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protocols::drug_design Namespace Reference

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  AtomExistsFilter
 
class  AtomExistsFilterCreator
 
class  ChemicalReaction
 
class  ConformationSelectionToRDMol
 
class  DrugDesignMover
 
class  DrugDesignMoverCreator
 
class  DrugPolishMover
 
class  DrugPolishMoverCreator
 
class  HeteroHeteroBondFilter
 
class  HeteroHeteroBondFilterCreator
 
class  LigandLocationFilter
 
class  LigandLocationFilterCreator
 
class  NChiFilter
 
class  NChiFilterCreator
 
class  RandomFragmentLigand
 
class  RandomFragmentLigandCreator
 
class  RDKitMetric
 A SimpleMetric which measures properties calcualted by RDKit on a ligand. More...
 
class  RDKitMetricCreator
 
class  RDKitMetricFilter
 
class  RDKitMetricFilterCreator
 
class  RDKitMetricsMover
 
class  RDKitMetricsMoverCreator
 
class  ReactionBasedAnalogSampler
 
class  ReactionBasedAnalogSamplerCreator
 
class  ReactionChemistry
 
class  ReactionFragment
 
class  ReactionFragmentCreator
 
class  ReactionGrow
 
class  ReactionGrowCreator
 
class  ReactionMultiTransform
 
class  ReactionMultiTransformCreator
 
class  SAScoreFilter
 
class  SAScoreData
 
class  SAScoreFilterCreator
 
class  SubstituentReplace
 
class  SubstituentReplaceCreator
 
class  AtomSubstitution
 A class representing a substitution of an atom from an original molecule through a pair of matched templates to a substituted molecule. Intended to be used through MoleculeSubstitution. More...
 
class  MoleculeSubstitution
 A class representing a substitution of a molecule from an original molecule through a pair of matched templates to a substituted molecule. More...
 
class  SubstructureReplace
 
class  SubstructureReplaceCreator
 

Typedefs

typedef utility::pointer::shared_ptr< ApplyChemistryMover > ApplyChemistryMoverOP
 
typedef utility::pointer::shared_ptr< ApplyChemistryMover const > ApplyChemistryMoverCOP
 
typedef utility::pointer::shared_ptr< ChemicalReaction > ChemicalReactionOP
 
typedef utility::pointer::shared_ptr< ChemicalReaction const > ChemicalReactionCOP
 
typedef utility::pointer::shared_ptr< DrugDesignMover > DrugDesignMoverOP
 
typedef utility::pointer::shared_ptr< DrugDesignMover const > DrugDesignMoverCOP
 
typedef utility::pointer::shared_ptr< DrugPolishMover > DrugPolishMoverOP
 
typedef utility::pointer::shared_ptr< DrugPolishMover const > DrugPolishMoverCOP
 
typedef utility::pointer::shared_ptr< RandomFragmentLigand > RandomFragmentLigandOP
 
typedef utility::pointer::shared_ptr< RandomFragmentLigand const > RandomFragmentLigandCOP
 
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
 
typedef utility::pointer::shared_ptr< ReactionBasedAnalogSampler > ReactionBasedAnalogSamplerOP
 
typedef utility::pointer::shared_ptr< ReactionBasedAnalogSampler const > ReactionBasedAnalogSamplerCOP
 
typedef utility::pointer::shared_ptr< ReactionFragment > ReactionFragmentOP
 
typedef utility::pointer::shared_ptr< ReactionFragment const > ReactionFragmentCOP
 
typedef utility::pointer::shared_ptr< ReactionGrow > ReactionGrowOP
 
typedef utility::pointer::shared_ptr< ReactionGrow const > ReactionGrowCOP
 
typedef utility::pointer::shared_ptr< ReactionMultiTransform > ReactionMultiTransformOP
 
typedef utility::pointer::shared_ptr< ReactionMultiTransform const > ReactionMultiTransformCOP
 
typedef utility::pointer::shared_ptr< SubstituentReplace > SubstituentReplaceOP
 
typedef utility::pointer::shared_ptr< SubstituentReplace const > SubstituentReplaceCOP
 
typedef utility::pointer::shared_ptr< AtomSubstitution > AtomSubstitutionOP
 
typedef utility::pointer::shared_ptr< AtomSubstitution const > AtomSubstitutionCOP
 
typedef utility::pointer::shared_ptr< MoleculeSubstitution > MoleculeSubstitutionOP
 
typedef utility::pointer::shared_ptr< MoleculeSubstitution const > MoleculeSubstitutionCOP
 
typedef utility::pointer::shared_ptr< SubstructureReplace > SubstructureReplaceOP
 
typedef utility::pointer::shared_ptr< SubstructureReplace const > SubstructureReplaceCOP
 

