io

Bindings for core::io namespace

class pyrosetta.rosetta.core.io.AtomInformation

Bases: pybind11_builtins.pybind11_object

Only fields that are present in the PDB file will be initialized; others will have the default value. This class basically reflects the structure of ‘ATOM’ lines in PDB file format.

property altLoc
assign(self: pyrosetta.rosetta.core.io.AtomInformation, : pyrosetta.rosetta.core.io.AtomInformation) pyrosetta.rosetta.core.io.AtomInformation

C++: core::io::AtomInformation::operator=(const struct core::io::AtomInformation &) –> struct core::io::AtomInformation &

property chainID
property chem_comp_type
property connected_indices
property connected_orders
property element
property formalcharge
property iCode
property isHet
property name
property occupancy
property resName
property resSeq
property segmentID
property serial
property temperature
property terCount
property x
property y
property z
class pyrosetta.rosetta.core.io.CisPeptideInformation

Bases: pybind11_builtins.pybind11_object

Labonte <JWLabonte.edu>

assign(self: pyrosetta.rosetta.core.io.CisPeptideInformation, : pyrosetta.rosetta.core.io.CisPeptideInformation) pyrosetta.rosetta.core.io.CisPeptideInformation

C++: core::io::CisPeptideInformation::operator=(const struct core::io::CisPeptideInformation &) –> struct core::io::CisPeptideInformation &

property chainID1
property chainID2
property icode1
property icode2
property measure
property pep1
property pep2
property seqNum1
property seqNum2
class pyrosetta.rosetta.core.io.CrystInfo

Bases: pybind11_builtins.pybind11_object

A(*args, **kwargs)

Overloaded function.

  1. A(self: pyrosetta.rosetta.core.io.CrystInfo) -> float

C++: core::io::CrystInfo::A() const –> double

  1. A(self: pyrosetta.rosetta.core.io.CrystInfo, Ain: float) -> None

C++: core::io::CrystInfo::A(double) –> void

B(*args, **kwargs)

Overloaded function.

  1. B(self: pyrosetta.rosetta.core.io.CrystInfo) -> float

C++: core::io::CrystInfo::B() const –> double

  1. B(self: pyrosetta.rosetta.core.io.CrystInfo, Bin: float) -> None

C++: core::io::CrystInfo::B(double) –> void

C(*args, **kwargs)

Overloaded function.

  1. C(self: pyrosetta.rosetta.core.io.CrystInfo) -> float

C++: core::io::CrystInfo::C() const –> double

  1. C(self: pyrosetta.rosetta.core.io.CrystInfo, Cin: float) -> None

C++: core::io::CrystInfo::C(double) –> void

alpha(*args, **kwargs)

Overloaded function.

  1. alpha(self: pyrosetta.rosetta.core.io.CrystInfo) -> float

C++: core::io::CrystInfo::alpha() const –> double

  1. alpha(self: pyrosetta.rosetta.core.io.CrystInfo, alphain: float) -> None

C++: core::io::CrystInfo::alpha(double) –> void

assign(self: pyrosetta.rosetta.core.io.CrystInfo, : pyrosetta.rosetta.core.io.CrystInfo) pyrosetta.rosetta.core.io.CrystInfo

C++: core::io::CrystInfo::operator=(const class core::io::CrystInfo &) –> class core::io::CrystInfo &

beta(*args, **kwargs)

Overloaded function.

  1. beta(self: pyrosetta.rosetta.core.io.CrystInfo) -> float

C++: core::io::CrystInfo::beta() const –> double

  1. beta(self: pyrosetta.rosetta.core.io.CrystInfo, betain: float) -> None

C++: core::io::CrystInfo::beta(double) –> void

gamma(*args, **kwargs)

Overloaded function.

  1. gamma(self: pyrosetta.rosetta.core.io.CrystInfo) -> float

C++: core::io::CrystInfo::gamma() const –> double

  1. gamma(self: pyrosetta.rosetta.core.io.CrystInfo, gammain: float) -> None

C++: core::io::CrystInfo::gamma(double) –> void

spacegroup(*args, **kwargs)

Overloaded function.

  1. spacegroup(self: pyrosetta.rosetta.core.io.CrystInfo) -> str

C++: core::io::CrystInfo::spacegroup() const –> std::string

  1. spacegroup(self: pyrosetta.rosetta.core.io.CrystInfo, spacegroupin: str) -> None

C++: core::io::CrystInfo::spacegroup(std::string) –> void

class pyrosetta.rosetta.core.io.HELIXInformation

Bases: pybind11_builtins.pybind11_object

Steven Lewis smlewi.com

assign(self: pyrosetta.rosetta.core.io.HELIXInformation, : pyrosetta.rosetta.core.io.HELIXInformation) pyrosetta.rosetta.core.io.HELIXInformation

C++: core::io::HELIXInformation::operator=(const struct core::io::HELIXInformation &) –> struct core::io::HELIXInformation &

property chainID1
property chainID2
property comment
property helixClass
property helixID
property helix_name
property icode1
property icode2
property length
property name3_1
property name3_2
property seqNum1
property seqNum2
class pyrosetta.rosetta.core.io.HeaderInformation

Bases: pybind11_builtins.pybind11_object

Information stored in the Title Section records http://www.wwpdb.org/documentation/format32/sect2.html HEADER PEPTIDASE 13-JAN-98 1A2Z

BIOLOGICAL_UNIT = <CompoundToken.BIOLOGICAL_UNIT: 3>
CHAIN = <CompoundToken.CHAIN: 4>
class CompoundToken

Bases: pybind11_builtins.pybind11_object

Members:

UNKNOWN_CMPD

MOL_ID

MOLECULE

BIOLOGICAL_UNIT

CHAIN

FRAGMENT

SYNONYM

EC

ENGINEERED

MUTATION

OTHER_DETAILS

CompoundToken_max

BIOLOGICAL_UNIT = <CompoundToken.BIOLOGICAL_UNIT: 3>
CHAIN = <CompoundToken.CHAIN: 4>
CompoundToken_max = <CompoundToken.OTHER_DETAILS: 10>
EC = <CompoundToken.EC: 7>
ENGINEERED = <CompoundToken.ENGINEERED: 8>
FRAGMENT = <CompoundToken.FRAGMENT: 5>
MOLECULE = <CompoundToken.MOLECULE: 2>
MOL_ID = <CompoundToken.MOL_ID: 1>
MUTATION = <CompoundToken.MUTATION: 9>
OTHER_DETAILS = <CompoundToken.OTHER_DETAILS: 10>
SYNONYM = <CompoundToken.SYNONYM: 6>
UNKNOWN_CMPD = <CompoundToken.UNKNOWN_CMPD: 0>
property name
CompoundToken_max = <CompoundToken.OTHER_DETAILS: 10>
EC = <CompoundToken.EC: 7>
ENGINEERED = <CompoundToken.ENGINEERED: 8>
FRAGMENT = <CompoundToken.FRAGMENT: 5>
MOLECULE = <CompoundToken.MOLECULE: 2>
MOL_ID = <CompoundToken.MOL_ID: 1>
MUTATION = <CompoundToken.MUTATION: 9>
OTHER_DETAILS = <CompoundToken.OTHER_DETAILS: 10>
SYNONYM = <CompoundToken.SYNONYM: 6>
UNKNOWN_CMPD = <CompoundToken.UNKNOWN_CMPD: 0>
add_author(self: pyrosetta.rosetta.core.io.HeaderInformation, author: str) None

C++: core::io::HeaderInformation::add_author(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.io.HeaderInformation, : pyrosetta.rosetta.core.io.HeaderInformation) pyrosetta.rosetta.core.io.HeaderInformation

C++: core::io::HeaderInformation::operator=(const class core::io::HeaderInformation &) –> class core::io::HeaderInformation &

author_in_progress(self: pyrosetta.rosetta.core.io.HeaderInformation) bool

C++: core::io::HeaderInformation::author_in_progress() const –> bool

authors(self: pyrosetta.rosetta.core.io.HeaderInformation) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

C++: core::io::HeaderInformation::authors() const –> const class std::list<std::string, class std::allocator<std::string > > &

classification(self: pyrosetta.rosetta.core.io.HeaderInformation) str

C++: core::io::HeaderInformation::classification() const –> std::string

clear_authors(self: pyrosetta.rosetta.core.io.HeaderInformation) None

C++: core::io::HeaderInformation::clear_authors() –> void

clear_compounds(self: pyrosetta.rosetta.core.io.HeaderInformation) None

C++: core::io::HeaderInformation::clear_compounds() –> void

clear_experimental_techniques(self: pyrosetta.rosetta.core.io.HeaderInformation) None

C++: core::io::HeaderInformation::clear_experimental_techniques() –> void

clear_keywords(self: pyrosetta.rosetta.core.io.HeaderInformation) None

C++: core::io::HeaderInformation::clear_keywords() –> void

clear_title(self: pyrosetta.rosetta.core.io.HeaderInformation) None

C++: core::io::HeaderInformation::clear_title() –> void

compound_in_progress(self: pyrosetta.rosetta.core.io.HeaderInformation) bool

C++: core::io::HeaderInformation::compound_in_progress() const –> bool

static compound_token_to_string(token: pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken) str

C++: core::io::HeaderInformation::compound_token_to_string(enum core::io::HeaderInformation::CompoundToken) –> std::string

compounds(self: pyrosetta.rosetta.core.io.HeaderInformation) pyrosetta.rosetta.utility.vector1_std_pair_core_io_HeaderInformation_CompoundToken_std_string_t

C++: core::io::HeaderInformation::compounds() const –> const class utility::vector1<struct std::pair<enum core::io::HeaderInformation::CompoundToken, std::string >, class std::allocator<struct std::pair<enum core::io::HeaderInformation::CompoundToken, std::string > > > &

deposition_date(*args, **kwargs)

Overloaded function.

