/** Process a mask from the command line. */ int Cpptraj::ProcessMask( Sarray const& topFiles, Sarray const& refFiles, std::string const& maskexpr, bool verbose, bool residue ) const { SetWorldSilent(true); if (topFiles.empty()) { mprinterr("Error: No topology file specified.\n"); return 1; } ParmFile pfile; Topology parm; if (pfile.ReadTopology(parm, topFiles[0], State_.Debug())) return 1; if (!refFiles.empty()) { DataSet_Coords_REF refCoords; if (refCoords.LoadRefFromFile( refFiles[0], parm, State_.Debug())) return 1; parm.SetDistMaskRef( refCoords.RefFrame() ); } if (!verbose) { AtomMask tempMask( maskexpr ); if (parm.SetupIntegerMask( tempMask )) return 1; loudPrintf("Selected="); if (residue) { int res = -1; for (AtomMask::const_iterator atom = tempMask.begin(); atom != tempMask.end(); ++atom) { if (parm[*atom].ResNum() > res) { loudPrintf(" %i", parm[*atom].ResNum()+1); res = parm[*atom].ResNum(); } } } else for (AtomMask::const_iterator atom = tempMask.begin(); atom != tempMask.end(); ++atom) loudPrintf(" %i", *atom + 1); loudPrintf("\n"); } else { if (residue) parm.PrintResidueInfo( maskexpr ); else parm.PrintAtomInfo( maskexpr ); } return 0; }