RDKit
Open-source cheminformatics and machine learning.
SequenceParsers.h
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1 //
2 // Copyright (C) 2015,2016 Greg Landrum and NextMove Software
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 #include <RDGeneral/export.h>
11 #ifndef _RD_SEQUENCEPARSE_H_
12 #define _RD_SEQUENCEPARSE_H_
13 #include <string>
14 
15 namespace RDKit {
16 class RWMol;
17 
18 // \brief construct a molecule from a sequence string (currently only supports
19 // peptides)
20 /*!
21  * \param seq - the string to be processed
22  * \param sanitize - toggles sanitization and stereochemistry perception of
23  *the molecule
24  * \param lowerD - if set, lower case letters will be parsed as the d form
25  *of the corresponding amino acid
26  *
27  */
28 RDKIT_FILEPARSERS_EXPORT RWMol *SequenceToMol(const char *seq, bool sanitize,
29  bool lowerD);
30 //! \overload
31 RDKIT_FILEPARSERS_EXPORT RWMol *SequenceToMol(const std::string &seq,
32  bool sanitize, bool lowerD);
33 
34 // \brief construct a protein, RNA or DNA molecule from a sequence string
35 /*!
36  * \param seq - the string to be processed
37  * \param sanitize - toggles sanitization and stereochemistry perception of
38  *the molecule
39  * \param flavor -
40  * 0 Protein, L amino acids (default)
41  * 1 Protein, D amino acids
42  * 2 RNA, no cap
43  * 3 RNA, 5' cap
44  * 4 RNA, 3' cap
45  * 5 RNA, both caps
46  * 6 DNA, no cap
47  * 7 DNA, 5' cap
48  * 8 DNA, 3' cap
49  * 9 DNA, both caps
50  *
51  */
52 RDKIT_FILEPARSERS_EXPORT RWMol *SequenceToMol(const char *seq,
53  bool sanitize = true,
54  int flavor = 0);
55 //! \overload
56 RDKIT_FILEPARSERS_EXPORT RWMol *SequenceToMol(const std::string &seq,
57  bool sanitize = true,
58  int flavor = 0);
59 
60 // \brief construct a molecule from a FASTA string (currently only supports
61 // peptides)
62 /*!
63  * \param seq - the string to be processed
64  * \param sanitize - toggles sanitization and stereochemistry perception of
65  *the molecule
66  * \param lowerD - if set, lower case letters will be parsed as the d form
67  *of the corresponding amino acid
68  *
69  */
70 RDKIT_FILEPARSERS_EXPORT RWMol *FASTAToMol(const char *seq, bool sanitize,
71  bool lowerD);
72 //! \overload
73 RDKIT_FILEPARSERS_EXPORT RWMol *FASTAToMol(const std::string &seq,
74  bool sanitize, bool lowerD);
75 
76 // \brief construct a protein, DNA or RNA molecule from a FASTA string
77 /*!
78  * \param seq - the string to be processed
79  * \param sanitize - toggles sanitization and stereochemistry perception of
80  *the molecule
81  * \param flavor -
82  * 0 Protein, L amino acids (default)
83  * 1 Protein, D amino acids
84  * 2 RNA, no cap
85  * 3 RNA, 5' cap
86  * 4 RNA, 3' cap
87  * 5 RNA, both caps
88  * 6 DNA, no cap
89  * 7 DNA, 5' cap
90  * 8 DNA, 3' cap
91  * 9 DNA, both caps
92  *
93  */
94 RDKIT_FILEPARSERS_EXPORT RWMol *FASTAToMol(const char *seq,
95  bool sanitize = true,
96  int flavor = 0);
97 //! \overload
98 RDKIT_FILEPARSERS_EXPORT RWMol *FASTAToMol(const std::string &seq,
99  bool sanitize = true,
100  int flavor = 0);
101 
102 // \brief construct a molecule from a HELM string (currently only supports
103 // peptides)
104 /*!
105  * \param seq - the string to be processed
106  * \param sanitize - toggles sanitization and stereochemistry perception of
107  *the molecule
108  *
109  */
110 RDKIT_FILEPARSERS_EXPORT RWMol *HELMToMol(const char *helm,
111  bool sanitize = true);
112 //! \overload
113 RDKIT_FILEPARSERS_EXPORT RWMol *HELMToMol(const std::string &helm,
114  bool sanitize = true);
115 } // namespace RDKit
116 
117 #endif
RDKIT_FILEPARSERS_EXPORT
#define RDKIT_FILEPARSERS_EXPORT
Definition: export.h:216
RDKit::HELMToMol
RDKIT_FILEPARSERS_EXPORT RWMol * HELMToMol(const char *helm, bool sanitize=true)
RDKit::SequenceToMol
RDKIT_FILEPARSERS_EXPORT RWMol * SequenceToMol(const char *seq, bool sanitize, bool lowerD)
RDKit
Std stuff.
Definition: Atom.h:30
RDKit::FASTAToMol
RDKIT_FILEPARSERS_EXPORT RWMol * FASTAToMol(const char *seq, bool sanitize, bool lowerD)
export.h