ga_ligand_dock

Bindings for protocols::ligand_docking::ga_ligand_dock namespace

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties

Bases: pybind11_object

the atom properties important in constraint generation

acceptor(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties) → bool

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::acceptor() const –> bool

ambiguity(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties) → float

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::ambiguity() const –> double

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::operator=(const class protocols::ligand_docking::ga_ligand_dock::AtomProperties &) –> class protocols::ligand_docking::ga_ligand_dock::AtomProperties &

donor(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties) → bool

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::donor() const –> bool

generic(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties) → bool

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::generic() const –> bool

match(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties, other: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties, polar_scale: float, halogen_specific: bool) → float

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::match(const class protocols::ligand_docking::ga_ligand_dock::AtomProperties &, double, bool) const –> double

polarH(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties) → bool

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::polarH() const –> bool

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties) -> float

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::score() const –> double

2. score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties, value: float) -> None

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::score(double) –> void

show(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties) → str

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::show() const –> std::string

tag(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties) → str

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::tag() const –> std::string

used_for_phore(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties) → bool

C++: protocols::ligand_docking::ga_ligand_dock::AtomProperties::used_for_phore() const –> bool

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ChiInfo

Bases: pybind11_object

property E

property ligchis

property recchis

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo

Bases: pybind11_object

Constraint information about AtomProperties and/or Pharmacophores

includes constrained xyzs & important properties we do not use a residue type (which already has this info)

because in “pharmicophore mode” we generate virtual sites from the protein side.

we want targets generated in both ways to run through the same machinery therefore, we instead we have two initialization routines:

• from the ligand side (from restype)

• from the receptor side (building programmatically)

align_to_current_phore_match(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, pose: pyrosetta.rosetta.core.pose.Pose, recinfo: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, marked_pairs: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, SrcPriorIDs: pyrosetta.rosetta.utility.vector1_unsigned_long, TgtPriorIDs: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

try aligning to the phore defined by current_phore_match_ (defined by select_phore_match)

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::align_to_current_phore_match(class core::pose::Pose &, const class protocols::ligand_docking::ga_ligand_dock::ConstraintInfo &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::operator=(const class protocols::ligand_docking::ga_ligand_dock::ConstraintInfo &) –> class protocols::ligand_docking::ga_ligand_dock::ConstraintInfo &

atomid(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, i: int) → pyrosetta.rosetta.core.id.AtomID

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::atomid(unsigned long) const –> const class core::id::AtomID &

coord(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, i: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::coord(unsigned long) const –> const class numeric::xyzVector<double> &

init_from_ligand(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

use a (non-identical) target ligand (for reference ligand matching)

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

init_from_ligand_pharmacophore(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, report_phore_info: bool) → None

defines pharmacophore partners in ligand (for pharmacophore matching)

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

init_from_map(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, density_points: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → None

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_map(class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >) –> void

init_from_receptor(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, pose: pyrosetta.rosetta.core.pose.Pose, gridscore: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, simple: bool) → None

build up binding locations from a receptor

gridscorer is used to define the bounding box

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_receptor(const class core::pose::Pose &, class std::shared_ptr<class protocols::ligand_docking::ga_ligand_dock::GridScorer>, const bool) –> void

limit(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo) → float

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::limit() –> double

map_phores(*args, **kwargs)

Overloaded function.

1. map_phores(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, receptor_phores: pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore, update: bool) -> None

2. map_phores(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, receptor_phores: pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore, update: bool, nmax: int) -> None

matches ligand phores (==own) to provided receptor phores and stores at phore_match_

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores(const class utility::vector1<class protocols::ligand_docking::ga_ligand_dock::Pharmacophore, class std::allocator<class protocols::ligand_docking::ga_ligand_dock::Pharmacophore> > &, const bool, const unsigned long) –> void

n_phore_match(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo) → int

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::n_phore_match() const –> unsigned long

natoms(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo) → int

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::natoms() const –> unsigned long

pharmacophores_defined(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo) → bool

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::pharmacophores_defined() const –> bool

phores(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo) → pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_Pharmacophore

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phores() const –> const class utility::vector1<class protocols::ligand_docking::ga_ligand_dock::Pharmacophore, class std::allocator<class protocols::ligand_docking::ga_ligand_dock::Pharmacophore> > &

polar_scale(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo) → float

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::polar_scale() –> double

properties(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, i: int) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.AtomProperties

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::properties(unsigned long) const –> const class protocols::ligand_docking::ga_ligand_dock::AtomProperties &

select_phore_match(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo, run_index: int) → None

selects a phore_match and updates current_phore_match_

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::select_phore_match(const unsigned long) –> void

weight(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo) → float

C++: protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::weight() –> double

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo

Bases: pybind11_object

property E

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfo

C++: protocols::ligand_docking::ga_ligand_dock::DensStructInfo::operator=(const struct protocols::ligand_docking::ga_ligand_dock::DensStructInfo &) –> struct protocols::ligand_docking::ga_ligand_dock::DensStructInfo &

property cst

property hbond_count

property lig_dens

property ligandname

property ligandscore

property native_hbond_ratio

property pocket_cc

property ranking_prerelax

property recscore

property rms

property str

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfoComp

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfoComp, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfoComp) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.DensStructInfoComp

C++: protocols::ligand_docking::ga_ligand_dock::DensStructInfoComp::operator=(const class protocols::ligand_docking::ga_ligand_dock::DensStructInfoComp &) –> class protocols::ligand_docking::ga_ligand_dock::DensStructInfoComp &

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.EntropyEstimator

Bases: pybind11_object

Estimates entropy change by ligand binding using short MC simulation

This class takes a full complex pose and ligand seqpos index to calculate entropy change upon ligand binding. MC simulation perturbs chi angles defined for the ligand at free state, and estimates effective entropy loss by binding by processing torsion probability during simulation assuming that ligand gets completely after binding.

apply(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.EntropyEstimator, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::apply(const class core::pose::Pose &) const –> double

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.EntropyEstimator, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.EntropyEstimator) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.EntropyEstimator

C++: protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::operator=(const class protocols::ligand_docking::ga_ligand_dock::EntropyEstimator &) –> class protocols::ligand_docking::ga_ligand_dock::EntropyEstimator &

set_niter(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.EntropyEstimator, setting: int) → None

C++: protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::set_niter(unsigned long) –> void