  1. deposition_date(self: pyrosetta.rosetta.core.io.HeaderInformation) -> str

C++: core::io::HeaderInformation::deposition_date() const –> std::string

  1. deposition_date(self: pyrosetta.rosetta.core.io.HeaderInformation, yy: int, mm: int, dd: int) -> None

get the deposition date using the format of two digit numbers

for the year, month and day of the month

C++: core::io::HeaderInformation::deposition_date(unsigned long &, unsigned long &, unsigned long &) const –> void

experimental_technique_in_progress(self: pyrosetta.rosetta.core.io.HeaderInformation) bool

C++: core::io::HeaderInformation::experimental_technique_in_progress() const –> bool

experimental_techniques(self: pyrosetta.rosetta.core.io.HeaderInformation) pyrosetta.rosetta.std.list_core_io_rcsb_ExperimentalTechnique_t

C++: core::io::HeaderInformation::experimental_techniques() const –> const class std::list<enum core::io::rcsb::ExperimentalTechnique, class std::allocator<enum core::io::rcsb::ExperimentalTechnique> > &

finalize_author_records(self: pyrosetta.rosetta.core.io.HeaderInformation) None

C++: core::io::HeaderInformation::finalize_author_records() –> void

finalize_compound_records(self: pyrosetta.rosetta.core.io.HeaderInformation) None

C++: core::io::HeaderInformation::finalize_compound_records() –> void

finalize_experimental_technique_records(self: pyrosetta.rosetta.core.io.HeaderInformation) None

C++: core::io::HeaderInformation::finalize_experimental_technique_records() –> void

finalize_keyword_records(self: pyrosetta.rosetta.core.io.HeaderInformation) None

C++: core::io::HeaderInformation::finalize_keyword_records() –> void

finalize_parse(self: pyrosetta.rosetta.core.io.HeaderInformation) None

C++: core::io::HeaderInformation::finalize_parse() –> void

idCode(self: pyrosetta.rosetta.core.io.HeaderInformation) str

C++: core::io::HeaderInformation::idCode() const –> std::string

is_experimental_technique(self: pyrosetta.rosetta.core.io.HeaderInformation, technique: pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique) bool

C++: core::io::HeaderInformation::is_experimental_technique(enum core::io::rcsb::ExperimentalTechnique) const –> bool

keyword_in_progress(self: pyrosetta.rosetta.core.io.HeaderInformation) bool

C++: core::io::HeaderInformation::keyword_in_progress() const –> bool

keywords(self: pyrosetta.rosetta.core.io.HeaderInformation) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

C++: core::io::HeaderInformation::keywords() const –> const class std::list<std::string, class std::allocator<std::string > > &

parse_in_progress(self: pyrosetta.rosetta.core.io.HeaderInformation) bool

C++: core::io::HeaderInformation::parse_in_progress() const –> bool

store_authors(self: pyrosetta.rosetta.core.io.HeaderInformation, authors: str) None

C++: core::io::HeaderInformation::store_authors(const std::string &) –> void

store_classification(self: pyrosetta.rosetta.core.io.HeaderInformation, classification: str) None

C++: core::io::HeaderInformation::store_classification(const std::string &) –> void

store_compound(*args, **kwargs)

Overloaded function.

  1. store_compound(self: pyrosetta.rosetta.core.io.HeaderInformation, compound: str) -> None

C++: core::io::HeaderInformation::store_compound(const std::string &) –> void

  1. store_compound(self: pyrosetta.rosetta.core.io.HeaderInformation, token: pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken, value: str) -> None

C++: core::io::HeaderInformation::store_compound(enum core::io::HeaderInformation::CompoundToken, const std::string &) –> void

store_deposition_date(*args, **kwargs)

Overloaded function.

  1. store_deposition_date(self: pyrosetta.rosetta.core.io.HeaderInformation, deposition_date: str) -> None

Store the deposition date using the format like “84-DEC-18”

C++: core::io::HeaderInformation::store_deposition_date(const std::string &) –> void

  1. store_deposition_date(self: pyrosetta.rosetta.core.io.HeaderInformation, yy: int, mm: int, dd: int) -> None

Store the deposition date using the format of two digit numbers

for the year, month and day of the month.

C++: core::io::HeaderInformation::store_deposition_date(unsigned long, unsigned long, unsigned long) –> void

store_experimental_technique(self: pyrosetta.rosetta.core.io.HeaderInformation, technique: pyrosetta.rosetta.core.io.rcsb.ExperimentalTechnique) None

C++: core::io::HeaderInformation::store_experimental_technique(enum core::io::rcsb::ExperimentalTechnique) –> void

store_experimental_techniques(self: pyrosetta.rosetta.core.io.HeaderInformation, exp: str) None
Parse the list of techniques string following the technique

field in the EXPDTA record of the pdb format and store the techniques

C++: core::io::HeaderInformation::store_experimental_techniques(const std::string &) –> void

store_idCode(self: pyrosetta.rosetta.core.io.HeaderInformation, id_code: str) None

C++: core::io::HeaderInformation::store_idCode(const std::string &) –> void

store_keywords(self: pyrosetta.rosetta.core.io.HeaderInformation, keywords: str) None

C++: core::io::HeaderInformation::store_keywords(const std::string &) –> void

store_title(self: pyrosetta.rosetta.core.io.HeaderInformation, title: str) None

Append title record onto current title string

C++: core::io::HeaderInformation::store_title(const std::string &) –> void

static string_to_compound_token(*args, **kwargs)

Overloaded function.

  1. string_to_compound_token(token: str) -> pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken

  2. string_to_compound_token(token: str, warn_on_unrecognized: bool) -> pyrosetta.rosetta.core.io.HeaderInformation.CompoundToken

C++: core::io::HeaderInformation::string_to_compound_token(const std::string &, bool) –> enum core::io::HeaderInformation::CompoundToken

title(self: pyrosetta.rosetta.core.io.HeaderInformation) str

C++: core::io::HeaderInformation::title() const –> const std::string &

class pyrosetta.rosetta.core.io.LinkInformation

Bases: pybind11_builtins.pybind11_object

Labonte <JWLabonte.edu>

assign(self: pyrosetta.rosetta.core.io.LinkInformation, : pyrosetta.rosetta.core.io.LinkInformation) pyrosetta.rosetta.core.io.LinkInformation

C++: core::io::LinkInformation::operator=(const struct core::io::LinkInformation &) –> struct core::io::LinkInformation &

property chainID1
property chainID2
property iCode1
property iCode2
property length
property name1
property name2
property resID1
property resID2
property resName1
property resName2
property resSeq1
property resSeq2
class pyrosetta.rosetta.core.io.ModifiedResidueInformation

Bases: pybind11_builtins.pybind11_object

Labonte <JWLabonte.edu>

assign(self: pyrosetta.rosetta.core.io.ModifiedResidueInformation, : pyrosetta.rosetta.core.io.ModifiedResidueInformation) pyrosetta.rosetta.core.io.ModifiedResidueInformation

C++: core::io::ModifiedResidueInformation::operator=(const struct core::io::ModifiedResidueInformation &) –> struct core::io::ModifiedResidueInformation &

property chainID
property comment
property iCode
property resName
property seqNum
property stdRes
class pyrosetta.rosetta.core.io.NomenclatureManager

Bases: pyrosetta.rosetta.utility.SingletonBase_core_io_NomenclatureManager_t

This class is a singleton and manages AltCodeMap data that should only be read from the database one time and shared among all processes constructing Poses.

static annotated_sequence_from_IUPAC_sequence(seq: str) str

C++: core::io::NomenclatureManager::annotated_sequence_from_IUPAC_sequence(const std::string &) –> std::string

static annotated_sequence_from_modomics_oneletter_sequence(seq: str) str

C++: core::io::NomenclatureManager::annotated_sequence_from_modomics_oneletter_sequence(const std::string &) –> std::string

static decide_is_d_aa(name3: str) bool

C++: core::io::NomenclatureManager::decide_is_d_aa(const std::string &) –> bool

static decide_is_known_achiral(name3: str) bool

C++: core::io::NomenclatureManager::decide_is_known_achiral(const std::string &) –> bool

static decide_is_l_aa(name3: str) bool

C++: core::io::NomenclatureManager::decide_is_l_aa(const std::string &) –> bool

static default_mainchain_connectivity_from_pdb_code(pdb_code: str) str

Return the default main-chain connectivity (if available) from the given pdb_code.

