LOOS  v2.3.2
charmm.hpp
1 /*
2  This file is part of LOOS.
3 
4  LOOS (Lightweight Object-Oriented Structure library)
5  Copyright (c) 2008, Tod D. Romo, Alan Grossfield
6  Department of Biochemistry and Biophysics
7  School of Medicine & Dentistry, University of Rochester
8 
9  This package (LOOS) is free software: you can redistribute it and/or modify
10  it under the terms of the GNU General Public License as published by
11  the Free Software Foundation under version 3 of the License.
12 
13  This package is distributed in the hope that it will be useful,
14  but WITHOUT ANY WARRANTY; without even the implied warranty of
15  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16  GNU General Public License for more details.
17 
18  You should have received a copy of the GNU General Public License
19  along with this program. If not, see <http://www.gnu.org/licenses/>.
20 */
21 
22 
23 
24 #if !(defined LOOS_CHARMM_HPP)
25 #define LOOS_CHARMM_HPP
26 
27 #include <ios>
28 #include <fstream>
29 #include <sstream>
30 #include <iostream>
31 
32 #include <stdexcept>
33 
34 #include <loos_defs.hpp>
35 #include <AtomicGroup.hpp>
36 
37 
38 namespace loos {
39 
41 
48  class CHARMM : public AtomicGroup {
49  public:
50  CHARMM() : _max_index(0) { }
51  virtual ~CHARMM() {}
52 
53  explicit CHARMM(const std::string fname) : _max_index(0), _filename(fname) {
54  std::ifstream ifs(fname.c_str());
55  if (!ifs) {
56  throw(FileOpenError(fname));
57  }
58  read(ifs);
59  }
60 
61  explicit CHARMM(std::istream &ifs) : _max_index(0), _filename("stream") {
62  read(ifs);
63  }
64 
65  static pAtomicGroup create(const std::string& fname) {
66  return(pAtomicGroup(new CHARMM(fname)));
67  }
68 
70  virtual CHARMM* clone(void) const;
71 
73  CHARMM copy(void) const;
74 
75  void read(std::istream& is);
76 
77 
78  private:
79 
80  CHARMM(const AtomicGroup& grp) : AtomicGroup(grp) { }
81 
82  uint _max_index;
83  std::string _filename;
84 
85  };
86 
87 
88 }
89 
90 #endif
CHARMM copy(void) const
Creates a deep copy (see AtomicGroup::copy() for more info)
Definition: charmm.cpp:36
Error while opening a file.
Definition: exceptions.hpp:170
Class for reading a CHARMM coordinate file.
Definition: charmm.hpp:48
Class for handling groups of Atoms (pAtoms, actually)
Definition: AtomicGroup.hpp:87
Namespace for most things not already encapsulated within a class.
void read(std::istream &is)
Definition: charmm.cpp:51
virtual CHARMM * clone(void) const
Clones an object for polymorphism (see AtomicGroup::clone() for more info)
Definition: charmm.cpp:32