citation_manager¶

Bindings for basic::citation_manager namespace

class pyrosetta.rosetta.basic.citation_manager.AuthorNames¶

Bases: pybind11_object

Data structure for author names.

assign(self: pyrosetta.rosetta.basic.citation_manager.AuthorNames, : pyrosetta.rosetta.basic.citation_manager.AuthorNames) → pyrosetta.rosetta.basic.citation_manager.AuthorNames¶

Assignment operator.

C++: basic::citation_manager::AuthorNames::operator=(const class basic::citation_manager::AuthorNames &) –> class basic::citation_manager::AuthorNames &

clone(self: pyrosetta.rosetta.basic.citation_manager.AuthorNames) → pyrosetta.rosetta.basic.citation_manager.AuthorNames¶: C++: basic::citation_manager::AuthorNames::clone() const –> class std::shared_ptr<class basic::citation_manager::AuthorNames>

given_names(self: pyrosetta.rosetta.basic.citation_manager.AuthorNames) → str¶

Get the given name(s).

C++: basic::citation_manager::AuthorNames::given_names() const –> const std::string &

initials(self: pyrosetta.rosetta.basic.citation_manager.AuthorNames) → str¶

Get the initial(s).

C++: basic::citation_manager::AuthorNames::initials() const –> const std::string &

surname(self: pyrosetta.rosetta.basic.citation_manager.AuthorNames) → str¶

Get the surname(s).

C++: basic::citation_manager::AuthorNames::surname() const –> const std::string &

class pyrosetta.rosetta.basic.citation_manager.Citation¶

Bases: pybind11_object

Data structure for storing a citation.

add_co_author(self: pyrosetta.rosetta.basic.citation_manager.Citation, given_names: str, surname: str, initials: str) → None¶

Add a co-author.

Must be added in order of appearance.

If I were adding “John Fitzgerald Kennedy Jr.”, I would set given_names=”John Fitzgerald”, surname=”Kennedy”, initials=”JF Jr.”.

C++: basic::citation_manager::Citation::add_co_author(const std::string &, const std::string &, const std::string &) –> void

add_primary_author(self: pyrosetta.rosetta.basic.citation_manager.Citation, given_names: str, surname: str, initials: str) → None¶

Add a primary author.

Must be added in order of appearance.

If I were adding “James Tiberius Kirk”, I would set given_names=”James Tiberius”, surname=”Kirk”, initials=”JT”.

C++: basic::citation_manager::Citation::add_primary_author(const std::string &, const std::string &, const std::string &) –> void

add_senior_author(self: pyrosetta.rosetta.basic.citation_manager.Citation, given_names: str, surname: str, initials: str) → None¶

Add a primary author.

Must be added in order of appearance.

If I were adding “Mary-Kate Olsen”, I would set given_names=”Mary-Kate”, surname=”Olsen”, initials=”M-K”.

C++: basic::citation_manager::Citation::add_senior_author(const std::string &, const std::string &, const std::string &) –> void

article_title(self: pyrosetta.rosetta.basic.citation_manager.Citation) → str¶

Get the article title.

C++: basic::citation_manager::Citation::article_title() const –> const std::string &

assign(self: pyrosetta.rosetta.basic.citation_manager.Citation, : pyrosetta.rosetta.basic.citation_manager.Citation) → pyrosetta.rosetta.basic.citation_manager.Citation¶: C++: basic::citation_manager::Citation::operator=(const class basic::citation_manager::Citation &) –> class basic::citation_manager::Citation &

clear(self: pyrosetta.rosetta.basic.citation_manager.Citation) → None¶

Completely clear the data in this citation.

C++: basic::citation_manager::Citation::clear() –> void

clone(self: pyrosetta.rosetta.basic.citation_manager.Citation) → pyrosetta.rosetta.basic.citation_manager.Citation¶: C++: basic::citation_manager::Citation::clone() const –> class std::shared_ptr<class basic::citation_manager::Citation>

co_authors(self: pyrosetta.rosetta.basic.citation_manager.Citation) → pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames¶

Access the list of coauthors.

