doxygen/chemical__features_8h_source.html

// -*-c++-*-

#ifndef STORMM_CHEMICAL_FEATURES_H

#define STORMM_CHEMICAL_FEATURES_H


#include "copyright.h"

#include "Accelerator/hybrid.h"

#include "DataTypes/common_types.h"

#include "DataTypes/stormm_vector_types.h"

#include "Math/vector_ops.h"

#include "Numerics/split_fixed_precision.h"

#include "Topology/atomgraph.h"

#include "Synthesis/condensate.h"

#include "Synthesis/phasespace_synthesis.h"

#include "Trajectory/coordinateframe.h"

#include "Trajectory/coordinate_series.h"

#include "Trajectory/phasespace.h"

#include "UnitTesting/stopwatch.h"

#include "chemistry_enumerators.h"

#include "match_bonding_pattern.h"


namespace stormm {

namespace chemistry {


using card::Hybrid;

using card::HybridTargetLevel;

using data_types::isFloatingPointScalarType;

using stmath::crossProduct;

using stmath::dot;

using stmath::project;

using stmath::roundUp;

using synthesis::Condensate;

using synthesis::CondensateReader;

using synthesis::PhaseSpaceSynthesis;

using synthesis::PsSynthesisReader;

using testing::StopWatch;

using topology::AtomGraph;

using topology::ChemicalDetailsKit;

using topology::NonbondedKit;

using topology::ValenceKit;

using trajectory::CoordinateFrame;

using trajectory::CoordinateFrameReader;

using trajectory::CoordinateSeries;

using trajectory::CoordinateSeriesReader;

using trajectory::PhaseSpace;

using trajectory::PhaseSpaceReader;


constexpr int max_fused_ring_tree_size = 33554432;


class BondedNode {

public:


  BondedNode();


  void setBranchPointer(std::vector<int> *vi, size_t pos, size_t max_branches);


  void addToTree(int previous_in, int current_atom, int current_layer,

                 const NonbondedKit<double> &nbk, const std::vector<bool> &valid_atom_mask);

  void addToTree(int previous_in, int current_atom, int current_layer, int previous_node_in,

                 const NonbondedKit<double> &nbk, const std::vector<bool> &valid_atom_mask);


  void addBondOrder(const ValenceKit<double> &vk, const Hybrid<double> &bond_orders);


  int getPreviousAtom() const;


  int getPreviousNode() const;


  int getAtom() const;


  int getLayer() const;


  int getBranchCount() const;


  int getBranchAtom(int index) const;


  int findBranchAtom(int search_index) const;


  uint getRingCompletion(int branch_index) const;


  double getRootBondOrder() const;


  void setRingCompletion(int partner_index);


  void wipeRingCompletion();


private:

  int previous_atom_index;

  int previous_node_index;

  int atom_index;

  int layer_index;

  double root_bond_order;

  int branch_count;

  int* branch_atoms;

  uint rings_completed;

};


class IsomerPlan {

public:


  IsomerPlan(ConformationEdit motion_in, ChiralInversionProtocol chiral_plan_in, int root_atom_in,

             int pivot_atom_in, const std::vector<int> &moving_atoms_in,

             const AtomGraph* ag_pointer_in);


  IsomerPlan(ConformationEdit motion_in, int root_atom_in, int pivot_atom_in,

             const std::vector<int> &moving_atoms_in, const AtomGraph* ag_pointer_in);


  IsomerPlan(ConformationEdit motion_in, ChiralInversionProtocol chiral_plan_in, int root_atom_in,

             int pivot_atom_in, const AtomGraph* ag_pointer_in);


  IsomerPlan(ConformationEdit motion_in, int root_atom_in, int pivot_atom_in,

             const AtomGraph* ag_pointer_in);


  IsomerPlan(const IsomerPlan &original) = default;

  IsomerPlan(IsomerPlan &&original) = default;

  IsomerPlan& operator=(const IsomerPlan &other) = default;

  IsomerPlan& operator=(IsomerPlan &&other) = default;


  ConformationEdit getMotion() const;


  ChiralInversionProtocol getChiralPlan() const;


  int getRootAtom() const;


  int getPivotAtom() const;


  int getRootHandle() const;


  int getPivotHandle() const;


  int getMovingAtomCount() const;


  int getRealMovingAtomCount() const;


  double getMovingAtomWeight() const;


  int getMovingAtom(const size_t index) const;


  const std::vector<int>& getMovingAtoms() const;


  void addMovingAtoms(const std::vector<int> &new_atom_idx);


  void eraseMovingAtoms();


private:

  ConformationEdit motion;

  ChiralInversionProtocol chiral_plan;

  int root_atom;

  int pivot_atom;

  int root_handle;

  int pivot_handle;

  int rotating_real_atom_count;

  std::vector<int> moving_atoms;

  double mass_of_rotators;

  AtomGraph *ag_pointer;

};


struct CoupledEdit {

public:


  CoupledEdit();

  CoupledEdit(ConformationEdit edit_in, int index_in);

  CoupledEdit(int2 data_in);


  CoupledEdit(const CoupledEdit &original) = default;

  CoupledEdit(CoupledEdit &&original) = default;

  CoupledEdit& operator=(const CoupledEdit &other) = default;

  CoupledEdit& operator=(CoupledEdit &&other) = default;


  CoupledEdit operator=(const int2 &other);


  ConformationEdit edit;

  int index;

};


struct ChemicalFeaturesReader {


  ChemicalFeaturesReader(int atom_count_in, int planar_atom_count_in, int ring_count_in,

                         int fused_ring_count_in, int twistable_ring_count_in,

                         int conjugated_group_count_in, int aromatic_group_count_in,

                         int polar_hydrogen_count_in, int hbond_donor_count_in,

                         int hbond_acceptor_count_in, int chiral_center_count_in,

                         int rotatable_bond_count_in, int cis_trans_bond_count_in,

                         int double_bond_count_in, int triple_bond_count_in,

                         int max_ring_size_in, double temperature_in,

                         bool rotating_groups_mapped_in, bool chiralities_computed_in,

                         const int* planar_centers_in, const int* ring_atoms_in,

                         const int* ring_atom_bounds_in, const int* aromatic_pi_electrons_in,

                         const int* aromatic_groups_in, const int* aromatic_group_bounds_in,

                         const int* polar_hydrogens_in, const int* hydrogen_bond_donors_in,

                         const int* hydrogen_bond_acceptors_in, const int* chiral_centers_in,

                         const int* chiral_inversion_methods_in, const int* rotatable_groups_in,

                         const int* rotatable_group_bounds_in, const int* cis_trans_groups_in,

                         const int* cis_trans_group_bounds_in, const int* invertible_groups_in,

                         const int* invertible_group_bounds_in, const int4* chiral_arm_atoms_in,

                         const double* formal_charges_in, const double* bond_orders_in,

                         const double* free_electrons_in, const ullint* ring_inclusion_in,

                         const AtomGraph *ag_pointer_in);