C++: core::io::NomenclatureManager::default_mainchain_connectivity_from_pdb_code(const std::string &) –> char

static get_instance() core::io::NomenclatureManager

C++: utility::SingletonBase<core::io::NomenclatureManager>::get_instance() –> class core::io::NomenclatureManager *

static is_NA(name3: str) bool

C++: core::io::NomenclatureManager::is_NA(const std::string &) –> bool

static is_metal(name3: str) bool

C++: core::io::NomenclatureManager::is_metal(const std::string &) –> bool

static is_old_DNA(name3: str) bool

C++: core::io::NomenclatureManager::is_old_DNA(const std::string &) –> bool

static is_old_RNA(name3: str) bool

C++: core::io::NomenclatureManager::is_old_RNA(const std::string &) –> bool

static is_sugar(name3: str) bool

C++: core::io::NomenclatureManager::is_sugar(const std::string &) –> bool

static pdb_code_from_rosetta_name(rosetta_name: str) str

This function returns the pdb code that corresponds to the residue name.

C++: core::io::NomenclatureManager::pdb_code_from_rosetta_name(const std::string &) –> std::string

static rosetta_names_from_pdb_code(pdb_code: str) Tuple[str, str]
Return a pair of Rosetta names (3-letter code and base ResidueType name, if available) from the given

pdb_code.

C++: core::io::NomenclatureManager::rosetta_names_from_pdb_code(const std::string &) –> struct std::pair<std::string, std::string >

class pyrosetta.rosetta.core.io.RemarkInfo

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.io.RemarkInfo, : pyrosetta.rosetta.core.io.RemarkInfo) pyrosetta.rosetta.core.io.RemarkInfo

C++: core::io::RemarkInfo::operator=(const class core::io::RemarkInfo &) –> class core::io::RemarkInfo &

property num
property value
class pyrosetta.rosetta.core.io.Remarks

Bases: pyrosetta.rosetta.std.vector_core_io_RemarkInfo

append(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo, x: core::io::RemarkInfo) None

Add an item to the end of the list

assign(self: pyrosetta.rosetta.core.io.Remarks, : pyrosetta.rosetta.core.io.Remarks) pyrosetta.rosetta.core.io.Remarks

C++: core::io::Remarks::operator=(const class core::io::Remarks &) –> class core::io::Remarks &

capacity(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo) int

returns the number of elements that can be held in currently allocated storage

clear(*args, **kwargs)

Overloaded function.

  1. clear(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo) -> None

Clear the contents

  1. clear(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo) -> None

clears the contents

empty(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo) bool

checks whether the container is empty

extend(*args, **kwargs)

Overloaded function.

  1. extend(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo, L: pyrosetta.rosetta.std.vector_core_io_RemarkInfo) -> None

Extend the list by appending all the items in the given list

  1. extend(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo, L: Iterable) -> None

Extend the list by appending all the items in the given list

insert(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo, i: int, x: core::io::RemarkInfo) None

Insert an item at a given position.

max_size(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo) int

returns the maximum possible number of elements

pop(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo) -> core::io::RemarkInfo

Remove and return the last item

  1. pop(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo, i: int) -> core::io::RemarkInfo

Remove and return the item at index i

reserve(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo, arg0: int) None

reserves storage

shrink_to_fit(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo) None

reduces memory usage by freeing unused memory

swap(self: pyrosetta.rosetta.std.vector_core_io_RemarkInfo, arg0: pyrosetta.rosetta.std.vector_core_io_RemarkInfo) None

swaps the contents

class pyrosetta.rosetta.core.io.ResidueInformation

Bases: pybind11_builtins.pybind11_object

Subset of data from “ATOM” lines that is shared by all atoms in a residue. This class is used for temporary storage of information during Pose building and “unbuilding”.

append_atom(self: pyrosetta.rosetta.core.io.ResidueInformation, atoms: pyrosetta.rosetta.core.io.AtomInformation) None

C++: core::io::ResidueInformation::append_atom(const struct core::io::AtomInformation &) –> void

append_atoms(self: pyrosetta.rosetta.core.io.ResidueInformation, source: pyrosetta.rosetta.core.io.ResidueInformation) None

C++: core::io::ResidueInformation::append_atoms(const class core::io::ResidueInformation &) –> void

assign(self: pyrosetta.rosetta.core.io.ResidueInformation, : pyrosetta.rosetta.core.io.ResidueInformation) pyrosetta.rosetta.core.io.ResidueInformation

C++: core::io::ResidueInformation::operator=(const class core::io::ResidueInformation &) –> class core::io::ResidueInformation &

atoms(self: pyrosetta.rosetta.core.io.ResidueInformation) pyrosetta.rosetta.utility.vector1_core_io_AtomInformation

C++: core::io::ResidueInformation::atoms() const –> const class utility::vector1<struct core::io::AtomInformation, class std::allocator<struct core::io::AtomInformation> > &

chainID(*args, **kwargs)

Overloaded function.

  1. chainID(self: pyrosetta.rosetta.core.io.ResidueInformation) -> str

C++: core::io::ResidueInformation::chainID() const –> char

  1. chainID(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: str) -> None

C++: core::io::ResidueInformation::chainID(char) –> void

iCode(*args, **kwargs)

Overloaded function.

  1. iCode(self: pyrosetta.rosetta.core.io.ResidueInformation) -> str

C++: core::io::ResidueInformation::iCode() const –> char

  1. iCode(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: str) -> None

C++: core::io::ResidueInformation::iCode(char) –> void

rename_atom(self: pyrosetta.rosetta.core.io.ResidueInformation, orig_name: str, new_name: str) None

C++: core::io::ResidueInformation::rename_atom(const std::string &, const std::string &) –> void

resName(*args, **kwargs)

Overloaded function.

  1. resName(self: pyrosetta.rosetta.core.io.ResidueInformation) -> str

C++: core::io::ResidueInformation::resName() const –> const std::string &

  1. resName(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: str) -> None

C++: core::io::ResidueInformation::resName(const std::string &) –> void

resSeq(*args, **kwargs)

Overloaded function.

  1. resSeq(self: pyrosetta.rosetta.core.io.ResidueInformation) -> int

C++: core::io::ResidueInformation::resSeq() const –> int

  1. resSeq(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: int) -> None

C++: core::io::ResidueInformation::resSeq(int) –> void

resid(self: pyrosetta.rosetta.core.io.ResidueInformation) str

Returns a short, printable designation for this residue.

C++: core::io::ResidueInformation::resid() const –> std::string

rosetta_resName(*args, **kwargs)

Overloaded function.

  1. rosetta_resName(self: pyrosetta.rosetta.core.io.ResidueInformation) -> str

C++: core::io::ResidueInformation::rosetta_resName() const –> const std::string &

  1. rosetta_resName(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: str) -> None

C++: core::io::ResidueInformation::rosetta_resName(const std::string &) –> void

segmentID(*args, **kwargs)

Overloaded function.

  1. segmentID(self: pyrosetta.rosetta.core.io.ResidueInformation) -> str

C++: core::io::ResidueInformation::segmentID() const –> const std::string &

  1. segmentID(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: str) -> None

C++: core::io::ResidueInformation::segmentID(const std::string &) –> void

set_temp(self: pyrosetta.rosetta.core.io.ResidueInformation, atomname: str, val: float) None

C++: core::io::ResidueInformation::set_temp(const std::string &, const double &) –> void

set_xyz(self: pyrosetta.rosetta.core.io.ResidueInformation, atomname: str, vect: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: core::io::ResidueInformation::set_xyz(const std::string &, const class numeric::xyzVector<double> &) –> void

temps(self: pyrosetta.rosetta.core.io.ResidueInformation) pyrosetta.rosetta.std.map_std_string_double

C++: core::io::ResidueInformation::temps() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

terCount(*args, **kwargs)

Overloaded function.

  1. terCount(self: pyrosetta.rosetta.core.io.ResidueInformation) -> int

C++: core::io::ResidueInformation::terCount() const –> int

  1. terCount(self: pyrosetta.rosetta.core.io.ResidueInformation, setting: int) -> None

C++: core::io::ResidueInformation::terCount(int) –> void

xyz(self: pyrosetta.rosetta.core.io.ResidueInformation) pyrosetta.rosetta.std.map_std_string_numeric_xyzVector_double_t

A convenience accessor for the coordinates.