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams

Bases: pybind11_object

represent options for a single “phase” of ligand docking

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GADockStageParams

C++: protocols::ligand_docking::ga_ligand_dock::GADockStageParams::operator=(const struct protocols::ligand_docking::ga_ligand_dock::GADockStageParams &) –> struct protocols::ligand_docking::ga_ligand_dock::GADockStageParams &

property elec_scale

property maxiter

property packcycles

property pmut

property pool

property ramp_schedule

property repeats

property rmsthreshold

property smoothing

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock

Bases: Mover

Ligand Docking protocol using Genetic Algorithm

Runs ligand docking using pre-computed full-atom grid score, binding-motif search, and genetic algorithm search on Ligand & flexible sidechains at receptor conformations. This docking method supports full on-the-fly search of ligand conformation hence ligand “conformer” generation is not required.

apply(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock, pose: pyrosetta.rosetta.core.pose.Pose) → None

main apply of GA ligand docking

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDock::operator=(const class protocols::ligand_docking::ga_ligand_dock::GALigandDock &) –> class protocols::ligand_docking::ga_ligand_dock::GALigandDock &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDock::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDock::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock) → pyrosetta.rosetta.core.pose.Pose

as this is a one->many mover, use this function to return multiple outputs from a single call to apply

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock) → str

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() → str

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDock::mover_name() –> std::string

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDock::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDock::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

setup_params_for_runmode(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDock, runmode: str) → None

parse options based on umbrella runmode option

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDock::setup_params_for_runmode(std::string) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDockCreator::operator=(const class protocols::ligand_docking::ga_ligand_dock::GALigandDockCreator &) –> class protocols::ligand_docking::ga_ligand_dock::GALigandDockCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDockCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator) → str

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDockCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GALigandDockCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::ligand_docking::ga_ligand_dock::GALigandDockCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer

Bases: pybind11_object

Genetic Algorithm Optimizer called by GALigandDock

Takes grid score & gene-representations of ligand (+flex sidechain) conformations returns multiple optimized gene-representations of ligand (+flex sidechain) conformations

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer

C++: protocols::ligand_docking::ga_ligand_dock::GAOptimizer::operator=(const class protocols::ligand_docking::ga_ligand_dock::GAOptimizer &) –> class protocols::ligand_docking::ga_ligand_dock::GAOptimizer &

set_align_reference_atom_ids(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer, newval: pyrosetta.rosetta.utility.vector1_core_id_AtomID) → None

C++: protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_align_reference_atom_ids(class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >) –> void

set_favor_native(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer, newval: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_favor_native(double) –> void

set_max_rot_cumulative_prob(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer, newval: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_max_rot_cumulative_prob(double) –> void

set_native(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer, native: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → None

C++: protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_native(const class protocols::ligand_docking::ga_ligand_dock::LigandConformer) –> void

set_protocol(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer, protocol_in: pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_GADockStageParams) → None

C++: protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_protocol(const class utility::vector1<struct protocols::ligand_docking::ga_ligand_dock::GADockStageParams, class std::allocator<struct protocols::ligand_docking::ga_ligand_dock::GADockStageParams> > &) –> void

set_rot_energy_cutoff(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GAOptimizer, newval: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::GAOptimizer::set_rot_energy_cutoff(double) –> void

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t

Bases: pybind11_object

add_point(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t, info: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbAcc) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridHash3D<protocols::ligand_docking::ga_ligand_dock::hbAcc>::add_point(struct protocols::ligand_docking::ga_ligand_dock::hbAcc) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t

C++: protocols::ligand_docking::ga_ligand_dock::GridHash3D<protocols::ligand_docking::ga_ligand_dock::hbAcc>::operator=(const class protocols::ligand_docking::ga_ligand_dock::GridHash3D<struct protocols::ligand_docking::ga_ligand_dock::hbAcc> &) –> class protocols::ligand_docking::ga_ligand_dock::GridHash3D<struct protocols::ligand_docking::ga_ligand_dock::hbAcc> &

npoints(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t) → int

C++: protocols::ligand_docking::ga_ligand_dock::GridHash3D<protocols::ligand_docking::ga_ligand_dock::hbAcc>::npoints() –> int

set_resolution(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbAcc_t, reso: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridHash3D<protocols::ligand_docking::ga_ligand_dock::hbAcc>::set_resolution(double) –> void

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t

Bases: pybind11_object

add_point(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t, info: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbDon) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridHash3D<protocols::ligand_docking::ga_ligand_dock::hbDon>::add_point(struct protocols::ligand_docking::ga_ligand_dock::hbDon) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t

C++: protocols::ligand_docking::ga_ligand_dock::GridHash3D<protocols::ligand_docking::ga_ligand_dock::hbDon>::operator=(const class protocols::ligand_docking::ga_ligand_dock::GridHash3D<struct protocols::ligand_docking::ga_ligand_dock::hbDon> &) –> class protocols::ligand_docking::ga_ligand_dock::GridHash3D<struct protocols::ligand_docking::ga_ligand_dock::hbDon> &

npoints(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t) → int

C++: protocols::ligand_docking::ga_ligand_dock::GridHash3D<protocols::ligand_docking::ga_ligand_dock::hbDon>::npoints() –> int

set_resolution(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridHash3D_protocols_ligand_docking_ga_ligand_dock_hbDon_t, reso: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridHash3D<protocols::ligand_docking::ga_ligand_dock::hbDon>::set_resolution(double) –> void

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer

Bases: pybind11_object

Grid representation of scorefunction

calculate_grid(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose, lig_resnos: pyrosetta.rosetta.utility.vector1_unsigned_long, movingSCs: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

calculate_ligand_density_correlation(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, resid: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_ligand_density_correlation(int, const class core::conformation::Residue &, const class core::pose::Pose &) –> double

calculate_pocket_density_correlation(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_pocket_density_correlation(const class core::pose::Pose &) –> double

calculate_pose_density_correlation(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_pose_density_correlation(const class core::pose::Pose &) –> double

debug_deriv(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, min_map: pyrosetta.rosetta.core.optimization.MinimizerMap) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::debug_deriv(class core::pose::Pose &, const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, class core::optimization::MinimizerMap &) –> void

density_score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → float

calculate electron density on the grid

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::density_score(const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &) –> double

derivatives(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, min_map: pyrosetta.rosetta.core.optimization.MinimizerMap) → None

calculate derivatives on the grid

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::derivatives(class core::pose::Pose &, const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, class core::optimization::MinimizerMap &) –> void

dof_derivative(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose, min_map: pyrosetta.rosetta.core.optimization.MinimizerMap, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: pyrosetta.rosetta.core.id.TorsionID) → float

(1b) dof derivatives

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::dof_derivative(class core::pose::Pose &, class core::optimization::MinimizerMap &, const class core::id::DOF_ID &, const class core::id::TorsionID &) –> double

get_1b_energy(*args, **kwargs)

Overloaded function.

