LOOS  v2.3.2
loos.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 
25 
26 
27 #if !defined(LOOS_HPP)
28 #define LOOS_HPP
29 
30 // These are common system includes that nearly anybody who uses LOOS
31 // will probably be including anyway...
32 
33 #include <iostream>
34 #include <iomanip>
35 #include <ios>
36 #include <sstream>
37 #include <fstream>
38 
39 #include <ctime>
40 #include <cmath>
41 
42 #include <string>
43 #include <vector>
44 #include <algorithm>
45 
46 #include <stdexcept>
47 
48 #include <cassert>
49 
50 // These are the LOOS-specific includes...
51 
52 #include <loos_defs.hpp>
53 #include <exceptions.hpp>
54 #include <utils.hpp>
55 #include <utils_random.hpp>
56 #include <utils_structural.hpp>
57 
58 #include <Kernel.hpp>
59 #include <Parser.hpp>
60 #include <Selectors.hpp>
61 
62 
63 #include <Matrix44.hpp>
64 #include <XForm.hpp>
65 #include <Matrix.hpp>
66 
67 #include <AtomicNumberDeducer.hpp>
68 #include <Atom.hpp>
69 #include <AtomicGroup.hpp>
70 #include <pdb.hpp>
71 #include <psf.hpp>
72 #include <amber.hpp>
73 #include <tinkerxyz.hpp>
74 
75 #include <Trajectory.hpp>
76 #include <dcd.hpp>
77 #include <dcd_utils.hpp>
78 
79 #include <trajwriter.hpp>
80 #include <dcdwriter.hpp>
81 #include <xtcwriter.hpp>
82 
83 #include <amber_traj.hpp>
84 
85 #if defined(HAS_NETCDF)
86 #include <amber_netcdf.hpp>
87 #endif
88 
89 #include <amber_rst.hpp>
90 #include <ccpdb.hpp>
91 #include <pdbtraj.hpp>
92 #include <tinker_arc.hpp>
93 #include <xtc.hpp>
94 #include <gro.hpp>
95 #include <trr.hpp>
96 
97 
98 
99 #include <Geometry.hpp>
100 #include <ensembles.hpp>
101 #include <TimeSeries.hpp>
102 
103 #include <Fmt.hpp>
104 
105 #include <sfactories.hpp>
106 
107 #include <timer.hpp>
108 #include <ProgressCounters.hpp>
109 #include <ProgressTriggers.hpp>
110 
111 #include <sorting.hpp>
112 
113 #include <OptionsFramework.hpp>
114 
115 #include <alignment.hpp>
116 #endif
117 
118