A 3D boolean array used for identifying core voxels in the VoidsPenaltyEnergy. More...
#include <VoidsPenaltyVoxelGrid.hh>
Public Member Functions | |
| VoidsPenaltyVoxelGrid () | |
| Default constructor. More... | |
| ~VoidsPenaltyVoxelGrid () override | |
| Default destructor. More... | |
| VoidsPenaltyVoxelGrid (VoidsPenaltyVoxelGrid const &src) | |
| Copy constructor. More... | |
| VoidsPenaltyVoxelGridOP | clone () const |
| Clone operator: copy this object and return an owning pointer to the copy. More... | |
| void | set_voxel_size_and_padding (core::Real const &size_in, core::Real const &padding_in) |
| Sets the voxel size and padding. More... | |
| void | set_cone_parameters (core::Real const &cone_dotproduct_cutoff_in, core::Real const cone_distance_cutoff_in, core::Size const containing_cones_cutoff_in) |
| Set the cone dotproduct cutoff and the cone distance cutoff. @detals The cone dotproduct cutoff is the cutoff value for the dot product of a cone vector and a cone base-test point vector below which we declare the test point not to be within the cone. Effectively, this is the cone width. Lower values make broader cones. Default 0.1. Can range from 1.0 (infinitely thin cone) to -1.0 (full spherical volume), with 0.0 represeting all points on one side of the plane perpendicular to the cone vector. The cone distance cutoff is the distance from the cone base that a test point must lie within to be in the cone. This is automatically converted to (and stored as) the square of the distance by this function for efficient comparison operations. the containing cones cutoff is the minimum number of cones that must contain a given voxel in order for that voxel to be considered to be "buried". More... | |
| void | reset () |
| Reset this object. More... | |
| void | set_up_voxel_grid_and_compute_burial (core::pose::Pose const &pose) |
| Set up voxel grid from a pose and determine which voxels are buried. More... | |
| void | prune_voxels_for_fixed_residues (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotsets, core::conformation::symmetry::SymmetryInfoCOP symminfo, core::conformation::symmetry::SymmetricConformationCOP symmconf) |
| Remove voxels from voxel grid for positions that cannot repack. More... | |
| void | compute_volumes_of_buried_rotamers (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotsets, utility::vector1< std::map< core::conformation::ResidueCOP, core::Real > > &rotamer_volume_maps, core::conformation::symmetry::SymmetryInfoCOP symminfo, core::conformation::symmetry::SymmetricConformationCOP symmconf) |
| Given a rotamer set and a place to store rotamer volume information, computes volumes of buried parts of rotamers. More... | |
| core::Real | compute_total_volume_of_current_residues (core::pose::Pose const &pose) const |
| Given a pose, compute the total volume of its buried residues. More... | |
| core::Real | compute_volume_of_this_buried_rotamer (core::conformation::ResidueCOP rot, numeric::MathNTensor< bool, 3 > &untouched_voxels, core::Size &untouched_voxel_count) const |
| Given a rotamer, compute the volume of the buried atoms. More... | |
| void | get_rotamer_bounding_box (core::conformation::ResidueCOP rot, utility::fixedsizearray1< core::Size, 3 > &bounding_box_start, utility::fixedsizearray1< core::Size, 3 > &bounding_box_end) const |
| Given a rotamer, determine the bounding box (in voxel grid indices) of that rotamer. More... | |
| bool | atom_overlaps_voxel (utility::fixedsizearray1< core::Size, 3 > const &voxel_index, numeric::xyzVector< core::Real > const &atom_xyz, core::Real const atomic_radius) const |
| Given a voxel index, the coordinates of an atom centre, and an atom radius, determine whether the atom overlaps the voxel. Returns true if it does and false otherwise. More... | |
| core::pose::PoseOP | visualize_voxel_grid (bool const only_buried_voxels) const |
| Only for debugging! This function returns a pose with a grid of copper atoms representing the voxels. More... | |
| numeric::xyzVector< core::Real > | get_voxel_coordinates (core::Size const index_x, core::Size const index_y, core::Size const index_z) const |
| Given the indices of a voxel (keeping in mind that indices are ZERO-based), get the 3D coordinates. More... | |
| bool | get_indices_of_voxel_from_coordinates (numeric::xyzVector< core::Real > point, utility::fixedsizearray1< core::Size, 3 > &output_indices) const |
| Given a point in 3D space, determine which voxel it lies in and return the indices of that voxel. More... | |
| core::Real | total_buried_volume () const |
| Get the total buried volume (including volume that cannot be reached by any rotamer), in cubic Angstroms. More... | |
| core::Real | reachable_buried_volume () const |
