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protocols::ligand_docking::ga_ligand_dock::ConstraintInfo Class Reference

Constraint information about AtomProperties and/or Pharmacophores. More...

#include <LigandAligner.hh>

Public Member Functions

 ConstraintInfo ()
 
 ConstraintInfo (core::conformation::Residue const &lig, bool use_pharmacophore, bool report_phore_info=false)
 
 ConstraintInfo (core::pose::Pose const &pose, GridScorerOP gridscore, bool const simple=false)
 
void init_from_ligand (core::conformation::Residue const &mylig)
 use a (non-identical) target ligand (for reference ligand matching) More...
 
void init_from_ligand_pharmacophore (core::conformation::Residue const &mylig, bool report_phore_info)
 defines pharmacophore partners in ligand (for pharmacophore matching) More...
 
void init_from_receptor (core::pose::Pose const &pose, GridScorerOP gridscore, bool const simple)
 
core::Size natoms () const
 
numeric::xyzVector< core::Real >
const & 
coord (core::Size i) const
 
AtomProperties const & properties (core::Size i) const
 
core::id::AtomID const & atomid (core::Size i) const
 
core::Real limit ()
 
core::Real weight ()
 
core::Real polar_scale ()
 
bool pharmacophores_defined () const
 
utility::vector1
< Pharmacophore > const & 
phores () const
 
core::Size n_phore_match () const
 
void select_phore_match (core::Size const run_index)
 selects a phore_match and updates current_phore_match_ More...
 
void align_to_current_phore_match (core::pose::Pose &pose, ConstraintInfo const &recinfo, core::Size const ligid, utility::vector1< std::pair< core::Size, core::Size > > &marked_pairs, utility::vector1< core::Size > &SrcPriorIDs, utility::vector1< core::Size > &TgtPriorIDs)
 try aligning to the phore defined by current_phore_match_ (defined by select_phore_match) More...
 
void map_phores (utility::vector1< Pharmacophore > const &receptor_phores, bool const update, core::Size const nmax=100)
 matches ligand phores (==own) to provided receptor phores and stores at phore_match_ More...
 

Private Member Functions

void set_default ()
 
void define_active_virtual_sites (core::pose::Pose const &pose, GridScorerOP gridscore, utility::vector1< std::pair< core::Real, core::Size > > &Vdonor_sort, utility::vector1< std::pair< core::Real, core::Size > > &Vacceptor_sort, core::Size const nneigh_cut_for_exposed_sc, core::Size const nneigh_cut_for_exposed_bb, bool const report=false)
 findes all virtual sites (for h-bonding candidates) in receptor More...
 
void append_metal_vsites (core::pose::Pose const &pose, core::Size const &ires, utility::vector1< std::pair< core::Real, core::Size > > &Vacceptor_sort, bool report=false)
 
void build_Dmtrx ()
 
void define_all_ligand_phores (core::Size const minsize, bool report_phore_info)
 defines all ligand phores More...
 
bool phore_overlaps_with_existing (Pharmacophore const &phore_i, core::Size &jphore) const
 
void define_receptor_phores (utility::vector1< std::pair< core::Real, core::Size > > &Vdonor_sort, utility::vector1< std::pair< core::Real, core::Size > > &Vacceptor_sort, core::Size const nmin=10, bool report_phore_info=false)
 defines receptor phores More...
 
void update_ligand_coord (core::conformation::Residue const &ligand)
 

Private Attributes

utility::vector1
< core::id::AtomID
atmids_
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
coords_
 
utility::vector1< AtomPropertiesproperties_
 
core::Real limit_
 
core::Real weight_
 
core::Real polar_scale_
 
bool is_ligand_
 
core::Real phore_dcut_
 
core::Size n_match_per_ligand_motif_
 
core::Size NNEIGH_CUT_FOR_EXPOSED_SC
 
core::Size NNEIGH_CUT_FOR_EXPOSED_BB
 
core::Size RECEPTOR_PHORE_MIN
 
core::Size RECEPTOR_PHORE_MAX
 
utility::vector1
< utility::vector1< core::Real > > 
Dmtrx_
 
utility::vector1< Pharmacophorephores_
 
utility::vector1< std::pair
< core::Size, Pharmacophore > > 
phore_match_
 
std::pair< core::Size,
Pharmacophore
current_phore_match_
 
bool debug_
 

Detailed Description

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:

