// ReferenceAction::InitRef()
int ReferenceAction::InitRef(bool previousIn, bool firstIn, bool massIn, bool fitIn,
std::string const& reftrajname, ReferenceFrame const& REF,
Topology* RefParm, std::string const& refmaskIn,
ArgList& actionArgs, const char* call)
{
refmode_ = UNKNOWN_REF;
previous_ = previousIn;
if (firstIn || previous_)
refmode_ = FIRST;
else {
if (REF.error()) return 1;
if (REF.empty()) {
if (!reftrajname.empty()) {
if (RefParm == 0) {
mprinterr("Error: %s: No parm found for reftraj %s. Make sure parm has been loaded.\n",
call, reftrajname.c_str());
return 1;
}
refmode_ = REFTRAJ;
} else {
// No reference keywords specified. Default to first.
mprintf("Warning: %s: No reference structure given. Defaulting to first.\n",call);
refmode_ = FIRST;
}
} else
refmode_ = REFFRAME;
}
// Set the reference mask expression
refMask_.SetMaskString(refmaskIn);
// Initialize reference if not 'first'
if (refmode_ != FIRST) {
if ( !reftrajname.empty() ) {
// Reference trajectory
if (SetRefMask( *RefParm, call )!=0) return 1;
// Attempt to open reference traj.
if (refTraj_.SetupTrajRead( reftrajname, actionArgs, RefParm)) {
mprinterr("Error: %s: Could not set up reftraj %s\n", call, reftrajname.c_str());
return 1;
}
refFrame_.SetupFrameV(RefParm->Atoms(), refTraj_.TrajCoordInfo());
if (refTraj_.BeginTraj()) {
mprinterr("Error: %s: Could not open reftraj %s\n", call, reftrajname.c_str());
return 1;
}
} else {
// Reference Frame
if (SetRefMask( REF.Parm(), call ) != 0) return 1;
SetRefStructure( REF.Coord(), fitIn, massIn );
}
}
// Set reference mode string
if (previous_)
modeString_ = "previous frame";
else if (refmode_ == FIRST)
modeString_ = "first frame";
else if (refmode_==REFTRAJ)
modeString_ = "trajectory " + refTraj_.Traj().Filename().Full();
else // REFFRAME
modeString_ = "\"" + REF.RefName() + "\"";
modeString_ += " (" + refMask_.MaskExpression() + ")";
return 0;
}