| Get the buried volume EXCLUDING volume that cannot be reached by any rotamer, in cubic Angstroms. More... | |
Private Member Functions | |
| void | compute_bounding_box (core::pose::Pose const &pose, core::Real const &padding, numeric::xyzVector< core::Real > &lower_left_coords, numeric::xyzVector< core::Real > &upper_right_coords) const |
| Given a pose, find the lower-left and upper-right corners of the bounding volume, with padding. More... | |
| void | resize_voxel_grid (numeric::xyzVector< core::Real > const &lower_left_coords, numeric::xyzVector< core::Real > &upper_right_coords, core::Real const &voxel_size, utility::fixedsizearray1< core::Size, 3 > &voxel_data_dimensions, numeric::MathNTensor< bool, 3 > &voxel_data) const |
| Given lower-left, upper-right, and voxel size data, resize the voxel grid appropriately. More... | |
| void | compute_burial (core::pose::Pose const &pose, utility::fixedsizearray1< core::Size, 3 > const &voxel_data_dimensions, numeric::MathNTensor< bool, 3 > &voxel_data, core::Size &buried_volume) const |
| Given a pose and a voxel grid that is already set up for the pose, compute whether each point is buried or not. More... | |
| bool | is_buried (numeric::xyzVector< core::Real > const &coords, utility::vector1< numeric::xyzVector< core::Real > > const &conevects, utility::vector1< numeric::xyzVector< core::Real > > const &conebases, utility::vector1< bool > const &skip_list) const |
| Given a pose and a point in space, determine whether the point is buried by the side-chain cones method. More... | |
| core::Size | get_current_res_symmetric (core::Size const index_in, core::conformation::symmetry::SymmetryInfoCOP symminfo) const |
| Given a residue index, get (a) the same residue index back in the asymmetric case, (b) the same residue index back in the symmetric case if this residue is independent, and (c) the residue index on which this residue depends in the symmetric case if this residue is dependent. More... | |
Private Attributes | |
| core::Real | voxel_size_ |
| The length, width, or height of a voxel, in Angstroms. More... | |
| core::Real | half_voxel_size_ |
| The voxel size divided by 2. Cached to avoid repeated computation. More... | |
| core::Real | voxel_volume_ |
| The volume of a voxel, in cubic Angstroms. Cached to avoid repeated computation. More... | |
| core::Real | padding_ |
| The padding around the pose for the voxel grid. More... | |
| numeric::xyzVector< core::Real > | lower_left_coords_ |
| The x, y, and z coordinates of the lower-left corner of the volume considered. More... | |
| numeric::xyzVector< core::Real > | upper_right_coords_ |
| The x, y, and z coordinates of the upper-right corner of the volume considered. More... | |
| numeric::MathNTensor< bool, 3 > | voxel_data_ |
| The actual volumetric data. More... | |
| utility::fixedsizearray1< core::Size, 3 > | voxel_data_dimensions_ |
| The dimensions, in cells, of the voxel data. More... | |
| core::Size | total_buried_volume_ |
| The total buried volume (including volume that cannot be reached by any rotamer). More... | |
| core::Size | reachable_buried_volume_ |
| The buried volume EXCLUDING volume that cannot be reached by any rotamer. More... | |
| bool | pose_setup_complete_ |
| Has this object been set up from a pose (i.e. has the voxel grid been initialized and the buried volume computed)? More... | |
| bool | non_packable_volume_pruned_ |
| Has the prune_voxels_for_fixed_residues() function been called? More... | |
| bool | rotamer_setup_complete_ |
| Has this object been used to set up rotmers? More... | |
| core::Real | cone_dotproduct_cutoff_ |
| The cutoff value for the dot product of a cone vector and a cone base-test point vector below which we declare the test point not to be within the cone. Effectively, this is the cone width. Lower values make broader cones. Default 0.1. Can range from 1.0 (infinitely thin cone) to -1.0 (full spherical volume), with 0.0 represeting all points on one side of the plane perpendicular to the cone vector. More... | |
| core::Real | cone_distance_cutoff_sq_ |
| The square of the cutoff value for the distance from the cone base at which we are considered no longer to be within the cone. Defaults to 64.0 (for a cutoff distance of 8.0). More... | |
| core::Size | containing_cones_cutoff_ |
| The minimum number of cones that must contain a particular voxel for that voxel to be considered "buried". More... | |
Friends | |
| class | ::VoidsPenaltyVoxelGridTests |
| class | ::VoidsPenaltyVoxelGridTests_rotamer_setup |
| class | ::VoidsPenaltyVoxelGridTests_rotamer_setup_2 |
Detailed Description
A 3D boolean array used for identifying core voxels in the VoidsPenaltyEnergy.
