LCOV - code coverage report
Current view: top level - multicolvar - AlphaBeta.cpp (source / functions) Hit Total Coverage
Test: plumed test coverage Lines: 44 47 93.6 %
Date: 2020-11-18 11:20:57 Functions: 10 12 83.3 %

          Line data    Source code
       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2019 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 "MultiColvarBase.h"
      23             : #include "AtomValuePack.h"
      24             : #include "tools/Torsion.h"
      25             : #include "core/ActionRegister.h"
      26             : 
      27             : #include <string>
      28             : #include <cmath>
      29             : 
      30             : using namespace std;
      31             : 
      32             : namespace PLMD {
      33             : namespace multicolvar {
      34             : 
      35             : //+PLUMEDOC COLVAR ALPHABETA
      36             : /*
      37             : Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values.
      38             : 
      39             : This colvar calculates the following quantity.
      40             : 
      41             : \f[
      42             : s = \frac{1}{2} \sum_i \left[ 1 + \cos( \phi_i - \phi_i^{\textrm{Ref}} ) \right]
      43             : \f]
      44             : 
      45             : where the \f$\phi_i\f$ values are the instantaneous values for the \ref TORSION angles of interest.
      46             : The \f$\phi_i^{\textrm{Ref}}\f$ values are the user-specified reference values for the torsional angles.
      47             : 
      48             : \par Examples
      49             : 
      50             : The following provides an example of the input for an alpha beta similarity.
      51             : 
      52             : \plumedfile
      53             : ALPHABETA ...
      54             : ATOMS1=168,170,172,188 REFERENCE1=3.14
      55             : ATOMS2=170,172,188,190 REFERENCE2=3.14
      56             : ATOMS3=188,190,192,230 REFERENCE3=3.14
      57             : LABEL=ab
      58             : ... ALPHABETA
      59             : PRINT ARG=ab FILE=colvar STRIDE=10
      60             : \endplumedfile
      61             : 
      62             : Because all the reference values are the same we can calculate the same quantity using
      63             : 
      64             : \plumedfile
      65             : ALPHABETA ...
      66             : ATOMS1=168,170,172,188 REFERENCE=3.14
      67             : ATOMS2=170,172,188,190
      68             : ATOMS3=188,190,192,230
      69             : LABEL=ab
      70             : ... ALPHABETA
      71             : PRINT ARG=ab FILE=colvar STRIDE=10
      72             : \endplumedfile
      73             : 
      74             : Writing out the atoms involved in all the torsions in this way can be rather tedious. Thankfully if you are working with protein you
      75             : can avoid this by using the \ref MOLINFO command.  PLUMED uses the pdb file that you provide to this command to learn
      76             : about the topology of the protein molecule.  This means that you can specify torsion angles using the following syntax:
      77             : 
      78             : \plumedfile
      79             : MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
      80             : ALPHABETA ...
      81             : ATOMS1=@phi-3 REFERENCE=3.14
      82             : ATOMS2=@psi-3
      83             : ATOMS3=@phi-4
      84             : LABEL=ab
      85             : ... ALPHABETA
      86             : PRINT ARG=ab FILE=colvar STRIDE=10
      87             : \endplumedfile
      88             : 
      89             : Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
      90             : Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein.
