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/*
* This file is part of the GROMACS molecular simulation package.
*
* Copyright 2020- The GROMACS Authors
* and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
* Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
*
* GROMACS 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 2.1
* of the License, or (at your option) any later version.
*
* GROMACS 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 GROMACS; if not, see
* https://www.gnu.org/licenses, or write to the Free Software Foundation,
* Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*
* If you want to redistribute modifications to GROMACS, please
* consider that scientific software is very special. Version
* control is crucial - bugs must be traceable. We will be happy to
* consider code for inclusion in the official distribution, but
* derived work must not be called official GROMACS. Details are found
* in the README & COPYING files - if they are missing, get the
* official version at https://www.gromacs.org.
*
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out https://www.gromacs.org.
*/
/*! \internal \file
* \brief
* Implements ParticleSequencer class
*
* \author Victor Holanda <victor.holanda@cscs.ch>
* \author Joe Jordan <ejjordan@kth.se>
* \author Prashanth Kanduri <kanduri@cscs.ch>
* \author Sebastian Keller <keller@cscs.ch>
* \author Artem Zhmurov <zhmurov@gmail.com>
*/
#include "nblib/particlesequencer.h"
#include <cstdio>
#include <algorithm>
#include <stdexcept>
#include "nblib/exception.h"
namespace nblib
{
int ParticleSequencer::operator()(const MoleculeName& moleculeName,
int moleculeNr,
const ResidueName& residueName,
const ParticleName& particleName) const
{
try
{
return data_.at(moleculeName).at(moleculeNr).at(residueName).at(particleName);
}
catch (const std::out_of_range& outOfRange)
{
if (moleculeName.value() == residueName.value())
{
printf("No particle %s in residue %s in molecule %s found\n",
particleName.value().c_str(),
residueName.value().c_str(),
moleculeName.value().c_str());
}
else
{
printf("No particle %s in molecule %s found\n",
particleName.value().c_str(),
moleculeName.value().c_str());
}
throw InputException(outOfRange.what());
}
}
void ParticleSequencer::build(const std::vector<std::tuple<Molecule, int>>& moleculesList)
{
int currentID = 0;
for (const auto& molNumberTuple : moleculesList)
{
const Molecule& molecule = std::get<0>(molNumberTuple);
const size_t numMols = std::get<1>(molNumberTuple);
auto& moleculeMap = data_[molecule.name()];
for (size_t i = 0; i < numMols; ++i)
{
auto& moleculeNrMap = moleculeMap[i];
for (int j = 0; j < molecule.numParticlesInMolecule(); ++j)
{
moleculeNrMap[molecule.residueName(j)][molecule.particleName(j)] = currentID++;
}
}
}
}
} // namespace nblib
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