Constructor & Destructor Documentation
◆ VoidsPenaltyVoxelGrid() [1/2]
| core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::VoidsPenaltyVoxelGrid | ( | ) |
Default constructor.
◆ ~VoidsPenaltyVoxelGrid()
|
override |
Default destructor.
◆ VoidsPenaltyVoxelGrid() [2/2]
| core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::VoidsPenaltyVoxelGrid | ( | VoidsPenaltyVoxelGrid const & | src | ) |
Copy constructor.
Member Function Documentation
◆ atom_overlaps_voxel()
| bool core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::atom_overlaps_voxel | ( | utility::fixedsizearray1< core::Size, 3 > const & | voxel_index, |
| numeric::xyzVector< core::Real > const & | atom_xyz, | ||
| core::Real const | atomic_radius | ||
| ) | const |
Given a voxel index, the coordinates of an atom centre, and an atom radius, determine whether the atom overlaps the voxel. Returns true if it does and false otherwise.
Requires that set_up_voxel_grid_and_compute_burial() was called first.
- Note
- This works in three steps. First, we determine whether the bonuding box of the atom and the voxel overlap, and return false if they don't. Next, we determine whether the atom centre is in the voxel, and return true if it is. Finally, we determine whether the voxel centre to atom centre distance is less than the atomic radius, and return true if and only if it is.
- This works in three steps. First, we determine whether the bonuding box of the atom and the voxel overlap, and return false if they don't. Next, we determine whether the atom centre is in the voxel, and return true if it is. Finally, we determine whether the voxel centre to atom centre distance is less than the atomic radius, and return true if and only if it is.
References get_voxel_coordinates(), half_voxel_size_, and pose_setup_complete_.
Referenced by compute_volume_of_this_buried_rotamer().
◆ clone()
| VoidsPenaltyVoxelGridOP core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::clone | ( | ) | const |
Clone operator: copy this object and return an owning pointer to the copy.
◆ compute_bounding_box()
|
private |
Given a pose, find the lower-left and upper-right corners of the bounding volume, with padding.
References core::chemical::ResidueType::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), core::pack::guidance_scoreterms::voids_penalty_energy::TR(), core::pose::Pose::xyz(), and core::conformation::Residue::xyz().
Referenced by set_up_voxel_grid_and_compute_burial().
◆ compute_burial()
|
private |
Given a pose and a voxel grid that is already set up for the pose, compute whether each point is buried or not.
References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_gly, core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::atom_name(), core::chemical::ICoorAtomID::atomno(), core::id::AtomID::atomno(), core::chemical::ResidueType::first_sidechain_atom(), get_voxel_coordinates(), core::chemical::ResidueType::icoor(), is_buried(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::is_virtual_residue(), core::chemical::ResidueTypeBase::name(), core::pose::Pose::residue_type(), core::chemical::AtomICoor::stub_atom1(), core::id::to_string(), core::pose::Pose::total_residue(), core::pack::guidance_scoreterms::voids_penalty_energy::TR(), and core::pose::Pose::xyz().
Referenced by set_up_voxel_grid_and_compute_burial().
◆ compute_total_volume_of_current_residues()
| core::Real core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_total_volume_of_current_residues | ( | core::pose::Pose const & | pose | ) | const |
Given a pose, compute the total volume of its buried residues.
Requires that set_up_voxel_grid_and_compute_burial() was called first.
References compute_volume_of_this_buried_rotamer(), core::pose::Pose::conformation(), pose_setup_complete_, core::conformation::Conformation::residue_cop(), total_buried_volume_, core::pose::Pose::total_residue(), and voxel_data_.
Referenced by core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy::finalize_total_energy().
