/usr/include/votca/csg/cgmoleculedef.h is in libvotca-csg2-dev 1.2.4-2.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 | /*
* 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 _cgmoleculedef_H
#define _cgmoleculedef_H
#include <string>
#include <vector>
#include <map>
#include <string>
#include <votca/tools/property.h>
#include "map.h"
#include <votca/tools/types.h>
#include "exclusionlist.h"
#include "molecule.h"
namespace votca { namespace csg {
using namespace votca::tools;
using namespace std;
/**
\brief definition of a coarse grained molecule
This class is to define a coarse grained molecule, which includes the topology, mapping, ...
\todo clean up this class, do the bonded interactions right!!!!
\todo check for consistency of xml file, seperate xml parser and class!!
*/
class CGMoleculeDef
{
public:
CGMoleculeDef() {}
~CGMoleculeDef();
Molecule *CreateMolecule(Topology & top);
Map *CreateMap(Molecule &in, Molecule &out);
void Load(string filename);
const string &getName() { return _name; }
const string &getIdent() { return _ident; }
private:
Property _options;
struct beaddef_t {
string _name;
string _type;
byte_t _symmetry;
string _mapping;
vector<string> _subbeads;
Property *_options;
};
// name of the coarse grained molecule
string _name;
// name of the molecule to coarse grain
string _ident;
// beads of the cg molecule
vector<beaddef_t *> _beads;
map<string, beaddef_t *> _beads_by_name;
// mapping schemes
map<string, Property *> _maps;
list<Property *> _bonded;
void ParseTopology(Property &options);
void ParseBeads(Property &options);
void ParseBonded(Property &options);
void ParseMapping(Property &options);
beaddef_t *getBeadByName(const string &name);
Property *getMapByName(const string &name);
};
}}
#endif /* _cgmoleculedef_H */
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