1. get_1b_energy(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, res_i: pyrosetta.rosetta.core.conformation.Residue, lkbrinfo: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, include_bb: bool) -> pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy

2. get_1b_energy(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, res_i: pyrosetta.rosetta.core.conformation.Residue, lkbrinfo: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, include_bb: bool, soft: bool) -> pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy

3. get_1b_energy(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, res_i: pyrosetta.rosetta.core.conformation.Residue, lkbrinfo: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, include_bb: bool, soft: bool, has_density_map: bool) -> pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy

get a residue:background energy

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_1b_energy(const class core::conformation::Residue &, class std::shared_ptr<class core::scoring::lkball::LKB_ResidueInfo>, bool, bool, bool) –> class protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy

get_2b_energy(*args, **kwargs)

Overloaded function.

1. get_2b_energy(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose, res_i: pyrosetta.rosetta.core.conformation.Residue, lkbrinfo_i: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, incl_bb_i: bool, res_j: pyrosetta.rosetta.core.conformation.Residue, lkbrinfo_j: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, incl_bb_j: bool) -> pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy

2. get_2b_energy(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose, res_i: pyrosetta.rosetta.core.conformation.Residue, lkbrinfo_i: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, incl_bb_i: bool, res_j: pyrosetta.rosetta.core.conformation.Residue, lkbrinfo_j: pyrosetta.rosetta.core.scoring.lkball.LKB_ResidueInfo, incl_bb_j: bool, soft: bool) -> pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy

get a residue:residue energy

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_2b_energy(class core::pose::Pose &, const class core::conformation::Residue &, class std::shared_ptr<class core::scoring::lkball::LKB_ResidueInfo>, bool, const class core::conformation::Residue &, class std::shared_ptr<class core::scoring::lkball::LKB_ResidueInfo>, bool, bool) –> class protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy

get_debug(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → bool

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_debug() –> bool

get_elec_scale(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → float

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_elec_scale() –> double

get_exact(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → bool

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_exact() –> bool

get_grid_all_atomtypes(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_grid_all_atomtypes() –> void

get_ligand_com(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_ligand_com() –> class numeric::xyzVector<double>

get_maxRad(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → float

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_maxRad() –> double

get_maxiterminimize(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → bool

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_maxiterminimize() –> bool

get_packer_cycles(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → int

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_packer_cycles() –> unsigned long

get_padding(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → float

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_padding() –> double

get_sfxn(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_sfxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_smoothing(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → float

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_smoothing() –> double

get_voxel_spacing(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → float

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_voxel_spacing() –> double

get_w_rep(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → float

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::get_w_rep() –> double

has_atom_type(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, atype: int) → bool

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::has_atom_type(int) –> bool

is_point_in_grid(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, x: pyrosetta.rosetta.numeric.xyzVector_double_t) → bool

check to see if a point falls w/i the grid boundaries

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::is_point_in_grid(class numeric::xyzVector<double>) const –> bool

is_residue_in_grid(*args, **kwargs)

Overloaded function.

1. is_residue_in_grid(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, res: pyrosetta.rosetta.core.conformation.Residue, angle_buffer: float, padding_buffer: float) -> bool

check to see if sidechain lies within the grid

“angle buffer” makes sure residues near the edge point toward middle (higer values == stricter, 0 = no filter) “padding buffer” adds a region on the outside where residues may not move

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(const class core::conformation::Residue &, double, double) const –> bool

2. is_residue_in_grid(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, res: pyrosetta.rosetta.core.conformation.Residue, padding_buffer: float, eigval: pyrosetta.rosetta.numeric.xyzVector_double_t, eigvec: pyrosetta.rosetta.numeric.xyzMatrix_double_t) -> bool

check to see if sidechain lies within the grid (ALTERNATE version)

similar to the above, but pass in eigenvalues/vectors that define pocket shape

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(const class core::conformation::Residue &, double, const class numeric::xyzVector<double> &, const class numeric::xyzMatrix<double> &) const –> bool

minimizer_loop(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, minopt: pyrosetta.rosetta.core.optimization.MinimizerOptions) → float

subroutine: min loop

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::minimizer_loop(class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, const class core::optimization::MinimizerOptions &) –> double

optimize(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ramp_schedule: pyrosetta.rosetta.utility.vector1_double, placeable_rotdb: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_ligand_docking_ga_ligand_dock_PlaceableRotamer_std_allocator_protocols_ligand_docking_ga_ligand_dock_PlaceableRotamer_t, rot_energies: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies) → float

minimize a ligand conformer

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::optimize(class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, class utility::vector1<double, class std::allocator<double> >, class utility::vector1<class utility::vector1<struct protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer, class std::allocator<struct protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer> >, class std::allocator<class utility::vector1<struct protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer, class std::allocator<struct protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer> > > > &, class protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies &) –> double

packer_loop(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, placeable_rotdb: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_ligand_docking_ga_ligand_dock_PlaceableRotamer_std_allocator_protocols_ligand_docking_ga_ligand_dock_PlaceableRotamer_t, rotamer_energies: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies) → float

subroutine: run packing

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, class utility::vector1<class utility::vector1<struct protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer, class std::allocator<struct protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer> >, class std::allocator<class utility::vector1<struct protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer, class std::allocator<struct protocols::ligand_docking::ga_ligand_dock::PlaceableRotamer> > > > &, class protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies &) –> double

point_clash_energy(*args, **kwargs)

Overloaded function.

1. point_clash_energy(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, X: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

2. point_clash_energy(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, X: pyrosetta.rosetta.numeric.xyzVector_double_t, atype_in: str) -> float

3. point_clash_energy(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, X: pyrosetta.rosetta.numeric.xyzVector_double_t, atype_in: str, soft: bool) -> float

gets the clash energy of a point

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::point_clash_energy(class numeric::xyzVector<double>, std::string, bool) –> double

point_energy(*args, **kwargs)

Overloaded function.

1. point_energy(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, X: pyrosetta.rosetta.numeric.xyzVector_double_t) -> float

2. point_energy(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, X: pyrosetta.rosetta.numeric.xyzVector_double_t, atype_in: str) -> float

3. point_energy(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, X: pyrosetta.rosetta.numeric.xyzVector_double_t, atype_in: str, weightelec_in: float) -> float

gets the solvation energy of a point

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::point_energy(class numeric::xyzVector<double>, std::string, double) –> double

prepare_grid(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose, lig_resnos: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

calulate the bounding box

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::prepare_grid(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) -> float

2. score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, soft: bool) -> float

calculate energies on the grid

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::score(const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, bool) –> double

3. score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) -> float

4. score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, soft: bool) -> float

calculate energies on the grid

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::score(class core::pose::Pose &, const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, bool) –> double

score_init(*args, **kwargs)

Overloaded function.

