RDKit: SequenceParsers.h Source File

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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 #ifndef _RD_SEQUENCEPARSE_H_
11 #define _RD_SEQUENCEPARSE_H_
12 #include <string>
13
14 namespace RDKit {
15 class RWMol;
16
17 // \brief construct a molecule from a sequence string (currently only supports
18 // peptides)
19 /*!
20 * \param seq - the string to be processed
21 * \param sanitize - toggles sanitization and stereochemistry perception of
22 *the molecule
23 * \param lowerD - if set, lower case letters will be parsed as the d form
24 *of the corresponding amino acid
25 *
26 */
27 RWMol *SequenceToMol(const char *seq, bool sanitize, bool lowerD);
28 //! \overload
29 RWMol *SequenceToMol(const std::string &seq, bool sanitize, bool lowerD);
30
31 // \brief construct a protein, RNA or DNA molecule from a sequence string
32 /*!
33 * \param seq - the string to be processed
34 * \param sanitize - toggles sanitization and stereochemistry perception of
35 *the molecule
36 * \param flavor -
37 * 0 Protein, L amino acids (default)
38 * 1 Protein, D amino acids
39 * 2 RNA, no cap
40 * 3 RNA, 5' cap
41 * 4 RNA, 3' cap
42 * 5 RNA, both caps
43 * 6 DNA, no cap
44 * 7 DNA, 5' cap
45 * 8 DNA, 3' cap
46 * 9 DNA, both caps
47 *
48 */
49 RWMol *SequenceToMol(const char *seq, bool sanitize = true, int flavor = 0);
50 //! \overload
51 RWMol *SequenceToMol(const std::string &seq, bool sanitize = true,
52 int flavor = 0);
53
54 // \brief construct a molecule from a FASTA string (currently only supports
55 // peptides)
56 /*!
57 * \param seq - the string to be processed
58 * \param sanitize - toggles sanitization and stereochemistry perception of
59 *the molecule
60 * \param lowerD - if set, lower case letters will be parsed as the d form
61 *of the corresponding amino acid
62 *
63 */
64 RWMol *FASTAToMol(const char *seq, bool sanitize, bool lowerD);
65 //! \overload
66 RWMol *FASTAToMol(const std::string &seq, bool sanitize, bool lowerD);
67
68 // \brief construct a protein, DNA or RNA molecule from a FASTA string
69 /*!
70 * \param seq - the string to be processed
71 * \param sanitize - toggles sanitization and stereochemistry perception of
72 *the molecule
73 * \param flavor -
74 * 0 Protein, L amino acids (default)
75 * 1 Protein, D amino acids
76 * 2 RNA, no cap
77 * 3 RNA, 5' cap
78 * 4 RNA, 3' cap
79 * 5 RNA, both caps
80 * 6 DNA, no cap
81 * 7 DNA, 5' cap
82 * 8 DNA, 3' cap
83 * 9 DNA, both caps
84 *
85 */
86 RWMol *FASTAToMol(const char *seq, bool sanitize = true, int flavor = 0);
87 //! \overload
88 RWMol *FASTAToMol(const std::string &seq, bool sanitize = true, int flavor = 0);
89
90 // \brief construct a molecule from a HELM string (currently only supports
91 // peptides)
92 /*!
93 * \param seq - the string to be processed
94 * \param sanitize - toggles sanitization and stereochemistry perception of
95 *the molecule
96 *
97 */
98 RWMol *HELMToMol(const char *helm, bool sanitize = true);
99 //! \overload
100 RWMol *HELMToMol(const std::string &helm, bool sanitize = true);
101 }
102
103 #endif
RDKit
Std stuff.
Definition: Atom.h:29
RDKit::SequenceToMol
RWMol * SequenceToMol(const char *seq, bool sanitize, bool lowerD)
RDKit::FASTAToMol
RWMol * FASTAToMol(const char *seq, bool sanitize, bool lowerD)
RDKit::HELMToMol
RWMol * HELMToMol(const char *helm, bool sanitize=true)