protocols::pdbinfo_manipulations::SequenceSpecification Struct Reference

Rosetta defines the pdbinfo of an object via possible chain IDs, segment IDs, and insertion codes. More...

#include <AlignPDBInfoToSequences.hh>

Public Member Functions
	SequenceSpecification ()
	SequenceSpecification (std::string const &sequence, utility::vector1< std::string > const &chains, utility::vector1< std::string > const &segmentIDs=utility::vector1< std::string >(), utility::vector1< std::string > const &insCodes=utility::vector1< std::string >(), utility::vector1< int > const &residue_numbers=utility::vector1< int >())
void	check_single_format () const
	make sure none of the non-sequence elements are larger than the sequence_. More...
void	update_multiple_format_residue_numbering ()
	make sure residue numbering is set to be the same size as the sequence_ More...
void	set_1_to_1_format (int const starting_number)
	duplicate the last element (or default last element if not set) to pad chains_, segmentIDs_, insCodes_, residue_numbers_, to be the same length as the sequence_. More...
bool	operator== (SequenceSpecification const &alt_ss) const
	This ignores current_idx_ because that is just a way to track how many times This has been used. More...

Public Attributes
std::string	sequence_
utility::vector1< std::string >	chains_
utility::vector1< std::string >	segmentIDs_
utility::vector1< std::string >	insCodes_
utility::vector1< int >	residue_numbers_
core::Size	current_idx_

Detailed Description

Rosetta defines the pdbinfo of an object via possible chain IDs, segment IDs, and insertion codes.

Constructor & Destructor Documentation

protocols::pdbinfo_manipulations::SequenceSpecification::SequenceSpecification ( )

inline

protocols::pdbinfo_manipulations::SequenceSpecification::SequenceSpecification ( std::string const &  sequence, utility::vector1< std::string > const &  chains, utility::vector1< std::string > const &  segmentIDs = utility::vector1<std::string>(), utility::vector1< std::string > const &  insCodes = utility::vector1<std::string>(), utility::vector1< int > const &  residue_numbers = utility::vector1<int>()  )

inline

Member Function Documentation

void protocols::pdbinfo_manipulations::SequenceSpecification::check_single_format

(

)

const

make sure none of the non-sequence elements are larger than the sequence_.

References chains_, insCodes_, residue_numbers_, segmentIDs_, and sequence_.

bool protocols::pdbinfo_manipulations::SequenceSpecification::operator==

(

SequenceSpecification const &

alt_ss

)

const

This ignores current_idx_ because that is just a way to track how many times This has been used.

References chains_, insCodes_, residue_numbers_, segmentIDs_, and sequence_.

void protocols::pdbinfo_manipulations::SequenceSpecification::set_1_to_1_format

(

int const

starting_number

)

duplicate the last element (or default last element if not set) to pad chains_, segmentIDs_, insCodes_, residue_numbers_, to be the same length as the sequence_.

duplicate the last element (or default last element if not set) to pad chains_, segmentIDs_, and insCodes_ to be the same length as the sequence_.

References chains_, insCodes_, residue_numbers_, segmentIDs_, and sequence_.

void protocols::pdbinfo_manipulations::SequenceSpecification::update_multiple_format_residue_numbering

(

)

make sure residue numbering is set to be the same size as the sequence_

make sure none of the non-sequence elements are larger than the sequence_.

References residue_numbers_, and sequence_.

Member Data Documentation

utility::vector1<std::string> protocols::pdbinfo_manipulations::SequenceSpecification::chains_

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence(), check_single_format(), protocols::pdbinfo_manipulations::from_json(), protocols::pdbinfo_manipulations::operator<<(), operator==(), set_1_to_1_format(), and protocols::pdbinfo_manipulations::to_json().

core::Size protocols::pdbinfo_manipulations::SequenceSpecification::current_idx_

Referenced by protocols::pdbinfo_manipulations::from_json(), protocols::pdbinfo_manipulations::operator<<(), and protocols::pdbinfo_manipulations::to_json().

utility::vector1<std::string> protocols::pdbinfo_manipulations::SequenceSpecification::insCodes_

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence(), check_single_format(), protocols::pdbinfo_manipulations::from_json(), protocols::pdbinfo_manipulations::operator<<(), operator==(), set_1_to_1_format(), and protocols::pdbinfo_manipulations::to_json().

utility::vector1<int> protocols::pdbinfo_manipulations::SequenceSpecification::residue_numbers_

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence(), check_single_format(), protocols::pdbinfo_manipulations::from_json(), protocols::pdbinfo_manipulations::operator<<(), operator==(), set_1_to_1_format(), protocols::pdbinfo_manipulations::to_json(), and update_multiple_format_residue_numbering().

utility::vector1<std::string> protocols::pdbinfo_manipulations::SequenceSpecification::segmentIDs_

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence(), check_single_format(), protocols::pdbinfo_manipulations::from_json(), protocols::pdbinfo_manipulations::operator<<(), operator==(), set_1_to_1_format(), and protocols::pdbinfo_manipulations::to_json().

std::string protocols::pdbinfo_manipulations::SequenceSpecification::sequence_

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence(), check_single_format(), protocols::pdbinfo_manipulations::from_json(), protocols::pdbinfo_manipulations::operator<<(), operator==(), set_1_to_1_format(), protocols::pdbinfo_manipulations::to_json(), and update_multiple_format_residue_numbering().

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The documentation for this struct was generated from the following files:

• src/protocols/pdbinfo_manipulations/AlignPDBInfoToSequences.hh
• src/protocols/pdbinfo_manipulations/AlignPDBInfoToSequences.cc