push_back( weights );
     127             :   // Now create fixed vectors using some sort of reference action
     128           1 :   mapping::Path::readPropertyInformation( pnames, getShortcutLabel(), reference, this );
     129             :   // Normalise the vector of weights
     130           2 :   readInputLine( getShortcutLabel() + "_wsum: SUM PERIODIC=NO ARG=" + weights + "_ref");
     131           2 :   readInputLine( getShortcutLabel() + "_weights: CUSTOM ARG=" + weights + "_ref," + getShortcutLabel() + "_wsum FUNC=x/y PERIODIC=NO");
     132             :   // Transform the high dimensional distances
     133             :   std::string hdfunc;
     134           1 :   parse("HIGH_DIM_FUNCTION",hdfunc);
     135           2 :   readInputLine( getShortcutLabel() + "_targ: MORE_THAN ARG=" + getShortcutLabel() + "_data SQUARED SWITCH={" + hdfunc + "}");
     136             :   // Create the projection object
     137             :   std::string ldfunc, cgtol;
     138           1 :   parse("LOW_DIM_FUNCTION",ldfunc);
     139           2 :   parse("CGTOL",cgtol);
     140           1 :   std::string argstr="ARG=" + pnames[0] + "_ref";
     141           2 :   for(unsigned i=1; i<pnames.size()-1; ++i) {
     142           2 :     argstr += "," + pnames[i] + "_ref";
     143             :   }
     144           3 :   readInputLine( getShortcutLabel() + ": PROJECT_POINTS " + argstr + " TARGET1=" + getShortcutLabel() + "_targ " +
     145           3 :                  "FUNC1={" + ldfunc + "} WEIGHTS1=" + getShortcutLabel() + "_weights CGTOL=" + cgtol );
     146           3 : }
     147             : 
     148             : }
     149             : }