C++: core::io::ResidueInformation::xyz() const –> const class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > > &

class pyrosetta.rosetta.core.io.SHEETInformation

Bases: pybind11_builtins.pybind11_object

Steven Lewis smlewi.com

assign(self: pyrosetta.rosetta.core.io.SHEETInformation, : pyrosetta.rosetta.core.io.SHEETInformation) pyrosetta.rosetta.core.io.SHEETInformation

C++: core::io::SHEETInformation::operator=(const struct core::io::SHEETInformation &) –> struct core::io::SHEETInformation &

property chainID1
property chainID2
property icode1
property icode2
property name3_1
property name3_2
property num_strands
property seqNum1
property seqNum2
property sheetID
property strandClass
property strand_num
class pyrosetta.rosetta.core.io.SSBondInformation

Bases: pybind11_builtins.pybind11_object

Watkins

assign(self: pyrosetta.rosetta.core.io.SSBondInformation, : pyrosetta.rosetta.core.io.SSBondInformation) pyrosetta.rosetta.core.io.SSBondInformation

C++: core::io::SSBondInformation::operator=(const struct core::io::SSBondInformation &) –> struct core::io::SSBondInformation &

property chainID1
property chainID2
property iCode1
property iCode2
property length
property name1
property name2
property resID1
property resID2
property resName1
property resName2
property resSeq1
property resSeq2
property sym1
property sym2
class pyrosetta.rosetta.core.io.StructFileReaderOptions

Bases: pyrosetta.rosetta.core.io.StructFileRepOptions

static append_schema_attributes(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None

C++: core::io::StructFileReaderOptions::append_schema_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

assign(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, : pyrosetta.rosetta.core.io.StructFileReaderOptions) pyrosetta.rosetta.core.io.StructFileReaderOptions

C++: core::io::StructFileReaderOptions::operator=(const class core::io::StructFileReaderOptions &) –> class core::io::StructFileReaderOptions &

auto_detect_glycan_connections(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::auto_detect_glycan_connections() const –> bool

chains_whose_residues_are_separate_chemical_entities(self: pyrosetta.rosetta.core.io.StructFileRepOptions) str

C++: core::io::StructFileRepOptions::chains_whose_residues_are_separate_chemical_entities() const –> const std::string &

check_if_residues_are_Ctermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions) str

C++: core::io::StructFileRepOptions::check_if_residues_are_Ctermini() const –> const std::string &

check_if_residues_are_Ntermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions) str

C++: core::io::StructFileRepOptions::check_if_residues_are_Ntermini() const –> const std::string &

clone(self: pyrosetta.rosetta.core.io.StructFileRepOptions) pyrosetta.rosetta.core.io.StructFileRepOptions

Copy this object and return an owning pointer to the copy.

C++: core::io::StructFileRepOptions::clone() const –> class std::shared_ptr<class core::io::StructFileRepOptions>

connect_info_cutoff(self: pyrosetta.rosetta.core.io.StructFileRepOptions) float

C++: core::io::StructFileRepOptions::connect_info_cutoff() const –> double

C++: core::io::StructFileRepOptions::constraints_from_link_records() const –> bool

do_not_autoassign_SS(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::do_not_autoassign_SS() const –> bool

exit_if_missing_heavy_atoms(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::exit_if_missing_heavy_atoms() const –> bool

fold_tree_io(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::fold_tree_io() const –> bool

glycam_pdb_format(self: pyrosetta.rosetta.core.io.StructFileReaderOptions) bool

C++: core::io::StructFileReaderOptions::glycam_pdb_format() const –> bool

guarantee_no_DNA(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::guarantee_no_DNA() const –> bool

ignore_sugars(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::ignore_sugars() const –> bool

ignore_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::ignore_unrecognized_res() const –> bool

ignore_waters(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::ignore_waters() const –> bool

ignore_zero_occupancy(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::ignore_zero_occupancy() const –> bool

integration_test_mode(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::integration_test_mode() const –> bool

keep_input_protonation_state(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::keep_input_protonation_state() const –> bool

C++: core::io::StructFileRepOptions::maintain_links() const –> bool

max_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions) float

C++: core::io::StructFileRepOptions::max_bond_length() const –> double

min_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions) float

C++: core::io::StructFileRepOptions::min_bond_length() const –> double

missing_dens_as_jump(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::missing_dens_as_jump() const –> bool

mmtf_extra_data_io(self: pyrosetta.rosetta.core.io.StructFileReaderOptions) bool

C++: core::io::StructFileReaderOptions::mmtf_extra_data_io() const –> bool

new_chain_order(self: pyrosetta.rosetta.core.io.StructFileReaderOptions) bool

C++: core::io::StructFileReaderOptions::new_chain_order() const –> bool

no_chainend_ter(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::no_chainend_ter() const –> bool

no_detect_pseudobonds(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::no_detect_pseudobonds() const –> bool

no_output_cen(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::no_output_cen() const –> bool

normalize_to_thk(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::normalize_to_thk() const –> bool

obey_ENDMDL(self: pyrosetta.rosetta.core.io.StructFileReaderOptions) bool

C++: core::io::StructFileReaderOptions::obey_ENDMDL() const –> bool

output_alternate_atomids(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_alternate_atomids() const –> bool

output_ligands_as_separate_chains(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_ligands_as_separate_chains() const –> bool

output_only_asymmetric_unit(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_only_asymmetric_unit() const –> bool

output_pose_cache(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_pose_cache() const –> bool

output_pose_energies_table(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_pose_energies_table() const –> bool

output_secondary_structure(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_secondary_structure() const –> bool

output_torsions(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_torsions() const –> bool

output_virtual(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_virtual() const –> bool

output_virtual_zero_occ(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_virtual_zero_occ() const –> bool

parse_my_tag(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, tag: utility::tag::Tag) None

C++: core::io::StructFileReaderOptions::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

pdb_author(self: pyrosetta.rosetta.core.io.StructFileRepOptions) str

C++: core::io::StructFileRepOptions::pdb_author() const –> const std::string &

pdb_comments(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::pdb_comments() const –> bool

pdb_parents(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::pdb_parents() const –> bool

per_chain_renumbering(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::per_chain_renumbering() const –> bool

preserve_crystinfo(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::preserve_crystinfo() const –> bool

preserve_header(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::preserve_header() const –> bool

randomize_missing_coords(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::randomize_missing_coords() const –> bool

read_only_ATOM_entries(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::read_only_ATOM_entries() const –> bool

read_pdb_header(self: pyrosetta.rosetta.core.io.StructFileReaderOptions) bool

C++: core::io::StructFileReaderOptions::read_pdb_header() const –> bool

remember_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::remember_unrecognized_res() const –> bool

remember_unrecognized_water(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::remember_unrecognized_water() const –> bool

renumber_pdb(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::renumber_pdb() const –> bool

residues_for_atom_name_remapping(self: pyrosetta.rosetta.core.io.StructFileRepOptions) pyrosetta.rosetta.utility.vector1_std_string

C++: core::io::StructFileRepOptions::residues_for_atom_name_remapping() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

set_auto_detect_glycan_connections(self: pyrosetta.rosetta.core.io.StructFileRepOptions, auto_detect_glycan_connections: bool) None

C++: core::io::StructFileRepOptions::set_auto_detect_glycan_connections(const bool) –> void

set_chains_whose_residues_are_separate_chemical_entities(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: str) None

C++: core::io::StructFileRepOptions::set_chains_whose_residues_are_separate_chemical_entities(const std::string &) –> void

set_check_if_residues_are_Ctermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions, check_if_residues_are_Ctermini: str) None

C++: core::io::StructFileRepOptions::set_check_if_residues_are_Ctermini(const std::string &) –> void

set_check_if_residues_are_Ntermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions, check_if_residues_are_Ntermini: str) None

C++: core::io::StructFileRepOptions::set_check_if_residues_are_Ntermini(const std::string &) –> void

set_connect_info_cutoff(self: pyrosetta.rosetta.core.io.StructFileRepOptions, connect_info_cutoff: float) None

C++: core::io::StructFileRepOptions::set_connect_info_cutoff(const double &) –> void

C++: core::io::StructFileRepOptions::set_constraints_from_link_records(const bool) –> void

set_do_not_autoassign_SS(self: pyrosetta.rosetta.core.io.StructFileRepOptions, do_not_autoassign_SS: bool) None

C++: core::io::StructFileRepOptions::set_do_not_autoassign_SS(const bool) –> void

set_exit_if_missing_heavy_atoms(self: pyrosetta.rosetta.core.io.StructFileRepOptions, exit_if_missing_heavy_atoms: bool) None

C++: core::io::StructFileRepOptions::set_exit_if_missing_heavy_atoms(const bool) –> void

set_fold_tree_io(self: pyrosetta.rosetta.core.io.StructFileRepOptions, fold_tree_io: bool) None

C++: core::io::StructFileRepOptions::set_fold_tree_io(const bool) –> void

set_glycam_pdb_format(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, setting: bool) None

C++: core::io::StructFileReaderOptions::set_glycam_pdb_format(bool) –> void

set_guarantee_no_DNA(self: pyrosetta.rosetta.core.io.StructFileRepOptions, guarantee_no_DNA: bool) None

C++: core::io::StructFileRepOptions::set_guarantee_no_DNA(const bool) –> void

set_ignore_sugars(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_ignore_sugars(const bool) –> void

set_ignore_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions, ignore_unrecognized_res: bool) None

C++: core::io::StructFileRepOptions::set_ignore_unrecognized_res(const bool) –> void

set_ignore_waters(self: pyrosetta.rosetta.core.io.StructFileRepOptions, ignore_waters: bool) None