C++: basic::citation_manager::Citation::co_authors() const –> const class utility::vector1<class basic::citation_manager::AuthorNames, class std::allocator<class basic::citation_manager::AuthorNames> > &

doi(self: pyrosetta.rosetta.basic.citation_manager.Citation) → str¶

Get the DOI.

C++: basic::citation_manager::Citation::doi() const –> const std::string &

get_formatted_citation(*args, **kwargs)¶

Overloaded function.

get_formatted_citation(self: pyrosetta.rosetta.basic.citation_manager.Citation, outstream: pyrosetta.rosetta.std.ostream) -> None
get_formatted_citation(self: pyrosetta.rosetta.basic.citation_manager.Citation, outstream: pyrosetta.rosetta.std.ostream, format: pyrosetta.rosetta.basic.citation_manager.CitationFormat) -> None

Get this citation as a string, in a particular format.

C++: basic::citation_manager::Citation::get_formatted_citation(std::ostream &, const enum basic::citation_manager::CitationFormat) const –> void

initialize_from_string(self: pyrosetta.rosetta.basic.citation_manager.Citation, citation_as_string: str) → None¶

Initializes from a string formatted as in the Rosetta database. See initialization

constructor’s description for an example.

Calls clear() before initializing.

C++: basic::citation_manager::Citation::initialize_from_string(const std::string &) –> void

journal_title(self: pyrosetta.rosetta.basic.citation_manager.Citation) → str¶

Get the journal title.

C++: basic::citation_manager::Citation::journal_title() const –> const std::string &

primary_authors(self: pyrosetta.rosetta.basic.citation_manager.Citation) → pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames¶

Access the list of primary authors.

C++: basic::citation_manager::Citation::primary_authors() const –> const class utility::vector1<class basic::citation_manager::AuthorNames, class std::allocator<class basic::citation_manager::AuthorNames> > &

senior_authors(self: pyrosetta.rosetta.basic.citation_manager.Citation) → pyrosetta.rosetta.utility.vector1_basic_citation_manager_AuthorNames¶

Access the list of senior authors.

C++: basic::citation_manager::Citation::senior_authors() const –> const class utility::vector1<class basic::citation_manager::AuthorNames, class std::allocator<class basic::citation_manager::AuthorNames> > &

set_year_and_article(self: pyrosetta.rosetta.basic.citation_manager.Citation, year_in: int, article_title: str, journal_title: str, volume_issue_pages: str, doi: str) → None¶

Set the year, article title, journal title, and the string for the volume/issue/pages.

C++: basic::citation_manager::Citation::set_year_and_article(const int, const std::string &, const std::string &, const std::string &, const std::string &) –> void

volume_issue_pages(self: pyrosetta.rosetta.basic.citation_manager.Citation) → str¶

Get the volume, issue, and pages.

C++: basic::citation_manager::Citation::volume_issue_pages() const –> const std::string &

year(self: pyrosetta.rosetta.basic.citation_manager.Citation) → int¶

Get the year.

C++: basic::citation_manager::Citation::year() const –> int

class pyrosetta.rosetta.basic.citation_manager.CitationCollection¶

Bases: CitationCollectionBase

A class for keeping track of a collection of citations for a particular Rosetta module.

add_citation(self: pyrosetta.rosetta.basic.citation_manager.CitationCollection, citation_in: pyrosetta.rosetta.basic.citation_manager.Citation) → None¶

Add a citation without cloning it.

Does nothing if citation_in is nullptr.

C++: basic::citation_manager::CitationCollection::add_citation(class std::shared_ptr<const class basic::citation_manager::Citation>) –> void

assign(self: pyrosetta.rosetta.basic.citation_manager.CitationCollection, : pyrosetta.rosetta.basic.citation_manager.CitationCollection) → pyrosetta.rosetta.basic.citation_manager.CitationCollection¶

Assignment operator.

C++: basic::citation_manager::CitationCollection::operator=(const class basic::citation_manager::CitationCollection &) –> class basic::citation_manager::CitationCollection &

clone(self: pyrosetta.rosetta.basic.citation_manager.CitationCollection) → pyrosetta.rosetta.basic.citation_manager.CitationCollection¶

Clone operator: copy this object and return an owning pointer to the copy.