  ChemicalFeaturesReader(const ChemicalFeaturesReader &original) = default;

  ChemicalFeaturesReader(ChemicalFeaturesReader &&original) = default;


  // Counts of atoms and features (see the parent object for more detailed information)

  const int atom_count;

  const int planar_atom_count;

  const int ring_count;

  const int fused_ring_count;

  const int twistable_ring_count;

  const int conjugated_group_count;

  const int aromatic_group_count;

  const int polar_hydrogen_count;

  const int hbond_donor_count;

  const int hbond_acceptor_count;

  const int chiral_center_count;

  const int rotatable_bond_count;

  const int cis_trans_bond_count;

  const int double_bond_count;

  const int triple_bond_count;

  const int max_ring_size;

  const double temperature;

  const bool rotating_groups_mapped;

  const bool chiralities_computed;


  // Lists of atom indices and atom properties (see the parent object for detailed descriptions)

  const int* planar_centers;

  const int* ring_atoms;

  const int* ring_atom_bounds;

  const int* aromatic_pi_electrons;

  const int* aromatic_groups;

  const int* aromatic_group_bounds;

  const int* polar_hydrogens;

  const int* hydrogen_bond_donors;

  const int* hydrogen_bond_acceptors;

  const int* chiral_centers;

  const int* chiral_inversion_methods;

  const int* rotatable_groups;

  const int* rotatable_group_bounds;

  const int* cis_trans_groups;

  const int* cis_trans_group_bounds;

  const int* invertible_groups;

  const int* invertible_group_bounds;

  const int4* chiral_arm_atoms;

  const double* formal_charges;

  const double* bond_orders;

  const double* free_electrons;

  const ullint* ring_inclusion;

  const AtomGraph *ag_pointer;

};


class ChemicalFeatures {

public:


  ChemicalFeatures(const AtomGraph *ag_in = nullptr,

                   MapRotatableGroups map_groups_in = MapRotatableGroups::NO,

                   double temperature_in = 300.0, StopWatch *timer_in = nullptr);


  ChemicalFeatures(const AtomGraph &ag_in,

                   MapRotatableGroups map_groups_in = MapRotatableGroups::NO,

                   double temperature_in = 300.0, StopWatch *timer_in = nullptr);


  ChemicalFeatures(const AtomGraph *ag_in, const CoordinateFrameReader &cfr,

                   MapRotatableGroups map_groups_in = MapRotatableGroups::NO,

                   double temperature_in = 300.0, StopWatch *timer_in = nullptr);


  ChemicalFeatures(const AtomGraph *ag_in, const CoordinateFrame &cf,

                   MapRotatableGroups map_groups_in = MapRotatableGroups::NO,

                   double temperature_in = 300.0, StopWatch *timer_in = nullptr);


  ChemicalFeatures(const AtomGraph *ag_in, const PhaseSpace &ps,

                   MapRotatableGroups map_groups_in = MapRotatableGroups::NO,

                   double temperature_in = 300.0, StopWatch *timer_in = nullptr);


  ChemicalFeatures(const AtomGraph &ag_in, const CoordinateFrame &cf,

                   MapRotatableGroups map_groups_in = MapRotatableGroups::NO,

                   double temperature_in = 300.0, StopWatch *timer_in = nullptr);


  ChemicalFeatures(const AtomGraph &ag_in, const PhaseSpace &ps,

                   MapRotatableGroups map_groups_in = MapRotatableGroups::NO,

                   double temperature_in = 300.0, StopWatch *timer_in = nullptr);


  ChemicalFeatures(const ChemicalFeatures &original);

  ChemicalFeatures(ChemicalFeatures &&original);


  ChemicalFeatures& operator=(const ChemicalFeatures &other);

  ChemicalFeatures& operator=(ChemicalFeatures &&other);


#ifdef STORMM_USE_HPC

  void upload();


  void download();

#endif


  int getAtomCount() const;


  int getPlanarAtomCount() const;


  int getRingCount() const;


  int getFusedRingCount() const;


  int getMutableRingCount() const;


  int getAromaticGroupCount() const;


  int getPolarHydrogenCount() const;


  int getHydrogenBondDonorCount() const;


  int getHydrogenBondAcceptorCount() const;


  int getChiralCenterCount() const;


  int getRotatableBondCount() const;


  int getCisTransBondCount() const;


  bool rotatableGroupsMapped() const;


  bool chiralitiesComputed() const;


  std::vector<uint> getRingMask(int min_ring_size, int max_ring_size) const;


  std::vector<uint> getAromaticMask(int min_pi_electrons, int max_pi_electrons) const;


  std::vector<int> getPolarHydrogenList() const;


  std::vector<int> getHydrogenBondDonorList() const;


  std::vector<int> getHydrogenBondAcceptorList() const;


  std::vector<uint> getPolarHydrogenMask() const;


  std::vector<uint> getHydrogenBondDonorMask() const;


  std::vector<uint> getHydrogenBondAcceptorMask() const;


  std::vector<int> getChiralCenters(ChiralOrientation direction = ChiralOrientation::NONE) const;


  std::vector<int4> getChiralArmBaseAtoms() const;