1. score_init(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) -> float

2. score_init(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, soft: bool) -> float

3. score_init(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, soft: bool, init_dens_weight: float) -> float

calculate energies on the grid for initial pool generation

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::score_init(const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, bool, double) –> double

4. score_init(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, soft: bool) -> float

5. score_init(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, pose: pyrosetta.rosetta.core.pose.Pose, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, soft: bool, init_dens_weight: float) -> float

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::score_init(class core::pose::Pose &, const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, bool, double) –> double

set_bbox_padding(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, bbox_padding_in: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_bbox_padding(double) –> void

set_debug(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, debugin: bool) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_debug(bool) –> void

set_elec_scale(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, setting: float) → bool

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_elec_scale(double) –> bool

set_exact(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, exactin: bool) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_exact(bool) –> void

set_force_exact_min(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, setting: bool) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_force_exact_min(bool) –> void

set_grid_dim_with_maxRad(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, inval: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_grid_dim_with_maxRad(double) –> void

set_hash_gridding(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, hash_gridding_in: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_hash_gridding(double) –> void

set_hash_subgridding(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, hash_subgridding_in: int) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_hash_subgridding(unsigned long) –> void

set_maxiter_minimize(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, setting: int) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_maxiter_minimize(unsigned long) –> void

set_out_of_bound_e(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, setting: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_out_of_bound_e(double) –> void

set_packer_cycles(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, setting: int) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_packer_cycles(unsigned long) –> void

set_smoothing(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, setting: float) → bool

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_smoothing(double) –> bool

set_voxel_spacing(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, voxel_spacing_in: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_voxel_spacing(double) –> void

set_w_rep(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer, setting: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::GridScorer::set_w_rep(double) –> void

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GriddedAtomTreeMultifunc

Bases: Multifunc

Atom tree multifunction class

abort_min(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double) → bool

Christophe added the following to allow premature end of minimization

If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!

C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

dfunc(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GriddedAtomTreeMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dump(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GriddedAtomTreeMultifunc, vars: pyrosetta.rosetta.utility.vector1_double, vars2: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::ligand_docking::ga_ligand_dock::GriddedAtomTreeMultifunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner

Bases: pybind11_object

Aligns ligand using defined constraint information

Performs ligand alignments using constraints derived from - reference ligand pose coords or - receptor pharmacophore info Constraint info should be properly provided in order to run this instance

apply(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → None

main apply function

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::apply(class protocols::ligand_docking::ga_ligand_dock::LigandConformer &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::operator=(const class protocols::ligand_docking::ga_ligand_dock::LigandAligner &) –> class protocols::ligand_docking::ga_ligand_dock::LigandAligner &

estimate_nstruct_sample(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, ntotal: int) → int

gets estimate of n-pharmacophore-search considering problem complexity

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::estimate_nstruct_sample(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long) –> unsigned long

points_to_search(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::points_to_search() const –> class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >

prealigned_input(*args, **kwargs)

Overloaded function.

1. prealigned_input(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, setting: bool) -> None

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::prealigned_input(bool) –> void

2. prealigned_input(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner) -> bool

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::prealigned_input() const –> bool

refine_input(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, setting: bool) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::refine_input(bool) –> void

sample_ring_conformers(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner) → bool

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::sample_ring_conformers() const –> bool

select_points(*args, **kwargs)

Overloaded function.

1. select_points(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, pose: pyrosetta.rosetta.core.pose.Pose, ligid: int) -> None

2. select_points(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, pose: pyrosetta.rosetta.core.pose.Pose, ligid: int, skeleton_threshold_const: float) -> None

3. select_points(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, pose: pyrosetta.rosetta.core.pose.Pose, ligid: int, skeleton_threshold_const: float, neighborhood_size: int) -> None

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::select_points(const class core::pose::Pose &, const unsigned long, double, unsigned long) –> void

set_chi_step(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, chi_step_in: int) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_chi_step(unsigned long) –> void

set_pharmacophore_reference(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, pose: pyrosetta.rosetta.core.pose.Pose) → None

setup pharmacophore info from receptor

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_pharmacophore_reference(const class core::pose::Pose &) –> void

set_rot_step(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, rot_step_in: int) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_rot_step(unsigned long) –> void

set_sample_ring_conformers(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, setting: bool) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_sample_ring_conformers(const bool) –> void

set_sf(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, sf_in: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.GridScorer) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_sf(class std::shared_ptr<class protocols::ligand_docking::ga_ligand_dock::GridScorer>) –> void

set_target(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, tgt_in: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ConstraintInfo) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_target(const class protocols::ligand_docking::ga_ligand_dock::ConstraintInfo &) –> void

set_trans_step(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, trans_step_in: int) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_trans_step(unsigned long) –> void

set_use_pharmacophore(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner, setting: bool) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_use_pharmacophore(bool) –> void

use_pharmacophore(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandAligner) → bool

C++: protocols::ligand_docking::ga_ligand_dock::LigandAligner::use_pharmacophore() const –> bool

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::operator=(const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &) –> class protocols::ligand_docking::ga_ligand_dock::LigandConformer &

assign_ligand_trans(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, transv: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::assign_ligand_trans(class numeric::xyzVector<double>) –> void

defined(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → bool

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::defined() const –> bool

density_score(*args, **kwargs)

Overloaded function.

1. density_score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, scorein: float) -> None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::density_score(double) –> void

2. density_score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) -> float

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::density_score() const –> double

dump_pose(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, pdbname: str) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::dump_pose(std::string) const –> void

generation_tag(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → str

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::generation_tag() const –> std::string

get_jumpid(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → int

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_jumpid() const –> unsigned long

get_ligandchi(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ichi: int) → float

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligandchi(unsigned long) const –> double

get_ligandchis(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligandchis() const –> const class utility::vector1<double, class std::allocator<double> > &

get_ligchi_type(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ndx: int) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionType

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligchi_type(unsigned long) const –> const struct protocols::ligand_docking::ga_ligand_dock::TorsionType &

get_ligchi_types(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_TorsionType

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ligchi_types() const –> const class utility::vector1<struct protocols::ligand_docking::ga_ligand_dock::TorsionType, class std::allocator<struct protocols::ligand_docking::ga_ligand_dock::TorsionType> > &

get_protein_chis(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ires: int) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_protein_chis(unsigned long) const –> class utility::vector1<double, class std::allocator<double> >

get_protein_restype(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ires: int) → pyrosetta.rosetta.core.chemical.ResidueType