C++: basic::citation_manager::CitationCollection::clone() const –> class std::shared_ptr<class basic::citation_manager::CitationCollection>

get_citations_formatted(*args, **kwargs)¶

Overloaded function.

get_citations_formatted(self: pyrosetta.rosetta.basic.citation_manager.CitationCollection, outstream: pyrosetta.rosetta.std.ostream) -> None
get_citations_formatted(self: pyrosetta.rosetta.basic.citation_manager.CitationCollection, outstream: pyrosetta.rosetta.std.ostream, format: pyrosetta.rosetta.basic.citation_manager.CitationFormat) -> None

Get the citations, written out prettily to a string stream.

Multiple citations will be on multiple lines, but there’s no newline at the start or the end of the output.

C++: basic::citation_manager::CitationCollection::get_citations_formatted(std::ostream &, const enum basic::citation_manager::CitationFormat) const –> void

static get_enumerated_module_type_name(module_type: pyrosetta.rosetta.basic.citation_manager.CitedModuleType) → str¶

Get the module type name.

The module_type cannot be CitedModuleType::CustomType (or this will throw).

C++: basic::citation_manager::CitationCollection::get_enumerated_module_type_name(const enum basic::citation_manager::CitedModuleType) –> const std::string &

has_multiple_citations(self: pyrosetta.rosetta.basic.citation_manager.CitationCollection) → bool¶

Does this collection have more than one citation?

C++: basic::citation_manager::CitationCollection::has_multiple_citations() const –> bool

module_name(self: pyrosetta.rosetta.basic.citation_manager.CitationCollection) → str¶

Get this module’s name.

C++: basic::citation_manager::CitationCollection::module_name() const –> const std::string &

module_type(self: pyrosetta.rosetta.basic.citation_manager.CitationCollection) → str¶

Get this module’s type.

C++: basic::citation_manager::CitationCollection::module_type() const –> const std::string &

class pyrosetta.rosetta.basic.citation_manager.CitationCollectionBase¶

Bases: pybind11_object

Base structure for storing a citation. This is a base class for vitual inheritance. There’s not much it actually does itself. Its main purpose is to allow us to put both CitationCollections and UnpublishedModuleInfos into the same list.

assign(self: pyrosetta.rosetta.basic.citation_manager.CitationCollectionBase, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionBase) → pyrosetta.rosetta.basic.citation_manager.CitationCollectionBase¶: C++: basic::citation_manager::CitationCollectionBase::operator=(const class basic::citation_manager::CitationCollectionBase &) –> class basic::citation_manager::CitationCollectionBase &

class pyrosetta.rosetta.basic.citation_manager.CitationCollectionList¶

Bases: pybind11_object

A collection of CitationCollectionBases

add(*args, **kwargs)¶

Overloaded function.

add(self: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList, citr: pyrosetta.rosetta.basic.citation_manager.CitationCollectionBase) -> None

Add the citation to the list, being aware of duplicates

C++: basic::citation_manager::CitationCollectionList::add(const class std::shared_ptr<const class basic::citation_manager::CitationCollectionBase> &) –> void

add(self: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList, other: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) -> None

Add all the citations in the other list

C++: basic::citation_manager::CitationCollectionList::add(const class basic::citation_manager::CitationCollectionList &) –> void

assign(self: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → pyrosetta.rosetta.basic.citation_manager.CitationCollectionList¶: C++: basic::citation_manager::CitationCollectionList::operator=(const class basic::citation_manager::CitationCollectionList &) –> class basic::citation_manager::CitationCollectionList &

citations(self: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_basic_citation_manager_CitationCollectionBase_t¶

The list of citation collections as a vector

C++: basic::citation_manager::CitationCollectionList::citations() const –> const class utility::vector1<class std::shared_ptr<const class basic::citation_manager::CitationCollectionBase>, class std::allocator<class std::shared_ptr<const class basic::citation_manager::CitationCollectionBase> > > &

empty(self: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → bool¶

Are we empty of citations?

C++: basic::citation_manager::CitationCollectionList::empty() const –> bool

class pyrosetta.rosetta.basic.citation_manager.CitationFormat¶

Bases: pybind11_object

The format for writing a citation.