C++: core::io::StructFileRepOptions::set_ignore_waters(const bool) –> void

set_ignore_zero_occupancy(self: pyrosetta.rosetta.core.io.StructFileRepOptions, ignore_zero_occupancy: bool) None

C++: core::io::StructFileRepOptions::set_ignore_zero_occupancy(const bool) –> void

set_integration_test_mode(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_integration_test_mode(const bool) –> void

set_keep_input_protonation_state(self: pyrosetta.rosetta.core.io.StructFileRepOptions, keep_input_protonation_state: bool) None

C++: core::io::StructFileRepOptions::set_keep_input_protonation_state(const bool) –> void

C++: core::io::StructFileRepOptions::set_maintain_links(const bool) –> void

set_max_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions, max_bond_length: float) None

C++: core::io::StructFileRepOptions::set_max_bond_length(const double) –> void

set_min_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions, min_bond_length: float) None

C++: core::io::StructFileRepOptions::set_min_bond_length(const double) –> void

set_missing_dens_as_jump(self: pyrosetta.rosetta.core.io.StructFileRepOptions, missing_dens_as_jump: bool) None

C++: core::io::StructFileRepOptions::set_missing_dens_as_jump(const bool) –> void

set_mmtf_extra_data_io(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, setting: bool) None

C++: core::io::StructFileReaderOptions::set_mmtf_extra_data_io(bool) –> void

set_new_chain_order(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, setting: bool) None

C++: core::io::StructFileReaderOptions::set_new_chain_order(bool) –> void

set_no_chainend_ter(self: pyrosetta.rosetta.core.io.StructFileRepOptions, no_chainend_ter: bool) None

C++: core::io::StructFileRepOptions::set_no_chainend_ter(const bool) –> void

set_no_detect_pseudobonds(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_no_detect_pseudobonds(const bool) –> void

set_no_output_cen(self: pyrosetta.rosetta.core.io.StructFileRepOptions, no_output_cen: bool) None

C++: core::io::StructFileRepOptions::set_no_output_cen(const bool) –> void

set_normalize_to_thk(self: pyrosetta.rosetta.core.io.StructFileRepOptions, normalize_to_thk: bool) None

C++: core::io::StructFileRepOptions::set_normalize_to_thk(const bool) –> void

set_obey_ENDMDL(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, setting: bool) None

C++: core::io::StructFileReaderOptions::set_obey_ENDMDL(bool) –> void

set_output_alternate_atomids(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_alternate_atomids: bool) None

C++: core::io::StructFileRepOptions::set_output_alternate_atomids(const bool) –> void

set_output_ligands_as_separate_chains(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_ligands_as_separate_chains: bool) None

C++: core::io::StructFileRepOptions::set_output_ligands_as_separate_chains(const bool) –> void

set_output_only_asymmetric_unit(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_only_asymmetric_unit: bool) None

C++: core::io::StructFileRepOptions::set_output_only_asymmetric_unit(const bool) –> void

set_output_pose_cache_data(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_output_pose_cache_data(const bool) –> void

set_output_pose_energies_table(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_output_pose_energies_table(const bool) –> void

set_output_secondary_structure(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_secondary_structure: bool) None

C++: core::io::StructFileRepOptions::set_output_secondary_structure(const bool) –> void

set_output_torsions(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_torsions: bool) None

C++: core::io::StructFileRepOptions::set_output_torsions(const bool) –> void

set_output_virtual(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_virtual: bool) None

C++: core::io::StructFileRepOptions::set_output_virtual(const bool) –> void

set_output_virtual_zero_occ(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_virtual_zero_occ: bool) None

C++: core::io::StructFileRepOptions::set_output_virtual_zero_occ(const bool) –> void

set_pdb_author(self: pyrosetta.rosetta.core.io.StructFileRepOptions, pdb_author: str) None

C++: core::io::StructFileRepOptions::set_pdb_author(const std::string &) –> void

set_pdb_comments(self: pyrosetta.rosetta.core.io.StructFileRepOptions, pdb_comments: bool) None

C++: core::io::StructFileRepOptions::set_pdb_comments(const bool) –> void

set_pdb_parents(self: pyrosetta.rosetta.core.io.StructFileRepOptions, pdb_parents: bool) None

C++: core::io::StructFileRepOptions::set_pdb_parents(const bool) –> void

set_per_chain_renumbering(self: pyrosetta.rosetta.core.io.StructFileRepOptions, per_chain_renumbering: bool) None

C++: core::io::StructFileRepOptions::set_per_chain_renumbering(const bool) –> void

set_preserve_crystinfo(self: pyrosetta.rosetta.core.io.StructFileRepOptions, preserve_crystinfo: bool) None

C++: core::io::StructFileRepOptions::set_preserve_crystinfo(const bool) –> void

set_preserve_header(self: pyrosetta.rosetta.core.io.StructFileRepOptions, preserve_header: bool) None

C++: core::io::StructFileRepOptions::set_preserve_header(const bool) –> void

set_randomize_missing_coords(self: pyrosetta.rosetta.core.io.StructFileRepOptions, randomize_missing_coords: bool) None

C++: core::io::StructFileRepOptions::set_randomize_missing_coords(const bool) –> void

set_read_only_ATOM_entries(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_read_only_ATOM_entries(const bool) –> void

set_read_pdb_header(self: pyrosetta.rosetta.core.io.StructFileReaderOptions, setting: bool) None

C++: core::io::StructFileReaderOptions::set_read_pdb_header(bool) –> void

set_remember_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions, remember_unrecognized_res: bool) None

C++: core::io::StructFileRepOptions::set_remember_unrecognized_res(const bool) –> void

set_remember_unrecognized_water(self: pyrosetta.rosetta.core.io.StructFileRepOptions, remember_unrecognized_water: bool) None

C++: core::io::StructFileRepOptions::set_remember_unrecognized_water(const bool) –> void

set_renumber_pdb(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_renumber_pdb(const bool) –> void

set_residues_for_atom_name_remapping(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: pyrosetta.rosetta.utility.vector1_std_string) None

C++: core::io::StructFileRepOptions::set_residues_for_atom_name_remapping(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_show_all_fixes(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_show_all_fixes(const bool) –> void

set_skip_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions, skip_connect_info: bool) None

C++: core::io::StructFileRepOptions::set_skip_connect_info(const bool) –> void

set_suppress_zero_occ_pdb_output(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_suppress_zero_occ_pdb_output(const bool) –> void

set_use_pdb_format_HETNAM_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_use_pdb_format_HETNAM_records(const bool) –> void

set_write_all_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_write_all_connect_info(const bool) –> void

set_write_glycan_pdb_codes(self: pyrosetta.rosetta.core.io.StructFileRepOptions, write_glycan_pdb_codes: bool) None

C++: core::io::StructFileRepOptions::set_write_glycan_pdb_codes(const bool) –> void

C++: core::io::StructFileRepOptions::set_write_pdb_link_records(const bool) –> void

set_write_pdb_parametric_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_write_pdb_parametric_info(const bool) –> void

set_write_pdb_title_section_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_write_pdb_title_section_records(const bool) –> void

set_write_seqres_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_write_seqres_records(const bool) –> void

show_all_fixes(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::show_all_fixes() const –> bool

skip_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::skip_connect_info() const –> bool

suppress_zero_occ_pdb_output(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::suppress_zero_occ_pdb_output() const –> bool

type(self: pyrosetta.rosetta.core.io.StructFileReaderOptions) str

C++: core::io::StructFileReaderOptions::type() const –> std::string

use_pdb_format_HETNAM_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::use_pdb_format_HETNAM_records() const –> bool

write_all_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::write_all_connect_info() const –> bool

write_glycan_pdb_codes(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::write_glycan_pdb_codes() const –> bool

C++: core::io::StructFileRepOptions::write_pdb_link_records() const –> bool

write_pdb_parametric_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::write_pdb_parametric_info() const –> bool

write_pdb_title_section_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::write_pdb_title_section_records() const –> bool

write_seqres_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::write_seqres_records() const –> bool

class pyrosetta.rosetta.core.io.StructFileRep

Bases: pybind11_builtins.pybind11_object

This class is designed to store information about a structure in a “non-Rosetta” way, such that it can serve as an intermediary between various file formats and a Pose.

This class is intended to be light, consisting primarily of simple accessors.

HELIXInformations(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.utility.vector1_core_io_HELIXInformation

C++: core::io::StructFileRep::HELIXInformations() –> class utility::vector1<struct core::io::HELIXInformation, class std::allocator<struct core::io::HELIXInformation> > &

SHEETInformations(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.utility.vector1_core_io_SHEETInformation

C++: core::io::StructFileRep::SHEETInformations() –> class utility::vector1<struct core::io::SHEETInformation, class std::allocator<struct core::io::SHEETInformation> > &

additional_string_output(self: pyrosetta.rosetta.core.io.StructFileRep) str

C++: core::io::StructFileRep::additional_string_output() –> std::string &

append_to_additional_string_output(self: pyrosetta.rosetta.core.io.StructFileRep, input_string: str) None

Append more string data to the additional_string_output_ string in the SFR.