      91             : 
      92             : 
      93             : */
      94             : //+ENDPLUMEDOC
      95             : 
      96           3 : class AlphaBeta : public MultiColvarBase {
      97             : private:
      98             :   std::vector<double> target;
      99             : public:
     100             :   static void registerKeywords( Keywords& keys );
     101             :   explicit AlphaBeta(const ActionOptions&);
     102             :   virtual double compute( const unsigned& tindex, AtomValuePack& myatoms ) const ;
     103           0 :   bool isPeriodic() { return false; }
     104             : };
     105             : 
     106        6453 : PLUMED_REGISTER_ACTION(AlphaBeta,"ALPHABETA")
     107             : 
     108           2 : void AlphaBeta::registerKeywords( Keywords& keys ) {
     109           2 :   MultiColvarBase::registerKeywords( keys );
     110           8 :   keys.add("numbered","ATOMS","the atoms involved in each of the alpha-beta variables you wish to calculate. "
     111             :            "Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one alpha-beta values will be "
     112             :            "calculated for each ATOM keyword you specify (all ATOM keywords should "
     113             :            "specify the indices of four atoms).  The eventual number of quantities calculated by this "
     114             :            "action will depend on what functions of the distribution you choose to calculate.");
     115           6 :   keys.reset_style("ATOMS","atoms");
     116           8 :   keys.add("numbered","REFERENCE","the reference values for each of the torsional angles.  If you use a single REFERENCE value the "
     117             :            "same reference value is used for all torsions");
     118           6 :   keys.reset_style("REFERENCE","compulsory");
     119           2 : }
     120             : 
     121           1 : AlphaBeta::AlphaBeta(const ActionOptions&ao):
     122             :   Action(ao),
     123           1 :   MultiColvarBase(ao)
     124             : {
     125             :   // Read in the atoms
     126             :   std::vector<AtomNumber> all_atoms;
     127           2 :   readAtomsLikeKeyword( "ATOMS", 4, all_atoms );
     128           1 :   setupMultiColvarBase( all_atoms );
     129             :   // Resize target
     130           1 :   target.resize( getFullNumberOfTasks() );
     131             :   // Setup central atom indices
     132           1 :   std::vector<bool> catom_ind(4, false);
     133             :   catom_ind[1]=catom_ind[2]=true;
     134           1 :   setAtomsForCentralAtom( catom_ind );
     135             : 
     136             :   // Read in reference values
     137             :   unsigned ntarget=0;
     138           2 :   for(unsigned i=0; i<target.size(); ++i) {
     139           3 :     if( !parseNumbered( "REFERENCE", i+1, target[i] ) ) break;
     140             :     ntarget++;
     141             :   }
     142           1 :   if( ntarget==0 ) {
     143           3 :     parse("REFERENCE",target[0]);
     144          23 :     for(unsigned i=1; i<target.size(); ++i) target[i]=target[0];
     145           0 :   } else if( ntarget!=target.size() ) {
     146           0 :     error("found wrong number of REFERENCE values");
     147             :   }
     148             : 
     149             :   // And setup the ActionWithVessel
     150           1 :   if( getNumberOfVessels()==0 ) {
     151             :     std::string fake_input;
     152           2 :     addVessel( "SUM", fake_input, -1 );  // -1 here means that this value will be named getLabel()
     153           1 :     readVesselKeywords();  // This makes sure resizing is done
     154             :   }
     155             : 
     156             :   // And check everything has been read in correctly
     157           1 :   checkRead();
     158           1 : }
     159             : 
     160          40 : double AlphaBeta::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
     161          80 :   const Vector d0=getSeparation(myatoms.getPosition(1),myatoms.getPosition(0));
     162          40 :   const Vector d1=getSeparation(myatoms.getPosition(2),myatoms.getPosition(1));
     163          40 :   const Vector d2=getSeparation(myatoms.getPosition(3),myatoms.getPosition(2));
     164             : 
     165          40 :   Vector dd0,dd1,dd2;
     166             :   PLMD::Torsion t;
     167          40 :   const double value  = t.compute(d0,d1,d2,dd0,dd1,dd2);
     168          80 :   const double svalue = -0.5*sin(value-target[tindex]);
     169          40 :   const double cvalue = 1.+cos(value-target[tindex]);
     170             : 
     171          40 :   dd0 *= svalue;
     172          40 :   dd1 *= svalue;
     173          40 :   dd2 *= svalue;
     174             : 
     175          40 :   addAtomDerivatives(1, 0, dd0, myatoms);
     176          40 :   addAtomDerivatives(1, 1, dd1-dd0, myatoms);
     177          40 :   addAtomDerivatives(1, 2, dd2-dd1, myatoms);
     178          40 :   addAtomDerivatives(1, 3, -dd2, myatoms);
     179             : 
     180          40 :   myatoms.addBoxDerivatives(1, -(extProduct(d0,dd0)+extProduct(d1,dd1)+extProduct(d2,dd2)));
     181             : 
     182          40 :   return 0.5*cvalue;
     183             : }
     184             : 
     185             : }
     186        4839 : }

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