Namespaces
	bcl

Classes
class	ApplyChemistryMover
	Apply a given Chemistry modifier to the ResidueType at a given position, then replace the ResidueType at that position. More...

class	ApplyChemistryMoverCreator

class	ConformationSelectionToRDMol

class	RDKitMetric
	A SimpleMetric which measures properties calcualted by RDKit on a ligand. More...

class	RDKitMetricCreator

class	RDKitMetricsMover

class	RDKitMetricsMoverCreator

Typedefs
typedef utility::pointer::shared_ptr< ApplyChemistryMover >	ApplyChemistryMoverOP

typedef utility::pointer::shared_ptr< ApplyChemistryMover const >	ApplyChemistryMoverCOP

using	RDKitMetricOP = utility::pointer::shared_ptr< RDKitMetric >

using	RDKitMetricCOP = utility::pointer::shared_ptr< RDKitMetric const >

typedef utility::pointer::shared_ptr< RDKitMetricsMover >	RDKitMetricsMoverOP

typedef utility::pointer::shared_ptr< RDKitMetricsMover const >	RDKitMetricsMoverCOP

Functions
std::ostream &	operator<< (std::ostream &os, ApplyChemistryMover const &mover)
	private methods /// More...

static basic::Tracer	TR ("protocols.drug_design.ConformationSelectionToRDMol")

static basic::Tracer	TR ("protocols.drug_design.RDKitMetricsMover")

void	align_residues (core::conformation::Residue &residue, core::conformation::Residue const &target, core::chemical::IndexIndexMapping const &map)
	Reassign the coordinates of `residue` to best match that of `target` using the provided mapping. More...

void	place_new_restype (core::pose::Pose &pose, core::Size position, core::chemical::ResidueType const &new_restype, core::chemical::IndexIndexMapping const &map, std::string const &method="default")
	Replace the residue at the given position in the pose with the new residue type, using the atom correspondence in the mapping The method used can be specified ("default") being whatever is currently thought of as "best". More...

void	place_new_restype_no_align (core::pose::Pose &pose, core::Size position, core::chemical::ResidueType const &new_restype)
	Replaces the residue at the given position in the pose with the new residue type. Does no alignment - assumes that the internal coordinates of the new restype are properly set. More...

void	place_new_restype_rotamer_align (core::pose::Pose &pose, core::Size position, core::chemical::ResidueType const &new_restype, core::chemical::IndexIndexMapping const &map)
	Replaces the residue at the given position in the pose with the new residue type, using the rotamer with the best alignment of mapped atoms and a fixed rigid body position of the neighbor atom. More...

Typedef Documentation

◆ ApplyChemistryMoverCOP

typedef utility::pointer::shared_ptr< ApplyChemistryMover const > protocols::drug_design::ApplyChemistryMoverCOP

◆ ApplyChemistryMoverOP

typedef utility::pointer::shared_ptr< ApplyChemistryMover > protocols::drug_design::ApplyChemistryMoverOP

◆ RDKitMetricCOP

using protocols::drug_design::RDKitMetricCOP = typedef utility::pointer::shared_ptr< RDKitMetric const >

◆ RDKitMetricOP

using protocols::drug_design::RDKitMetricOP = typedef utility::pointer::shared_ptr< RDKitMetric >

◆ RDKitMetricsMoverCOP

typedef utility::pointer::shared_ptr< RDKitMetricsMover const > protocols::drug_design::RDKitMetricsMoverCOP

◆ RDKitMetricsMoverOP

typedef utility::pointer::shared_ptr< RDKitMetricsMover > protocols::drug_design::RDKitMetricsMoverOP

Function Documentation

◆ align_residues()

void protocols::drug_design::align_residues	(	core::conformation::Residue &	residue,
		core::conformation::Residue const &	target,
		core::chemical::IndexIndexMapping const &	map
	)

Reassign the coordinates of residue to best match that of target using the provided mapping.

References core::pose::center_of_mass(), protocols::splice::coords(), core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_entry(), core::conformation::Residue::natoms(), core::scoring::residue_rmsd_nosuper(), core::scoring::residue_rmsd_super(), core::conformation::Residue::set_xyz(), TR(), and core::conformation::Residue::xyz().

Referenced by place_new_restype_rotamer_align().

◆ operator<<()

std::ostream & protocols::drug_design::operator<<	(	std::ostream &	os,
		ApplyChemistryMover const &	mover
	)

private methods ///

References protocols::drug_design::ApplyChemistryMover::show().

◆ place_new_restype()

void protocols::drug_design::place_new_restype	(	core::pose::Pose &	pose,
		core::Size	position,
		core::chemical::ResidueType const &	new_restype,
		core::chemical::IndexIndexMapping const &	map,
		std::string const &	method_mc
	)

Replace the residue at the given position in the pose with the new residue type, using the atom correspondence in the mapping The method used can be specified ("default") being whatever is currently thought of as "best".

References place_new_restype_no_align(), and place_new_restype_rotamer_align().

Referenced by protocols::drug_design::ApplyChemistryMover::apply().

◆ place_new_restype_no_align()

void protocols::drug_design::place_new_restype_no_align	(	core::pose::Pose &	pose,
		core::Size	position,
		core::chemical::ResidueType const &	new_restype
	)

Replaces the residue at the given position in the pose with the new residue type. Does no alignment - assumes that the internal coordinates of the new restype are properly set.

References core::pose::Pose::replace_residue().

Referenced by place_new_restype().

◆ place_new_restype_rotamer_align()

void protocols::drug_design::place_new_restype_rotamer_align	(	core::pose::Pose &	pose,
		core::Size	position,
		core::chemical::ResidueType const &	new_restype,
		core::chemical::IndexIndexMapping const &	map
	)

Replaces the residue at the given position in the pose with the new residue type, using the rotamer with the best alignment of mapped atoms and a fixed rigid body position of the neighbor atom.

References protocols::cluster::calibur::aa, core::pose::Pose::add_constraints(), align_residues(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::pack::task::TaskFactory::create_packer_task(), core::chemical::AtomRefMapping< FromRef, ToRef >::empty(), core::sequence::end, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::fa_intra_rep_xover4, core::scoring::fa_rep, core::pose::Pose::fold_tree(), core::chemical::ResidueType::get_self_ptr(), core::chemical::AtomRefMapping< FromRef, ToRef >::invalid_entry(), core::conformation::Residue::natoms(), core::chemical::ResidueType::nchi(), core::pose::Pose::remove_constraints(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::scoring::residue_rmsd_super(), core::kinematics::FoldTree::root(), core::scoring::ScoreFunction::set_weight(), core::pose::Pose::total_residue(), TR(), and core::conformation::Residue::xyz().

Referenced by place_new_restype().

◆ TR() [1/2]

static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.ConformationSelectionToRDMol" )

static

Referenced by align_residues(), protocols::drug_design::RDKitMetric::calculate(), protocols::drug_design::ConformationSelectionToRDMol::Mol(), place_new_restype_rotamer_align(), and protocols::drug_design::RDKitMetric::rdkit_metric().

◆ TR() [2/2]

static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.RDKitMetricsMover" )