Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2020 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 "MultiColvarShortcuts.h"
      25             : 
      26             : //+PLUMEDOC MCOLVAR TORSIONS
      27             : /*
      28             : Calculate whether or not a set of torsional angles are within a particular range.
      29             : 
      30             : \par Examples
      31             : 
      32             : The following provides an example of the input for the TORSIONS command
      33             : 
      34             : \plumedfile
      35             : TORSIONS ...
      36             : ATOMS1=168,170,172,188
      37             : ATOMS2=170,172,188,190
      38             : ATOMS3=188,190,192,230
      39             : BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
      40             : LABEL=ab
      41             : ... TORSIONS
      42             : PRINT ARG=ab.* FILE=colvar STRIDE=10
      43             : \endplumedfile
      44             : 
      45             : 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
      46             : can avoid this by using the \ref MOLINFO command.  PLUMED uses the pdb file that you provide to this command to learn
      47             : about the topology of the protein molecule.  This means that you can specify torsion angles using the following syntax:
      48             : 
      49             : \plumedfile
      50             : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
      51             : MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb
      52             : TORSIONS ...
      53             : ATOMS1=@phi-3
      54             : ATOMS2=@psi-3
      55             : ATOMS3=@phi-4
      56             : BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}
      57             : LABEL=ab
      58             : ... TORSIONS
      59             : PRINT ARG=ab.* FILE=colvar STRIDE=10
      60             : \endplumedfile
      61             : 
      62             : Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.
      63             : Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the fourth residue of the protein.
      64             : 
      65             : 
      66             : */
      67             : //+ENDPLUMEDOC
      68             : 
      69             : namespace PLMD {
      70             : namespace multicolvar {
      71             : 
      72             : class Torsions : public ActionShortcut {
      73             : public:
      74             :   static void registerKeywords(Keywords& keys);
      75             :   explicit Torsions(const ActionOptions&);
      76             : };
      77             : 
      78             : PLUMED_REGISTER_ACTION(Torsions,"TORSIONS")
      79             : 
      80           8 : void Torsions::registerKeywords(Keywords& keys) {
      81           8 :   ActionShortcut::registerKeywords( keys ); MultiColvarShortcuts::shortcutKeywords( keys );
      82           8 :   keys.needsAction("TORSION");
      83          16 :   keys.setValueDescription("vector","the TORSION for each set of three atoms that were specified");
      84           8 : }
      85             : 
      86           6 : Torsions::Torsions(const ActionOptions& ao):
      87             :   Action(ao),
      88           6 :   ActionShortcut(ao)
      89             : {
      90           6 :   log.printf("Action TORSION\n");
      91           6 :   log.printf("  with label %s \n", getShortcutLabel().c_str() );
      92          12 :   readInputLine( getShortcutLabel() + ": TORSION " + convertInputLineToString() );
      93             :   // Add shortcuts to label
      94           6 :   MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this );
      95           6 : }
      96             : 
      97             : }
      98             : }