filters¶

Bindings for protocols::protein_interface_design::filters namespace

pyrosetta.rosetta.protocols.protein_interface_design.filters.Ca_coords(pose: pyrosetta.rosetta.core.pose.Pose, positions: pyrosetta.rosetta.utility.vector1_unsigned_long) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t¶: C++: protocols::protein_interface_design::filters::Ca_coords(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

class pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

Filters for structures which could form a disulfide bond across the docking interface.

Use this filter when you are trying to design one docking member so that it forms a disulfide bond to one or more target residues of the other docking partner. The filter does not consider the indentities of the residues involved, only their Cb position.

This filter only applies to centroid poses. Calling it with a full atom pose will result in everything failing.

Spencer Bliven <blivens.washington.edu>

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter) -> None
__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter, arg0: pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter) -> None
__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter, targetResidue: int) -> None
__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter, targetResidues: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

apply(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::protein_interface_design::filters::DisulfideFilter::apply(const class core::pose::Pose &) const –> bool

class_name() → str¶: C++: protocols::protein_interface_design::filters::DisulfideFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::protein_interface_design::filters::DisulfideFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::protein_interface_design::filters::DisulfideFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter) → str¶: C++: protocols::protein_interface_design::filters::DisulfideFilter::name() const –> std::string

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::protein_interface_design::filters::DisulfideFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::protein_interface_design::filters::DisulfideFilter::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.DisulfideFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::protein_interface_design::filters::DisulfideFilter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter) -> None
__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter, arg0: int, arg1: int) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter, arg0: int, arg1: int, arg2: float) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter, arg0: int, arg1: int, arg2: float, arg3: bool) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter, resnum: int, partners: int, energy_cutoff: float, backbone: bool, sidechain: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter, arg0: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

apply(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::protein_interface_design::filters::HbondsToAtomFilter::apply(const class core::pose::Pose &) const –> bool

class_name() → str¶: C++: protocols::protein_interface_design::filters::HbondsToAtomFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::protein_interface_design::filters::HbondsToAtomFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter, pose: pyrosetta.rosetta.core.pose.Pose) → int¶: C++: protocols::protein_interface_design::filters::HbondsToAtomFilter::compute(const class core::pose::Pose &) const –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::protein_interface_design::filters::HbondsToAtomFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter) → str¶: C++: protocols::protein_interface_design::filters::HbondsToAtomFilter::name() const –> std::string

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::protein_interface_design::filters::HbondsToAtomFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::protein_interface_design::filters::HbondsToAtomFilter::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToAtomFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::protein_interface_design::filters::HbondsToAtomFilter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) -> None
__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, arg0: int, arg1: int) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, arg0: int, arg1: int, arg2: float) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, arg0: int, arg1: int, arg2: float, arg3: bool) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, arg0: int, arg1: int, arg2: float, arg3: bool, arg4: bool) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, arg0: int, arg1: int, arg2: float, arg3: bool, arg4: bool, arg5: bool) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, arg0: int, arg1: int, arg2: float, arg3: bool, arg4: bool, arg5: bool, arg6: bool) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, resnum: int, partners: int, energy_cutoff: float, backbone: bool, sidechain: bool, bb_bb: bool, from_other_chains: bool, from_same_chain: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, arg0: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

apply(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::apply(const class core::pose::Pose &) const –> bool

backbone(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) → bool¶

Get whether to include backbone hydrogen bonds.

I’m not sure that this is implemented properly. (VKM – 6 July 2015).

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::backbone() const –> bool

bb_bb(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) → bool¶

Get whether to include backbone-backbone hydrogen bonds.

I’m not sure that this is implemented properly. (VKM – 6 July 2015).

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::bb_bb() const –> bool

class_name() → str¶: C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, pose: pyrosetta.rosetta.core.pose.Pose, resnum_rosetta: int) → int¶

Actually compute the number of hydrogen bonds to the target residue.

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::compute(const class core::pose::Pose &, const unsigned long) const –> unsigned long

energy_cutoff(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) → float¶

Get the threshold for the hbond score term at which two residues are counted as being hydrogen bonded.

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::energy_cutoff() const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

from_other_chains(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) → bool¶

Get whether hydrogen bonds from other chains should be counted.

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::from_other_chains() const –> bool

from_same_chain(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) → bool¶

Get whether hydrogen bonds from the same chain should be counted.

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::from_same_chain() const –> bool

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) → str¶: C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::name() const –> std::string

partners(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) → int¶

Get the minimum number of H-bond partners that this residue must have for the filter to pass.