Enumerations

enum  MoleculeSelection { OriginalMol , TemplateMol , ReplaceMol , NewMol }
 

Functions

std::ostream & operator<< (std::ostream &os, ApplyChemistryMover const &mover)
 private methods /// More...
 
static basic::Tracer TR ("protocols.drug_design.AtomExistsFilter")
 
static basic::Tracer TR ("protocols.drug_design.ChemicalReaction")
 
static basic::Tracer TR ("protocols.drug_design.ConformationSelectionToRDMol")
 
static basic::Tracer TR ("protocols.drug_design.DrugDesignMover")
 
void replace_residue_type_with_mask (core::pose::Pose &pose, core::Size seqpos, core::chemical::ResidueType const &new_rsd_type, utility::vector1< bool > const &mask)
 Replace residues using only those atoms which are true in mask. More...
 
static basic::Tracer TR ("protocols.drug_design.DrugPolishMover")
 
static basic::Tracer TR ("protocols.drug_design.HeteroHeteroBondFilter")
 
static basic::Tracer TR ("protocols.drug_design.LigandLocationFilter")
 
static basic::Tracer TR ("protocols.drug_design.NChiFilter")
 
static basic::Tracer TR ("protocols.drug_design.RandomFragmentLigand")
 
static basic::Tracer TR ("protocols.drug_design.RDKitMetricFilter")
 
static basic::Tracer TR ("protocols.drug_design.RDKitMetricsMover")
 
static basic::Tracer TR ("protocols.drug_design.ReactionBasedAnalogSampler")
 
static basic::Tracer TR ("protocols.drug_design.ReactionChemistry")
 
static basic::Tracer TR ("protocols.drug_design.ReactionFragment")
 
bool invalid_products (::RDKit::MOL_SPTR_VECT const &products, ::RDKit::ChemicalReactionCOP rxn)
 Check if the produced products are valid given the reaction. (The ability to run the reaction comes from matching the reacting templates the product templates may have additional restrictions which could invalidate a product.) More...
 
static basic::Tracer TR ("protocols.drug_design.ReactionGrow")
 
static basic::Tracer TR ("protocols.drug_design.ReactionMultiTransform")
 
static basic::Tracer TR ("protocols.drug_design.SAScoreFilter")
 
static basic::Tracer TR ("protocols.drug_design.SubstituentReplace")
 
static basic::Tracer TR ("protocols.drug_design.substructure_support")
 
::RDKit::Bond::BondType get_first_bondtype (::RDKit::ROMol const &mol, ::RDKit::Atom const *atom)
 Get the RDKit bond type of the first bond to atom. More...
 
::RDKit::Bond::BondType get_first_bondtype (::RDKit::ROMol const &mol, unsigned int idx)
 Get the RDKit bond type of the first bond to the given atom. More...
 
::RDKit::Bond const & get_first_bond (::RDKit::ROMol const &mol, unsigned int idx)
 Get the RDKit bond of the first bond to the given atom. More...
 
unsigned int get_bonded_atom (::RDKit::ROMol const &mol, unsigned int idx)
 Get the atom number of the atom bonded to idx (it's the first atom) More...
 
bool is_dummy (::RDKit::ROMol const &mol, unsigned int idx)
 Is the given atom a dummy (atom number 0)? More...
 
void find_dummies (::RDKit::ROMol const &mol, utility::vector1< unsigned int > &dummy_list)
 Populate the list with the index of all the dummies in the molecule. More...
 
bool bond_is_in_ring (::RDKit::ROMol const &rdmol, unsigned int atm1, unsigned int atm2)
 Is the bond between the atoms in a ring? More...
 
std::map< unsigned int, unsigned int > convert_matchvect_to_map (::RDKit::MatchVectType const &pairings)
 Convert the RDKit MatcVect into a map (real molecule index to query index) More...
 