  ChiralOrientation getAtomChirality(int atom_index) const;

  std::vector<ChiralOrientation> getAtomChirality(int low_index, int high_index) const;

  std::vector<ChiralOrientation> getAtomChirality() const;


  std::vector<uint> getChiralityMask(ChiralOrientation direction) const;


  std::vector<double> getFormalCharges() const;


  std::vector<double> getBondOrders() const;


  double getFreeElectrons(int atom_index) const;

  std::vector<double> getFreeElectrons(int low_index, int high_index) const;

  std::vector<double> getFreeElectrons() const;


  const std::vector<int>& getZeroKelvinFormalCharges() const;


  const std::vector<int>& getZeroKelvinBondOrders() const;


  const std::vector<int>& getZeroKelvinFreeElectrons() const;


  ullint getRingInclusion(int atom_index) const;

  std::vector<ullint> getRingInclusion(int low_index, int high_index) const;

  std::vector<ullint> getRingInclusion() const;


  bool bondIsInRing(int atom_i, int atom_j) const;

  bool bondIsInRing(int bond_index) const;


  std::vector<IsomerPlan> getRotatableBondGroups() const;

  std::vector<IsomerPlan> getRotatableBondGroups(int cutoff, int mol_index = 0) const;


  std::vector<IsomerPlan> getCisTransIsomerizationGroups() const;


  std::vector<IsomerPlan> getChiralInversionGroups() const;


  std::vector<ChiralInversionProtocol> getChiralInversionMethods() const;

  ChiralInversionProtocol getChiralInversionMethods(int index) const;


  const AtomGraph* getTopologyPointer() const;


  const ChemicalFeatures* getSelfPointer() const;


  ChemicalFeaturesReader data(HybridTargetLevel tier = HybridTargetLevel::HOST) const;


  void findChiralOrientations(const CoordinateFrameReader &cfr);


  void findRotatableBondGroups(StopWatch *timer = nullptr);


private:

  int atom_count;

  int planar_atom_count;

  int ring_count;

  int fused_ring_count;

  int twistable_ring_count;

  int conjugated_group_count;

  int aromatic_group_count;

  int polar_hydrogen_count;

  int hbond_donor_count;

  int hbond_acceptor_count;

  int chiral_center_count;

  int rotatable_bond_count;

  int cis_trans_bond_count;

  int double_bond_count;

  int triple_bond_count;

  int max_ring_size;

  double temperature;

  bool rotating_groups_mapped;

  bool chiralities_computed;


  Hybrid<int> planar_centers;


  Hybrid<ullint> ring_inclusion;


  Hybrid<int> ring_atom_bounds;


  Hybrid<int> ring_atoms;


  Hybrid<int> aromatic_group_bounds;


  Hybrid<int> aromatic_pi_electrons;


  Hybrid<int> aromatic_groups;


  Hybrid<int> polar_hydrogens;


  Hybrid<int> hydrogen_bond_donors;


  Hybrid<int> hydrogen_bond_acceptors;


  Hybrid<int4> chiral_arm_atoms;


  Hybrid<int> chiral_centers;


  Hybrid<int> chiral_inversion_methods;


  Hybrid<int> rotatable_groups;


  Hybrid<int> rotatable_group_bounds;


  Hybrid<int> cis_trans_groups;


  Hybrid<int> cis_trans_group_bounds;


  Hybrid<int> invertible_groups;


  Hybrid<int> invertible_group_bounds;


  Hybrid<int> anchor_a_branches;


  Hybrid<int> anchor_b_branches;


  Hybrid<double> formal_charges;


  Hybrid<double> bond_orders;


  Hybrid<double> free_electrons;


  Hybrid<int> int_data;


  Hybrid<int> mutable_group_data;


  Hybrid<double> double_data;


  std::vector<int> zerok_formal_charges;


  std::vector<int> zerok_bond_orders;


  std::vector<int> zerok_free_electrons;


  std::vector<bool> bond_in_ring;


  AtomGraph *ag_pointer;


  StopWatch *timer;


  void analyzeTopology(MapRotatableGroups map_groups_in);


  std::vector<int> findPlanarAtoms(const ValenceKit<double> &vk) const;


  void traceTopologicalRings(const NonbondedKit<double> &nbk, const ChemicalDetailsKit &cdk,

                             std::vector<ullint> *tmp_ring_inclusion,

                             std::vector<int> *tmp_ring_atoms,

                             std::vector<int> *tmp_ring_atom_bounds);


  void markRingAtoms(int j_atom, int k_atom, const std::vector<int> &tree_positions,

                     int node_count, std::vector<BondedNode> *links,

                     std::vector<ullint> *tmp_ring_inclusion, std::vector<int> *tmp_ring_atoms,

                     std::vector<int> *tmp_ring_atom_bounds,

                     const ChemicalDetailsKit &cdk);


  void drawLewisStructures(const ValenceKit<double> &vk, const NonbondedKit<double> &nbk,

                           const ChemicalDetailsKit &cdk);


  void findAromaticGroups(const ChemicalDetailsKit &cdk, const ValenceKit<double> &vk,

                          const std::vector<int> &tmp_ring_atoms,

                          const std::vector<int> &tmp_ring_atom_bounds,

                          std::vector<int> *tmp_aromatic_group_bounds,

                          std::vector<int> *tmp_aromatic_pi_electrons,

                          std::vector<int> *tmp_aromatic_groups);


  std::vector<int> detailChiralCenters(const NonbondedKit<double> &nbk,

                                       const ValenceKit<double> &vk,

                                       const ChemicalDetailsKit &cdk);


  std::vector<int> findChiralInversionMethods(const std::vector<int> &tmp_chiral_centers,

                                              const std::vector<int> &tmp_ring_atoms,

                                              const std::vector<int> &tmp_ring_atom_bounds);


  void findRotatableBonds(const ValenceKit<double> &vk, const ChemicalDetailsKit &cdk,

                          const NonbondedKit<double> &nbk, const std::vector<int> &ring_atoms,

                          const std::vector<int> &ring_atom_bounds,

                          std::vector<int> *tmp_rotatable_groups,

                          std::vector<int> *tmp_rotatable_group_bounds,

                          std::vector<int> *tmp_cis_trans_groups,

                          std::vector<int> *tmp_cis_trans_group_bounds);


  void findInvertibleGroups(const std::vector<int> &tmp_chiral_centers,

                            const std::vector<int> &tmp_inversion_methods,

                            std::vector<int> *tmp_anchor_a_branches,

                            std::vector<int> *tmp_anchor_b_branches,

                            std::vector<int> *tmp_invertible_groups,

                            std::vector<int> *tmp_invertible_group_bounds);


  void findHydrogenBondElements(const NonbondedKit<double> &nbk, const ChemicalDetailsKit &cdk,

