Add support for reading/writing Hybrid36 fields from PDB files (Amber-MD#1171)

* Adapt hybrid36 routines from https://raw.githubusercontent.com/cctbx/cctbx_project/master/iotbx/pdb/hybrid_36_c.c

* Fix issue comparing int to unsigned

* Start adding a hybrid36 mode

* Add hybrid36 keyword

* Update depends

* Ensure error messages from h36 are trapped

* Add hybrid36 to SSBOND/CONECT; allow overflow for these instead of reset to match original behavior when wrap is RESET

* Add the flush command

* Automatically detect and decode hybrid36 fields

* Print message if hybrid36 detected on read

* Make hybrid36 the default

* V7.3.0. Hybrid36 is now the default for large PDBs

* Add note about Hybrid36 code origin to README

* Add specific author

---------

Co-authored-by: Daniel R. Roe <daniel.roe@nih.gov>

Author: drroe

README.md

@@ -250,3 +250,5 @@ External code/libraries bundled with CPPTRAJ
 * The code for quaternion RMSD calculation was adapted from code in [qcprot.c](https://theobald.brandeis.edu/qcp/qcprot.c) originally written by Douglas L. Theobald and Pu Lio (Brandeis University).
 
 * The code for reading numpy arrays in `src/libnpy` is from [libnpy](https://github.com/llohse/libnpy) written by Leon Merten Lohse et al. (Universität Göttingen).
+
+* The code for reading/writing atom/residue number fields in large PDB files (in `Hybrid36.cpp`) is adapted from code written by Ralf W. Grosse-Kunstleve in the Computational Crystallography Toolbox, https://doi.org/10.1107/S0021889801017824, https://raw.githubusercontent.com/cctbx/cctbx_project/master/iotbx/pdb/hybrid_36_c.c

src/Command.cpp

@@ -41,6 +41,7 @@
 #include "Exec_Random.h"
 #include "Exec_CompareClusters.h"
 #include "Exec_ParseTiming.h"
+#include "Exec_Flush.h"
 // ----- SYSTEM ----------------------------------------------------------------
 #include "Exec_System.h"
 // ----- COORDS ----------------------------------------------------------------
@@ -245,6 +246,7 @@ void Command::Init() {
   Command::AddCmd( new Exec_DataSetCmd(),      Cmd::EXE, 1, "dataset" );
   Command::AddCmd( new Exec_EnsFileExt(),      Cmd::EXE, 1, "ensextension" );
   Command::AddCmd( new Exec_Flatten(),         Cmd::EXE, 1, "flatten" );
+  Command::AddCmd( new Exec_Flush(),           Cmd::EXE, 1, "flush" );
   Command::AddCmd( new Exec_GenerateAmberRst(),Cmd::EXE, 1, "rst" );
   Command::AddCmd( new Exec_Help(),            Cmd::EXE, 1, "help" );
   Command::AddCmd( new Exec_ListAll(),         Cmd::EXE, 1, "list" );

src/DataFileList.cpp

@@ -356,6 +356,17 @@ void DataFileList::List() const {
   }
 }
 
+/** Call write for all data files. and close out and clear all CpptrajFiles. */
+void DataFileList::Flush() {
+  WriteAllDF();
+  for (CFarray::iterator it = cfList_.begin(); it != cfList_.end(); ++it) {
+    (*it)->CloseFile();
+    delete *it;
+  }
+  cfList_.clear();
+  cfData_.clear();
+}
+
 // DataFileList::WriteAllDF()
 /** Call write for all DataFiles in list for which writeFile is true. Once
   * a file has been written set writeFile to false; it can be reset to

src/DataFileList.h

@@ -70,6 +70,8 @@ class DataFileList {
     void List() const;
     /// Write all DataFiles in list that have not yet been written.
     void WriteAllDF();
+    /// Write all DataFiles and close out all CpptrajFiles
+    void Flush();
     /// \return true if DataFiles have not yet been written.
     bool UnwrittenData() const;
     /// Reset the write status of all DataFiles so they will be written

src/Exec_Flush.cpp

@@ -0,0 +1,15 @@
+#include "Exec_Flush.h"
+#include "CpptrajStdio.h"
+
+// Exec_Flush::Help()
+void Exec_Flush::Help() const
+{
+  mprintf("  Write any pending data files; close all other files.\n");
+}
+
+// Exec_Flush::Execute()
+Exec::RetType Exec_Flush::Execute(CpptrajState& State, ArgList& argIn)
+{
+  State.DFL().Flush();
+  return CpptrajState::OK;
+}

src/Exec_Flush.h

@@ -0,0 +1,12 @@
+#ifndef INC_EXEC_FLUSH_H
+#define INC_EXEC_FLUSH_H
+#include "Exec.h"
+/// <Enter description of Exec_Flush here>
+class Exec_Flush : public Exec {
+  public:
+    Exec_Flush() : Exec(GENERAL) {}
+    void Help() const;
+    DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Flush(); }
+    RetType Execute(CpptrajState&, ArgList&);
+};
+#endif