If this is altered, update Citation::get_formatted_citation().

Members:

DefaultStyle

NatureStyle

end_of_list

DefaultStyle = <CitationFormat.DefaultStyle: 1>¶

NatureStyle = <CitationFormat.NatureStyle: 2>¶

end_of_list = <CitationFormat.NatureStyle: 2>¶

property name¶

property value¶

class pyrosetta.rosetta.basic.citation_manager.CitationManager¶

Bases: SingletonBase_basic_citation_manager_CitationManager_t

A class that receives lists of works to cite from Rosetta modules, then returns a list of all works to cite on demand. Threadsafe.

add_citation(self: pyrosetta.rosetta.basic.citation_manager.CitationManager, input: pyrosetta.rosetta.basic.citation_manager.CitationCollectionBase) → None¶

Add a single citation to the citation manger

Will not add if a duplicate

Threadsafe

C++: basic::citation_manager::CitationManager::add_citation(const class std::shared_ptr<const class basic::citation_manager::CitationCollectionBase> &) –> void

add_citations(self: pyrosetta.rosetta.basic.citation_manager.CitationManager, input: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Add citations to the list of citations that have been collected.

Only adds citations that have not been already added.

Threadsafe.

C++: basic::citation_manager::CitationManager::add_citations(const class basic::citation_manager::CitationCollectionList &) –> void

clear_citations(self: pyrosetta.rosetta.basic.citation_manager.CitationManager) → None¶

Clear all citations that have been collected.

Does not clear the map of DOI->Rosetta citation that was loaded from the Rosetta database.

Threadsafe.

C++: basic::citation_manager::CitationManager::clear_citations() –> void

get_citation_by_doi(self: pyrosetta.rosetta.basic.citation_manager.CitationManager, doi: str) → pyrosetta.rosetta.basic.citation_manager.Citation¶

Given a DOI string, get a Rosetta citation.

Throws if the DOI string isn’t in the list of Rosetta papers in the database.

C++: basic::citation_manager::CitationManager::get_citation_by_doi(const std::string &) const –> class std::shared_ptr<const class basic::citation_manager::Citation>

static get_instance() → basic::citation_manager::CitationManager¶: C++: utility::SingletonBase<basic::citation_manager::CitationManager>::get_instance() –> class basic::citation_manager::CitationManager *

write_all_citations_and_unpublished_author_info(self: pyrosetta.rosetta.basic.citation_manager.CitationManager) → None¶

Write out all unpublished modules and citations to the CitationManager’s tracer.

C++: basic::citation_manager::CitationManager::write_all_citations_and_unpublished_author_info() const –> void

write_all_citations_and_unpublished_author_info_from_list_to_stream(self: pyrosetta.rosetta.basic.citation_manager.CitationManager, list: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList, outstream: pyrosetta.rosetta.std.ostream) → None¶

Write out all unpublished modules and citations in a CitationCollectionList to a given output stream.

C++: basic::citation_manager::CitationManager::write_all_citations_and_unpublished_author_info_from_list_to_stream(const class basic::citation_manager::CitationCollectionList &, std::ostream &) const –> void

class pyrosetta.rosetta.basic.citation_manager.CitedModuleType¶

Bases: pybind11_object

What type of Rosetta module are we providing a citation for?

If this list is added to, then the CitationCollection::get_enumerated_module_type_name() function must be updated.

Members:

Mover

Filter

ScoreTerm

ResidueSelector

TaskOperation

PackerPalette

ScoreFunction

EnergyMethod

SimpleMetric

ConstraintGenerator

NeuralNetwork

Singleton

Application

CrosslinkerMoverHelper

CustomType

end_of_list

Application = <CitedModuleType.Application: 13>¶

ConstraintGenerator = <CitedModuleType.ConstraintGenerator: 10>¶

CrosslinkerMoverHelper = <CitedModuleType.CrosslinkerMoverHelper: 14>¶

CustomType = <CitedModuleType.CustomType: 15>¶

EnergyMethod = <CitedModuleType.EnergyMethod: 8>¶

Filter = <CitedModuleType.Filter: 2>¶

Mover = <CitedModuleType.Mover: 1>¶

NeuralNetwork = <CitedModuleType.NeuralNetwork: 11>¶

PackerPalette = <CitedModuleType.PackerPalette: 6>¶

ResidueSelector = <CitedModuleType.ResidueSelector: 4>¶

ScoreFunction = <CitedModuleType.ScoreFunction: 7>¶

ScoreTerm = <CitedModuleType.ScoreTerm: 3>¶

SimpleMetric = <CitedModuleType.SimpleMetric: 9>¶

Singleton = <CitedModuleType.Singleton: 12>¶

TaskOperation = <CitedModuleType.TaskOperation: 5>¶

end_of_list = <CitedModuleType.CustomType: 15>¶

property name¶

property value¶

class pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor¶

Bases: pybind11_object

Authorship information for a single author in an unpublished Rosetta module.

Vikram K. Mulligan (vmulligan.org)

affiliation(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor) → str¶

Get his or her institutional affiliation.

C++: basic::citation_manager::UnpublishedModuleAuthor::affiliation() const –> const std::string &

assign(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor, : pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor) → pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor¶: C++: basic::citation_manager::UnpublishedModuleAuthor::operator=(const class basic::citation_manager::UnpublishedModuleAuthor &) –> class basic::citation_manager::UnpublishedModuleAuthor &

author_name(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor) → str¶

Get the author’s name.

C++: basic::citation_manager::UnpublishedModuleAuthor::author_name() const –> const std::string &

clone(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor) → pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor¶

Clone operation: make a copy of this object, and return an owning pointer to the copy.

C++: basic::citation_manager::UnpublishedModuleAuthor::clone() const –> class std::shared_ptr<class basic::citation_manager::UnpublishedModuleAuthor>

email_address(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor) → str¶

Get his or her e-mail address.

C++: basic::citation_manager::UnpublishedModuleAuthor::email_address() const –> const std::string &

notes(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleAuthor) → str¶

Get the notes, if any.

C++: basic::citation_manager::UnpublishedModuleAuthor::notes() const –> const std::string &

class pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo¶

Bases: CitationCollectionBase

Authorship information for an unpublished Rosetta module.

Vikram K. Mulligan (vmulligan.org)

add_author(*args, **kwargs)¶

Overloaded function.

add_author(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo, author_name: str, affiliation: str, email: str) -> None

Add an author for this unpublished module.

The author name must be nonempty; the other fields may be empty.

C++: basic::citation_manager::UnpublishedModuleInfo::add_author(const std::string &, const std::string &, const std::string &) –> void

add_author(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo, author_name: str, affiliation: str, email: str, notes: str) -> None

Add an author for this unpublished module.

The author name must be nonempty; the other fields may be empty. This version has a field for notes.

C++: basic::citation_manager::UnpublishedModuleInfo::add_author(const std::string &, const std::string &, const std::string &, const std::string &) –> void

assign(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo, : pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo) → pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo¶: C++: basic::citation_manager::UnpublishedModuleInfo::operator=(const class basic::citation_manager::UnpublishedModuleInfo &) –> class basic::citation_manager::UnpublishedModuleInfo &

clone(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo) → pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo¶

Clone operation: make a copy of this object, and return an owning pointer to the copy.

C++: basic::citation_manager::UnpublishedModuleInfo::clone() const –> class std::shared_ptr<class basic::citation_manager::UnpublishedModuleInfo>

get_author_list(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo, outstream: pyrosetta.rosetta.std.ostream) → None¶

List authors in the format:: Name, Institution [email] Name, Institution [email] Name, Institution [email] …

C++: basic::citation_manager::UnpublishedModuleInfo::get_author_list(std::ostream &) const –> void

module_name(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo) → str¶

Get the unpublished module’s name.

C++: basic::citation_manager::UnpublishedModuleInfo::module_name() const –> const std::string &

module_type(self: pyrosetta.rosetta.basic.citation_manager.UnpublishedModuleInfo) → str¶

Get the unpublished module’s type.

C++: basic::citation_manager::UnpublishedModuleInfo::module_type() const –> const std::string &