protocols::pdbinfo_manipulations Namespace Reference

Classes
struct	SequenceSpecification
	Rosetta defines the pdbinfo of an object via possible chain IDs, segment IDs, and insertion codes. More...
class	AlignPDBInfoToSequences
	Realign poses to sequences after losing pdb_info. More...
class	AlignPDBInfoToSequencesCreator

Typedefs
using	AlignPDBInfoToSequencesOP = utility::pointer::shared_ptr< AlignPDBInfoToSequences >
using	AlignPDBInfoToSequencesCOP = utility::pointer::shared_ptr< AlignPDBInfoToSequences const >

Enumerations
enum class	AlignPDBInfoToSequencesMode { unset , single , multiple }

Functions
AlignPDBInfoToSequencesMode	get_alignpdbinfotosequencesmode_from_string (std::string const &str)
std::string	alignpdbinfotosequencesmode_to_string (AlignPDBInfoToSequencesMode const &mode)
std::ostream &	operator<< (std::ostream &os, SequenceSpecification const &ss)
void	to_json (nlohmann::json &j, SequenceSpecification const &ss)
	serialization (json) of SequenceSpecification More...
void	from_json (const json &j, SequenceSpecification &ss)
utility::vector1< core::sequence::SequenceOP >	get_pose_sequences (core::pose::Pose const &pose)
utility::vector1< std::string >	split_string_based_on_inserts (std::string const &str_in)
	take something like -—HELLO-—MY—BOY— More...
std::string	AlignPDBInfoToSequences_namer (std::string const &name)
std::ostream &	operator<< (std::ostream &os, AlignPDBInfoToSequences const &mover)
	private methods /// More...
void	pad_sequences (std::string const &full_seq_1, core::sequence::SequenceOP const &aln_seq_1, std::string const &full_seq_2, core::sequence::SequenceOP const &aln_seq_2)
	Take two sequences that have been aligned, and their parent sequences and align/pad them with '-' as shown below: More...

Typedef Documentation

AlignPDBInfoToSequencesCOP

using protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesCOP = typedef utility::pointer::shared_ptr< AlignPDBInfoToSequences const >

AlignPDBInfoToSequencesOP

using protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesOP = typedef utility::pointer::shared_ptr< AlignPDBInfoToSequences >

Enumeration Type Documentation

AlignPDBInfoToSequencesMode

enum protocols::pdbinfo_manipulations::AlignPDBInfoToSequencesMode

strong

Enumerator
unset
single
multiple

Function Documentation

AlignPDBInfoToSequences_namer()

std::string protocols::pdbinfo_manipulations::AlignPDBInfoToSequences_namer

(

std::string const &

name

)

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::provide_xml_schema().

alignpdbinfotosequencesmode_to_string()

std::string protocols::pdbinfo_manipulations::alignpdbinfotosequencesmode_to_string

(

AlignPDBInfoToSequencesMode const &

mode

)

References multiple, and single.

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::get_mode_as_string().

from_json()

void protocols::pdbinfo_manipulations::from_json	(	const json &	j,
		SequenceSpecification &	ss
	)

References protocols::pdbinfo_manipulations::SequenceSpecification::chains_, protocols::pdbinfo_manipulations::SequenceSpecification::current_idx_, protocols::pdbinfo_manipulations::SequenceSpecification::insCodes_, protocols::pdbinfo_manipulations::SequenceSpecification::residue_numbers_, protocols::pdbinfo_manipulations::SequenceSpecification::segmentIDs_, and protocols::pdbinfo_manipulations::SequenceSpecification::sequence_.

get_alignpdbinfotosequencesmode_from_string()

AlignPDBInfoToSequencesMode protocols::pdbinfo_manipulations::get_alignpdbinfotosequencesmode_from_string

(

std::string const &

str

)

References multiple, single, and protocols::kinmatch::str().

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::parse_my_tag(), and protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::set_mode_from_string().

get_pose_sequences()

utility::vector1< core::sequence::SequenceOP > protocols::pdbinfo_manipulations::get_pose_sequences

(

core::pose::Pose const &

pose

)

References core::pose::Pose::chain_sequence(), core::pose::Pose::num_chains(), and core::id::to_string().

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence().

operator<<() [1/2]

std::ostream & protocols::pdbinfo_manipulations::operator<<	(	std::ostream &	os,
		AlignPDBInfoToSequences const &	mover
	)

private methods ///

References protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::show().

operator<<() [2/2]

std::ostream & protocols::pdbinfo_manipulations::operator<<	(	std::ostream &	os,
		SequenceSpecification const &	ss
	)

References protocols::pdbinfo_manipulations::SequenceSpecification::chains_, protocols::pdbinfo_manipulations::SequenceSpecification::current_idx_, protocols::pdbinfo_manipulations::SequenceSpecification::insCodes_, protocols::pdbinfo_manipulations::SequenceSpecification::residue_numbers_, protocols::pdbinfo_manipulations::SequenceSpecification::segmentIDs_, and protocols::pdbinfo_manipulations::SequenceSpecification::sequence_.

pad_sequences()

void protocols::pdbinfo_manipulations::pad_sequences	(	std::string const &	full_seq_1,
		core::sequence::SequenceOP const &	aln_seq_1,
		std::string const &	full_seq_2,
		core::sequence::SequenceOP const &	aln_seq_2
	)

Take two sequences that have been aligned, and their parent sequences and align/pad them with '-' as shown below:

given to align from SWAlign: query: CLGIGSCNDFAGCGYAVVCFW target: XXXXXXXXXXXXXXCLGIGSCNDFAGCGXXXXXXYAVVCFWXXXXX

from: (aka a result from SWAlign) query 1 CLGIGSCNDFAGCG---—YAVVCFW target 15 CLGIGSCNDFAGCGXXXXXXYAVVCFW

to: query 1 -----------—CLGIGSCNDFAGCG---—YAVVCFW--— target 1 XXXXXXXXXXXXXXCLGIGSCNDFAGCGXXXXXXYAVVCFWXXXXX

References protocols::mean_field::max().

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence(), and protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_single_sequence().

split_string_based_on_inserts()

utility::vector1< std::string > protocols::pdbinfo_manipulations::split_string_based_on_inserts

(

std::string const &

str_in

)

take something like -—HELLO-—MY—BOY—

Referenced by protocols::pdbinfo_manipulations::AlignPDBInfoToSequences::apply_multi_sequence().

to_json()

void protocols::pdbinfo_manipulations::to_json	(	nlohmann::json &	j,
		SequenceSpecification const &	ss
	)

serialization (json) of SequenceSpecification

References protocols::pdbinfo_manipulations::SequenceSpecification::chains_, protocols::pdbinfo_manipulations::SequenceSpecification::current_idx_, protocols::pdbinfo_manipulations::SequenceSpecification::insCodes_, protocols::pdbinfo_manipulations::SequenceSpecification::residue_numbers_, protocols::pdbinfo_manipulations::SequenceSpecification::segmentIDs_, and protocols::pdbinfo_manipulations::SequenceSpecification::sequence_.