◆ compute_volume_of_this_buried_rotamer()
| core::Real core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_volume_of_this_buried_rotamer | ( | core::conformation::ResidueCOP | rot, |
| numeric::MathNTensor< bool, 3 > & | untouched_voxels, | ||
| core::Size & | untouched_voxel_count | ||
| ) | const |
Given a rotamer, compute the volume of the buried atoms.
This is a bit approximate. The algorithm is as follows:
- Deterine the bounding box of the residue.
- Loop through every voxel in the bounding box.
- Check whether any atom in the residue overlaps the voxel. If it does, add 1 voxel volume to the total volume.
- Return the total volume.
References atom_overlaps_voxel(), get_rotamer_bounding_box(), rot(), voxel_data_, and voxel_volume_.
Referenced by compute_total_volume_of_current_residues(), compute_volumes_of_buried_rotamers(), and prune_voxels_for_fixed_residues().
◆ compute_volumes_of_buried_rotamers()
| void core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_volumes_of_buried_rotamers | ( | core::pose::Pose const & | pose, |
| core::pack::rotamer_set::RotamerSets const & | rotsets, | ||
| utility::vector1< std::map< core::conformation::ResidueCOP, core::Real > > & | rotamer_volume_maps, | ||
| core::conformation::symmetry::SymmetryInfoCOP | symminfo, | ||
| core::conformation::symmetry::SymmetricConformationCOP | symmconf | ||
| ) |
Given a rotamer set and a place to store rotamer volume information, computes volumes of buried parts of rotamers.
Requires that set_up_voxel_grid_and_compute_burial() was called first. Input is a RotamersSet object. Output is a vector of maps of ResidueOP to floats. The float values are the total volume of each rotamer that lies within the buried volume.
- Note
- If symminfo == nullptr, then we assume this is the asymmetric case (in which case symmconf can also be nullptr). Otherwise, we use the symmetry information to simplify the calculation, returning rotamer volumes multiplied by the number of symmetry copies ONLY for the independent positions.
Requires that set_up_voxel_grd_and_compute_burial was called first. Input is a RotamersSet object. Output is a vector of maps of ResidueOP to floats. The float values are the total volume of each rotamer that lies within the buried volume.
- Note
- If symminfo == nullptr, then we assume this is the asymmetric case (in which case symmconf can also be nullptr). Otherwise, we use the symmetry information to simplify the calculation, returning rotamer volumes multiplied by the number of symmetry copies ONLY for the independent positions.
References compute_volume_of_this_buried_rotamer(), core::pose::Pose::conformation(), core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(), non_packable_volume_pruned_, pose_setup_complete_, reachable_buried_volume_, core::conformation::Conformation::residue_cop(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), rotamer_setup_complete_, total_buried_volume_, core::pack::rotamer_set::RotamerSets::total_residue(), and voxel_data_.
Referenced by core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy::set_up_residuearrayannealableenergy_for_packing().
◆ get_current_res_symmetric()
|
private |
Given a residue index, get (a) the same residue index back in the asymmetric case, (b) the same residue index back in the symmetric case if this residue is independent, and (c) the residue index on which this residue depends in the symmetric case if this residue is dependent.
Referenced by prune_voxels_for_fixed_residues().
◆ get_indices_of_voxel_from_coordinates()
| bool core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::get_indices_of_voxel_from_coordinates | ( | numeric::xyzVector< core::Real > | point, |
| utility::fixedsizearray1< core::Size, 3 > & | output_indices | ||
| ) | const |
Given a point in 3D space, determine which voxel it lies in and return the indices of that voxel.
Returns false if the point lies outside of the voxel grid. Returns true otherwise and sets output_indices to the indices of the voxel grid cell. If return value is false, the out-of-range indices are set to the values of the edge of the voxel grid (0 or voxel_data_dimensions_[n]-1, where n is 1, 2, or 3 for x, y, and z respectively), and all other indices are set appropriately.
- Note
- The xyzVector is deliberately copied in instead of being passed by reference because I'd otherwise need to allocate a new xyzVector and copy values that I want to modify as part of the calculation.
References half_voxel_size_, lower_left_coords_, protocols::mean_field::max(), protocols::mean_field::min(), pose_setup_complete_, upper_right_coords_, voxel_data_dimensions_, and voxel_size_.
Referenced by get_rotamer_bounding_box().
