Fix spurious hybrid36 detect in PDB messages

README.md

@@ -207,6 +207,9 @@ Original code for the 'xtalsymm' Action.
 * Johannes Kraml, Franz Waibl & Klaus R. Liedl (Department of General, Inorganic, and Theoretical Chemistry, University of Innsbruck)
 Improvements and enhancements for GIST.
 
+* Nikolai Skrynnikov, Danil Yevdokimov, Olga O. Lebedenko and Ivan S. Podkorytov (Purdue University, IN)
+Fix for truncated octahedron cell solvation of large systems.
+
 #### Various Contributions
 * David A. Case (Rutgers University, Piscataway, NJ, USA)
 * Hai Nguyen (Rutgers University, Piscataway, NJ, USA)

src/PDBfile.cpp

@@ -190,13 +190,19 @@ PDBfile::PDBfile() :
   has_large_chainid_(false)
 {}
 
-/** Set atom/residue number wrap type */
+/** Set atom/residue number wrap type. Verbose, intended when setting up for writes. */
 void PDBfile::SetWrapType(NumWrapType typeIn)
 {
   wrapType_ = typeIn;
   mprintf("\tPDB atom/residue number out of range mode: %s\n", NumWrapTypeStr_[wrapType_]);
 }
 
+/** Set atom/residue number wrap type. Silent, intended when setting up for reads. */
+void PDBfile::SetWrapTypeSilent(NumWrapType typeIn)
+{
+  wrapType_ = typeIn;
+}
+
 // PDBfile::IsPDBkeyword()
 /** \return true if given string is a recognized PDB record keyword.
   * PDB record keywords are typically 6 characters long (including spaces),

src/PDBfile.h

@@ -19,6 +19,8 @@ class PDBfile : public CpptrajFile {
 
     /// Set out of range atom/residue number wrap type
     void SetWrapType(NumWrapType);
+    /// Set out of range atom/residue number wrap type (silent)
+    void SetWrapTypeSilent(NumWrapType);
 
     /// Check if either of the first two lines contain valid PDB records.
     static bool ID_PDB(CpptrajFile&);

src/Parm_PDB.cpp

@@ -57,6 +57,8 @@ int Parm_PDB::ReadParm(FileName const& fname, Topology &TopIn) {
   int barray[5];                // Hold CONECT atom and bonds
   char altLoc = ' ';            // For reading in altLoc.
   Frame Coords;
+  // Wrap type is not known a priori; it will be detected if present.
+  infile.SetWrapTypeSilent(PDBfile::RESET);
   // Determine if CONECT records should be read.
   bool readConect;
   if (ConectMode_ == SKIP)

src/Traj_PDBfile.cpp

@@ -90,6 +90,8 @@ int Traj_PDBfile::setupTrajin(FileName const& fname, Topology* trajParm)
     mprintf("\tWhen present, only reading alternate location ID %c\n", keepAltLoc_);
   int atom;
   pdbWriteMode_ = NONE;
+  // Wrap type is not known a priori; it will be detected if present.
+  file_.SetWrapTypeSilent(PDBfile::RESET);
   if (file_.SetupRead( fname, debug_ )) return TRAJIN_ERR;
   if (file_.OpenFile()) return TRAJIN_ERR;
   // Two strats - check for MODEL keywords or see how many times natom ATOM

src/Version.h

@@ -12,7 +12,7 @@
  * Whenever a number that precedes <revision> is incremented, all subsequent
  * numbers should be reset to 0.
  */
-#define CPPTRAJ_INTERNAL_VERSION "V7.6.0"
+#define CPPTRAJ_INTERNAL_VERSION "V7.6.1"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif