/usr/include/votca/csg/molecule.h is in libvotca-csg-dev 1.4.1-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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* Copyright 2009-2011 The VOTCA Development Team (http://www.votca.org)
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*/
#ifndef _MOLECULE_H
#define _MOLECULE_H
#include <vector>
#include <map>
#include <string>
#include <assert.h>
#include "topologyitem.h"
#include "bead.h"
namespace votca { namespace csg {
using namespace votca::tools;
using namespace std;
class Interaction;
/**
\brief information about molecules
The Molecule class stores which beads belong to a molecule.
The organization of beads into molecules is needed for the CG mapping.
\todo sort atoms in molecule
*/
class Molecule : public TopologyItem
{
public:
/// get the molecule ID
int getId() const { return _id; }
/// get the name of the molecule
const string &getName() const { return _name; }
/// set the name of the molecule
void setName(const string &name) { _name=name; }
/// Add a bead to the molecule
void AddBead(Bead *bead, const string &name);
/// get the id of a bead in the molecule
Bead *getBead(int bead) { return _beads[bead]; }
int getBeadId(int bead) { return _beads[bead]->getId(); }
int getBeadIdByName(const string &name);
/// get the number of beads in the molecule
int BeadCount() const { return _beads.size(); }
/// find a bead by it's name
int getBeadByName(const string &name);
string getBeadName(int bead) {return _bead_names[bead]; }
/// Add an interaction to the molecule
void AddInteraction(Interaction *ic) { _interactions.push_back(ic);
}
vector<Interaction *> Interactions() { return _interactions; }
template<typename T>
void setUserData(T *userdata) { _userdata = (void*)userdata; }
template<typename T>
T *getUserData() { return (T *)_userdata; }
private:
// maps a name to a bead id
map<string, int> _beadmap;
vector<Interaction*> _interactions;
// id of the molecules
int _id;
// name of the molecule
string _name;
// the beads in the molecule
vector<Bead *> _beads;
vector<string> _bead_names;
void *_userdata;
/// constructor
Molecule(Topology *parent, int id, string name)
: TopologyItem(parent), _id(id), _name(name)
{}
friend class Topology;
};
inline int Molecule::getBeadIdByName(const string &name)
{
int i = getBeadByName(name);
if(i<0)
return i;
return _beads[i]->getId();
}
}}
#endif /* _Molecule_H */
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