MoleculeSubstitutionOP pick_template (::RDKit::ROMolOP rdmol, utility::vector1< ::RDKit::ROMolOP > &templates, bool dummy_only)
 Pick a template to use, return it and the atom pairing of template->rdmol. More...
 
MoleculeSubstitutionOP test_replacement (MoleculeSubstitutionOP current_molsub, ::RDKit::ROMolOP possible_replacement, core::Real dist_threshold)
 Is the replacement molecule template compatible with the molecule and template in template_frag_infos If the replacement is appropriate, the return value will be a new MoleculeSubstitution which has the appropriate replacement entries set. If the replacement doesn't work, it will return a null pointer. More...
 
MoleculeSubstitutionOP pick_replacement (MoleculeSubstitutionOP current_molsub, utility::vector1< ::RDKit::ROMolOP > &possible_replacements, core::Real distance_threshold, std::string weighting_property="")
 Given the molecule and template info in template_frag_infos, pick a possible replacement molecule from possible_replacements. More...
 
void copy_attached_atoms (MoleculeSubstitution &molsub, MoleculeSelection source, ::RDGeom::Transform3D const &transform, unsigned int start, unsigned int skip)
 Copies all atom and bonds attached to start in the source molecule to the new molecule. If skip is a valid index, it will be supressed in the source molecule, and will not be counted for copying or for attachment purposes The transform is applied to the coordinates of the atom to get the coordinates of the new atom. More...
 
static basic::Tracer TR ("protocols.drug_design.SubstructureReplace")
 
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

◆ AtomSubstitutionCOP

typedef utility::pointer::shared_ptr< AtomSubstitution const > protocols::drug_design::AtomSubstitutionCOP

◆ AtomSubstitutionOP

typedef utility::pointer::shared_ptr< AtomSubstitution > protocols::drug_design::AtomSubstitutionOP

◆ ChemicalReactionCOP

typedef utility::pointer::shared_ptr< ChemicalReaction const > protocols::drug_design::ChemicalReactionCOP

◆ ChemicalReactionOP

typedef utility::pointer::shared_ptr< ChemicalReaction > protocols::drug_design::ChemicalReactionOP

◆ DrugDesignMoverCOP

typedef utility::pointer::shared_ptr< DrugDesignMover const > protocols::drug_design::DrugDesignMoverCOP

◆ DrugDesignMoverOP

typedef utility::pointer::shared_ptr< DrugDesignMover > protocols::drug_design::DrugDesignMoverOP

◆ DrugPolishMoverCOP

typedef utility::pointer::shared_ptr< DrugPolishMover const > protocols::drug_design::DrugPolishMoverCOP

◆ DrugPolishMoverOP

typedef utility::pointer::shared_ptr< DrugPolishMover > protocols::drug_design::DrugPolishMoverOP

◆ MoleculeSubstitutionCOP

typedef utility::pointer::shared_ptr< MoleculeSubstitution const > protocols::drug_design::MoleculeSubstitutionCOP

◆ MoleculeSubstitutionOP

typedef utility::pointer::shared_ptr< MoleculeSubstitution > protocols::drug_design::MoleculeSubstitutionOP

◆ RandomFragmentLigandCOP

typedef utility::pointer::shared_ptr< RandomFragmentLigand const > protocols::drug_design::RandomFragmentLigandCOP

◆ RandomFragmentLigandOP

typedef utility::pointer::shared_ptr< RandomFragmentLigand > protocols::drug_design::RandomFragmentLigandOP

◆ 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

◆ ReactionBasedAnalogSamplerCOP

typedef utility::pointer::shared_ptr< ReactionBasedAnalogSampler const > protocols::drug_design::ReactionBasedAnalogSamplerCOP

◆ ReactionBasedAnalogSamplerOP

typedef utility::pointer::shared_ptr< ReactionBasedAnalogSampler > protocols::drug_design::ReactionBasedAnalogSamplerOP

◆ ReactionFragmentCOP

typedef utility::pointer::shared_ptr< ReactionFragment const > protocols::drug_design::ReactionFragmentCOP

◆ ReactionFragmentOP

typedef utility::pointer::shared_ptr< ReactionFragment > protocols::drug_design::ReactionFragmentOP

◆ ReactionGrowCOP

typedef utility::pointer::shared_ptr< ReactionGrow const > protocols::drug_design::ReactionGrowCOP

