Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2020 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 "MultiColvarShortcuts.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : #include <string>
      26             : #include <cmath>
      27             : 
      28             : namespace PLMD {
      29             : namespace multicolvar {
      30             : 
      31             : //+PLUMEDOC COLVAR DIHCOR
      32             : /*
      33             : Measures the degree of similarity between dihedral angles.
      34             : 
      35             : This colvar calculates the following quantity.
      36             : 
      37             : $$
      38             : s = \frac{1}{2} \sum_i \left[ 1 + \cos( \phi_i - \psi_i ) \right]
      39             : $$
      40             : 
      41             : where the $\phi_i$ and $\psi_i$ values are the instantaneous values for the TORSION angles of interest.
      42             : 
      43             : You can see an example input for the DIHCOR action below
      44             : 
      45             : ```plumed
      46             : dih: DIHCOR ...
      47             :   ATOMS1=1,2,3,4,5,6,7,8
      48             :   ATOMS2=5,6,7,8,9,10,11,12
      49             : ...
      50             : PRINT ARG=dih FILE=colvar STRIDE=10
      51             : ```
      52             : 
      53             : In the above input we are calculating the correlation between the torsion angle involving atoms 1, 2, 3 and 4 and the torsion angle
      54             : involving atoms 5, 6, 7 and 8.  This is then added to the correlation between the torsion angle involving atoms 5, 6, 7 and 8 and the
      55             : correlation angle involving atoms 9, 10, 11 and 12.
      56             : 
      57             : Writing out the atoms involved in all the torsion angles in this way can be rather tedious. Thankfully if you are working with protein you
      58             : can avoid this by using the [MOLINFO](MOLINFO.md) command.  PLUMED uses the pdb file that you provide to this command to learn
      59             : about the topology of the protein molecule.  This means that you can specify torsion angles using the following syntax:
      60             : 
      61             : ```plumed
      62             : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
      63             : MOLINFO MOLTYPE=protein STRUCTURE=regtest/basic/rt32/helix.pdb
      64             : dih: DIHCOR ...
      65             : ATOMS1=@phi-3,@psi-3
      66             : ATOMS2=@psi-3,@phi-4
      67             : ATOMS3=@phi-4,@psi-4
      68             : ...
      69             : PRINT ARG=dih FILE=colvar STRIDE=10
      70             : ```
      71             : 
      72             : Here, `@phi-3` tells plumed that you would like to calculate the $\phi$ angle in the third residue of the protein.
      73             : Similarly `@psi-4` tells plumed that you want to calculate the $\psi$ angle of the fourth residue of the protein.
      74             : 
      75             : Notice, last of all, that if you want not to reassemble the atoms that have been broken by the periodic boundary conditions using a procedure
      76             : like that outlined in [WHOLEMOLECULES](WHOLEMOLECULES.md) you can add a NOPBC as shown below:
      77             : 
      78             : ```plumed
      79             : dih: DIHCOR ...
      80             :   ATOMS1=1,2,3,4,5,6,7,8
      81             :   ATOMS2=5,6,7,8,9,10,11,12
      82             :   NOPBC
      83             : ...
      84             : PRINT ARG=dih FILE=colvar STRIDE=10
      85             : ```
      86             : 
      87             : */
      88             : //+ENDPLUMEDOC
      89             : 
      90             : // We have a little helper class here to ensure that we actually do what is required by this action
      91             : class Dihcor : public ActionShortcut {
      92             : public:
      93             :   static void registerKeywords( Keywords& keys );
      94             :   Dihcor(const ActionOptions&);
      95             : };
      96             : 
      97             : PLUMED_REGISTER_ACTION(Dihcor,"DIHCOR")
      98             : 
      99           4 : void Dihcor::registerKeywords( Keywords& keys ) {
     100           4 :   ActionShortcut::registerKeywords( keys );
     101           4 :   keys.needsAction("DIHEDRAL_CORRELATION");
     102           8 :   keys.needsAction("SUM");
     103           4 :   keys.add("atoms","ATOMS","the set of 8 atoms that are being used each of the dihedral correlation values");
     104           4 :   keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
     105           8 :   keys.setValueDescription("scalar","the sum of all the dihedral correlations");
     106           4 : }
     107             : 
     108           1 : Dihcor::Dihcor(const ActionOptions&ao):
     109             :   Action(ao),
     110           1 :   ActionShortcut(ao) {
     111           2 :   readInputLine( getShortcutLabel() +"_data: DIHEDRAL_CORRELATION " + convertInputLineToString() );
     112           2 :   readInputLine( getShortcutLabel() + ": SUM ARG=" + getShortcutLabel() + "_data PERIODIC=NO");
     113           1 : }
     114             : 
     115             : }
     116             : }