RDKit
Open-source cheminformatics and machine learning.
SequenceParsers.h
Go to the documentation of this file.
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//
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// Copyright (C) 2015,2016 Greg Landrum and NextMove Software
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <
RDGeneral/export.h
>
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#ifndef _RD_SEQUENCEPARSE_H_
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#define _RD_SEQUENCEPARSE_H_
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#include <string>
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namespace
RDKit
{
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class
RWMol;
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// \brief construct a molecule from a sequence string (currently only supports
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// peptides)
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/*!
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* \param seq - the string to be processed
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* \param sanitize - toggles sanitization and stereochemistry perception of
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*the molecule
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* \param lowerD - if set, lower case letters will be parsed as the d form
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*of the corresponding amino acid
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*
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*/
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RDKIT_FILEPARSERS_EXPORT
RWMol *
SequenceToMol
(
const
char
*seq,
bool
sanitize,
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bool
lowerD);
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//! \overload
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RDKIT_FILEPARSERS_EXPORT
RWMol *
SequenceToMol
(
const
std::string &seq,
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bool
sanitize,
bool
lowerD);
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// \brief construct a protein, RNA or DNA molecule from a sequence string
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/*!
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* \param seq - the string to be processed
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* \param sanitize - toggles sanitization and stereochemistry perception of
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*the molecule
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* \param flavor -
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* 0 Protein, L amino acids (default)
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* 1 Protein, D amino acids
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* 2 RNA, no cap
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* 3 RNA, 5' cap
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* 4 RNA, 3' cap
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* 5 RNA, both caps
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* 6 DNA, no cap
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* 7 DNA, 5' cap
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* 8 DNA, 3' cap
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* 9 DNA, both caps
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*
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*/
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RDKIT_FILEPARSERS_EXPORT
RWMol *
SequenceToMol
(
const
char
*seq,
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bool
sanitize =
true
,
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int
flavor = 0);
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//! \overload
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RDKIT_FILEPARSERS_EXPORT
RWMol *
SequenceToMol
(
const
std::string &seq,
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bool
sanitize =
true
,
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int
flavor = 0);
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// \brief construct a molecule from a FASTA string (currently only supports
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// peptides)
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/*!
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* \param seq - the string to be processed
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* \param sanitize - toggles sanitization and stereochemistry perception of
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*the molecule
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* \param lowerD - if set, lower case letters will be parsed as the d form
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*of the corresponding amino acid
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*
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*/
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RDKIT_FILEPARSERS_EXPORT
RWMol *
FASTAToMol
(
const
char
*seq,
bool
sanitize,
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bool
lowerD);
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//! \overload
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RDKIT_FILEPARSERS_EXPORT
RWMol *
FASTAToMol
(
const
std::string &seq,
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bool
sanitize,
bool
lowerD);
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// \brief construct a protein, DNA or RNA molecule from a FASTA string
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/*!
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* \param seq - the string to be processed
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* \param sanitize - toggles sanitization and stereochemistry perception of
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*the molecule
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* \param flavor -
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* 0 Protein, L amino acids (default)
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* 1 Protein, D amino acids
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* 2 RNA, no cap
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* 3 RNA, 5' cap
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* 4 RNA, 3' cap
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* 5 RNA, both caps
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* 6 DNA, no cap
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* 7 DNA, 5' cap
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* 8 DNA, 3' cap
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* 9 DNA, both caps
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*
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*/
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RDKIT_FILEPARSERS_EXPORT
RWMol *
FASTAToMol
(
const
char
*seq,
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bool
sanitize =
true
,
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int
flavor = 0);
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//! \overload
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RDKIT_FILEPARSERS_EXPORT
RWMol *
FASTAToMol
(
const
std::string &seq,
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bool
sanitize =
true
,
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int
flavor = 0);
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// \brief construct a molecule from a HELM string (currently only supports
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// peptides)
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/*!
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* \param seq - the string to be processed
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* \param sanitize - toggles sanitization and stereochemistry perception of
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*the molecule
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*
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*/
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RDKIT_FILEPARSERS_EXPORT
RWMol *
HELMToMol
(
const
char
*helm,
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bool
sanitize =
true
);
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//! \overload
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RDKIT_FILEPARSERS_EXPORT
RWMol *
HELMToMol
(
const
std::string &helm,
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bool
sanitize =
true
);
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}
// namespace RDKit
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#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
GraphMol
FileParsers
SequenceParsers.h
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