◆ get_rotamer_bounding_box()
| void core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::get_rotamer_bounding_box | ( | core::conformation::ResidueCOP | rot, |
| utility::fixedsizearray1< core::Size, 3 > & | bounding_box_start, | ||
| utility::fixedsizearray1< core::Size, 3 > & | bounding_box_end | ||
| ) | const |
Given a rotamer, determine the bounding box (in voxel grid indices) of that rotamer.
Requires that set_up_voxel_grid_and_compute_burial() was called first.
- Note
- If a rotamer exceeds the bounding box of the overall voxel grid, the edge indices are returned. Outputs are bounding_box_start and bounding_box_end.
References get_indices_of_voxel_from_coordinates(), pose_setup_complete_, and rot().
Referenced by compute_volume_of_this_buried_rotamer().
◆ get_voxel_coordinates()
| numeric::xyzVector< core::Real > core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::get_voxel_coordinates | ( | core::Size const | index_x, |
| core::Size const | index_y, | ||
| core::Size const | index_z | ||
| ) | const |
Given the indices of a voxel (keeping in mind that indices are ZERO-based), get the 3D coordinates.
Note: This returns the 3D coordinates of the CENTRE of the voxel.
References lower_left_coords_, pose_setup_complete_, voxel_data_dimensions_, and voxel_size_.
Referenced by atom_overlaps_voxel(), compute_burial(), and visualize_voxel_grid().
◆ is_buried()
|
private |
Given a pose and a point in space, determine whether the point is buried by the side-chain cones method.
References cone_distance_cutoff_sq_, cone_dotproduct_cutoff_, containing_cones_cutoff_, and protocols::simple_filters::coords().
Referenced by compute_burial().
◆ prune_voxels_for_fixed_residues()
| void core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::prune_voxels_for_fixed_residues | ( | core::pose::Pose const & | pose, |
| core::pack::rotamer_set::RotamerSets const & | rotsets, | ||
| core::conformation::symmetry::SymmetryInfoCOP | symminfo, | ||
| core::conformation::symmetry::SymmetricConformationCOP | symmconf | ||
| ) |
Remove voxels from voxel grid for positions that cannot repack.
set_up_voxel_grid_and_compute_burial() must be called first.
- Note
- If symminfo == nullptr, then we assume this is the asymmetric case. Otherwise, we use the symmetry information to aid the pruning.
References compute_volume_of_this_buried_rotamer(), core::pose::Pose::conformation(), get_current_res_symmetric(), core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(), core::chemical::ResidueType::is_inverted_virtual_residue(), core::chemical::ResidueType::is_virtual_residue(), non_packable_volume_pruned_, pose_setup_complete_, core::conformation::Conformation::residue_cop(), core::pose::Pose::residue_type(), total_buried_volume_, core::pose::Pose::total_residue(), core::pack::guidance_scoreterms::voids_penalty_energy::TR(), and voxel_data_.
Referenced by core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy::set_up_residuearrayannealableenergy_for_packing().
◆ reachable_buried_volume()
| core::Real core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::reachable_buried_volume | ( | ) | const |
Get the buried volume EXCLUDING volume that cannot be reached by any rotamer, in cubic Angstroms.
References reachable_buried_volume_, rotamer_setup_complete_, and voxel_volume_.
Referenced by core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy::set_up_residuearrayannealableenergy_for_packing().
◆ reset()
| void core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::reset | ( | ) |
Reset this object.
Clears stored volumetric data. Does not clear settings, such as voxel size or cone dotproduct cutoff.
References lower_left_coords_, non_packable_volume_pruned_, pose_setup_complete_, reachable_buried_volume_, rotamer_setup_complete_, total_buried_volume_, upper_right_coords_, voxel_data_, and voxel_data_dimensions_.
Referenced by set_cone_parameters(), and set_voxel_size_and_padding().
◆ resize_voxel_grid()
|
private |
Given lower-left, upper-right, and voxel size data, resize the voxel grid appropriately.
This also updates upper_right_coords to be the centre of the maximum voxel (pushing it a little beyond the old bounding box).
References core::pack::guidance_scoreterms::voids_penalty_energy::TR(), and voxel_size_.
Referenced by set_up_voxel_grid_and_compute_burial().