◆ ReactionGrowOP

typedef utility::pointer::shared_ptr< ReactionGrow > protocols::drug_design::ReactionGrowOP

◆ ReactionMultiTransformCOP

typedef utility::pointer::shared_ptr< ReactionMultiTransform const > protocols::drug_design::ReactionMultiTransformCOP

◆ ReactionMultiTransformOP

typedef utility::pointer::shared_ptr< ReactionMultiTransform > protocols::drug_design::ReactionMultiTransformOP

◆ SubstituentReplaceCOP

typedef utility::pointer::shared_ptr< SubstituentReplace const > protocols::drug_design::SubstituentReplaceCOP

◆ SubstituentReplaceOP

typedef utility::pointer::shared_ptr< SubstituentReplace > protocols::drug_design::SubstituentReplaceOP

◆ SubstructureReplaceCOP

typedef utility::pointer::shared_ptr< SubstructureReplace const > protocols::drug_design::SubstructureReplaceCOP

◆ SubstructureReplaceOP

typedef utility::pointer::shared_ptr< SubstructureReplace > protocols::drug_design::SubstructureReplaceOP

Enumeration Type Documentation

◆ MoleculeSelection

enum protocols::drug_design::MoleculeSelection
Enumerator
OriginalMol 
TemplateMol 
ReplaceMol 
NewMol 

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().

◆ bond_is_in_ring()

bool protocols::drug_design::bond_is_in_ring ( ::RDKit::ROMol const &  rdmol,
unsigned int  atm1,
unsigned int  atm2 
)

Is the bond between the atoms in a ring?

Referenced by protocols::drug_design::SubstituentReplace::pick_replacement().

◆ convert_matchvect_to_map()

std::map< unsigned int, unsigned int > protocols::drug_design::convert_matchvect_to_map ( ::RDKit::MatchVectType const &  pairings)

Convert the RDKit MatcVect into a map (real molecule index to query index)

Referenced by protocols::drug_design::SubstituentReplace::pick_replacement(), and pick_template().

◆ copy_attached_atoms()

void protocols::drug_design::copy_attached_atoms ( MoleculeSubstitution &  molsub,
MoleculeSelection  source,
::RDGeom::Transform3D const &  transform,
unsigned int  start,
unsigned int  skip 
)

Copies all atom and bonds attached to start in the source molecule to the new molecule. If skip is a valid index, it will be supressed in the source molecule, and will not be counted for copying or for attachment purposes The transform is applied to the coordinates of the atom to get the coordinates of the new atom.

References protocols::drug_design::MoleculeSubstitution::get_romol(), protocols::drug_design::AtomSubstitution::invalid_index, protocols::drug_design::AtomSubstitution::ndx(), protocols::drug_design::MoleculeSubstitution::newmol(), protocols::drug_design::AtomSubstitution::set_ndx(), protocols::loops::start, and protocols::drug_design::MoleculeSubstitution::substitution_for_idx().

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

◆ find_dummies()

void protocols::drug_design::find_dummies ( ::RDKit::ROMol const &  mol,
utility::vector1< unsigned int > &  dummy_list 
)

Populate the list with the index of all the dummies in the molecule.

Existing contents will be cleared.

References is_dummy().

Referenced by protocols::drug_design::MoleculeSubstitution::add_replacement(), protocols::drug_design::MoleculeSubstitution::add_template(), protocols::drug_design::SubstructureReplace::substructure_database(), protocols::drug_design::SubstituentReplace::template_database(), and test_replacement().

◆ get_bonded_atom()

unsigned int protocols::drug_design::get_bonded_atom ( ::RDKit::ROMol const &  mol,
unsigned int  idx 
)

Get the atom number of the atom bonded to idx (it's the first atom)

References get_first_bond().

Referenced by protocols::drug_design::SubstituentReplace::apply(), protocols::drug_design::SubstructureReplace::apply(), and protocols::drug_design::SubstituentReplace::pick_replacement().

◆ get_first_bond()

RDKit::Bond const & protocols::drug_design::get_first_bond ( ::RDKit::ROMol const &  mol,
unsigned int  idx 
)

Get the RDKit bond of the first bond to the given atom.

Referenced by get_bonded_atom().

