/** Attempt to set up all actions in the action list with the given parm
* If an action cannot be set up skip it.
*/
int ActionList::SetupActions(Topology **ParmAddress) {
if (actionlist_.empty()) return 0;
Topology *OriginalParm = *ParmAddress;
mprintf(".....................................................\n");
mprintf("ACTION SETUP FOR PARM '%s' (%zu actions):\n",(*ParmAddress)->c_str(),actionlist_.size());
if (actionsAreSilent_) SetWorldSilent( true );
unsigned int actnum = 0;
for (Aarray::iterator act = actionlist_.begin(); act != actionlist_.end(); ++act)
{
// Only attempt to set up action if active
if (actionstatus_[actnum] != INACTIVE) {
mprintf(" %u: [%s]\n", actnum, actioncmd_[actnum].c_str());
actionstatus_[actnum] = SETUP;
Action::RetType err = (*act)->Setup(*ParmAddress, ParmAddress);
if (err == Action::ERR) {
mprintf("Warning: Setup failed for [%s]: Skipping\n",
actioncmd_[actnum].c_str());
// Reset action status to INIT (pre-setup)
actionstatus_[actnum] = INIT;
} else if (err == Action::USEORIGINALFRAME) {
*ParmAddress = OriginalParm;
}
}
++actnum;
}
if (actionsAreSilent_) SetWorldSilent( false );
return 0;
}
// ActionList::AddAction()
int ActionList::AddAction(DispatchObject::DispatchAllocatorType Alloc, ArgList& argIn,
TopologyList* PFL, DataSetList* DSL, DataFileList* DFL)
{
int err = 0;
if (actionsAreSilent_) SetWorldSilent( true );
Action* act = (Action*)Alloc();
// Attempt to initialize action
if ( act->Init( argIn, PFL, DSL, DFL, debug_ ) != Action::OK ) {
mprinterr("Error: Could not initialize action [%s]\n", argIn.Command());
delete act;
err = 1;
} else {
actionlist_.push_back( act );
actioncmd_.push_back( argIn.ArgLine() );
actionAlloc_.push_back( Alloc );
actionstatus_.push_back( INIT );
if (argIn.CheckForMoreArgs()) err = 1;
}
if (actionsAreSilent_) SetWorldSilent( false );
return err;
}
/** 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;
}
/** Read command line args. */
Cpptraj::Mode Cpptraj::ProcessCmdLineArgs(int argc, char** argv) {
bool hasInput = false;
bool interactive = false;
Sarray inputFiles;
Sarray topFiles;
Sarray trajinFiles;
Sarray trajoutFiles;
Sarray refFiles;
for (int i = 1; i < argc; i++) {
std::string arg(argv[i]);
if ( arg == "--help" || arg == "-h" ) {
// --help, -help: Print usage and exit
SetWorldSilent(true);
Usage();
return QUIT;
}
if ( arg == "-V" || arg == "--version" ) {
// -V, --version: Print version number and exit
SetWorldSilent( true );
loudPrintf("CPPTRAJ: Version %s\n", CPPTRAJ_VERSION_STRING);
return QUIT;
}
if ( arg == "--internal-version" ) {
// --internal-version: Print internal version number and quit.
SetWorldSilent( true );
loudPrintf("CPPTRAJ: Internal version # %s\n", CPPTRAJ_INTERNAL_VERSION);
return QUIT;
}
if ( arg == "--defines" ) {
// --defines: Print information on compiler defines used and exit
SetWorldSilent( true );
loudPrintf("Compiled with:");
loudPrintf("%s\n", Cpptraj::Defines().c_str());
return QUIT;
}
if (arg == "-tl") {
// -tl: Trajectory length
if (topFiles.empty()) {
mprinterr("Error: No topology file specified.\n");
return ERROR;
}
SetWorldSilent( true );
if (State_.TrajLength( topFiles[0], trajinFiles )) return ERROR;
return QUIT;
}
if ( arg == "--interactive" )
interactive = true;
else if ( arg == "-debug" && i+1 != argc) {
// -debug: Set overall debug level
ArgList dbgarg( argv[++i] );
State_.SetListDebug( dbgarg );
} else if ( arg == "--log" && i+1 != argc)
// --log: Set up log file for interactive mode
logfilename_ = argv[++i];
else if ( arg == "-p" && i+1 != argc) {
// -p: Topology file
topFiles.push_back( argv[++i] );
