/usr/include/rdkit/GraphMol/FileParsers/SequenceParsers.h is in librdkit-dev 201603.5-2.
This file is owned by root:root, with mode 0o644.
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// Copyright (C) 2015 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.
//
#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
*
*/
RWMol *SequenceToMol(const char *seq, bool sanitize = true,
bool lowerD = false);
//! \overload
RWMol *SequenceToMol(const std::string &seq, bool sanitize = true,
bool lowerD = false);
// \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
*
*/
RWMol *FASTAToMol(const char *seq, bool sanitize = true, bool lowerD = false);
//! \overload
RWMol *FASTAToMol(const std::string &seq, bool sanitize = true,
bool lowerD = false);
// \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
*
*/
RWMol *HELMToMol(const char *helm, bool sanitize = true);
//! \overload
RWMol *HELMToMol(const std::string &helm, bool sanitize = true);
}
#endif
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