C++: core::io::StructFileRep::append_to_additional_string_output(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.io.StructFileRep, : pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.core.io.StructFileRep

C++: core::io::StructFileRep::operator=(const class core::io::StructFileRep &) –> class core::io::StructFileRep &

chain_sequences(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_char_utility_vector1_std_string_std_allocator_std_string_t

C++: core::io::StructFileRep::chain_sequences() –> class std::map<char, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<char>, class std::allocator<struct std::pair<const char, class utility::vector1<std::string, class std::allocator<std::string > > > > > &

chains(self: pyrosetta.rosetta.core.io.StructFileRep) utility::vector0<utility::vector0<core::io::AtomInformation, std::allocator<core::io::AtomInformation> >, std::allocator<utility::vector0<core::io::AtomInformation, std::allocator<core::io::AtomInformation> > > >

C++: core::io::StructFileRep::chains() –> class utility::vector0<utility::vector0<core::io::AtomInformation> > &

cispep_map(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_std_string_core_io_CisPeptideInformation

C++: core::io::StructFileRep::cispep_map() –> class std::map<std::string, struct core::io::CisPeptideInformation, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::CisPeptideInformation> > > &

clone(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.core.io.StructFileRep

Create a copy and return an owning pointer to the copy.

C++: core::io::StructFileRep::clone() const –> class std::shared_ptr<class core::io::StructFileRep>

crystinfo(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.core.io.CrystInfo

C++: core::io::StructFileRep::crystinfo() –> class core::io::CrystInfo &

default_mainchain_connectivity(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_std_string_char

C++: core::io::StructFileRep::default_mainchain_connectivity() –> class std::map<std::string, char, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, char> > > &

filename(self: pyrosetta.rosetta.core.io.StructFileRep) str

C++: core::io::StructFileRep::filename() –> std::string &

foldtree_string(self: pyrosetta.rosetta.core.io.StructFileRep) str

C++: core::io::StructFileRep::foldtree_string() –> std::string &

header(self: pyrosetta.rosetta.core.io.StructFileRep) core::io::HeaderInformation

C++: core::io::StructFileRep::header() –> class std::shared_ptr<class core::io::HeaderInformation> &

heterogen_formulae(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::StructFileRep::heterogen_formulae() –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

heterogen_names(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::StructFileRep::heterogen_names() –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

heterogen_synonyms(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_std_string_utility_vector1_std_string_std_allocator_std_string_t

C++: core::io::StructFileRep::heterogen_synonyms() –> class std::map<std::string, class utility::vector1<std::string, class std::allocator<std::string > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<std::string, class std::allocator<std::string > > > > > &

C++: core::io::StructFileRep::link_map() –> class std::map<std::string, class utility::vector1<struct core::io::LinkInformation, class std::allocator<struct core::io::LinkInformation> >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<struct core::io::LinkInformation, class std::allocator<struct core::io::LinkInformation> > > > > &

modeltag(self: pyrosetta.rosetta.core.io.StructFileRep) str

C++: core::io::StructFileRep::modeltag() –> std::string &

modres_map(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_std_string_core_io_ModifiedResidueInformation

C++: core::io::StructFileRep::modres_map() –> class std::map<std::string, struct core::io::ModifiedResidueInformation, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct core::io::ModifiedResidueInformation> > > &

pdb_comments(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::StructFileRep::pdb_comments() –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

pose_cache_real_data(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_std_string_double

C++: core::io::StructFileRep::pose_cache_real_data() –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

pose_cache_string_data(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_std_string_std_string

C++: core::io::StructFileRep::pose_cache_string_data() –> class std::map<std::string, std::string, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, std::string > > > &

remarks(self: pyrosetta.rosetta.core.io.StructFileRep) core::io::Remarks

C++: core::io::StructFileRep::remarks() –> class std::shared_ptr<class core::io::Remarks> &

residue_type_base_names(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_std_string_std_pair_std_string_std_string_t

C++: core::io::StructFileRep::residue_type_base_names() –> class std::map<std::string, struct std::pair<std::string, std::string >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct std::pair<std::string, std::string > > > > &

score_table_filename(self: pyrosetta.rosetta.core.io.StructFileRep) str

C++: core::io::StructFileRep::score_table_filename() –> std::string &

score_table_labels(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.utility.vector1_std_string

C++: core::io::StructFileRep::score_table_labels() –> class utility::vector1<std::string, class std::allocator<std::string > > &

score_table_lines(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.utility.vector1_std_vector_std_string_std_allocator_std_string_t

C++: core::io::StructFileRep::score_table_lines() –> class utility::vector1<class std::vector<std::string, class std::allocator<std::string > >, class std::allocator<class std::vector<std::string, class std::allocator<std::string > > > > &

score_table_weights(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.utility.vector1_double

C++: core::io::StructFileRep::score_table_weights() –> class utility::vector1<double, class std::allocator<double> > &

simple_metric_data(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.core.simple_metrics.SimpleMetricStruct

C++: core::io::StructFileRep::simple_metric_data() –> struct core::simple_metrics::SimpleMetricStruct &

ssbond_map(self: pyrosetta.rosetta.core.io.StructFileRep) pyrosetta.rosetta.std.map_std_string_utility_vector1_core_io_SSBondInformation_std_allocator_core_io_SSBondInformation_t

C++: core::io::StructFileRep::ssbond_map() –> class std::map<std::string, class utility::vector1<struct core::io::SSBondInformation, class std::allocator<struct core::io::SSBondInformation> >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<struct core::io::SSBondInformation, class std::allocator<struct core::io::SSBondInformation> > > > > &

class pyrosetta.rosetta.core.io.StructFileRepOptions

Bases: pybind11_builtins.pybind11_object

static append_schema_attributes(attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) None

Describe the XML Schema for this ResourceOption object

C++: core::io::StructFileRepOptions::append_schema_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

assign(self: pyrosetta.rosetta.core.io.StructFileRepOptions, : pyrosetta.rosetta.core.io.StructFileRepOptions) pyrosetta.rosetta.core.io.StructFileRepOptions

C++: core::io::StructFileRepOptions::operator=(const class core::io::StructFileRepOptions &) –> class core::io::StructFileRepOptions &

auto_detect_glycan_connections(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::auto_detect_glycan_connections() const –> bool

chains_whose_residues_are_separate_chemical_entities(self: pyrosetta.rosetta.core.io.StructFileRepOptions) str

C++: core::io::StructFileRepOptions::chains_whose_residues_are_separate_chemical_entities() const –> const std::string &

check_if_residues_are_Ctermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions) str

C++: core::io::StructFileRepOptions::check_if_residues_are_Ctermini() const –> const std::string &

check_if_residues_are_Ntermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions) str

C++: core::io::StructFileRepOptions::check_if_residues_are_Ntermini() const –> const std::string &

clone(self: pyrosetta.rosetta.core.io.StructFileRepOptions) pyrosetta.rosetta.core.io.StructFileRepOptions

Copy this object and return an owning pointer to the copy.

C++: core::io::StructFileRepOptions::clone() const –> class std::shared_ptr<class core::io::StructFileRepOptions>

connect_info_cutoff(self: pyrosetta.rosetta.core.io.StructFileRepOptions) float

C++: core::io::StructFileRepOptions::connect_info_cutoff() const –> double

C++: core::io::StructFileRepOptions::constraints_from_link_records() const –> bool

do_not_autoassign_SS(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::do_not_autoassign_SS() const –> bool

exit_if_missing_heavy_atoms(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::exit_if_missing_heavy_atoms() const –> bool

fold_tree_io(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::fold_tree_io() const –> bool

guarantee_no_DNA(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::guarantee_no_DNA() const –> bool

ignore_sugars(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::ignore_sugars() const –> bool

ignore_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::ignore_unrecognized_res() const –> bool

ignore_waters(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::ignore_waters() const –> bool

ignore_zero_occupancy(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::ignore_zero_occupancy() const –> bool

integration_test_mode(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::integration_test_mode() const –> bool

keep_input_protonation_state(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::keep_input_protonation_state() const –> bool

C++: core::io::StructFileRepOptions::maintain_links() const –> bool

max_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions) float

C++: core::io::StructFileRepOptions::max_bond_length() const –> double

min_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions) float

C++: core::io::StructFileRepOptions::min_bond_length() const –> double

missing_dens_as_jump(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::missing_dens_as_jump() const –> bool

mmtf_extra_data_io(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::mmtf_extra_data_io() const –> bool

no_chainend_ter(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::no_chainend_ter() const –> bool

no_detect_pseudobonds(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::no_detect_pseudobonds() const –> bool

no_output_cen(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::no_output_cen() const –> bool

normalize_to_thk(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::normalize_to_thk() const –> bool

output_alternate_atomids(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_alternate_atomids() const –> bool

output_ligands_as_separate_chains(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_ligands_as_separate_chains() const –> bool

output_only_asymmetric_unit(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_only_asymmetric_unit() const –> bool

output_pose_cache(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_pose_cache() const –> bool

output_pose_energies_table(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_pose_energies_table() const –> bool

output_secondary_structure(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_secondary_structure() const –> bool

output_torsions(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_torsions() const –> bool

output_virtual(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_virtual() const –> bool

output_virtual_zero_occ(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::output_virtual_zero_occ() const –> bool

parse_my_tag(self: pyrosetta.rosetta.core.io.StructFileRepOptions, tag: utility::tag::Tag) None