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_protein_restype(unsigned long) const –> class std::shared_ptr<const class core::chemical::ResidueType>

get_ref_pose(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_ref_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_reference_ft(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::get_reference_ft() const –> const class core::kinematics::FoldTree &

has_density_map(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → bool

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::has_density_map() const –> bool

init_params(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::init_params() –> void

initialize(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, movingscs: pyrosetta.rosetta.utility.vector1_unsigned_long, freeze_ligand_backbone: bool, freeze_ligand: bool) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::initialize(class std::shared_ptr<const class core::pose::Pose>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, bool, bool) –> void

is_ligand_bb_frozen(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → bool

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::is_ligand_bb_frozen() const –> bool

is_ligand_frozen(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → bool

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::is_ligand_frozen() const –> bool

is_ligand_terminal(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → bool

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::is_ligand_terminal() const –> bool

ligand_ids(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_ids() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

ligand_residue(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ires: int) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_residue(unsigned long) const –> class core::conformation::Residue

ligand_rg(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → float

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_rg() const –> double

ligand_typename(*args, **kwargs)

Overloaded function.

1. ligand_typename(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) -> str

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_typename() const –> std::string

2. ligand_typename(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, i: int) -> str

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_typename(unsigned long) const –> std::string

ligand_xyz(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::ligand_xyz() –> const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &

moving_scs(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::moving_scs() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

n_ligandchis(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → int

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::n_ligandchis() const –> unsigned long

neg_Tds(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → float

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::neg_Tds() const –> double

protein_residue(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ires: int) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::protein_residue(unsigned long) const –> class core::conformation::Residue

quat(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.numeric.Quaternion_double_t

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::quat() const –> const class numeric::Quaternion<double>

randomize(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, transmax: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::randomize(double) –> void

receptor(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::receptor() const –> class std::shared_ptr<class core::pose::Pose>

rms(*args, **kwargs)

Overloaded function.

1. rms(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, rmsin: float) -> None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::rms(double) –> void

2. rms(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) -> float

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::rms() const –> double

sample_conformation(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, transmax: float, sampler: protocols::ligand_docking::ga_ligand_dock::TorsionSampler) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::sample_conformation(double, const class std::shared_ptr<const class protocols::ligand_docking::ga_ligand_dock::TorsionSampler> &) –> void

sample_ring_conformers(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → bool

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::sample_ring_conformers() const –> bool

score(*args, **kwargs)

Overloaded function.

1. score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, scorein: float) -> None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::score(double) –> void

2. score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) -> float

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::score() const –> double

set_chiwidth(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, setting: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_chiwidth(double) –> void

set_generation_tag(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, tag: str) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_generation_tag(std::string) –> void

set_has_density_map(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, setting: bool) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_has_density_map(bool) –> void

set_ligandchi(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ichi: int, value: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_ligandchi(unsigned long, double) –> void

set_moving_scs(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_moving_scs(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

set_negTds(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, inval: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_negTds(double) –> void

set_protein_chis(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ires: int, newchis: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_protein_chis(unsigned long, const class utility::vector1<double, class std::allocator<double> > &) –> void

set_protein_restype(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ires: int, restype: pyrosetta.rosetta.core.chemical.ResidueType) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_protein_restype(unsigned long, class std::shared_ptr<const class core::chemical::ResidueType>) –> void

set_rotwidth(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, setting: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_rotwidth(double) –> void

set_rtmutrate(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, setting: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_rtmutrate(double) –> void

set_sample_ring_conformers(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, setting: bool) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_sample_ring_conformers(bool) –> void

set_torsmutrate(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, setting: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_torsmutrate(double) –> void

set_transwidth(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, setting: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::set_transwidth(double) –> void

superimpose_to_ref_pose(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ids: pyrosetta.rosetta.utility.vector1_core_id_AtomID) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::superimpose_to_ref_pose(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &) –> void

to_minipose(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, pose: pyrosetta.rosetta.core.pose.Pose, minilig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_minipose(class std::shared_ptr<class core::pose::Pose>, class protocols::ligand_docking::ga_ligand_dock::LigandConformer &) const –> void

to_pose(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_pose(class std::shared_ptr<class core::pose::Pose>) const –> void

to_string(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → str

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::to_string() const –> std::string

trans(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::trans() const –> const class numeric::xyzVector<double>

update_conf(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(class std::shared_ptr<const class core::pose::Pose>) –> void

update_conf_from_minipose(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf_from_minipose(class std::shared_ptr<const class core::pose::Pose>) –> void

update_ligand_conf(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf(class std::shared_ptr<const class core::pose::Pose>) –> void

update_ligchi_types(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, ligres: pyrosetta.rosetta.core.conformation.Residue) → None

C++: protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligchi_types(const class core::conformation::Residue &) –> void

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner

Bases: pybind11_object

align_pose(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner, template_pose: pyrosetta.rosetta.core.pose.Pose, ligand_pose: pyrosetta.rosetta.core.pose.Pose, pair_indices_map: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, template_idx: int, ligand_idx: int) → None

C++: protocols::ligand_docking::ga_ligand_dock::MCSAligner::align_pose(const class core::pose::Pose &, class core::pose::Pose &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const unsigned long &, const unsigned long &) –> void

apply(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner, lig: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → None

main apply function

C++: protocols::ligand_docking::ga_ligand_dock::MCSAligner::apply(class protocols::ligand_docking::ga_ligand_dock::LigandConformer &) –> void

set_options(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner, options: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions) → None

set MCSAligner options

C++: protocols::ligand_docking::ga_ligand_dock::MCSAligner::set_options(const struct protocols::ligand_docking::ga_ligand_dock::MCSAlignerOptions &) –> void

set_torsion_and_align(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner, template_pose: pyrosetta.rosetta.core.pose.Pose, ligand_pose: pyrosetta.rosetta.core.pose.Pose, pair_indices_map: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long, template_idx: int, ligand_idx: int) → None

C++: protocols::ligand_docking::ga_ligand_dock::MCSAligner::set_torsion_and_align(const class core::pose::Pose &, class core::pose::Pose &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &, const unsigned long &, const unsigned long &) –> void

torsion_in_align(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAligner) → pyrosetta.rosetta.utility.vector1_bool

C++: protocols::ligand_docking::ga_ligand_dock::MCSAligner::torsion_in_align() const –> const class utility::vector1<bool, class std::allocator<bool> > &

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions

Bases: pybind11_object

Aligns ligand using maximum commom substructure (MCS)

Performs ligand alignments using MCS bewteen - reference ligand pose - ligand to dock