                                std::vector<int> *tmp_polar_h, std::vector<int> *tmp_hb_don,

                                std::vector<int> *tmp_hb_acc);


  void allocateMutableData(const std::vector<int> &tmp_rotatable_groups,

                           const std::vector<int> &tmp_rotatable_group_bounds,

                           const std::vector<int> &tmp_cis_trans_groups,

                           const std::vector<int> &tmp_cis_trans_group_bounds,

                           const std::vector<int> &tmp_cis_invertible_groups,

                           const std::vector<int> &tmp_cis_invertible_group_bounds,

                           const std::vector<int> &tmp_anchor_a_branches,

                           const std::vector<int> &tmp_anchor_b_branches);


  void repairPointers();

};


void unpackRotatableGroups(const std::vector<int2> &bond_endpoints,

                           const std::vector<std::vector<int>> &moving_lists,

                           std::vector<int> *tmp_groups, std::vector<int> *tmp_group_bounds);


bool scoreChiralBranches(const std::vector<std::vector<BondedNode>> &links,

                         const std::vector<int> &layer_llim, const std::vector<int> &layer_hlim,

                         const ChemicalDetailsKit &cdk, std::vector<int> *chiral_dominance,

                         std::vector<int> *parallel_growth);


template <typename T>

int getChiralOrientation(const T* xcrd, const T* ycrd, const T* zcrd, int center_atom,

                         int root_atom, int branch_a_atom, int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const CoordinateFrameReader &cfr, int center_atom, int root_atom,

                         int branch_a_atom, int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const CoordinateFrame *cf, int center_atom, int root_atom,

                         int branch_a_atom, int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const CoordinateFrame &cf, int center_atom, int root_atom,

                         int branch_a_atom, int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const PhaseSpaceReader &psr, int center_atom, int root_atom,

                         int branch_a_atom, int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const PhaseSpace *ps, int center_atom, int root_atom, int branch_a_atom,

                         int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const PhaseSpace &ps, int center_atom, int root_atom, int branch_a_atom,

                         int branch_b_atom, int branch_c_atom);


template <typename T>

int getChiralOrientation(const CoordinateSeriesReader<T> &csr, size_t frame_index, int center_atom,

                         int root_atom, int branch_a_atom, int branch_b_atom, int branch_c_atom);


template <typename T>

int getChiralOrientation(const CoordinateSeries<T> *cs, size_t frame_index, int center_atom,

                         int root_atom, int branch_a_atom, int branch_b_atom, int branch_c_atom);


template <typename T>

int getChiralOrientation(const CoordinateSeries<T> &cs, size_t frame_index, int center_atom,

                         int root_atom, int branch_a_atom, int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const CondensateReader &cdnsr, int system_index, int center_atom,

                         int root_atom, int branch_a_atom, int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const Condensate *cdns, int system_index, int center_atom,

                         int root_atom, int branch_a_atom, int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const Condensate &cdns, int system_index, int center_atom,

                         int root_atom, int branch_a_atom, int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const PsSynthesisReader &poly_psr, int system_index, int center_atom,

                         int root_atom, int branch_a_atom, int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const PhaseSpaceSynthesis *poly_ps, int system_index, int center_atom,

                         int root_atom, int branch_a_atom, int branch_b_atom, int branch_c_atom);


int getChiralOrientation(const PhaseSpaceSynthesis &poly_ps, int system_index, int center_atom,

                         int root_atom, int branch_a_atom, int branch_b_atom, int branch_c_atom);


bool matchBondingPattern(const AtomGraph &ag, const ChemicalFeatures &chemfe, int atom_a,

                         int atom_b);


bool permutationsAreLinked(const std::vector<IsomerPlan> &isomerizers, int permi, int permj,

                           const NonbondedKit<double> &nbk);


} // namespace chemistry

} // namespace stormm


#include "chemical_features.tpp"


#endif

stormm::card::Hybrid
An evolution of GpuBuffer in pmemd.cuda, the Composite array has elements that are accessible from ei...
Definition hybrid.h:202

stormm::chemistry::BondedNode::findBranchAtom
int findBranchAtom(int search_index) const
Get the branch index of a specific atom in a BondedNode.
Definition chemical_features.cpp:137

stormm::chemistry::BondedNode::getPreviousAtom
int getPreviousAtom() const
Get the previous atom index.
Definition chemical_features.cpp:107

stormm::chemistry::BondedNode::BondedNode
BondedNode()
Basic constructor simply initializes the members to blank values.
Definition chemical_features.cpp:45

stormm::chemistry::BondedNode::getBranchAtom
int getBranchAtom(int index) const
Get the topological atom index of a specific branch that can come off of this BondedNode.
Definition chemical_features.cpp:132

stormm::chemistry::BondedNode::getPreviousNode
int getPreviousNode() const
Get the previous node's list index.
Definition chemical_features.cpp:112

stormm::chemistry::BondedNode::getBranchCount
int getBranchCount() const
Get the number of branches associated with this BondedNode's central atom (this is the total number o...
Definition chemical_features.cpp:127

stormm::chemistry::BondedNode::setBranchPointer
void setBranchPointer(std::vector< int > *vi, size_t pos, size_t max_branches)
Take a pre-existing std::vector<int> in order to set the object's own next_links pointer....
Definition chemical_features.cpp:51

stormm::chemistry::BondedNode::addBondOrder
void addBondOrder(const ValenceKit< double > &vk, const Hybrid< double > &bond_orders)
Add the bond order between this atom and its previous atom.
Definition chemical_features.cpp:90

stormm::chemistry::BondedNode::wipeRingCompletion
void wipeRingCompletion()
Wipe clean the ring completion for this object.
Definition chemical_features.cpp:164

stormm::chemistry::BondedNode::getLayer
int getLayer() const
Get the layer of which this BondedNode is a part.
Definition chemical_features.cpp:122

stormm::chemistry::BondedNode::getAtom
int getAtom() const
Get the central atom for this BondedNode.
Definition chemical_features.cpp:117

stormm::chemistry::BondedNode::setRingCompletion
void setRingCompletion(int partner_index)
Set the ring completion for this object (this relies on no atom having more bonds than the number of ...
Definition chemical_features.cpp:159

stormm::chemistry::BondedNode::getRingCompletion
uint getRingCompletion(int branch_index) const
Get the ring completion status for a particular node.
Definition chemical_features.cpp:149

stormm::chemistry::BondedNode::addToTree
void addToTree(int previous_in, int current_atom, int current_layer, const NonbondedKit< double > &nbk, const std::vector< bool > &valid_atom_mask)
Set this as the next link in the chain, or as the chain initiator.
Definition chemical_features.cpp:62

