RDKit: SequenceParsers.h Source File

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SequenceParsers.h
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1 //
2 // Copyright (C) 2015 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 = true,
28 bool lowerD = false);
29 //! \overload
30 RWMol *SequenceToMol(const std::string &seq, bool sanitize = true,
31 bool lowerD = false);
32
33 // \brief construct a molecule from a FASTA string (currently only supports
34 // peptides)
35 /*!
36 * \param seq - the string to be processed
37 * \param sanitize - toggles sanitization and stereochemistry perception of
38 *the molecule
39 * \param lowerD - if set, lower case letters will be parsed as the d form
40 *of the corresponding amino acid
41 *
42 */
43 RWMol *FASTAToMol(const char *seq, bool sanitize = true, bool lowerD = false);
44 //! \overload
45 RWMol *FASTAToMol(const std::string &seq, bool sanitize = true,
46 bool lowerD = false);
47
48 // \brief construct a molecule from a HELM string (currently only supports
49 // peptides)
50 /*!
51 * \param seq - the string to be processed
52 * \param sanitize - toggles sanitization and stereochemistry perception of
53 *the molecule
54 *
55 */
56 RWMol *HELMToMol(const char *helm, bool sanitize = true);
57 //! \overload
58 RWMol *HELMToMol(const std::string &helm, bool sanitize = true);
59 }
60
61 #endif
RDKit::FASTAToMol
RWMol * FASTAToMol(const char *seq, bool sanitize=true, bool lowerD=false)
RDKit::SequenceToMol
RWMol * SequenceToMol(const char *seq, bool sanitize=true, bool lowerD=false)
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::HELMToMol
RWMol * HELMToMol(const char *helm, bool sanitize=true)