// Action_Esander::Init()
Action::RetType Action_Esander::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
trajComm_ = init.TrajComm();
# endif
SANDER_.SetDebug( debugIn );
Init_ = init;
// Get keywords
outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
save_forces_ = actionArgs.hasKey("saveforces");
ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
if (REF.error()) return Action::ERR;
if (!REF.empty()) {
refFrame_ = REF.Coord();
currentParm_ = REF.ParmPtr();
}
if (SANDER_.SetInput( actionArgs )) return Action::ERR;
// DataSet name and array
setname_ = actionArgs.GetStringNext();
if (setname_.empty())
setname_ = init.DSL().GenerateDefaultName("ENE");
Esets_.clear();
Esets_.resize( (int)Energy_Sander::N_ENERGYTYPES, 0 );
mprintf(" ESANDER: Calculating energy using Sander.\n");
mprintf("\tTemporary topology file name is '%s'\n", SANDER_.TopFilename().full());
if (save_forces_) mprintf("\tSaving force information to frame.\n");
mprintf("\tReference for initialization");
if (!REF.empty())
mprintf(" is '%s'\n", REF.refName());
else
mprintf(" will be first frame.\n");
return Action::OK;
}
// Action_Unwrap::Init()
Action::RetType Action_Unwrap::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Get Keywords
center_ = actionArgs.hasKey("center");
if (actionArgs.hasKey("bymol"))
imageMode_ = Image::BYMOL;
else if (actionArgs.hasKey("byres"))
imageMode_ = Image::BYRES;
else if (actionArgs.hasKey("byatom")) {
imageMode_ = Image::BYATOM;
// Unwrapping to center by atom makes no sense
if (center_) center_ = false;
} else
imageMode_ = Image::BYATOM;
// Get reference
ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
if (REF.error()) return Action::ERR;
if (!REF.empty()) {
RefFrame_ = REF.Coord();
// Get reference parm for frame
RefParm_ = REF.ParmPtr();
}
// Get mask string
maskExpression_ = actionArgs.GetMaskNext();
mprintf(" UNWRAP: By %s", Image::ModeString(imageMode_));
if (!maskExpression_.empty())
mprintf(" using mask '%s'", maskExpression_.c_str());
else
mprintf(" using all atoms");
if (imageMode_ != Image::BYATOM) {
if (center_)
mprintf(" based on center of mass.");
else
mprintf(" based on first atom position.");
}
mprintf("\n");
if ( !REF.empty())
mprintf("\tReference is %s", REF.refName());
else
mprintf("\tReference is first frame.");
mprintf("\n");
return Action::OK;
}
/** Called once before traj processing. Set up reference info. */
Action::RetType Action_Rmsd::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
debug_ = debugIn;
// Check for keywords
fit_ = !actionArgs.hasKey("nofit");
if (fit_)
rotate_ = !actionArgs.hasKey("norotate");
useMass_ = actionArgs.hasKey("mass");
DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
bool saveMatrices = actionArgs.hasKey("savematrices");
// Reference keywords
bool previous = actionArgs.hasKey("previous");
bool first = actionArgs.hasKey("first");
ReferenceFrame refFrm = init.DSL().GetReferenceFrame( actionArgs );
std::string reftrajname = actionArgs.GetStringKey("reftraj");
if (!reftrajname.empty())
RefParm_ = init.DSL().GetTopology( actionArgs );
// Per-res keywords
perres_ = actionArgs.hasKey("perres");
if (perres_) {
perresout_ = init.DFL().AddDataFile( actionArgs.GetStringKey("perresout") );
perresinvert_ = actionArgs.hasKey("perresinvert");
TgtRange_.SetRange( actionArgs.GetStringKey("range") );
RefRange_.SetRange( actionArgs.GetStringKey("refrange") );
perresmask_ = actionArgs.GetStringKey("perresmask");
if (perresmask_.empty())
perresmask_.assign("");
else {
// If perresmask does not start with ampersand, insert one.
if (perresmask_[0] != '&')
perresmask_ = '&' + perresmask_;
}
perrescenter_ = actionArgs.hasKey("perrescenter");
perresavg_ = init.DFL().AddDataFile( actionArgs.GetStringKey("perresavg") );
}
// Get the RMS mask string for target
std::string tMaskExpr = actionArgs.GetMaskNext();
tgtMask_.SetMaskString(tMaskExpr);
// Get the RMS mask string for reference
std::string rMaskExpr = actionArgs.GetMaskNext();
if (rMaskExpr.empty())
rMaskExpr = tMaskExpr;
// Initialize reference
if (REF_.InitRef(previous, first, useMass_, fit_, reftrajname, refFrm,
RefParm_, rMaskExpr, actionArgs, "rmsd"))
return Action::ERR;
// Set RefParm for perres if not empty
if (perres_ && RefParm_ == 0 && !refFrm.empty())
RefParm_ = refFrm.ParmPtr();
// Set up the RMSD data set.
MetaData md( actionArgs.GetStringNext(), MetaData::M_RMS );
rmsd_ = init.DSL().AddSet(DataSet::DOUBLE, md, "RMSD");
if (rmsd_==0) return Action::ERR;
// Add dataset to data file list
if (outfile != 0) outfile->AddDataSet( rmsd_ );
// Set up rotation matrix data set if specified
if (saveMatrices) {
md.SetAspect("RM");
if (!fit_) {
mprinterr("Error: Must be fitting in order to save rotation matrices.\n");
return Action::ERR;
}
rmatrices_ = init.DSL().AddSet(DataSet::MAT3X3, md);
if (rmatrices_ == 0) return Action::ERR;
}
mprintf(" RMSD: (%s), reference is %s", tgtMask_.MaskString(),
REF_.RefModeString());
if (!fit_)
mprintf(", no fitting");
else {
mprintf(", with fitting");
if (!rotate_)
mprintf(" (no rotation)");
}
if (useMass_)
mprintf(", mass-weighted");
mprintf(".\n");
if (rmatrices_ != 0)
mprintf("\tRotation matrices will be saved to set '%s'\n", rmatrices_->legend());
// Per-residue RMSD info.
if (perres_) {
mprintf(" No-fit RMSD will also be calculated for ");
if (TgtRange_.Empty())
mprintf("each solute residue");
else
mprintf("residues %s",TgtRange_.RangeArg());
if (!RefRange_.Empty())
mprintf(" (reference residues %s)",RefRange_.RangeArg());
mprintf(" using mask [:X%s].\n",perresmask_.c_str());
if (perresout_ != 0)
mprintf(" Per-residue output file is %s\n",perresout_->DataFilename().base());
if (perresavg_ != 0)
mprintf(" Avg per-residue output file is %s\n",perresavg_->DataFilename().base());
if (perrescenter_)
mprintf(" perrescenter: Each residue will be centered prior to RMS calc.\n");
if (perresinvert_)
mprintf(" perresinvert: Frames will be written in rows instead of columns.\n");
}
if (perres_)
init.DSL().SetDataSetsPending(true);
masterDSL_ = init.DslPtr();
return Action::OK;
}