LOOS  v2.3.2
utils_structural.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 #if !defined(LOOS_UTILS_STRUCTURAL_HPP)
26 #define LOOS_UTILS_STRUCTURAL_HPP
27 
28 #include <vector>
29 
30 #include <loos_defs.hpp>
31 #include <exceptions.hpp>
32 
33 namespace loos {
35 
38  GCoord boxFromRemarks(const Remarks&);
39 
41  bool remarksHasBox(const Remarks&);
42 
44  AtomicGroup loadStructureWithCoords(const std::string& model, const std::string& cooords);
45 
46  AtomicGroup loadStructureWithCoords(const std::string& model, const std::string& type, const std::string& cooords);
47 
49  std::vector<uint> assignTrajectoryFrames(const pTraj& traj, const std::string& frame_index_spec, uint skip = 0, uint stride = 1);
50 
51 };
52 
53 #endif
54 
55 
AtomicGroup loadStructureWithCoords(const std::string &model_name, const std::string &coord_name)
Loads a structure and optional coordinates.
GCoord boxFromRemarks(const Remarks &r)
Extract the Alan-style box-size from a PDB Remarks block.
Namespace for most things not already encapsulated within a class.
bool remarksHasBox(const Remarks &r)
Checks to see if a Remarks block has an Alan-style box size in it.
std::vector< uint > assignTrajectoryFrames(const pTraj &traj, const std::string &frame_index_spec, uint skip, uint stride)
Builds a list of trajectory indices (frame_index_spec supercedes skip)