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
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
|
//
// Copyright (C) 2015,2016 Greg Landrum and NextMove Software
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef _RD_SEQUENCEPARSE_H_
#define _RD_SEQUENCEPARSE_H_
#include <string>
namespace RDKit {
class RWMol;
// \brief construct a molecule from a sequence string (currently only supports
// peptides)
/*!
* \param seq - the string to be processed
* \param sanitize - toggles sanitization and stereochemistry perception of
*the molecule
* \param lowerD - if set, lower case letters will be parsed as the d form
*of the corresponding amino acid
*
*/
RDKIT_FILEPARSERS_EXPORT RWMol *SequenceToMol(const char *seq, bool sanitize, bool lowerD);
//! \overload
RDKIT_FILEPARSERS_EXPORT RWMol *SequenceToMol(const std::string &seq, bool sanitize, bool lowerD);
// \brief construct a protein, RNA or DNA molecule from a sequence string
/*!
* \param seq - the string to be processed
* \param sanitize - toggles sanitization and stereochemistry perception of
*the molecule
* \param flavor -
* 0 Protein, L amino acids (default)
* 1 Protein, D amino acids
* 2 RNA, no cap
* 3 RNA, 5' cap
* 4 RNA, 3' cap
* 5 RNA, both caps
* 6 DNA, no cap
* 7 DNA, 5' cap
* 8 DNA, 3' cap
* 9 DNA, both caps
*
*/
RDKIT_FILEPARSERS_EXPORT RWMol *SequenceToMol(const char *seq, bool sanitize = true, int flavor = 0);
//! \overload
RDKIT_FILEPARSERS_EXPORT RWMol *SequenceToMol(const std::string &seq, bool sanitize = true,
int flavor = 0);
// \brief construct a molecule from a FASTA string (currently only supports
// peptides)
/*!
* \param seq - the string to be processed
* \param sanitize - toggles sanitization and stereochemistry perception of
*the molecule
* \param lowerD - if set, lower case letters will be parsed as the d form
*of the corresponding amino acid
*
*/
RDKIT_FILEPARSERS_EXPORT RWMol *FASTAToMol(const char *seq, bool sanitize, bool lowerD);
//! \overload
RDKIT_FILEPARSERS_EXPORT RWMol *FASTAToMol(const std::string &seq, bool sanitize, bool lowerD);
// \brief construct a protein, DNA or RNA molecule from a FASTA string
/*!
* \param seq - the string to be processed
* \param sanitize - toggles sanitization and stereochemistry perception of
*the molecule
* \param flavor -
* 0 Protein, L amino acids (default)
* 1 Protein, D amino acids
* 2 RNA, no cap
* 3 RNA, 5' cap
* 4 RNA, 3' cap
* 5 RNA, both caps
* 6 DNA, no cap
* 7 DNA, 5' cap
* 8 DNA, 3' cap
* 9 DNA, both caps
*
*/
RDKIT_FILEPARSERS_EXPORT RWMol *FASTAToMol(const char *seq, bool sanitize = true, int flavor = 0);
//! \overload
RDKIT_FILEPARSERS_EXPORT RWMol *FASTAToMol(const std::string &seq, bool sanitize = true, int flavor = 0);
// \brief construct a molecule from a HELM string (currently only supports
// peptides)
/*!
* \param seq - the string to be processed
* \param sanitize - toggles sanitization and stereochemistry perception of
*the molecule
*
*/
RDKIT_FILEPARSERS_EXPORT RWMol *HELMToMol(const char *helm, bool sanitize = true);
//! \overload
RDKIT_FILEPARSERS_EXPORT RWMol *HELMToMol(const std::string &helm, bool sanitize = true);
}
#endif
|