C++: core::io::StructFileRepOptions::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

pdb_author(self: pyrosetta.rosetta.core.io.StructFileRepOptions) str

C++: core::io::StructFileRepOptions::pdb_author() const –> const std::string &

pdb_comments(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::pdb_comments() const –> bool

pdb_parents(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::pdb_parents() const –> bool

per_chain_renumbering(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::per_chain_renumbering() const –> bool

preserve_crystinfo(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::preserve_crystinfo() const –> bool

preserve_header(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::preserve_header() const –> bool

randomize_missing_coords(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::randomize_missing_coords() const –> bool

read_only_ATOM_entries(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::read_only_ATOM_entries() const –> bool

remember_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::remember_unrecognized_res() const –> bool

remember_unrecognized_water(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::remember_unrecognized_water() const –> bool

renumber_pdb(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::renumber_pdb() const –> bool

residues_for_atom_name_remapping(self: pyrosetta.rosetta.core.io.StructFileRepOptions) pyrosetta.rosetta.utility.vector1_std_string

C++: core::io::StructFileRepOptions::residues_for_atom_name_remapping() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

set_auto_detect_glycan_connections(self: pyrosetta.rosetta.core.io.StructFileRepOptions, auto_detect_glycan_connections: bool) None

C++: core::io::StructFileRepOptions::set_auto_detect_glycan_connections(const bool) –> void

set_chains_whose_residues_are_separate_chemical_entities(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: str) None

C++: core::io::StructFileRepOptions::set_chains_whose_residues_are_separate_chemical_entities(const std::string &) –> void

set_check_if_residues_are_Ctermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions, check_if_residues_are_Ctermini: str) None

C++: core::io::StructFileRepOptions::set_check_if_residues_are_Ctermini(const std::string &) –> void

set_check_if_residues_are_Ntermini(self: pyrosetta.rosetta.core.io.StructFileRepOptions, check_if_residues_are_Ntermini: str) None

C++: core::io::StructFileRepOptions::set_check_if_residues_are_Ntermini(const std::string &) –> void

set_connect_info_cutoff(self: pyrosetta.rosetta.core.io.StructFileRepOptions, connect_info_cutoff: float) None

C++: core::io::StructFileRepOptions::set_connect_info_cutoff(const double &) –> void

C++: core::io::StructFileRepOptions::set_constraints_from_link_records(const bool) –> void

set_do_not_autoassign_SS(self: pyrosetta.rosetta.core.io.StructFileRepOptions, do_not_autoassign_SS: bool) None

C++: core::io::StructFileRepOptions::set_do_not_autoassign_SS(const bool) –> void

set_exit_if_missing_heavy_atoms(self: pyrosetta.rosetta.core.io.StructFileRepOptions, exit_if_missing_heavy_atoms: bool) None

C++: core::io::StructFileRepOptions::set_exit_if_missing_heavy_atoms(const bool) –> void

set_fold_tree_io(self: pyrosetta.rosetta.core.io.StructFileRepOptions, fold_tree_io: bool) None

C++: core::io::StructFileRepOptions::set_fold_tree_io(const bool) –> void

set_guarantee_no_DNA(self: pyrosetta.rosetta.core.io.StructFileRepOptions, guarantee_no_DNA: bool) None

C++: core::io::StructFileRepOptions::set_guarantee_no_DNA(const bool) –> void

set_ignore_sugars(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_ignore_sugars(const bool) –> void

set_ignore_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions, ignore_unrecognized_res: bool) None

C++: core::io::StructFileRepOptions::set_ignore_unrecognized_res(const bool) –> void

set_ignore_waters(self: pyrosetta.rosetta.core.io.StructFileRepOptions, ignore_waters: bool) None

C++: core::io::StructFileRepOptions::set_ignore_waters(const bool) –> void

set_ignore_zero_occupancy(self: pyrosetta.rosetta.core.io.StructFileRepOptions, ignore_zero_occupancy: bool) None

C++: core::io::StructFileRepOptions::set_ignore_zero_occupancy(const bool) –> void

set_integration_test_mode(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_integration_test_mode(const bool) –> void

set_keep_input_protonation_state(self: pyrosetta.rosetta.core.io.StructFileRepOptions, keep_input_protonation_state: bool) None

C++: core::io::StructFileRepOptions::set_keep_input_protonation_state(const bool) –> void

C++: core::io::StructFileRepOptions::set_maintain_links(const bool) –> void

set_max_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions, max_bond_length: float) None

C++: core::io::StructFileRepOptions::set_max_bond_length(const double) –> void

set_min_bond_length(self: pyrosetta.rosetta.core.io.StructFileRepOptions, min_bond_length: float) None

C++: core::io::StructFileRepOptions::set_min_bond_length(const double) –> void

set_missing_dens_as_jump(self: pyrosetta.rosetta.core.io.StructFileRepOptions, missing_dens_as_jump: bool) None

C++: core::io::StructFileRepOptions::set_missing_dens_as_jump(const bool) –> void

set_mmtf_extra_data_io(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_mmtf_extra_data_io(const bool) –> void

set_no_chainend_ter(self: pyrosetta.rosetta.core.io.StructFileRepOptions, no_chainend_ter: bool) None

C++: core::io::StructFileRepOptions::set_no_chainend_ter(const bool) –> void

set_no_detect_pseudobonds(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_no_detect_pseudobonds(const bool) –> void

set_no_output_cen(self: pyrosetta.rosetta.core.io.StructFileRepOptions, no_output_cen: bool) None

C++: core::io::StructFileRepOptions::set_no_output_cen(const bool) –> void

set_normalize_to_thk(self: pyrosetta.rosetta.core.io.StructFileRepOptions, normalize_to_thk: bool) None

C++: core::io::StructFileRepOptions::set_normalize_to_thk(const bool) –> void

set_output_alternate_atomids(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_alternate_atomids: bool) None

C++: core::io::StructFileRepOptions::set_output_alternate_atomids(const bool) –> void

set_output_ligands_as_separate_chains(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_ligands_as_separate_chains: bool) None

C++: core::io::StructFileRepOptions::set_output_ligands_as_separate_chains(const bool) –> void

set_output_only_asymmetric_unit(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_only_asymmetric_unit: bool) None

C++: core::io::StructFileRepOptions::set_output_only_asymmetric_unit(const bool) –> void

set_output_pose_cache_data(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_output_pose_cache_data(const bool) –> void

set_output_pose_energies_table(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_output_pose_energies_table(const bool) –> void

set_output_secondary_structure(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_secondary_structure: bool) None

C++: core::io::StructFileRepOptions::set_output_secondary_structure(const bool) –> void

set_output_torsions(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_torsions: bool) None

C++: core::io::StructFileRepOptions::set_output_torsions(const bool) –> void

set_output_virtual(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_virtual: bool) None

C++: core::io::StructFileRepOptions::set_output_virtual(const bool) –> void

set_output_virtual_zero_occ(self: pyrosetta.rosetta.core.io.StructFileRepOptions, output_virtual_zero_occ: bool) None

C++: core::io::StructFileRepOptions::set_output_virtual_zero_occ(const bool) –> void

set_pdb_author(self: pyrosetta.rosetta.core.io.StructFileRepOptions, pdb_author: str) None

C++: core::io::StructFileRepOptions::set_pdb_author(const std::string &) –> void

set_pdb_comments(self: pyrosetta.rosetta.core.io.StructFileRepOptions, pdb_comments: bool) None

C++: core::io::StructFileRepOptions::set_pdb_comments(const bool) –> void

set_pdb_parents(self: pyrosetta.rosetta.core.io.StructFileRepOptions, pdb_parents: bool) None

C++: core::io::StructFileRepOptions::set_pdb_parents(const bool) –> void

set_per_chain_renumbering(self: pyrosetta.rosetta.core.io.StructFileRepOptions, per_chain_renumbering: bool) None

C++: core::io::StructFileRepOptions::set_per_chain_renumbering(const bool) –> void

set_preserve_crystinfo(self: pyrosetta.rosetta.core.io.StructFileRepOptions, preserve_crystinfo: bool) None

C++: core::io::StructFileRepOptions::set_preserve_crystinfo(const bool) –> void

set_preserve_header(self: pyrosetta.rosetta.core.io.StructFileRepOptions, preserve_header: bool) None

C++: core::io::StructFileRepOptions::set_preserve_header(const bool) –> void

set_randomize_missing_coords(self: pyrosetta.rosetta.core.io.StructFileRepOptions, randomize_missing_coords: bool) None