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.MCSAlignerOptions

C++: protocols::ligand_docking::ga_ligand_dock::MCSAlignerOptions::operator=(const struct protocols::ligand_docking::ga_ligand_dock::MCSAlignerOptions &) –> struct protocols::ligand_docking::ga_ligand_dock::MCSAlignerOptions &

property perturb_rb

property perturb_rb_rotation

property perturb_rb_translation

property perturb_torsion

property perturb_torsion_rotation

property restype_to_rdmol_options

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OptHMode

Bases: pybind11_object

Members:

OPTH_NONE

OPTH_FULL

OPTH_NO_FLIP_HNQ

OPTH_FLEXIBLE_SIDECHAINS

OPTH_REDEFINE_SIDECHAINS

OPTH_FLEXIBLE_SIDECHAINS = <OptHMode.OPTH_FLEXIBLE_SIDECHAINS: 3>

OPTH_FULL = <OptHMode.OPTH_FULL: 1>

OPTH_NONE = <OptHMode.OPTH_NONE: 0>

OPTH_NO_FLIP_HNQ = <OptHMode.OPTH_NO_FLIP_HNQ: 2>

OPTH_REDEFINE_SIDECHAINS = <OptHMode.OPTH_REDEFINE_SIDECHAINS: 4>

property name

property value

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore

Bases: pybind11_object

helper class to manage multiple outputs

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::operator=(const class protocols::ligand_docking::ga_ligand_dock::OutputStructureStore &) –> class protocols::ligand_docking::ga_ligand_dock::OutputStructureStore &

clear(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore) → None

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::clear() –> void

dH_pop(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, complexscore: float, ligandscore: float, recscore: float, ranking_prerelax: int, ligandname: str) → None

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::dH_pop(class core::pose::Pose &, double &, double &, double &, double &, double &, unsigned long &, std::string &) –> void

dens_clear(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore) → None

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::dens_clear() –> void

dens_has_data(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore) → bool

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::dens_has_data() –> bool

dens_pop(*args, **kwargs)

Overloaded function.

1. dens_pop(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, ligandscore: float, recscore: float, ranking_prerelax: int, ligandname: str, lig_dens: float, native_hbond_ratio: float, hbond_count: float, pocket_cc: float) -> None

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::dens_pop(class core::pose::Pose &, double &, double &, double &, double &, unsigned long &, std::string &, double &, double &, double &, double &) –> void

2. dens_pop(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::dens_pop() –> class std::shared_ptr<class core::pose::Pose>

dens_push(*args, **kwargs)

Overloaded function.

1. dens_push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float) -> None

2. dens_push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float) -> None

3. dens_push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, ligandscore: float) -> None

4. dens_push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, ligandscore: float, recscore: float) -> None

5. dens_push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, ligandscore: float, recscore: float, ranking_prerelax: int) -> None

6. dens_push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, ligandscore: float, recscore: float, ranking_prerelax: int, ligandname: str) -> None

7. dens_push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, ligandscore: float, recscore: float, ranking_prerelax: int, ligandname: str, lig_dens: float) -> None

8. dens_push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, ligandscore: float, recscore: float, ranking_prerelax: int, ligandname: str, lig_dens: float, native_hbond_ratio: float) -> None

9. dens_push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, ligandscore: float, recscore: float, ranking_prerelax: int, ligandname: str, lig_dens: float, native_hbond_ratio: float, hbond_count: float) -> None

10. dens_push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, ligandscore: float, recscore: float, ranking_prerelax: int, ligandname: str, lig_dens: float, native_hbond_ratio: float, hbond_count: float, pocket_cc: float) -> None

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::dens_push(const class core::pose::Pose &, double, double, double, double, unsigned long, std::string, double, double, double, double) –> void

dens_size(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore) → int

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::dens_size() –> unsigned long

has_data(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore) → bool

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::has_data() –> bool

pop(*args, **kwargs)

Overloaded function.

1. pop(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, complexscore: float, ligandscore: float, recscore: float, ranking_prerelax: int, ligandname: str) -> None

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::pop(class core::pose::Pose &, double &, double &, double &, double &, double &, unsigned long &, std::string &) –> void

2. pop(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore) -> pyrosetta.rosetta.core.pose.Pose

3. pop(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, metric: str) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::pop(std::string) –> class std::shared_ptr<class core::pose::Pose>

push(*args, **kwargs)

Overloaded function.

1. push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float) -> None

2. push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float) -> None

3. push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, complexscore: float) -> None

4. push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, complexscore: float, ligandscore: float) -> None

5. push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, complexscore: float, ligandscore: float, recscore: float) -> None

6. push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, complexscore: float, ligandscore: float, recscore: float, ranking_prerelax: int) -> None

7. push(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore, pose: pyrosetta.rosetta.core.pose.Pose, E: float, rms: float, complexscore: float, ligandscore: float, recscore: float, ranking_prerelax: int, ligandname: str) -> None

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::push(const class core::pose::Pose &, double, double, double, double, double, unsigned long, std::string) –> void

size(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.OutputStructureStore) → int

C++: protocols::ligand_docking::ga_ligand_dock::OutputStructureStore::size() –> unsigned long

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore

Bases: pybind11_object

Pharmacophore (aka binding-motif) definition

Stores collection of atom properties and their clustering info

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::operator=(const class protocols::ligand_docking::ga_ligand_dock::Pharmacophore &) –> class protocols::ligand_docking::ga_ligand_dock::Pharmacophore &

atm(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, i: int) → int

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::atm(unsigned long) const –> unsigned long

atms(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::atms() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

com(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::com() const –> const class numeric::xyzVector<double> &

dist(*args, **kwargs)

Overloaded function.

1. dist(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore) -> pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::dist() const –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

2. dist(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, i: int, j: int) -> float

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::dist(unsigned long, unsigned long) const –> double

find_type_matches(*args, **kwargs)

Overloaded function.