◆ get_first_bondtype() [1/2]

RDKit::Bond::BondType protocols::drug_design::get_first_bondtype ( ::RDKit::ROMol const &  mol,
::RDKit::Atom const *  atom 
)

Get the RDKit bond type of the first bond to atom.

Referenced by protocols::drug_design::SubstructureReplace::apply(), get_first_bondtype(), and test_replacement().

◆ get_first_bondtype() [2/2]

RDKit::Bond::BondType protocols::drug_design::get_first_bondtype ( ::RDKit::ROMol const &  mol,
unsigned int  idx 
)

Get the RDKit bond type of the first bond to the given atom.

References get_first_bondtype().

◆ invalid_products()

bool protocols::drug_design::invalid_products ( ::RDKit::MOL_SPTR_VECT const &  products,
::RDKit::ChemicalReactionCOP  rxn 
)

Check if the produced products are valid given the reaction. (The ability to run the reaction comes from matching the reacting templates the product templates may have additional restrictions which could invalidate a product.)

References TR().

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

◆ is_dummy()

bool protocols::drug_design::is_dummy ( ::RDKit::ROMol const &  mol,
unsigned int  idx 
)

Is the given atom a dummy (atom number 0)?

Referenced by find_dummies(), protocols::drug_design::MoleculeSubstitution::rdx_is_dummy(), and protocols::drug_design::MoleculeSubstitution::tdx_is_dummy().

◆ operator<<()

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

private methods ///

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

◆ pick_replacement()

MoleculeSubstitutionOP protocols::drug_design::pick_replacement ( MoleculeSubstitutionOP  current_molsub,
utility::vector1< ::RDKit::ROMolOP > &  possible_replacements,
core::Real  distance_threshold,
std::string  weighting_property = "" 
)

Given the molecule and template info in template_frag_infos, pick a possible replacement molecule from possible_replacements.

current_molsub should have the original and template molecules set. If multiple replacements are possible, one will be picked randomly, based on the value of weighting_property in the replacement ROMol properties

References test_replacement(), and TR().

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

◆ pick_template()

MoleculeSubstitutionOP protocols::drug_design::pick_template ( ::RDKit::ROMolOP  rdmol,
utility::vector1< ::RDKit::ROMolOP > &  templates,
bool  dummy_only 
)

Pick a template to use, return it and the atom pairing of template->rdmol.

References convert_matchvect_to_map(), TR(), and core::pack::tt().

Referenced by protocols::drug_design::SubstituentReplace::apply(), and protocols::drug_design::SubstructureReplace::apply().

◆ 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(), and protocols::drug_design::DrugDesignMover::emplace_residue_type().

◆ 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().

◆ replace_residue_type_with_mask()

void protocols::drug_design::replace_residue_type_with_mask ( core::pose::Pose &  pose,
core::Size  seqpos,
core::chemical::ResidueType const &  new_rsd_type,
utility::vector1< bool > const &  mask 
)

Replace residues using only those atoms which are true in mask.

References core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::conformation::Residue::chain(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::conformation::Residue::fill_missing_atoms(), core::conformation::Residue::has(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::conformation::Residue::seqpos(), TR(), and core::conformation::Atom::xyz().

◆ test_replacement()

MoleculeSubstitutionOP protocols::drug_design::test_replacement ( MoleculeSubstitutionOP  current_molsub,
::RDKit::ROMolOP  possible_replacement,
core::Real  dist_threshold 
)

Is the replacement molecule template compatible with the molecule and template in template_frag_infos If the replacement is appropriate, the return value will be a new MoleculeSubstitution which has the appropriate replacement entries set. If the replacement doesn't work, it will return a null pointer.

current_molsub should have the original and template molecules set.

References find_dummies(), get_first_bondtype(), and protocols::drug_design::AtomSubstitution::invalid_index.

Referenced by pick_replacement().

