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coord_group.hh
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1 //------------------------------------------------------------------------------
2 // This file is part of the OpenStructure project <www.openstructure.org>
3 //
4 // Copyright (C) 2008-2011 by the OpenStructure authors
5 //
6 // This library is free software; you can redistribute it and/or modify it under
7 // the terms of the GNU Lesser General Public License as published by the Free
8 // Software Foundation; either version 3.0 of the License, or (at your option)
9 // any later version.
10 // This library is distributed in the hope that it will be useful, but WITHOUT
11 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
12 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
13 // details.
14 //
15 // You should have received a copy of the GNU Lesser General Public License
16 // along with this library; if not, write to the Free Software Foundation, Inc.,
17 // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
18 //------------------------------------------------------------------------------
19 #ifndef OST_COORD_GROUP_HH
20 #define OST_COORD_GROUP_HH
21 
22 /*
23  Author: Ansgar Philippsen, Marco Biasini
24 */
25 
26 #include <vector>
27 #include <boost/shared_array.hpp>
28 #include "atom_handle.hh"
29 #include "coord_source.hh"
30 
31 namespace geom {
32  // we should really have fw headers...
33  class Transform;
34 }
35 
36 namespace ost { namespace mol {
37 
40 public:
45 
47  EntityHandle GetEntity() const;
48 
49  //EntityGroupHandle ExtractFromTo(int start, int end, int step=1);
50  //EntityGroupHandle ExtractEvery(int step, int start=0);
51 
53  uint GetAtomCount() const;
54 
56  uint GetFrameCount() const;
57 
59  float GetDelta() const;
60 
62  void SetDelta(float d);
63 
65  float GetStartTime() const;
66 
68  void SetStartTime(float t);
69 
72  void SetFramePositions(uint frame, const std::vector<geom::Vec3>& clist);
73 
75  geom::Vec3List GetFramePositions(uint frame);
76 
78  void CopyFrame(uint frame);
79 
81  void Capture();
82 
83  void CaptureInto(int pos);
84 
86  void Capture(uint frame);
87 
89  //void AddFrame(const std::vector<geom::Vec3>& clist);
90  void AddFrame(const geom::Vec3List& clist);
91  void AddFrame(const geom::Vec3List& clist,const geom::Vec3& cell_size,const geom::Vec3& cell_angles);
92 
93  void AddFrames(const CoordGroupHandle& cg);
95  void SetAtomPos(uint frame, AtomHandle atom, const geom::Vec3& pos);
96 
98  geom::Vec3 GetAtomPos(uint frame, AtomHandle atom) const;
99 
101  bool IsValid() const;
102 
104  operator bool() const;
105 
106  AtomHandleList GetAtomList() const;
107  CoordFramePtr GetFrame(uint frame) const;
108  CoordFrame GetFrame2(uint frame);
109 
112  CoordGroupHandle Filter(const EntityView& selected,int first=0,int last=-1) const;
113 
115  void ApplyTransform(const geom::Transform& tf);
116 
117 
118 private:
119  void CheckValidity() const;
120  CoordSourcePtr source_;
121 };
122 
123 // factory method
124 // create with a reference set of atoms and zero frames
126 
127 }} // ns
128 
129 #endif