1. find_type_matches(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, other: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore) -> float

2. find_type_matches(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, other: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, just_count: bool) -> float

find matches with proper types (e.g. acceptor - donor)

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::find_type_matches(const class protocols::ligand_docking::ga_ligand_dock::Pharmacophore &, const bool) const –> double

has(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, i: int) → bool

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::has(unsigned long) const –> bool

index(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore) → str

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::index() const –> std::string

is_acceptor(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, i: int) → bool

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::is_acceptor(unsigned long) const –> bool

is_close(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, Dcol: pyrosetta.rosetta.utility.vector1_double, dcut: float) → bool

whether j is close to all own members (Dcol == Dmtrx[j])

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::is_close(const class utility::vector1<double, class std::allocator<double> > &, double) const –> bool

is_donor(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, i: int) → bool

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::is_donor(unsigned long) const –> bool

is_polarH(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, i: int) → bool

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::is_polarH(unsigned long) const –> bool

map_index(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::map_index() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

match(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, other: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, map_index: pyrosetta.rosetta.utility.vector1_unsigned_long, unmatch_score: float) → float

find matches with the partner pharmacophore provided

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::match(const class protocols::ligand_docking::ga_ligand_dock::Pharmacophore &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double) const –> double

props(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore) → pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ga_ligand_dock_AtomProperties

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::props() const –> class utility::vector1<class protocols::ligand_docking::ga_ligand_dock::AtomProperties, class std::allocator<class protocols::ligand_docking::ga_ligand_dock::AtomProperties> >

set_map_index(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, map_index: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::set_map_index(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

show(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore) → str

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::show() const –> std::string

size(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore) → int

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::size() const –> unsigned long

update_com(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.Pharmacophore, coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → None

C++: protocols::ligand_docking::ga_ligand_dock::Pharmacophore::update_com(const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PlaceableRotamer

Bases: pybind11_object

property chis

property lkbrinfo

property prob

property prob_accum

property resid

property restype

property rotno

property score

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.PointScoreComparator

Bases: pybind11_object

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy

Bases: pybind11_object

Rotamer data used for packing in GALigandDock

Stores energy information of rotamers to facilitate rotamer packing

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy

C++: protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::operator=(const class protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy &) –> class protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy &

property bonus_wtd_

property cst_wtd_

property elec_dens_wtd_

property fa_atr_wtd_

property fa_elec_wtd_

property fa_rep_

property fa_sol_wtd_

property hbond_wtd_

property lk_ball_wtd_

property oneb_wtd_

property penalty_wtd_

reset(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy) → None

C++: protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::reset() –> void

score(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy, farep_scale: float) → float

C++: protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy::score(double) –> float

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies

Bases: pybind11_object

add_residue(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies, nrots_i: int) → None

C++: protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::add_residue(unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies

C++: protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::operator=(const class protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies &) –> class protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies &

clear(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies) → None

C++: protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::clear() –> void

energy1b(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies, ires: int, irot: int) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy

C++: protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::energy1b(unsigned long, unsigned long) –> class protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy &

energy2b(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies, ires: int, irot: int, jres: int, jrot: int) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy

C++: protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::energy2b(unsigned long, unsigned long, unsigned long, unsigned long) –> class protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy &

energyBG(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies, ires: int, irot: int) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.ReweightableRepEnergy

C++: protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::energyBG(unsigned long, unsigned long) –> class protocols::ligand_docking::ga_ligand_dock::ReweightableRepEnergy &

finalize(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.RotamerPairEnergies) → None

C++: protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::finalize() –> void

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo

Bases: pybind11_object

property E

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfo

C++: protocols::ligand_docking::ga_ligand_dock::StructInfo::operator=(const struct protocols::ligand_docking::ga_ligand_dock::StructInfo &) –> struct protocols::ligand_docking::ga_ligand_dock::StructInfo &

property complexscore

property cst

property dH

property ligandname

property ligandscore

property ranking_prerelax

property recscore

property rms

property str

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoComp

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoComp, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoComp) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoComp

C++: protocols::ligand_docking::ga_ligand_dock::StructInfoComp::operator=(const class protocols::ligand_docking::ga_ligand_dock::StructInfoComp &) –> class protocols::ligand_docking::ga_ligand_dock::StructInfoComp &

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoCompdH

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoCompdH, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoCompdH) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.StructInfoCompdH

C++: protocols::ligand_docking::ga_ligand_dock::StructInfoCompdH::operator=(const class protocols::ligand_docking::ga_ligand_dock::StructInfoCompdH &) –> class protocols::ligand_docking::ga_ligand_dock::StructInfoCompdH &

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams

Bases: pybind11_object

add_mode(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams, A: float, mu: float, sigma: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams::add_mode(double, double, double) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams

C++: protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams::operator=(const class protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams &) –> class protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams &

get_mode_i(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams, i: int, A_out: float, mu_out: float, sigma_out: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams::get_mode_i(unsigned long, double &, double &, double &) const –> void

multiplicity(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams) → int

C++: protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams::multiplicity() const –> unsigned long

n_mode(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams) → int

C++: protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams::n_mode() const –> unsigned long

normalize(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams) → None

C++: protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams::normalize() –> void

sample_mode(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams, A_out: float, mu_out: float, sigma_out: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams::sample_mode(double &, double &, double &) const –> void

set_multiplicity(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams, mult_in: float) → None

C++: protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams::set_multiplicity(double) –> void

set_torsion_type(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams, ttype_in: str) → None

C++: protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams::set_torsion_type(const std::string &) –> void

torsion_type(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams) → str

C++: protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams::torsion_type() const –> std::string

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionSampler

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionSampler, : pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionSampler) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionSampler

C++: protocols::ligand_docking::ga_ligand_dock::TorsionSampler::operator=(const class protocols::ligand_docking::ga_ligand_dock::TorsionSampler &) –> class protocols::ligand_docking::ga_ligand_dock::TorsionSampler &

lookup_tors_distr_params(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionSampler, bn: pyrosetta.rosetta.core.chemical.BondName, br: pyrosetta.rosetta.core.chemical.BondRingness, type1: int, type2: int, type3: int, type4: int) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionDistrParams

C++: protocols::ligand_docking::ga_ligand_dock::TorsionSampler::lookup_tors_distr_params(enum core::chemical::BondName, enum core::chemical::BondRingness, unsigned long, unsigned long, unsigned long, unsigned long) const –> const class protocols::ligand_docking::ga_ligand_dock::TorsionDistrParams &

sample(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionSampler, bn: pyrosetta.rosetta.core.chemical.BondName, br: pyrosetta.rosetta.core.chemical.BondRingness, type1: int, type2: int, type3: int, type4: int) → float

C++: protocols::ligand_docking::ga_ligand_dock::TorsionSampler::sample(enum core::chemical::BondName, enum core::chemical::BondRingness, unsigned long, unsigned long, unsigned long, unsigned long) const –> double

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.TorsionType

Bases: pybind11_object

Gene representation of ligand & flexible sidechains in receptor

Gene is preresented by rigid body (rb_), ligandchis, and receptorchis Also has functions to tranform back and forth to pose object Uses friend functions to perform mutation / crossovers with others within gene representation

property at1

property at2

property at3

property at4

property bn

property br

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.atmInfo

Bases: pybind11_object

property atom

property atomWaters

property atomicCharge

property nAtomWaters

nbr_atom(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.atmInfo) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::ligand_docking::ga_ligand_dock::atmInfo::nbr_atom() –> class numeric::xyzVector<double>

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.compute_nhbonds(pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, resids: pyrosetta.rosetta.utility.vector1_unsigned_long, nhbonds_total: int, nhbonds_max1: int, include_bb: bool, hb_metric: str) → None

C++: protocols::ligand_docking::ga_ligand_dock::compute_nhbonds(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, unsigned long &, unsigned long &, const bool &, const std::string &) –> void

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.constraint_relax(*args, **kwargs)

Overloaded function.

