Exec::RetType Exec_ParmStrip::Execute(CpptrajState& State, ArgList& argIn) {
Topology* parm = State.DSL().GetTopByIndex( argIn );
if (parm == 0) return CpptrajState::ERR;
// Check if this topology has already been used to set up an input
// trajectory, as this will break the traj read.
bool topology_in_use = false;
const char* fname = 0;
for (TrajinList::trajin_it tIn = State.InputTrajList().trajin_begin();
tIn != State.InputTrajList().trajin_end(); ++tIn)
if ( (*tIn)->Traj().Parm() == parm ) {
topology_in_use = true;
fname = (*tIn)->Traj().Filename().full();
break;
}
if (!topology_in_use) {
for (TrajinList::ensemble_it eIn = State.InputTrajList().ensemble_begin();
eIn != State.InputTrajList().ensemble_end(); ++eIn)
if ( (*eIn)->Traj().Parm() == parm ) {
topology_in_use = true;
fname = (*eIn)->Traj().Filename().full();
break;
}
}
if (topology_in_use) {
mprinterr("Error: Topology '%s' has already been used to set up trajectory '%s'.\n"
"Error: To strip this topology use the 'strip' action.\n",
parm->c_str(), fname);
return CpptrajState::ERR;
}
AtomMask tempMask( argIn.GetMaskNext() );
// Since want to keep atoms outside mask, invert selection
tempMask.InvertMaskExpression();
if (parm->SetupIntegerMask( tempMask )) return CpptrajState::ERR;
mprintf("\tStripping atoms in mask [%s] (%i) from %s\n",tempMask.MaskString(),
parm->Natom() - tempMask.Nselected(), parm->c_str());
Topology* tempParm = parm->modifyStateByMask(tempMask);
if (tempParm==0) {
mprinterr("Error: %s: Could not strip parm.\n", argIn.Command());
return CpptrajState::ERR;
} else {
// Replace parm with stripped version
*parm = *tempParm;
parm->Brief("Stripped parm:");
delete tempParm;
}
return CpptrajState::OK;
}
Exec::RetType Exec_LoadTraj::Execute(CpptrajState& State, ArgList& argIn) {
// Get Keywords
std::string setname = argIn.GetStringKey("name");
if (setname.empty()) {
mprinterr("Error: Must provide data set name ('name <setname>')\n");
return CpptrajState::ERR;
}
DataSet_Coords_TRJ* trj = (DataSet_Coords_TRJ*)
State.DSL().FindSetOfType(setname, DataSet::TRAJ);
if (trj == 0)
trj = (DataSet_Coords_TRJ*)
State.DSL().AddSet(DataSet::TRAJ, setname, "__DTRJ__");
if (trj == 0) {
mprinterr("Error: Could not set up TRAJ data set.\n");
return CpptrajState::ERR;
}
std::string trajname = argIn.GetStringNext();
if (trajname.empty()) {
// Add all existing input trajectories
if (State.InputTrajList().empty()) {
mprinterr("Error: No input trajectories loaded.\n");
return CpptrajState::ERR;
}
if (State.InputTrajList().Mode() != TrajinList::NORMAL) {
mprinterr("Error: Cannot convert ensemble input trajectories to data.\n");
return CpptrajState::ERR;
}
mprintf("\tSaving currently loaded input trajectories as data set with name '%s'\n",
setname.c_str());
for (TrajinList::trajin_it Trajin = State.InputTrajList().trajin_begin();
Trajin != State.InputTrajList().trajin_end(); ++Trajin)
if (trj->AddInputTraj( *Trajin )) return CpptrajState::ERR;
// TODO: Clear input trajectories from trajinList?
} else {
// Add the named trajectory
if (trj->AddSingleTrajin( trajname, argIn, State.DSL().GetTopology(argIn) ))
return CpptrajState::ERR;
}
return CpptrajState::OK;
}
/** Set up variable with value. In this case allow any amount of whitespace,
* so re-tokenize the original argument line (minus the command).
*/
CpptrajState::RetType
Control_Set::SetupControl(CpptrajState& State, ArgList& argIn, Varray& CurrentVars)
{
ArgList remaining = argIn.RemainingArgs();
size_t pos0 = remaining.ArgLineStr().find_first_of("=");
if (pos0 == std::string::npos) {
mprinterr("Error: Expected <var>=<value>\n");
return CpptrajState::ERR;
}
size_t pos1 = pos0;
bool append = false;
if (pos0 > 0 && remaining.ArgLineStr()[pos0-1] == '+') {
pos0--;
append = true;
}
std::string variable = NoWhitespace( remaining.ArgLineStr().substr(0, pos0) );
if (variable.empty()) {
mprinterr("Error: No variable name.\n");
return CpptrajState::ERR;
}
ArgList equals( NoLeadingWhitespace(remaining.ArgLineStr().substr(pos1+1)) );
std::string value;
if (equals.Contains("inmask")) {
AtomMask mask( equals.GetStringKey("inmask") );
Topology* top = State.DSL().GetTopByIndex( equals );
if (top == 0) return CpptrajState::ERR;
if (top->SetupIntegerMask( mask )) return CpptrajState::ERR;
if (equals.hasKey("atoms"))
value = integerToString( mask.Nselected() );
else if (equals.hasKey("residues")) {
int curRes = -1;
int nres = 0;
for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) {
int res = (*top)[*at].ResNum();
if (res != curRes) {
nres++;
curRes = res;
}
}
value = integerToString( nres );
} else if (equals.hasKey("molecules")) {
int curMol = -1;
int nmol = 0;
for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) {
int mol = (*top)[*at].MolNum();
if (mol != curMol) {
nmol++;
curMol = mol;
}
}
value = integerToString( nmol );
} else {
mprinterr("Error: Expected 'atoms', 'residues', or 'molecules'.\n");
return CpptrajState::ERR;
}
} else if (equals.hasKey("trajinframes")) {
value = integerToString(State.InputTrajList().MaxFrames());
} else
value = equals.ArgLineStr();
if (append)
CurrentVars.AppendVariable( "$" + variable, value );
else
CurrentVars.UpdateVariable( "$" + variable, value );
mprintf("\tVariable '%s' set to '%s'\n", variable.c_str(), value.c_str());
for (int iarg = 0; iarg < argIn.Nargs(); iarg++)
argIn.MarkArg( iarg );
return CpptrajState::OK;
}