LOOS 4.1.0
The Lightweight Object Oriented Structural analysis library/toolkit
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tinker_arc.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#if !defined(LOOS_TINKER_ARC_HPP)
23#define LOOS_TINKER_ARC_HPP
24
25
26#include <iostream>
27#include <string>
28#include <stdexcept>
29
30#include <loos_defs.hpp>
31#include <Trajectory.hpp>
32
33#include <tinkerxyz.hpp>
34
35
36namespace loos {
37
39
60 class TinkerArc : public Trajectory {
61 public:
62 explicit TinkerArc(const std::string& s) : Trajectory(s), _natoms(0), _nframes(0),
63 current_index(0), at_end(false) { init(); }
64
65 explicit TinkerArc(std::istream& is) : Trajectory(is), _natoms(0),
66 _nframes(0), current_index(0), at_end(false) { init(); }
67
68 std::string description() const { return("Tinker Archive"); }
69
70 static pTraj create(const std::string& fname, const AtomicGroup& model) {
71 return(pTraj(new TinkerArc(fname)));
72 }
73
74 virtual uint nframes(void) const { return(_nframes); }
75 virtual uint natoms(void) const { return(_natoms); }
76 virtual std::vector<GCoord> coords(void) const;
77
78 virtual bool hasPeriodicBox(void) const { return(frame.isPeriodic()); }
79 virtual GCoord periodicBox(void) const { return(frame.periodicBox()); }
80
81 virtual float timestep(void) const { return(0.001); }
82
84
87 TinkerXYZ currentFrame(void) const { return(frame); }
88
89 virtual bool parseFrame(void);
90
91
92 private:
93 void init(void);
94 virtual void rewindImpl(void) { ifs->clear(); ifs->seekg(0); current_index = 0; at_end = false; }
95 virtual void seekNextFrameImpl(void);
96 virtual void seekFrameImpl(const uint);
97 virtual void updateGroupCoordsImpl(AtomicGroup& g);
98
99
100 private:
101 uint _natoms, _nframes;
102 uint current_index;
103 bool at_end;
104 TinkerXYZ frame;
105 std::vector<long> indices;
106 };
107
108
109}
110
111
112#endif
Class for handling groups of Atoms (pAtoms, actually)
Definition AtomicGroup.hpp:108
Class for handling Tinker ARC files (concatenation of .xyz files)
Definition tinker_arc.hpp:60
virtual float timestep(void) const
Timestep per frame.
Definition tinker_arc.hpp:81
virtual GCoord periodicBox(void) const
Returns the periodic box for the current frame/trajectory.
Definition tinker_arc.hpp:79
virtual std::vector< GCoord > coords(void) const
Returns the current frames coordinates as a vector of GCoords.
Definition tinker_arc.cpp:100
virtual bool parseFrame(void)
Parse an actual frame.
Definition tinker_arc.cpp:76
virtual uint nframes(void) const
Number of frames in the trajectory.
Definition tinker_arc.hpp:74
std::string description() const
Return a string describing trajectory format.
Definition tinker_arc.hpp:68
TinkerXYZ currentFrame(void) const
Returns the contained TinkerXYZ object.
Definition tinker_arc.hpp:87
virtual uint natoms(void) const
Definition tinker_arc.hpp:75
virtual bool hasPeriodicBox(void) const
Definition tinker_arc.hpp:78
Class for reading a subset of the TinkerXYZ format.
Definition tinkerxyz.hpp:47
Base-class for polymorphic trajectories.
Definition Trajectory.hpp:65
-picker
Namespace for most things not already encapsulated within a class.
Definition version.cpp:3