MolInfo.cpp

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/* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   Copyright (c) 2013 The plumed team
   (see the PEOPLE file at the root of the distribution for a list of names)

   See http://www.plumed-code.org for more information.

   This file is part of plumed, version 2.0.

   plumed is free software: you can redistribute it and/or modify
   it under the terms of the GNU Lesser General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.

   plumed is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU Lesser General Public License for more details.

   You should have received a copy of the GNU Lesser General Public License
   along with plumed.  If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "core/ActionRegister.h"
#include "core/SetupMolInfo.h"

namespace PLMD{
namespace setup{

//+PLUMEDOC TOPOLOGY MOLINFO
/*
This command is used to provide information on the molecules that are present in your system.

The information on the molecules in your system can either be provided in the form of a pdb file
or as a set of lists of atoms that describe the various chains in your system. If a pdb file
is used plumed the MOLINFO command will endeavor to recognize the various chains and residues that
make up the molecules in your system using the chainIDs and resnumbers from the pdb file. You can
then use this information in later commands to specify atom lists in terms residues.  For example
using this command you can find the backbone atoms in your structure automatically. 

Please be aware that the pdb parser in plumed is far from perfect. You should thus check the log file
and examine what plumed is actually doing whenenver you use the MOLINFO action.

\bug At the moment all atoms named HA1 are treated as if they are CB atoms.  This makes it possible to deal
with GLY residues in colvars like \ref ALPHARMSD. 

\par Examples

In the following example the MOLINFO command is used to provide the information on which atoms
are in the backbone of a protein to the ALPHARMSD CV.

\verbatim
MOLINFO STRUCTURE=reference.pdb
ALPHARMSD BACKBONE=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a 
\endverbatim
(see also \ref ALPHARMSD)

*/
//+ENDPLUMEDOC


/*
This action is defined in core/ as it is used by other actions.
Anyway, it is registered here, so that excluding this module from
compilation will exclude it from plumed.
*/

typedef PLMD::SetupMolInfo MolInfo;

PLUMED_REGISTER_ACTION(MolInfo,"MOLINFO")

}
}