Speed and functionality improvements for 'hbond' command

src/Action_Hbond.h

@@ -1,121 +0,0 @@
-#ifndef INC_ACTION_HBOND_H
-#define INC_ACTION_HBOND_H
-#include <vector>
-#include <map>
-#include <set>
-#include "Action.h"
-#include "ImagedAction.h"
-#include "DataSet_integer.h"
-/// Action to calculate the Hbonds present in each frame.
-class Action_Hbond : public Action {
-  public:
-    Action_Hbond();
-    DispatchObject* Alloc() const { return (DispatchObject*)new Action_Hbond(); }
-    void Help() const;
-  private:
-    Action::RetType Init(ArgList&, ActionInit&, int);
-    Action::RetType Setup(ActionSetup&);
-    Action::RetType DoAction(int, ActionFrame&);
-#   ifdef MPI
-    int SyncAction();
-    Parallel::Comm trajComm_;
-#   endif
-    void Print();
-
-    struct HbondType {
-      double dist;  ///< Used to calc avg distance of this hbond
-      double angle; ///< Used to calc avg angle of this hbond
-      DataSet_integer* data_; ///< If series, keep track of frames hbond is present.
-      int A;        ///< Acceptor atom#
-      int H;        ///< Hydrogen atom#
-      int D;        ///< Donor atom#
-      int Frames;   ///< # frames this hbond has been present
-    };
-
-    ImagedAction Image_;
-    Matrix_3x3 ucell_, recip_;
-    int debug_;
-    int Nframes_;
-    CpptrajFile* avgout_;
-    CpptrajFile* solvout_;
-    CpptrajFile* bridgeout_;
-    DataFile* UUseriesout_;
-    DataFile* UVseriesout_;
-    bool useAtomNum_;
-    typedef std::map<int,HbondType> HBmapType;
-    HBmapType HbondMap_;   ///< Track all solute-solute hbonds found
-    HBmapType SolventMap_; ///< Track all solute-solvent hbonds found
-    typedef std::map< std::set<int>, int > BridgeType;
-    BridgeType BridgeMap_; ///< Track all combos of residues bridged by solvent.
-    typedef std::vector<int> HBlistType;
-    HBlistType Donor_;                 ///< Array of hbond donor atoms (D0, H0, D1, H1, ...)
-    HBlistType Acceptor_;              ///< Array of hbond acceptor atoms (A0, A1, ...)
-    HBlistType SolventDonor_;
-    HBlistType SolventAcceptor_;
-    AtomMask Mask_;
-    AtomMask DonorMask_;
-    AtomMask DonorHmask_;
-    AtomMask AcceptorMask_;
-    AtomMask SolventDonorMask_;
-    AtomMask SolventAcceptorMask_;
-    bool hasDonorMask_;
-    bool hasDonorHmask_;
-    bool hasAcceptorMask_;
-    bool hasSolventDonor_;
-    bool hasSolventAcceptor_;
-    bool calcSolvent_;
-    bool noIntramol_;
-    double acut_;
-    double dcut2_;
-    Topology* CurrentParm_;
-
-    bool series_;
-    bool seriesUpdated_;
-    std::string hbsetname_;
-    DataSet* NumHbonds_;
-    DataSet* NumSolvent_;
-    DataSet* NumBridge_;
-    DataSet* BridgeID_;
-    // TODO: Replace these with new DataSet type
-    DataSetList* masterDSL_;
-    /// Return true if the first hbond has more frames than the second.
-    /** If both have the same # of frames, pick something arbitrary just to
-      * be sure that we have a well-defined ordering (otherwise we could get
-      * spurious test failures) -- Order equivalent frames based on atom number
-      * of Acceptor.
-      */
-    struct hbond_cmp {
-      inline bool operator()(HbondType const& first, HbondType const& second) const {
-        if (first.Frames == second.Frames)
-          return (first.dist < second.dist);
-        else
-          return (first.Frames > second.Frames);
-      }
-    };
-    /// Return true if first bridge has more frames than second.
-    struct bridge_cmp {
-      inline bool operator()(std::pair< std::set<int>, int> const& first, 
-                             std::pair< std::set<int>, int> const& second) const
-      {
-        if (first.second > second.second)
-          return true;
-        else if (first.second < second.second)
-          return false;
-        else
-          return (first.second < second.second);
-      }
-    };
-
-    void SearchAcceptor(HBlistType&,AtomMask&,bool);
-    void SearchDonor(HBlistType&,AtomMask&,bool,bool);
-    std::string MemoryUsage(size_t, size_t) const;
-    void UpdateSeries();
-    inline int AtomsAreHbonded(Frame const&, int, int, int, int, int,bool);
-    inline void HbondTypeCalcAvg(HbondType&);
-    inline double ImagedAngle(const double*, const double*, const double*) const;
-#   ifdef MPI
-    void SyncMap(HBmapType&, std::vector<int> const&, std::vector<int> const&,
-                 const char*, Parallel::Comm const&) const;
-#   endif
-};
-#endif