◆ set_cone_parameters()
| void core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::set_cone_parameters | ( | core::Real const & | cone_dotproduct_cutoff_in, |
| core::Real const | cone_distance_cutoff_in, | ||
| core::Size const | containing_cones_cutoff_in | ||
| ) |
Set the cone dotproduct cutoff and the cone distance cutoff. @detals The cone dotproduct cutoff is the cutoff value for the dot product of a cone vector and a cone base-test point vector below which we declare the test point not to be within the cone. Effectively, this is the cone width. Lower values make broader cones. Default 0.1. Can range from 1.0 (infinitely thin cone) to -1.0 (full spherical volume), with 0.0 represeting all points on one side of the plane perpendicular to the cone vector. The cone distance cutoff is the distance from the cone base that a test point must lie within to be in the cone. This is automatically converted to (and stored as) the square of the distance by this function for efficient comparison operations. the containing cones cutoff is the minimum number of cones that must contain a given voxel in order for that voxel to be considered to be "buried".
Set the cone dotproduct cutoff and the cone distance cutoff. @detals The cone dotproduct cutoff is the cutoff value for the dot product of a cone vector and a cone base-test point vector below which we declare the test point not to be within the cone. Effectively, this is the cone width. Lower values make broader cones. Default 0.1. Can range from 1.0 (infinitely thin cone) to -1.0 (full spherical volume), with 0.0 represeting all points on one side of the plane perpendicular to the cone vector. The cone distance cutoff is the distance from the cone base that a test point must lie within to be in the cone. This is automatically converted to (and stored as) the square of the distance by this function for efficient comparison operations.
- Note
- Calls reset(), necessitating subsequent initialization from pose.
References cone_distance_cutoff_sq_, cone_dotproduct_cutoff_, containing_cones_cutoff_, and reset().
Referenced by core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy::configure_voxel_grid().
◆ set_up_voxel_grid_and_compute_burial()
| void core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::set_up_voxel_grid_and_compute_burial | ( | core::pose::Pose const & | pose | ) |
Set up voxel grid from a pose and determine which voxels are buried.
This function must be called before compute_volumes_of_buried_rotamers().
References compute_bounding_box(), compute_burial(), lower_left_coords_, padding_, pose_setup_complete_, resize_voxel_grid(), rotamer_setup_complete_, total_buried_volume_, upper_right_coords_, voxel_data_, voxel_data_dimensions_, and voxel_size_.
Referenced by core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy::finalize_total_energy(), and core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy::set_up_residuearrayannealableenergy_for_packing().
◆ set_voxel_size_and_padding()
| void core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::set_voxel_size_and_padding | ( | core::Real const & | size_in, |
| core::Real const & | padding_in | ||
| ) |
Sets the voxel size and padding.
Calls reset(), necessitating subsequent initialization from pose. Computes half_voxel_size_ and voxel_volume_.
References half_voxel_size_, padding_, reset(), voxel_size_, and voxel_volume_.
Referenced by core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy::configure_voxel_grid().
◆ total_buried_volume()
| core::Real core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::total_buried_volume | ( | ) | const |
Get the total buried volume (including volume that cannot be reached by any rotamer), in cubic Angstroms.
References pose_setup_complete_, total_buried_volume_, and voxel_volume_.
Referenced by core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyEnergy::finalize_total_energy().
◆ visualize_voxel_grid()
| core::pose::PoseOP core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::visualize_voxel_grid | ( | bool const | only_buried_voxels | ) | const |
Only for debugging! This function returns a pose with a grid of copper atoms representing the voxels.
If only_buried_voxels is true, then the voxel grid only has copper atoms at the "true" positions; otherwise, the full grid is dumped to the pose.
References core::chemical::FULL_ATOM_t, get_voxel_coordinates(), pose_setup_complete_, voxel_data_, and voxel_data_dimensions_.
Friends And Related Function Documentation
◆ ::VoidsPenaltyVoxelGridTests
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friend |
◆ ::VoidsPenaltyVoxelGridTests_rotamer_setup
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◆ ::VoidsPenaltyVoxelGridTests_rotamer_setup_2
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friend |
Member Data Documentation
◆ cone_distance_cutoff_sq_
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private |
The square of the cutoff value for the distance from the cone base at which we are considered no longer to be within the cone. Defaults to 64.0 (for a cutoff distance of 8.0).
Referenced by is_buried(), and set_cone_parameters().
◆ cone_dotproduct_cutoff_
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private |
The cutoff value for the dot product of a cone vector and a cone base-test point vector below which we declare the test point not to be within the cone. Effectively, this is the cone width. Lower values make broader cones. Default 0.1. Can range from 1.0 (infinitely thin cone) to -1.0 (full spherical volume), with 0.0 represeting all points on one side of the plane perpendicular to the cone vector.