stormm::chemistry::BondedNode::getRootBondOrder
double getRootBondOrder() const
Get the bond order of the bond between this atom and the previous atom in the tree.
Definition chemical_features.cpp:154

stormm::chemistry::ChemicalFeatures
An object to store information about chemical motifs: participation in rings, planarity,...
Definition chemical_features.h:400

stormm::chemistry::ChemicalFeatures::getRotatableBondCount
int getRotatableBondCount() const
Get the number of rotatable bonds in the system.
Definition chemical_features.cpp:2690

stormm::chemistry::ChemicalFeatures::operator=
ChemicalFeatures & operator=(const ChemicalFeatures &other)
Copy assignment and move assignment operators.
Definition chemical_features.cpp:606

stormm::chemistry::ChemicalFeatures::getChiralCenters
std::vector< int > getChiralCenters(ChiralOrientation direction=ChiralOrientation::NONE) const
List the chiral centers in a system, using topological indices.
Definition chemical_features.cpp:2782

stormm::chemistry::ChemicalFeatures::getAromaticGroupCount
int getAromaticGroupCount() const
Get the number of aromatic groups in the system.
Definition chemical_features.cpp:2665

stormm::chemistry::ChemicalFeatures::getRingMask
std::vector< uint > getRingMask(int min_ring_size, int max_ring_size) const
Return a mask of rings within a given size range for this system.
Definition chemical_features.cpp:2710

stormm::chemistry::ChemicalFeatures::getHydrogenBondAcceptorList
std::vector< int > getHydrogenBondAcceptorList() const
Get a list of all hydrogen bond acceptor atoms.
Definition chemical_features.cpp:2762

stormm::chemistry::ChemicalFeatures::getPolarHydrogenCount
int getPolarHydrogenCount() const
Get the number of polar hydrogens in the system.
Definition chemical_features.cpp:2670

stormm::chemistry::ChemicalFeatures::getAromaticMask
std::vector< uint > getAromaticMask(int min_pi_electrons, int max_pi_electrons) const
Return a mask of atomatic atoms in the system.
Definition chemical_features.cpp:2731

stormm::chemistry::ChemicalFeatures::getHydrogenBondAcceptorCount
int getHydrogenBondAcceptorCount() const
Get the number of hydrogen bond acceptors in the system.
Definition chemical_features.cpp:2680

stormm::chemistry::ChemicalFeatures::getHydrogenBondAcceptorMask
std::vector< uint > getHydrogenBondAcceptorMask() const
Get a bit mask of all hydrogen bond acceptors in the system, acceptable for inputs to creating new at...
Definition chemical_features.cpp:2777

stormm::chemistry::ChemicalFeatures::getZeroKelvinFreeElectrons
const std::vector< int > & getZeroKelvinFreeElectrons() const
Return the free electron content of atoms in a representative Lewis structure of the molecules in thi...
Definition chemical_features.cpp:2957

stormm::chemistry::ChemicalFeatures::getFreeElectrons
double getFreeElectrons(int atom_index) const
Return the (resonance-averaged) free electron content for one or more atoms in the system.
Definition chemical_features.cpp:2931

stormm::chemistry::ChemicalFeatures::getFormalCharges
std::vector< double > getFormalCharges() const
Return a vector containing the formal charges on all particles in the system (this includes virtual s...
Definition chemical_features.cpp:2921

stormm::chemistry::ChemicalFeatures::chiralitiesComputed
bool chiralitiesComputed() const
Indicate whether chiralities have been determined for this set of chemical features.
Definition chemical_features.cpp:2705

stormm::chemistry::ChemicalFeatures::getFusedRingCount
int getFusedRingCount() const
Get the number of fused rings in the system.
Definition chemical_features.cpp:2655

stormm::chemistry::ChemicalFeatures::ChemicalFeatures
ChemicalFeatures(const AtomGraph *ag_in=nullptr, MapRotatableGroups map_groups_in=MapRotatableGroups::NO, double temperature_in=300.0, StopWatch *timer_in=nullptr)
The constructor requires a topology and some coordinate set.
Definition chemical_features.cpp:396

stormm::chemistry::ChemicalFeatures::data
ChemicalFeaturesReader data(HybridTargetLevel tier=HybridTargetLevel::HOST) const
Get the abstract.
Definition chemical_features.cpp:3148

stormm::chemistry::ChemicalFeatures::getAtomCount
int getAtomCount() const
Get the total number of atoms.
Definition chemical_features.cpp:2640

stormm::chemistry::ChemicalFeatures::getRotatableBondGroups
std::vector< IsomerPlan > getRotatableBondGroups() const
Get the atom endpoints of a rotatable bond. The bond root atom is returned in the x member of the tup...
Definition chemical_features.cpp:3017

stormm::chemistry::ChemicalFeatures::getPolarHydrogenList
std::vector< int > getPolarHydrogenList() const
Get a list of all polar hydrogen atoms.
Definition chemical_features.cpp:2752

stormm::chemistry::ChemicalFeatures::getZeroKelvinBondOrders
const std::vector< int > & getZeroKelvinBondOrders() const
Return the bond orders for a representative Lewis structure of the molecules in this topology.
Definition chemical_features.cpp:2952

stormm::chemistry::ChemicalFeatures::getChiralCenterCount
int getChiralCenterCount() const
Get the number of chiral centers in the system.
Definition chemical_features.cpp:2685

stormm::chemistry::ChemicalFeatures::getCisTransIsomerizationGroups
std::vector< IsomerPlan > getCisTransIsomerizationGroups() const
Get the moving atom groups and bond endpoints involved in cis-trans isomerization....
Definition chemical_features.cpp:3082

stormm::chemistry::ChemicalFeatures::getMutableRingCount
int getMutableRingCount() const
Get the number of malleable, non-aromatic twistable rings in the system.
Definition chemical_features.cpp:2660

stormm::chemistry::ChemicalFeatures::getSelfPointer
const ChemicalFeatures * getSelfPointer() const
Get a const pointer to the object itself in host memory.
Definition chemical_features.cpp:3143

stormm::chemistry::ChemicalFeatures::getHydrogenBondDonorList
std::vector< int > getHydrogenBondDonorList() const
Get a list of all hydrogen bond donor atoms.
Definition chemical_features.cpp:2757