Constructor & Destructor Documentation

protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::ConstraintInfo ( )
inline
protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::ConstraintInfo ( core::conformation::Residue const &  lig,
bool  use_pharmacophore,
bool  report_phore_info = false 
)
inline
protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::ConstraintInfo ( core::pose::Pose const &  pose,
GridScorerOP  gridscore,
bool const  simple = false 
)
inline

Member Function Documentation

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::align_to_current_phore_match ( core::pose::Pose pose,
ConstraintInfo const &  recinfo,
core::Size const  ligid,
utility::vector1< std::pair< core::Size, core::Size > > &  marked_pairs,
utility::vector1< core::Size > &  SrcPriorIDs,
utility::vector1< core::Size > &  TgtPriorIDs 
)
void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::append_metal_vsites ( core::pose::Pose const &  pose,
core::Size const &  ires,
utility::vector1< std::pair< core::Real, core::Size > > &  Vacceptor_sort,
bool  report = false 
)
private
core::id::AtomID const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::atomid ( core::Size  i) const
inline

Referenced by update_ligand_coord().

void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::build_Dmtrx ( )
private
numeric::xyzVector< core::Real > const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::coord ( core::Size  i) const
inline
void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites ( core::pose::Pose const &  pose,
GridScorerOP  gridscore,
utility::vector1< std::pair< core::Real, core::Size > > &  Vdonor_sort,
utility::vector1< std::pair< core::Real, core::Size > > &  Vacceptor_sort,
core::Size const  nneigh_cut_for_exposed_sc,
core::Size const  nneigh_cut_for_exposed_bb,
bool const  report = false 
)
private
void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_all_ligand_phores ( core::Size const  minsize,
bool  report_phore_info 
)
private
void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_receptor_phores ( utility::vector1< std::pair< core::Real, core::Size > > &  Vdonor_sort,
utility::vector1< std::pair< core::Real, core::Size > > &  Vacceptor_sort,
core::Size const  nmin = 10,
bool  report_phore_info = false 
)
private
void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand ( core::conformation::Residue const &  mylig)
void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_ligand_pharmacophore ( core::conformation::Residue const &  mylig,
bool  report_phore_info 
)
void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::init_from_receptor ( core::pose::Pose const &  pose,
GridScorerOP  gridscore,
bool const  simple 
)
core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::limit ( )
inline
void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::map_phores ( utility::vector1< Pharmacophore > const &  receptor_phores,
bool const  update,
core::Size const  nmax = 100 
)
core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::n_phore_match ( ) const
inline
core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::natoms ( ) const
inline
bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::pharmacophores_defined ( ) const
inline
bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_overlaps_with_existing ( Pharmacophore const &  phore_i,
core::Size jphore 
) const
private
utility::vector1< Pharmacophore > const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phores ( ) const
inline
core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::polar_scale ( )
inline
AtomProperties const& protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::properties ( core::Size  i) const
inline
void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::select_phore_match ( core::Size const  run_index)
void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::set_default ( )
private
void protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::update_ligand_coord ( core::conformation::Residue const &  ligand)
private
core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::weight ( )
inline

Member Data Documentation

utility::vector1< core::id::AtomID > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::atmids_
private
utility::vector1< numeric::xyzVector< core::Real > > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::coords_
private
std::pair< core::Size, Pharmacophore > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::current_phore_match_
private
bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::debug_
private
utility::vector1< utility::vector1< core::Real > > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::Dmtrx_
private
bool protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::is_ligand_
private
core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::limit_
private

Referenced by set_default().

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::n_match_per_ligand_motif_
private

Referenced by map_phores(), and set_default().

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::NNEIGH_CUT_FOR_EXPOSED_BB
private

Referenced by init_from_receptor(), and set_default().

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::NNEIGH_CUT_FOR_EXPOSED_SC
private

Referenced by init_from_receptor(), and set_default().

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_dcut_
private
utility::vector1< std::pair< core::Size, Pharmacophore > > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_match_
private

Referenced by map_phores(), and select_phore_match().

utility::vector1< Pharmacophore > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phores_
private
core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::polar_scale_
private

Referenced by set_default().

utility::vector1< AtomProperties > protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::properties_
private
core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::RECEPTOR_PHORE_MAX
private

Referenced by init_from_receptor(), and set_default().

core::Size protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::RECEPTOR_PHORE_MIN
private

Referenced by init_from_receptor(), and set_default().

core::Real protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::weight_
private

Referenced by set_default().


The documentation for this class was generated from the following files: