Add the 'keep' action. Opposite of 'strip'; can also be used to only …

…keep bridging waters from 'hbond' (#957)

* Start adding Keep action

* Start parsing bridge ID set

* Start testing keep

* Add modified topology and frame

* Start modifying top and frame

* Add topwriter

* Indices in bridge res ID data start from 1

* Start keep tests

* Add test for bridge with keepmask

* Allow keepmask to work on its own

* Make nobox option a part of ActionTopWriter

* Add basic test for keep, use strip test save

* Add nobox to other ActionTopWriter actions

* Add residue status array. Check that bridging residue specified by data
set was also specified as a bridge residue for command.

* Start adding bridgeresonly; allow fine tuning of what atoms to keep when
keeping bridging waters

* Ensure that only the requested number of bridges are retained (fewer or
more will invalidate the topology)

* Add test keeping only 1 bridging water

* Actually set the status

* Add keep two bridging waters at specified residues test

* Reorganize vars to keep everything set in Init in one place

* Fix up help

* Test reading in hb bridge data

* Add 'keep' entry. Fix actions table to indicate when actions modify
state (like strip).

* Hide some debug info. Improve warnings

* Add nobridgewarn option

* Add nobridgewarn to manual

* Enable keep test and protect in parallel. Add warning when run in
parallel with bridgedata

* 6.4.3. Revision bump for addition of keep action.

* Add code docs

src/ActionTopWriter.cpp

@@ -1,27 +1,39 @@
 #include "ActionTopWriter.h"
+#include "ActionState.h"
 #include "ArgList.h"
+#include "CoordinateInfo.h"
 #include "CpptrajStdio.h"
 #include "Topology.h"
 #include "ParmFile.h"
 
-static const char* keywords_ = "\t[outprefix <prefix>] [parmout <filename>]\n"
-                               "\t[parmopts <comma-separated-list>]\n";
-static const char* options_ = 
-          "    outprefix <prefix> : Write modified topology to <prefix>.<originalname>\n"
-          "    parmout <filename> : Write modified topology to <filename>\n"
-          "    parmopts <list>    : Options for writing topology file\n";
+const char* ActionTopWriter::keywords_ =
+  "\t[outprefix <prefix>] [nobox] [parmout <filename>]\n"
+  "\t[parmopts <comma-separated-list>]\n";
+const char* ActionTopWriter::options_ = 
+  "    outprefix <prefix> : Write modified topology to <prefix>.<originalname>\n"
+  "    nobox              : If specified, remove box information from topology\n"
+  "    parmout <filename> : Write modified topology to <filename>\n"
+  "    parmopts <list>    : Options for writing topology file\n";
 
 const char* ActionTopWriter::Keywords() { return keywords_; }
 const char* ActionTopWriter::Options() { return options_; }
 
 /** CONSTRUCTOR */
 ActionTopWriter::ActionTopWriter() :
-  debug_(0)
+  debug_(0),
+  removeBoxInfo_(false),
+  newCinfo_(0)
 {}
 
+/** DESTRUCTOR */
+ActionTopWriter::~ActionTopWriter() {
+  if (newCinfo_ != 0) delete newCinfo_;
+}
+
 /** Parse arguments. */
 int ActionTopWriter::InitTopWriter(ArgList& argIn, const char* typeStrIn, int debugIn) {
   debug_ = debugIn;
+  removeBoxInfo_ = argIn.hasKey("nobox");
   prefix_ = argIn.GetStringKey("outprefix");
   parmoutName_ = argIn.GetStringKey("parmout");
   parmOpts_ = argIn.GetStringKey("parmopts");
@@ -35,6 +47,8 @@ int ActionTopWriter::InitTopWriter(ArgList& argIn, const char* typeStrIn, int de
 
 /** Print arguments to stdout. */
 void ActionTopWriter::PrintOptions() const {
+  if (removeBoxInfo_)
+    mprintf("\tAny existing box information will be removed.\n");
   if (!prefix_.empty())
     mprintf("\tWriting '%s' topology file with prefix '%s'\n", typeStr_.c_str(), prefix_.c_str());
   if (!parmoutName_.empty())
@@ -72,3 +86,26 @@ int ActionTopWriter::WriteTops(Topology const& topIn) const {
   }
   return err;
 }
+
+/** Modify given ActionSetup. */
+int ActionTopWriter::ModifyActionState(ActionSetup& setup, Topology* topIn)
+{
+  // Remove box information if asked
+  if (removeBoxInfo_) {
+    topIn->SetParmBox( Box() );
+    newCinfo_ = new CoordinateInfo( setup.CoordInfo() );
+    newCinfo_->SetBox( Box() );
+    setup.SetCoordInfo( newCinfo_ );
+  }
+  return 0;
+}
+
+/** Modify given Topology only. */
+int ActionTopWriter::ModifyTop(Topology* topIn)
+{
+  // Remove box information if asked
+  if (removeBoxInfo_) {
+    topIn->SetParmBox( Box() );
+  }
+  return 0;
+}

src/ActionTopWriter.h

@@ -2,12 +2,15 @@
 #define INC_ACTIONTOPWRITER_H
 #include <string>
 // Forward declares
+class ActionSetup;
 class ArgList;
+class CoordinateInfo;
 class Topology;
 /// Class to hold common functionality for actions that will write modified topologies.
 class ActionTopWriter {
   public:
     ActionTopWriter();
+    ~ActionTopWriter();
 
     static const char* Keywords();
     static const char* Options();
@@ -18,11 +21,20 @@ class ActionTopWriter {
     void PrintOptions() const;
     /// Write the Topology to file(s)
     int WriteTops(Topology const&) const;
+    /// Remove box information from Topology/CoordinateInfo
+    int ModifyActionState(ActionSetup&, Topology*);
+    /// Remove box information from Topology
+    int ModifyTop(Topology*);
   private:
     std::string prefix_;      ///< Prefix for writing topology as <prefix>.<originalname>
     std::string parmoutName_; ///< Output topology file name
     std::string parmOpts_;    ///< Topology file write args
     std::string typeStr_;     ///< Label for kind of topology being written.
     int debug_;               ///< Debug level to pass to Topology file writer.
+    bool removeBoxInfo_;       ///< If true, remove box information from Topology/CoordinateInfo
+    CoordinateInfo* newCinfo_; ///< Hold any modified CoordinateInfo
+
+    static const char* keywords_;
+    static const char* options_;
 };
 #endif

src/Action_Closest.cpp

@@ -295,6 +295,9 @@ Action::RetType Action_Closest::Setup(ActionSetup& setup) {
     return Action::ERR;
   }
   setup.SetTopology( newParm_ );
+  // Remove box information if asked
+  if (topWriter_.ModifyActionState(setup, newParm_))
+    return Action::ERR;
   newParm_->Brief("Closest topology:");
   // Allocate space for new frame
   newFrame_.SetupFrameV( setup.Top().Atoms(), setup.CoordInfo() );

src/Action_FixAtomOrder.cpp

@@ -83,8 +83,11 @@ Action::RetType Action_FixAtomOrder::Setup(ActionSetup& setup) {
     mprinterr("Error: Could not create re-ordered topology.\n");
     return Action::ERR;
   }
-  newParm_->Brief("Re-ordered parm:");
   setup.SetTopology( newParm_ );
+  // Remove box information if asked
+  if (topWriter_.ModifyActionState(setup, newParm_))
+    return Action::ERR;
+  newParm_->Brief("Re-ordered parm:");
   // Allocate space for new frame
   newFrame_.SetupFrameV( setup.Top().Atoms(), setup.CoordInfo() );