C++: core::io::StructFileRepOptions::set_randomize_missing_coords(const bool) –> void

set_read_only_ATOM_entries(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_read_only_ATOM_entries(const bool) –> void

set_remember_unrecognized_res(self: pyrosetta.rosetta.core.io.StructFileRepOptions, remember_unrecognized_res: bool) None

C++: core::io::StructFileRepOptions::set_remember_unrecognized_res(const bool) –> void

set_remember_unrecognized_water(self: pyrosetta.rosetta.core.io.StructFileRepOptions, remember_unrecognized_water: bool) None

C++: core::io::StructFileRepOptions::set_remember_unrecognized_water(const bool) –> void

set_renumber_pdb(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_renumber_pdb(const bool) –> void

set_residues_for_atom_name_remapping(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: pyrosetta.rosetta.utility.vector1_std_string) None

C++: core::io::StructFileRepOptions::set_residues_for_atom_name_remapping(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_show_all_fixes(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_show_all_fixes(const bool) –> void

set_skip_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions, skip_connect_info: bool) None

C++: core::io::StructFileRepOptions::set_skip_connect_info(const bool) –> void

set_suppress_zero_occ_pdb_output(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_suppress_zero_occ_pdb_output(const bool) –> void

set_use_pdb_format_HETNAM_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_use_pdb_format_HETNAM_records(const bool) –> void

set_write_all_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_write_all_connect_info(const bool) –> void

set_write_glycan_pdb_codes(self: pyrosetta.rosetta.core.io.StructFileRepOptions, write_glycan_pdb_codes: bool) None

C++: core::io::StructFileRepOptions::set_write_glycan_pdb_codes(const bool) –> void

C++: core::io::StructFileRepOptions::set_write_pdb_link_records(const bool) –> void

set_write_pdb_parametric_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_write_pdb_parametric_info(const bool) –> void

set_write_pdb_title_section_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_write_pdb_title_section_records(const bool) –> void

set_write_seqres_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions, setting: bool) None

C++: core::io::StructFileRepOptions::set_write_seqres_records(const bool) –> void

show_all_fixes(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::show_all_fixes() const –> bool

skip_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::skip_connect_info() const –> bool

suppress_zero_occ_pdb_output(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::suppress_zero_occ_pdb_output() const –> bool

type(self: pyrosetta.rosetta.core.io.StructFileRepOptions) str

C++: core::io::StructFileRepOptions::type() const –> std::string

use_pdb_format_HETNAM_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::use_pdb_format_HETNAM_records() const –> bool

write_all_connect_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::write_all_connect_info() const –> bool

write_glycan_pdb_codes(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::write_glycan_pdb_codes() const –> bool

C++: core::io::StructFileRepOptions::write_pdb_link_records() const –> bool

write_pdb_parametric_info(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::write_pdb_parametric_info() const –> bool

write_pdb_title_section_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::write_pdb_title_section_records() const –> bool

write_seqres_records(self: pyrosetta.rosetta.core.io.StructFileRepOptions) bool

C++: core::io::StructFileRepOptions::write_seqres_records() const –> bool

C++: core::io::explicit_links_from_sfr_linkage(const class std::map<std::string, class utility::vector1<struct core::io::LinkInformation, class std::allocator<struct core::io::LinkInformation> >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class utility::vector1<struct core::io::LinkInformation, class std::allocator<struct core::io::LinkInformation> > > > > &, const class utility::vector1<class core::io::ResidueInformation, class std::allocator<class core::io::ResidueInformation> > &) –> class std::map<std::string, class std::map<std::string, struct std::pair<std::string, std::string >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct std::pair<std::string, std::string > > > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, struct std::pair<std::string, std::string >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct std::pair<std::string, std::string > > > > > > >

pyrosetta.rosetta.core.io.fix_glycan_order(rinfos: pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation, glycan_positions: pyrosetta.rosetta.utility.vector1_unsigned_long, options: pyrosetta.rosetta.core.io.StructFileRepOptions, known_links: pyrosetta.rosetta.std.map_std_string_std_map_std_string_std_pair_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_pair_std_string_std_string_t) pyrosetta.rosetta.utility.vector1_unsigned_long

Reorganize the given glycan residues such that they’re in tree order

Not 100% great, as it won’t move any non-glycan residue, which may result in a funky order if there are non-glycans interspersed with the glycan residues Return the positions (in the rinfos) of the known (non-reducing) ends of the glycan chains

C++: core::io::fix_glycan_order(class utility::vector1<class core::io::ResidueInformation, class std::allocator<class core::io::ResidueInformation> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::io::StructFileRepOptions &, const class std::map<std::string, class std::map<std::string, struct std::pair<std::string, std::string >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct std::pair<std::string, std::string > > > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::map<std::string, struct std::pair<std::string, std::string >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, struct std::pair<std::string, std::string > > > > > > > &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

Is the LinkInformation in the given vector?

C++: core::io::link_in_vector(const class utility::vector1<struct core::io::LinkInformation, class std::allocator<struct core::io::LinkInformation> > &, const struct core::io::LinkInformation &) –> bool

pyrosetta.rosetta.core.io.pose_data_cache_from_sfr(*args, **kwargs)

Overloaded function.

  1. pose_data_cache_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep) -> str

Extract the pose data cache from the SFR as a string representation for PDB output.

C++: core::io::pose_data_cache_from_sfr(const class core::io::StructFileRep &) –> std::string

  1. pose_data_cache_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep, out: pyrosetta.rosetta.std.stringstream) -> None

Extract the pose data cache from the SFR as a string representation for PDB output.

C++: core::io::pose_data_cache_from_sfr(const class core::io::StructFileRep &, class std::basic_stringstream<char> &) –> void

pyrosetta.rosetta.core.io.pose_energies_from_sfr(*args, **kwargs)

Overloaded function.

  1. pose_energies_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep) -> str

Extract the pose energies table from an SFR as a string representation for PDB output.

C++: core::io::pose_energies_from_sfr(const class core::io::StructFileRep &) –> std::string

  1. pose_energies_from_sfr(sfr: pyrosetta.rosetta.core.io.StructFileRep, out: pyrosetta.rosetta.std.stringstream) -> None

Extract the pose energies table from an SFR as a string representation for PDB output.

C++: core::io::pose_energies_from_sfr(const class core::io::StructFileRep &, class std::basic_stringstream<char> &) –> void

pyrosetta.rosetta.core.io.pose_from_pose(*args, **kwargs)

Overloaded function.

  1. pose_from_pose(new_pose: pyrosetta.rosetta.core.pose.Pose, old_pose: pyrosetta.rosetta.core.pose.Pose, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::io::pose_from_pose(class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. pose_from_pose(new_pose: pyrosetta.rosetta.core.pose.Pose, old_pose: pyrosetta.rosetta.core.pose.Pose, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

C++: core::io::pose_from_pose(class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::io::StructFileRepOptions &) –> void

  1. pose_from_pose(new_pose: pyrosetta.rosetta.core.pose.Pose, old_pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::io::pose_from_pose(class core::pose::Pose &, const class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. pose_from_pose(new_pose: pyrosetta.rosetta.core.pose.Pose, old_pose: pyrosetta.rosetta.core.pose.Pose, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet, residue_indices: pyrosetta.rosetta.utility.vector1_unsigned_long, options: pyrosetta.rosetta.core.io.StructFileRepOptions) -> None

C++: core::io::pose_from_pose(class core::pose::Pose &, const class core::pose::Pose &, const class core::chemical::ResidueTypeSet &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class core::io::StructFileRepOptions &) –> void

pyrosetta.rosetta.core.io.read_alternative_3_letter_codes_from_database_file(filename: str) pyrosetta.rosetta.std.map_std_string_std_tuple_std_string_std_string_char_utility_vector1_std_string_std_allocator_std_string_t
Return a mapping of alternative PDB 3-letter codes to a paired set including the Rosetta 3-letter code and,

optionally, any HETNAM information for the residue desired.

C++: core::io::read_alternative_3_letter_codes_from_database_file(const std::string &) –> class std::map<std::string, class std::tuple<std::string, std::string, char, class utility::vector1<std::string, class std::allocator<std::string > > >, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::tuple<std::string, std::string, char, class utility::vector1<std::string, class std::allocator<std::string > > > > > >

pyrosetta.rosetta.core.io.reorder_glycan_residues(rinfos: pyrosetta.rosetta.utility.vector1_core_io_ResidueInformation, correct_order: pyrosetta.rosetta.utility.vector1_unsigned_long, glycan_positions: pyrosetta.rosetta.utility.vector1_unsigned_long) None
Bring glycans into the correct order, which corresponds to connectivity of each glycan tree

This requires reordering rinfos and rosetta_residue_name3s.

C++: core::io::reorder_glycan_residues(class utility::vector1<class core::io::ResidueInformation, class std::allocator<class core::io::ResidueInformation> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

Do these link information correspond to the same connection (ignoring order)

C++: core::io::same_link(const struct core::io::LinkInformation &, const struct core::io::LinkInformation &) –> bool