1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
|
// $Id$
//
// Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
/*! \file ConformerParser.h
\brief Contains functionality to load conformers from a MD trajectory
*/
#ifndef __RD_ConformerParser_H__
#define __RD_ConformerParser_H__
#include <sstream>
namespace RDKit {
class ROMol;
class Conformer;
namespace ConformerParser {
/*!
Adds the conformations read from a list of doubles
\param mol the molecule of interest
\param coords list with coordinates
\param numConf number of conformers to read (default: all)
Returns: integer vector with confIds
*/
RDKIT_CONFORMERPARSER_EXPORT INT_VECT addConformersFromList(
ROMol &mol, const std::vector<std::vector<double>> &coords,
int numConf = -1);
/*!
Converts an Amber trajectory into a list of doubles
\param inStream input file
\param coords list with coordinates
*/
RDKIT_CONFORMERPARSER_EXPORT void readAmberTrajectory(
const std::string &fName, std::vector<std::vector<double>> &coords,
unsigned int numAtoms);
} // end namespace ConformerParser
} // end namespace RDKit
#endif
|