◆ TR() [1/20]

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

Referenced by protocols::drug_design::ReactionChemistry::add_reaction(), protocols::drug_design::ReactionFragment::add_reaction(), protocols::drug_design::ReactionGrow::add_reaction(), protocols::drug_design::ReactionMultiTransform::add_reaction(), align_residues(), protocols::drug_design::RandomFragmentLigand::apply(), protocols::drug_design::ReactionBasedAnalogSampler::apply(), protocols::drug_design::ReactionFragment::apply(), protocols::drug_design::ReactionGrow::apply(), protocols::drug_design::ReactionMultiTransform::apply(), protocols::drug_design::SubstituentReplace::apply(), protocols::drug_design::SubstructureReplace::apply(), protocols::drug_design::DrugDesignMover::apply(), protocols::drug_design::DrugPolishMover::apply(), protocols::drug_design::AtomExistsFilter::apply(), protocols::drug_design::HeteroHeteroBondFilter::apply(), protocols::drug_design::LigandLocationFilter::apply(), protocols::drug_design::NChiFilter::apply(), protocols::drug_design::RDKitMetricFilter::apply(), protocols::drug_design::RDKitMetric::calculate(), protocols::drug_design::ChemicalReaction::ChemicalReaction(), protocols::drug_design::ReactionChemistry::cleanup_product(), protocols::drug_design::AtomExistsFilter::compute(), protocols::drug_design::HeteroHeteroBondFilter::compute(), protocols::drug_design::NChiFilter::compute(), protocols::drug_design::RDKitMetricFilter::compute(), protocols::drug_design::SAScoreFilter::compute(), protocols::drug_design::DrugDesignMover::emplace_residue_type(), protocols::drug_design::DrugDesignMover::find_design_position(), protocols::drug_design::ReactionBasedAnalogSampler::find_O3A_mapping(), protocols::drug_design::ReactionGrow::fragment_database(), invalid_products(), protocols::drug_design::ReactionBasedAnalogSampler::load_all_reagents(), protocols::drug_design::SAScoreData::load_data_from_file(), protocols::drug_design::ChemicalReaction::load_file(), protocols::drug_design::ReactionBasedAnalogSampler::load_reactions(), protocols::drug_design::ChemicalReaction::load_reagents(), protocols::drug_design::RDKitMetricFilter::metric(), protocols::drug_design::ConformationSelectionToRDMol::Mol(), protocols::drug_design::AtomExistsFilter::parse_my_tag(), protocols::drug_design::HeteroHeteroBondFilter::parse_my_tag(), protocols::drug_design::NChiFilter::parse_my_tag(), protocols::drug_design::RDKitMetricFilter::parse_my_tag(), protocols::drug_design::SAScoreFilter::parse_my_tag(), protocols::drug_design::ReactionBasedAnalogSampler::parse_my_tag(), protocols::drug_design::SubstituentReplace::parse_my_tag(), pick_replacement(), protocols::drug_design::SubstituentReplace::pick_replacement(), pick_template(), place_new_restype_rotamer_align(), protocols::drug_design::DrugDesignMover::post_process_restype(), protocols::drug_design::DrugDesignMover::pre_process_restype(), protocols::drug_design::ReactionGrow::prefilter_fragments(), protocols::drug_design::ReactionChemistry::prefilter_reactions(), protocols::drug_design::RDKitMetric::rdkit_metric(), protocols::drug_design::ReactionChemistry::reaction_file(), protocols::drug_design::ChemicalReaction::reaction_result(), protocols::drug_design::ChemicalReaction::reagent(), replace_residue_type_with_mask(), protocols::drug_design::SAScoreFilter::report(), protocols::drug_design::ReactionBasedAnalogSampler::run_reaction(), protocols::drug_design::ReactionBasedAnalogSampler::sample(), protocols::drug_design::ReactionBasedAnalogSampler::sample_candidate(), protocols::drug_design::ReactionBasedAnalogSampler::sample_fragment(), protocols::drug_design::SubstituentReplace::substituents_database(), protocols::drug_design::SubstructureReplace::substructure_database(), and protocols::drug_design::SubstituentReplace::template_database().

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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.ChemicalReaction"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.ConformationSelectionToRDMol"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.DrugDesignMover"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.DrugPolishMover"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.HeteroHeteroBondFilter"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.LigandLocationFilter"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.NChiFilter"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.RandomFragmentLigand"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.RDKitMetricFilter"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.RDKitMetricsMover"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.ReactionBasedAnalogSampler"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.ReactionChemistry"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.ReactionFragment"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.ReactionGrow"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.ReactionMultiTransform"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.SAScoreFilter"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.SubstituentReplace"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.substructure_support"  )
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static basic::Tracer protocols::drug_design::TR ( "protocols.drug_design.SubstructureReplace"  )
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