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::partners() const –> unsigned long

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::report_sm(const class core::pose::Pose &) const –> double

resnum(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) → str¶

Get the residue number (a string to be parsed at apply time).

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::resnum() const –> std::string

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_backbone(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, val: bool) → None¶

Set whether to include backbone hydrogen bonds.

I’m not sure that this is implemented properly. (VKM – 6 July 2015).

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::set_backbone(const bool) –> void

set_bb_bb(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, val: bool) → None¶

Set whether to include backbone-backbone hydrogen bonds.

I’m not sure that this is implemented properly. (VKM – 6 July 2015).

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::set_bb_bb(const bool) –> void

set_energy_cutoff(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, val: float) → None¶

Set the threshold for the hbond score term at which two residues are counted as being hydrogen bonded.

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::set_energy_cutoff(const double) –> void

set_from_other_chains(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, val: bool) → None¶

Set whether hydrogen bonds from other chains should be counted.

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::set_from_other_chains(const bool) –> void

set_from_same_chain(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, val: bool) → None¶

Set whether hydrogen bonds from the same chain should be counted.

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::set_from_same_chain(const bool) –> void

set_partners(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, val: int) → None¶

Set the minimum number of H-bond partners that this residue must have for the filter to pass.

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::set_partners(const unsigned long) –> void

set_resnum(*args, **kwargs)¶

Overloaded function.

set_resnum(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, input: str) -> None

Set the residue number (as a string to be parsed at apply time).

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::set_resnum(const class std::basic_string<char> &) –> void

set_resnum(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, val: int) -> None

Set the residue number (as an integer – Rosetta numbering).

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::set_resnum(const unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

Set the scorefunction to use for hbond calculation.

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_selector(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None¶

Set the ResidueSelector to use.

Only hydrogen bonds between this residue and the residues selected by the ResidueSelector will be counted, if a ResidueSelector is provided.

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_sidechain(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter, val: bool) → None¶

Set whether to include backbone hydrogen bonds.

I’m not sure that this is implemented properly. (VKM – 6 July 2015).

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::set_sidechain(const bool) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

sidechain(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.HbondsToResidueFilter) → bool¶

Get whether to include backbone hydrogen bonds.

I’m not sure that this is implemented properly. (VKM – 6 July 2015).

C++: protocols::protein_interface_design::filters::HbondsToResidueFilter::sidechain() const –> bool

class pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

returns the residues aligned to a segment on the input pdb to the source pdb

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter) -> None
__init__(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter, arg0: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

apply(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::apply(const class core::pose::Pose &) const –> bool

class_name() → str¶: C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter) → str¶: C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::name() const –> std::string

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

source_pose(*args, **kwargs)¶

Overloaded function.

source_pose(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter) -> str

C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::source_pose() const –> std::string

source_pose(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter, s: str) -> None

C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::source_pose(const class std::basic_string<char> &) –> void

start_res(*args, **kwargs)¶

Overloaded function.

start_res(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter) -> int

C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::start_res() const –> unsigned long

start_res(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter, s: int) -> None

C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::start_res(const unsigned long) –> void

stop_res(*args, **kwargs)¶

Overloaded function.

stop_res(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter) -> int

C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::stop_res() const –> unsigned long

stop_res(self: pyrosetta.rosetta.protocols.protein_interface_design.filters.RelativeSegmentFilter, s: int) -> None

C++: protocols::protein_interface_design::filters::RelativeSegmentFilter::stop_res(const unsigned long) –> void

pyrosetta.rosetta.protocols.protein_interface_design.filters.atom_distance(r1: pyrosetta.rosetta.core.conformation.Residue, a1: str, r2: pyrosetta.rosetta.core.conformation.Residue, a2: str) → float¶: C++: protocols::protein_interface_design::filters::atom_distance(const class core::conformation::Residue &, const class std::basic_string<char> &, const class core::conformation::Residue &, const class std::basic_string<char> &) –> double

pyrosetta.rosetta.protocols.protein_interface_design.filters.res_rmsd(pose_res_for_rmsd: pyrosetta.rosetta.utility.vector1_unsigned_long, template_res_for_rmsd: pyrosetta.rosetta.utility.vector1_unsigned_long, copy_pose: pyrosetta.rosetta.core.pose.Pose, template_pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::protein_interface_design::filters::res_rmsd(const class utility::vector1<unsigned long, class std::allocator<unsigned long> >, const class utility::vector1<unsigned long, class std::allocator<unsigned long> >, const class core::pose::Pose &, const class core::pose::Pose &) –> double