} else if ( arg == "-y" && i+1 != argc) {
// -y: Trajectory file in
trajinFiles.push_back( argv[++i] );
} else if ( arg == "-x" && i+1 != argc) {
// -x: Trajectory file out
trajoutFiles.push_back( argv[++i] );
} else if ( arg == "-c" && i+1 != argc) {
// -c: Reference file
refFiles.push_back( argv[++i] );
} else if (arg == "-i" && i+1 != argc) {
// -i: Input file(s)
inputFiles.push_back( argv[++i] );
} else if (arg == "-ms" && i+1 != argc) {
// -ms: Parse mask string, print selected atom #s
if (ProcessMask( topFiles, refFiles, std::string(argv[++i]), false, false )) return ERROR;
return QUIT;
} else if (arg == "-mr" && i+1 != argc) {
// -mr: Parse mask string, print selected res #s
if (ProcessMask( topFiles, refFiles, std::string(argv[++i]), false, true )) return ERROR;
return QUIT;
} else if (arg == "--mask" && i+1 != argc) {
// --mask: Parse mask string, print selected atom details
if (ProcessMask( topFiles, refFiles, std::string(argv[++i]), true, false )) return ERROR;
return QUIT;
} else if (arg == "--resmask" && i+1 != argc) {
// --resmask: Parse mask string, print selected residue details
if (ProcessMask( topFiles, refFiles, std::string(argv[++i]), true, true )) return ERROR;
return QUIT;
} else if ( i == 1 ) {
// For backwards compatibility with PTRAJ; Position 1 = TOP file
topFiles.push_back( argv[i] );
} else if ( i == 2 ) {
// For backwards compatibility with PTRAJ; Position 2 = INPUT file
inputFiles.push_back( argv[i] );
} else {
// Unrecognized
mprintf(" Unrecognized input on command line: %i: %s\n", i,argv[i]);
Usage();
return ERROR;
}
}
Cpptraj::Intro();
// Add all topology files specified on command line.
for (Sarray::const_iterator topFilename = topFiles.begin();
topFilename != topFiles.end();
++topFilename)
if (State_.AddTopology( *topFilename, ArgList() )) return ERROR;
// Add all reference trajectories specified on command line.
for (Sarray::const_iterator refName = refFiles.begin();
refName != refFiles.end();
++refName)
if (State_.AddReference( *refName )) return ERROR;
// Add all input trajectories specified on command line.
for (Sarray::const_iterator trajinName = trajinFiles.begin();
trajinName != trajinFiles.end();
++trajinName)
if (State_.AddTrajin( *trajinName )) return ERROR;
// Add all output trajectories specified on command line.
if (!trajoutFiles.empty()) {
hasInput = true; // This allows direct traj conversion with no other input
for (Sarray::const_iterator trajoutName = trajoutFiles.begin();
trajoutName != trajoutFiles.end();
++trajoutName)
if (State_.AddOutputTrajectory( *trajoutName )) return ERROR;
}
// Process all input files specified on command line.
if ( !inputFiles.empty() ) {
hasInput = true;
for (Sarray::const_iterator inputFilename = inputFiles.begin();
inputFilename != inputFiles.end();
++inputFilename)
{
Command::RetType c_err = Command::ProcessInput( State_, *inputFilename );
if (c_err == Command::C_ERR && State_.ExitOnError()) return ERROR;
if (c_err == Command::C_QUIT) return QUIT;
}
}
// Determine whether to enter interactive mode
if (!hasInput || interactive) {
// Test if input is really from a console
if ( isatty(fileno(stdin)) )
return INTERACTIVE;
else {
// "" means read from STDIN
Command::RetType c_err = Command::ProcessInput( State_, "" );
if (c_err == Command::C_ERR && State_.ExitOnError()) return ERROR;
if (c_err == Command::C_QUIT) return QUIT;
}
}
return BATCH;
}
// ----- M A I N ---------------------------------------------------------------
int main(int argc, char** argv) {
SetWorldSilent(true); // No STDOUT output from cpptraj routines.
std::string topname, crdname, title, bres, pqr, sybyltype, writeconect;
std::string aatm(" pdbatom"), ter_opt(" terbyres"), box(" sg \"P 1\"");
TrajectoryFile::TrajFormatType fmt = TrajectoryFile::PDBFILE;
bool ctr_origin = false;
bool useExtendedInfo = false;
int res_offset = 0;
int debug = 0;
int numSoloArgs = 0;
for (int i = 1; i < argc; ++i) {
std::string arg( argv[i] );
if (arg == "-p" && i+1 != argc && topname.empty()) // Topology
topname = std::string( argv[++i] );
else if (arg == "-c" && i+1 != argc && crdname.empty()) // Coords
crdname = std::string( argv[++i] );
else if (arg == "-tit" && i+1 != argc && title.empty()) // Title
title = " title " + std::string( argv[++i] );
else if (arg == "-offset" && i+1 != argc) // Residue # offset
res_offset = convertToInteger( argv[++i] );
else if ((arg == "-d" || arg == "--debug") && i+1 != argc) // Debug level
debug = convertToInteger( argv[++i] );
else if (arg == "-h" || arg == "--help") { // Help
Help(argv[0], true);
return 0;
} else if (arg == "-v" || arg == "--version") { // Version info
WriteVersion();
return 0;
} else if (arg == "-aatm") // Amber atom names, include extra pts
aatm.assign(" include_ep");
else if (arg == "-sybyl") // Amber atom types to SYBYL
sybyltype.assign(" sybyltype");
else if (arg == "-conect") // Write CONECT records from bond info
writeconect.assign(" conect");
else if (arg == "-ep") // PDB atom names, include extra pts
aatm.append(" include_ep");
else if (arg == "-bres") // PDB residue names
bres.assign(" pdbres");
else if (arg == "-ext") // Use extended PDB info from Topology
useExtendedInfo = true;
else if (arg == "-ctr") // Center on origin
ctr_origin = true;
else if (arg == "-noter") // No TER cards
ter_opt.assign(" noter");
else if (arg == "-nobox") // No CRYST1 record
box.assign(" nobox");
else if (arg == "-pqr") { // Charge/Radii in occ/bfactor cols
pqr.assign(" dumpq");
++numSoloArgs;
} else if (arg == "-mol2") { // output as mol2
fmt = TrajectoryFile::MOL2FILE;
++numSoloArgs;
} else if (Unsupported(arg)) {
mprinterr("Error: Option '%s' is not yet supported.\n\n", arg.c_str());
return 1;
} else {
mprinterr("Error: Unrecognized option '%s'\n", arg.c_str());
Help(argv[0], false);
return 1;
}
}
if (debug > 0) WriteVersion();
// Check command line for errors.
if (topname.empty()) topname.assign("prmtop");
if (debug > 0 && crdname.empty())
mprinterr("| Reading Amber restart from STDIN\n");
if (numSoloArgs > 1) {
mprinterr("Error: Only one alternate output format option may be specified (found %i)\n",
numSoloArgs);
Help(argv[0], true);
return 1;
}
if (!sybyltype.empty() && fmt != TrajectoryFile::MOL2FILE) {
mprinterr("Warning: -sybyl is only valid for MOL2 file output.\n");
sybyltype.clear();
}
if (debug > 0) {
mprinterr("Warning: debug is %i; debug info will be written to STDOUT.\n", debug);
SetWorldSilent(false);
}
// Topology
ParmFile pfile;
Topology parm;
if (pfile.ReadTopology(parm, topname, debug)) {
if (topname == "prmtop") Help(argv[0], false);
return 1;
}
if (!useExtendedInfo)
parm.ResetPDBinfo();
if (res_offset != 0)
for (int r = 0; r < parm.Nres(); r++)
parm.SetRes(r).SetOriginalNum( parm.Res(r).OriginalResNum() + res_offset );
ArgList trajArgs;
// Input coords
Frame TrajFrame;
CoordinateInfo cInfo;
if (!crdname.empty()) {
Trajin_Single trajin;
if (trajin.SetupTrajRead(crdname, trajArgs, &parm)) return 1;
cInfo = trajin.TrajCoordInfo();
TrajFrame.SetupFrameV(parm.Atoms(), cInfo);
trajin.BeginTraj();
if (trajin.ReadTrajFrame(0, TrajFrame)) return 1;
trajin.EndTraj();
} else {
// Assume Amber restart from STDIN
// Check that input is from a redirect.
if ( isatty(fileno(stdin)) ) {
mprinterr("Error: No coordinates specified with '-c' and no STDIN '<'.\n");
return 1;
}
Traj_AmberRestart restartIn;
restartIn.SetDebug( debug );
//restartIn.processReadArgs( trajArgs );
int total_frames = restartIn.setupTrajin("", &parm);
if (total_frames < 1) return 1;
cInfo = restartIn.CoordInfo();
TrajFrame.SetupFrameV(parm.Atoms(), cInfo);
if (restartIn.openTrajin()) return 1;
if (restartIn.readFrame(0, TrajFrame)) return 1;
restartIn.closeTraj();
}
if (ctr_origin)
TrajFrame.CenterOnOrigin(false);
// Output coords
Trajout_Single trajout;
trajArgs.SetList( aatm + bres + pqr + title + ter_opt + box + sybyltype + writeconect, " " );
if ( trajout.PrepareStdoutTrajWrite(trajArgs, &parm, cInfo, 1, fmt) ) return 1;
trajout.WriteSingle(0, TrajFrame);
trajout.EndTraj();
return 0;
}