1. constraint_relax(pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, movable_scs: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. constraint_relax(pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, movable_scs: pyrosetta.rosetta.utility.vector1_unsigned_long, maxiter: float) -> None

C++: protocols::ligand_docking::ga_ligand_dock::constraint_relax(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, double) –> void

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.count_neighbors(pose: pyrosetta.rosetta.core.pose.Pose, atomname: str, dcut: float) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ligand_docking::ga_ligand_dock::count_neighbors(const class core::pose::Pose &, const std::string, const double) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.count_neighbors_on_coord(pose: pyrosetta.rosetta.core.pose.Pose, xyz1: pyrosetta.rosetta.numeric.xyzVector_double_t, atomname: str, dcut: float) → int

C++: protocols::ligand_docking::ga_ligand_dock::count_neighbors_on_coord(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const std::string, const double) –> unsigned long

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.crossover(l1: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, l2: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer

C++: protocols::ligand_docking::ga_ligand_dock::crossover(const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &) –> class protocols::ligand_docking::ga_ligand_dock::LigandConformer

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.distance_fast(gene1: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, gene2: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → float

C++: protocols::ligand_docking::ga_ligand_dock::distance_fast(class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, class protocols::ligand_docking::ga_ligand_dock::LigandConformer &) –> double

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.distance_internal(gene1: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, gene2: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → Tuple[float, float]

C++: protocols::ligand_docking::ga_ligand_dock::distance_internal(const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &) –> struct std::pair<double, double>

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.distance_slow(gene1: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer, gene2: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → float

C++: protocols::ligand_docking::ga_ligand_dock::distance_slow(class protocols::ligand_docking::ga_ligand_dock::LigandConformer &, class protocols::ligand_docking::ga_ligand_dock::LigandConformer &) –> double

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.get_atomic_contacting_sidechains(*args, **kwargs)

Overloaded function.

1. get_atomic_contacting_sidechains(pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.utility.vector1_unsigned_long

2. get_atomic_contacting_sidechains(pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, atomic_distance_cut: float) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.get_hbond_score_weighted(sf: pyrosetta.rosetta.core.scoring.ScoreFunction, database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbopt: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, hbt: pyrosetta.rosetta.core.scoring.hbonds.HBEvalTuple, D: pyrosetta.rosetta.numeric.xyzVector_double_t, H: pyrosetta.rosetta.numeric.xyzVector_double_t, A: pyrosetta.rosetta.numeric.xyzVector_double_t, B: pyrosetta.rosetta.numeric.xyzVector_double_t, B_0: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: protocols::ligand_docking::ga_ligand_dock::get_hbond_score_weighted(class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<const class core::scoring::hbonds::HBondDatabase>, const class core::scoring::hbonds::HBondOptions &, const class core::scoring::hbonds::HBEvalTuple &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> double

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.get_ligand_jumpid(pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long) → int

C++: protocols::ligand_docking::ga_ligand_dock::get_ligand_jumpid(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.get_ligand_resids(pose: pyrosetta.rosetta.core.pose.Pose, lig_resids: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::ligand_docking::ga_ligand_dock::get_ligand_resids(const class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbAcc

Bases: pybind11_object

property A

property B

property B_0

property acctype

nbr_atom(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbAcc) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::ligand_docking::ga_ligand_dock::hbAcc::nbr_atom() –> class numeric::xyzVector<double>

class pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbDon

Bases: pybind11_object

property D

property H

property dontype

nbr_atom(self: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbDon) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::ligand_docking::ga_ligand_dock::hbDon::nbr_atom() –> class numeric::xyzVector<double>

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.is_hb_satisfied(sf: pyrosetta.rosetta.core.scoring.ScoreFunction, hb_database: pyrosetta.rosetta.core.scoring.hbonds.HBondDatabase, hbopt: pyrosetta.rosetta.core.scoring.hbonds.HBondOptions, acc: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbAcc, don: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.hbDon, maxHbdis2: float, hb_energy_cutoff: float, metric: str) → bool

C++: protocols::ligand_docking::ga_ligand_dock::is_hb_satisfied(class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<const class core::scoring::hbonds::HBondDatabase>, const class core::scoring::hbonds::HBondOptions &, const struct protocols::ligand_docking::ga_ligand_dock::hbAcc &, const struct protocols::ligand_docking::ga_ligand_dock::hbDon &, const double &, const double &, const std::string &) –> bool

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.make_ligand_only_pose(pose_new: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose, lig_resnos: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::ligand_docking::ga_ligand_dock::make_ligand_only_pose(class std::shared_ptr<class core::pose::Pose>, class std::shared_ptr<const class core::pose::Pose>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.mutate(l: pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer) → pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.LigandConformer

C++: protocols::ligand_docking::ga_ligand_dock::mutate(const class protocols::ligand_docking::ga_ligand_dock::LigandConformer &) –> class protocols::ligand_docking::ga_ligand_dock::LigandConformer

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.perturb_ligand_rb(*args, **kwargs)

Overloaded function.

1. perturb_ligand_rb(pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. perturb_ligand_rb(pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, trans_step: float) -> None

3. perturb_ligand_rb(pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, trans_step: float, rot_step: float) -> None

C++: protocols::ligand_docking::ga_ligand_dock::perturb_ligand_rb(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, double, double) –> void

pyrosetta.rosetta.protocols.ligand_docking.ga_ligand_dock.perturb_ligand_torsions(*args, **kwargs)

Overloaded function.

1. perturb_ligand_torsions(pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, freeze_chi: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. perturb_ligand_torsions(pose: pyrosetta.rosetta.core.pose.Pose, ligids: pyrosetta.rosetta.utility.vector1_unsigned_long, freeze_chi: pyrosetta.rosetta.utility.vector1_unsigned_long, chi_step: float) -> None

C++: protocols::ligand_docking::ga_ligand_dock::perturb_ligand_torsions(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, double) –> void