stormm::chemistry::ChemicalFeatures::getPolarHydrogenMask
std::vector< uint > getPolarHydrogenMask() const
Get a bit mask of all polar hydrogen atoms in the system, acceptable for inputs to creating new atom ...
Definition chemical_features.cpp:2767

stormm::chemistry::ChemicalFeatures::getPlanarAtomCount
int getPlanarAtomCount() const
Get the number of planar atoms.
Definition chemical_features.cpp:2645

stormm::chemistry::ChemicalFeatures::getChiralInversionMethods
std::vector< ChiralInversionProtocol > getChiralInversionMethods() const
Get the means for inverting one or more chiral centers.
Definition chemical_features.cpp:3124

stormm::chemistry::ChemicalFeatures::getRingInclusion
ullint getRingInclusion(int atom_index) const
Return the ring inclusion specifications for one or more atoms in the system.
Definition chemical_features.cpp:2962

stormm::chemistry::ChemicalFeatures::findRotatableBondGroups
void findRotatableBondGroups(StopWatch *timer=nullptr)
Find the rotatable (and cis-trans invertible, and chiral invertible) atom groups in the topology base...
Definition chemical_features.cpp:3188

stormm::chemistry::ChemicalFeatures::getHydrogenBondDonorCount
int getHydrogenBondDonorCount() const
Get the number of hydrogen bond donors in the system.
Definition chemical_features.cpp:2675

stormm::chemistry::ChemicalFeatures::getRingCount
int getRingCount() const
Get the number of rings in the system.
Definition chemical_features.cpp:2650

stormm::chemistry::ChemicalFeatures::getChiralArmBaseAtoms
std::vector< int4 > getChiralArmBaseAtoms() const
Get the bases of each arm for all chiral centers. The result returns the lowest priority arm in the "...
Definition chemical_features.cpp:2834

stormm::chemistry::ChemicalFeatures::findChiralOrientations
void findChiralOrientations(const CoordinateFrameReader &cfr)
Find the chiral orientations of the system's chiral centers. This function will be called once by the...
Definition chemical_features.cpp:3169

stormm::chemistry::ChemicalFeatures::getChiralInversionGroups
std::vector< IsomerPlan > getChiralInversionGroups() const
Get the group of atoms that can invert a chiral center by a C2 symmetry rotation. This re-uses the Is...
Definition chemical_features.cpp:3102

stormm::chemistry::ChemicalFeatures::rotatableGroupsMapped
bool rotatableGroupsMapped() const
Indicate whether the rotatable groups (including rotatable bonds as well as cis-trans bonds) have bee...
Definition chemical_features.cpp:2700

stormm::chemistry::ChemicalFeatures::getTopologyPointer
const AtomGraph * getTopologyPointer() const
Get a pointer to the AtomGraph which built this object.
Definition chemical_features.cpp:3138

stormm::chemistry::ChemicalFeatures::getChiralityMask
std::vector< uint > getChiralityMask(ChiralOrientation direction) const
Return a mask of chiral centers in the system.
Definition chemical_features.cpp:2887

stormm::chemistry::ChemicalFeatures::getAtomChirality
ChiralOrientation getAtomChirality(int atom_index) const
Return the chiral orientations for one or more atoms in the system.
Definition chemical_features.cpp:2839

stormm::chemistry::ChemicalFeatures::getHydrogenBondDonorMask
std::vector< uint > getHydrogenBondDonorMask() const
Get a bit mask of all hydrogen bond donors in the system, acceptable for inputs to creating new atom ...
Definition chemical_features.cpp:2772

stormm::chemistry::ChemicalFeatures::getZeroKelvinFormalCharges
const std::vector< int > & getZeroKelvinFormalCharges() const
Return the formal charges for a representative Lewis structure of the molecules in this topology.
Definition chemical_features.cpp:2947

stormm::chemistry::ChemicalFeatures::getCisTransBondCount
int getCisTransBondCount() const
Get the number of bonds involved in cis-trans isomerization.
Definition chemical_features.cpp:2695

stormm::chemistry::ChemicalFeatures::bondIsInRing
bool bondIsInRing(int atom_i, int atom_j) const
Return whether a bond in the system is in a ring group or not.
Definition chemical_features.cpp:2978

stormm::chemistry::ChemicalFeatures::getBondOrders
std::vector< double > getBondOrders() const
Return a vector containing the orders of all bonds in the system (this includes bonds to virtual site...
Definition chemical_features.cpp:2926

stormm::chemistry::IsomerPlan::getRootHandle
int getRootHandle() const
Get the root atom handle (for a rotatable bond J-K, this might be I of the sequence I-J-K-L).
Definition chemical_features.cpp:260

stormm::chemistry::IsomerPlan::getMotion
ConformationEdit getMotion() const
Get the isomerizing motion.
Definition chemical_features.cpp:240

stormm::chemistry::IsomerPlan::getMovingAtom
int getMovingAtom(const size_t index) const
Get the index of an individual moving atom from within this plan.
Definition chemical_features.cpp:285

stormm::chemistry::IsomerPlan::IsomerPlan
IsomerPlan(const IsomerPlan &original)=default
The default copy and move constructors will suffice, and with no const members the copy and move assi...

stormm::chemistry::IsomerPlan::getPivotAtom
int getPivotAtom() const
Get the pivot atom for the motion.
Definition chemical_features.cpp:255

stormm::chemistry::IsomerPlan::getRootAtom
int getRootAtom() const
Get the root atom for the motion.
Definition chemical_features.cpp:250

stormm::chemistry::IsomerPlan::getMovingAtomCount
int getMovingAtomCount() const
Get the number of moving atoms.
Definition chemical_features.cpp:270

stormm::chemistry::IsomerPlan::getMovingAtomWeight
double getMovingAtomWeight() const
Get the total mass of moving atoms.
Definition chemical_features.cpp:280

stormm::chemistry::IsomerPlan::addMovingAtoms
void addMovingAtoms(const std::vector< int > &new_atom_idx)
Add atoms to the moving atoms list.
Definition chemical_features.cpp:299

stormm::chemistry::IsomerPlan::getMovingAtoms
const std::vector< int > & getMovingAtoms() const
Get a const reference to the stored list of atoms that move as a consequence of the isomerization.
Definition chemical_features.cpp:294

stormm::chemistry::IsomerPlan::getPivotHandle
int getPivotHandle() const
Get the pivot atom handle (for a rotatable bond J-K, this might be L of the sequence I-J-K-L).
Definition chemical_features.cpp:265