Referenced by is_buried(), and set_cone_parameters().
◆ containing_cones_cutoff_
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private |
The minimum number of cones that must contain a particular voxel for that voxel to be considered "buried".
Defaults to 6.
Referenced by is_buried(), and set_cone_parameters().
◆ half_voxel_size_
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private |
The voxel size divided by 2. Cached to avoid repeated computation.
Referenced by atom_overlaps_voxel(), get_indices_of_voxel_from_coordinates(), and set_voxel_size_and_padding().
◆ lower_left_coords_
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private |
The x, y, and z coordinates of the lower-left corner of the volume considered.
Referenced by get_indices_of_voxel_from_coordinates(), get_voxel_coordinates(), reset(), and set_up_voxel_grid_and_compute_burial().
◆ non_packable_volume_pruned_
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private |
Has the prune_voxels_for_fixed_residues() function been called?
This must precede rotamer setup.
Referenced by compute_volumes_of_buried_rotamers(), prune_voxels_for_fixed_residues(), and reset().
◆ padding_
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private |
The padding around the pose for the voxel grid.
Referenced by set_up_voxel_grid_and_compute_burial(), and set_voxel_size_and_padding().
◆ pose_setup_complete_
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private |
Has this object been set up from a pose (i.e. has the voxel grid been initialized and the buried volume computed)?
This step must precede rotamer setup.
Referenced by atom_overlaps_voxel(), compute_total_volume_of_current_residues(), compute_volumes_of_buried_rotamers(), get_indices_of_voxel_from_coordinates(), get_rotamer_bounding_box(), get_voxel_coordinates(), prune_voxels_for_fixed_residues(), reset(), set_up_voxel_grid_and_compute_burial(), total_buried_volume(), and visualize_voxel_grid().
◆ reachable_buried_volume_
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The buried volume EXCLUDING volume that cannot be reached by any rotamer.
Referenced by compute_volumes_of_buried_rotamers(), reachable_buried_volume(), and reset().
◆ rotamer_setup_complete_
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private |
Has this object been used to set up rotmers?
This step must follow setup from pose, and can only be performed once.
Referenced by compute_volumes_of_buried_rotamers(), reachable_buried_volume(), reset(), and set_up_voxel_grid_and_compute_burial().
◆ total_buried_volume_
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private |
The total buried volume (including volume that cannot be reached by any rotamer).
Referenced by compute_total_volume_of_current_residues(), compute_volumes_of_buried_rotamers(), prune_voxels_for_fixed_residues(), reset(), set_up_voxel_grid_and_compute_burial(), and total_buried_volume().
◆ upper_right_coords_
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private |
The x, y, and z coordinates of the upper-right corner of the volume considered.
Referenced by get_indices_of_voxel_from_coordinates(), reset(), and set_up_voxel_grid_and_compute_burial().
◆ voxel_data_
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private |
The actual volumetric data.
Referenced by compute_total_volume_of_current_residues(), compute_volume_of_this_buried_rotamer(), compute_volumes_of_buried_rotamers(), prune_voxels_for_fixed_residues(), reset(), set_up_voxel_grid_and_compute_burial(), and visualize_voxel_grid().
◆ voxel_data_dimensions_
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private |
The dimensions, in cells, of the voxel data.
Referenced by get_indices_of_voxel_from_coordinates(), get_voxel_coordinates(), reset(), set_up_voxel_grid_and_compute_burial(), and visualize_voxel_grid().
◆ voxel_size_
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private |
The length, width, or height of a voxel, in Angstroms.
Defaults to 0.5 A. Smaller is not necessarily better.
Referenced by get_indices_of_voxel_from_coordinates(), get_voxel_coordinates(), resize_voxel_grid(), set_up_voxel_grid_and_compute_burial(), and set_voxel_size_and_padding().
◆ voxel_volume_
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private |
The volume of a voxel, in cubic Angstroms. Cached to avoid repeated computation.
Referenced by compute_volume_of_this_buried_rotamer(), reachable_buried_volume(), set_voxel_size_and_padding(), and total_buried_volume().
The documentation for this class was generated from the following files:
- src/core/pack/guidance_scoreterms/voids_penalty_energy/VoidsPenaltyVoxelGrid.hh
- src/core/pack/guidance_scoreterms/voids_penalty_energy/VoidsPenaltyVoxelGrid.cc
