diff --git a/README.md b/README.md index e2655e5b50..921e3d9ea1 100644 --- a/README.md +++ b/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) diff --git a/src/PDBfile.cpp b/src/PDBfile.cpp index d6cc421427..4d1638300f 100644 --- a/src/PDBfile.cpp +++ b/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), diff --git a/src/PDBfile.h b/src/PDBfile.h index 718eecf8cf..09a76ee992 100644 --- a/src/PDBfile.h +++ b/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&); diff --git a/src/Parm_PDB.cpp b/src/Parm_PDB.cpp index 73cd2077d9..96996a5c24 100644 --- a/src/Parm_PDB.cpp +++ b/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) diff --git a/src/Traj_PDBfile.cpp b/src/Traj_PDBfile.cpp index 9c4cc315b0..9c67e6d588 100644 --- a/src/Traj_PDBfile.cpp +++ b/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 diff --git a/src/Version.h b/src/Version.h index ff93a2f878..22db6c9b55 100644 --- a/src/Version.h +++ b/src/Version.h @@ -12,7 +12,7 @@ * Whenever a number that precedes 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