stormm::chemistry::IsomerPlan::getRealMovingAtomCount
int getRealMovingAtomCount() const
Get the number of real moving atoms.
Definition chemical_features.cpp:275

stormm::chemistry::IsomerPlan::eraseMovingAtoms
void eraseMovingAtoms()
Erase the list of moving atoms to start over. This will resize the vector to zero.
Definition chemical_features.cpp:304

stormm::chemistry::IsomerPlan::getChiralPlan
ChiralInversionProtocol getChiralPlan() const
Get the plan for inverting a chiral center.
Definition chemical_features.cpp:245

stormm::chemistry::IsomerPlan::IsomerPlan
IsomerPlan(ConformationEdit motion_in, ChiralInversionProtocol chiral_plan_in, int root_atom_in, int pivot_atom_in, const std::vector< int > &moving_atoms_in, const AtomGraph *ag_pointer_in)
The constructor takes all applicable arguments. Different overloads check the value of the Conformati...
Definition chemical_features.cpp:169

stormm::synthesis::Condensate
Condense the data format, and possibly offer a reduced representation of coordinates,...
Definition condensate.h:146

stormm::synthesis::PhaseSpaceSynthesis
A fixed-precision representation of coordinates, velocities, and forces to manage a set of simulation...
Definition phasespace_synthesis.h:325

stormm::testing::StopWatch
Object for managing calls to the C-standard function gettimeofday(), calculating deltas and categoriz...
Definition stopwatch.h:23

stormm::topology::AtomGraph
A struct to hold information relating to an Amber topology. This struct's member functions are limite...
Definition atomgraph.h:50

stormm::trajectory::CoordinateFrame
Store the coordinates and box information for a frame, only. This abridged struct can serve when the ...
Definition coordinateframe.h:111

stormm::trajectory::CoordinateSeries
Store the coordinates and box information for a series of frames, in one of several levels of precisi...
Definition coordinate_series.h:137

stormm::trajectory::PhaseSpace
An object to complement a topology and hold positions, velocities, and forces of all particles in a s...
Definition phasespace.h:141

stormm::chemistry::ChemicalFeaturesReader
Abstract of the chemical features object: this is about as complex as an object with a single abstrac...
Definition chemical_features.h:298

stormm::chemistry::ChemicalFeaturesReader::hydrogen_bond_acceptors
const int * hydrogen_bond_acceptors
List of topological indices for H-bond acceptors.
Definition chemical_features.h:369

stormm::chemistry::ChemicalFeaturesReader::aromatic_groups
const int * aromatic_groups
Definition chemical_features.h:363

stormm::chemistry::ChemicalFeaturesReader::invertible_group_bounds
const int * invertible_group_bounds
Bounds array for invertible_groups.
Definition chemical_features.h:382

stormm::chemistry::ChemicalFeaturesReader::hbond_donor_count
const int hbond_donor_count
Number of hydrogen bond donors.
Definition chemical_features.h:341

stormm::chemistry::ChemicalFeaturesReader::hbond_acceptor_count
const int hbond_acceptor_count
Number of hydrogen bond acceptors.
Definition chemical_features.h:342

stormm::chemistry::ChemicalFeaturesReader::conjugated_group_count
const int conjugated_group_count
Number of separate conjugated pi-systems.
Definition chemical_features.h:338

stormm::chemistry::ChemicalFeaturesReader::formal_charges
const double * formal_charges
Definition chemical_features.h:387

stormm::chemistry::ChemicalFeaturesReader::hydrogen_bond_donors
const int * hydrogen_bond_donors
Definition chemical_features.h:367

stormm::chemistry::ChemicalFeaturesReader::cis_trans_group_bounds
const int * cis_trans_group_bounds
Bounds array for cis_trans_groups.
Definition chemical_features.h:378

stormm::chemistry::ChemicalFeaturesReader::chiral_center_count
const int chiral_center_count
Number of chiral centers.
Definition chemical_features.h:343

stormm::chemistry::ChemicalFeaturesReader::ChemicalFeaturesReader
ChemicalFeaturesReader(const ChemicalFeaturesReader &original)=default
The default copy and move constructors are acceptable, but assignment operators are implicitly delete...

stormm::chemistry::ChemicalFeaturesReader::aromatic_group_count
const int aromatic_group_count
Number of distinct aromatic groups.
Definition chemical_features.h:339

stormm::chemistry::ChemicalFeaturesReader::cis_trans_bond_count
const int cis_trans_bond_count
Number of cis-trans flippable bonds.
Definition chemical_features.h:345

stormm::chemistry::ChemicalFeaturesReader::twistable_ring_count
const int twistable_ring_count
Number of twistable (i.e. boat-chair) rings.
Definition chemical_features.h:337

stormm::chemistry::ChemicalFeaturesReader::double_bond_count
const int double_bond_count
Number of double bonds.
Definition chemical_features.h:346

stormm::chemistry::ChemicalFeaturesReader::rotating_groups_mapped
const bool rotating_groups_mapped
Definition chemical_features.h:350

stormm::chemistry::ChemicalFeaturesReader::polar_hydrogen_count
const int polar_hydrogen_count
Number of polar hydrogens.
Definition chemical_features.h:340

stormm::chemistry::ChemicalFeaturesReader::aromatic_group_bounds
const int * aromatic_group_bounds
Bounds array for aromatic_groups.
Definition chemical_features.h:365

stormm::chemistry::ChemicalFeaturesReader::cis_trans_groups
const int * cis_trans_groups
Definition chemical_features.h:376

stormm::chemistry::ChemicalFeaturesReader::ring_count
const int ring_count
Number of rings.
Definition chemical_features.h:335

stormm::chemistry::ChemicalFeaturesReader::chiral_inversion_methods
const int * chiral_inversion_methods
Definition chemical_features.h:371

stormm::chemistry::ChemicalFeaturesReader::ring_atom_bounds
const int * ring_atom_bounds
Bounds array for ring_atoms.
Definition chemical_features.h:359

stormm::chemistry::ChemicalFeaturesReader::polar_hydrogens
const int * polar_hydrogens
List of topological indices for polar hydrogen atoms.
Definition chemical_features.h:366

stormm::chemistry::ChemicalFeaturesReader::planar_centers
const int * planar_centers
Topological indices of atoms with enforced planarity.
Definition chemical_features.h:356

stormm::chemistry::ChemicalFeaturesReader::chiral_arm_atoms
const int4 * chiral_arm_atoms
Definition chemical_features.h:383

stormm::chemistry::ChemicalFeaturesReader::temperature
const double temperature
Temperature at which resonance structures were computed.
Definition chemical_features.h:349

stormm::chemistry::ChemicalFeaturesReader::aromatic_pi_electrons
const int * aromatic_pi_electrons
Definition chemical_features.h:360

stormm::chemistry::ChemicalFeaturesReader::ChemicalFeaturesReader
ChemicalFeaturesReader(int atom_count_in, int planar_atom_count_in, int ring_count_in, int fused_ring_count_in, int twistable_ring_count_in, int conjugated_group_count_in, int aromatic_group_count_in, int polar_hydrogen_count_in, int hbond_donor_count_in, int hbond_acceptor_count_in, int chiral_center_count_in, int rotatable_bond_count_in, int cis_trans_bond_count_in, int double_bond_count_in, int triple_bond_count_in, int max_ring_size_in, double temperature_in, bool rotating_groups_mapped_in, bool chiralities_computed_in, const int *planar_centers_in, const int *ring_atoms_in, const int *ring_atom_bounds_in, const int *aromatic_pi_electrons_in, const int *aromatic_groups_in, const int *aromatic_group_bounds_in, const int *polar_hydrogens_in, const int *hydrogen_bond_donors_in, const int *hydrogen_bond_acceptors_in, const int *chiral_centers_in, const int *chiral_inversion_methods_in, const int *rotatable_groups_in, const int *rotatable_group_bounds_in, const int *cis_trans_groups_in, const int *cis_trans_group_bounds_in, const int *invertible_groups_in, const int *invertible_group_bounds_in, const int4 *chiral_arm_atoms_in, const double *formal_charges_in, const double *bond_orders_in, const double *free_electrons_in, const ullint *ring_inclusion_in, const AtomGraph *ag_pointer_in)
The constructor takes a straight list of critical constants and pointers.
Definition chemical_features.cpp:330

stormm::chemistry::ChemicalFeaturesReader::ag_pointer
const AtomGraph * ag_pointer
Definition chemical_features.h:394

stormm::chemistry::ChemicalFeaturesReader::chiral_centers
const int * chiral_centers
List of topological indices for chiral centers.
Definition chemical_features.h:370

stormm::chemistry::ChemicalFeaturesReader::atom_count
const int atom_count
Total number of atoms in the system.
Definition chemical_features.h:333

stormm::chemistry::ChemicalFeaturesReader::ring_atoms
const int * ring_atoms
Definition chemical_features.h:357

stormm::chemistry::ChemicalFeaturesReader::fused_ring_count
const int fused_ring_count
Number of fused rings.
Definition chemical_features.h:336

stormm::chemistry::ChemicalFeaturesReader::invertible_groups
const int * invertible_groups
Definition chemical_features.h:379

stormm::chemistry::ChemicalFeaturesReader::triple_bond_count
const int triple_bond_count
Number of triple bonds.
Definition chemical_features.h:347

stormm::chemistry::ChemicalFeaturesReader::planar_atom_count
const int planar_atom_count
Number of atoms with enforced planarity.
Definition chemical_features.h:334

stormm::chemistry::ChemicalFeaturesReader::rotatable_bond_count
const int rotatable_bond_count
Number of rotatable single bonds.
Definition chemical_features.h:344

stormm::chemistry::ChemicalFeaturesReader::bond_orders
const double * bond_orders
Definition chemical_features.h:389

stormm::chemistry::ChemicalFeaturesReader::chiralities_computed
const bool chiralities_computed
Definition chemical_features.h:352

stormm::chemistry::ChemicalFeaturesReader::max_ring_size
const int max_ring_size
The maximum ring size found.
Definition chemical_features.h:348

stormm::chemistry::ChemicalFeaturesReader::free_electrons
const double * free_electrons
Free electron content of each atom.
Definition chemical_features.h:391

stormm::chemistry::ChemicalFeaturesReader::rotatable_groups
const int * rotatable_groups
Definition chemical_features.h:373

stormm::chemistry::ChemicalFeaturesReader::rotatable_group_bounds
const int * rotatable_group_bounds
Bounds array for rotatable groups.
Definition chemical_features.h:375

stormm::chemistry::ChemicalFeaturesReader::ring_inclusion
const ullint * ring_inclusion
Definition chemical_features.h:392

stormm::chemistry::CoupledEdit::CoupledEdit
CoupledEdit(const CoupledEdit &original)=default
The copy and move constructors, as well as assignment operators, can take their default forms.

stormm::chemistry::CoupledEdit::edit
ConformationEdit edit
Definition chemical_features.h:291

stormm::chemistry::CoupledEdit::CoupledEdit
CoupledEdit()
Definition chemical_features.cpp:309

stormm::chemistry::CoupledEdit::index
int index
Index of the connected feature from whatever appropriate list.
Definition chemical_features.h:293

stormm::data_types::int2
Definition stormm_vector_types.h:22

stormm::data_types::int4
Definition stormm_vector_types.h:33

stormm::synthesis::CondensateReader
Read-only abstract for the Condensate class. In most cases, the read-only abstract will be preferred ...
Definition condensate.h:102

stormm::synthesis::PsSynthesisReader
The reader for a PhaseSpaceSynthesis object, containing all of the data relevant for propagating dyna...
Definition phasespace_synthesis.h:199

stormm::topology::ChemicalDetailsKit
Information on atoms and residues which may be useful for applying atom masks or identifying specific...
Definition atomgraph_abstracts.h:382

stormm::topology::NonbondedKit
Information needed for non-bonded real-space calculations. Templating is used as above,...
Definition atomgraph_abstracts.h:287

stormm::topology::ValenceKit
Information need for bonded calculations. Templating is used to serve either of two levels of precisi...
Definition atomgraph_abstracts.h:88

stormm::trajectory::CoordinateFrameReader
Collect C-style pointers for the elements of a read-only CoordinateFrame object.
Definition coordinateframe.h:65

stormm::trajectory::CoordinateSeriesReader
Collect C-style pointers and critical constants for a read-only CoordinateSeries object.
Definition coordinate_series.h:96

stormm::trajectory::PhaseSpaceReader
Collect constants and pointers to the components of a read-only PhaseSpace object.
Definition phasespace.h:81