/** Like the strip action, closest will modify the current parm keeping info
* for atoms in mask plus the closestWaters solvent molecules. Set up the
* vector of MolDist objects, one for every solvent molecule in the original
* parm file. Atom masks for each solvent molecule will be set up.
*/
Action_Closest::RetType Action_Closest::Setup(Topology const& topIn, CoordinateInfo const& cInfoIn)
{
// If there are no solvent molecules this action is not valid.
if (topIn.Nsolvent()==0) {
mprintf("Warning: Parm %s does not contain solvent.\n",topIn.c_str());
return Action_Closest::SKIP;
}
// If # solvent to keep >= solvent in this parm the action is not valid.
if (closestWaters_ >= topIn.Nsolvent()) {
mprintf("Warning: # solvent to keep (%i) >= # solvent molecules in '%s' (%i)\n",
closestWaters_, topIn.c_str(), topIn.Nsolvent());
return Action_Closest::SKIP;
}
image_.SetupImaging( cInfoIn.TrajBox().Type() );
if (image_.ImagingEnabled())
mprintf("\tDistances will be imaged.\n");
else
mprintf("\tImaging off.\n");
// LOOP OVER MOLECULES
// 1: Check that all solvent molecules contain same # atoms. Solvent
// molecules must be identical for the command to work properly;
// the prmtop strip occurs only once so the solvent params become fixed.
// 2: Set up a mask for all solvent molecules.
SolventMols_.clear();
// NOTE: May not be necessary to init 'solvent'
MolDist solvent;
solvent.D = 0.0;
solvent.mol = 0;
SolventMols_.resize(topIn.Nsolvent(), solvent);
std::vector<MolDist>::iterator mdist = SolventMols_.begin();
// 3: Set up the soluteMask for all non-solvent molecules.
int molnum = 1;
int nclosest = 0;
int NsolventAtoms = -1;
for (Topology::mol_iterator Mol = topIn.MolStart();
Mol != topIn.MolEnd(); ++Mol)
{
if ( Mol->IsSolvent() ) {
// Solvent, check for same # of atoms.
if (NsolventAtoms == -1)
NsolventAtoms = Mol->NumAtoms();
else if ( NsolventAtoms != Mol->NumAtoms() ) {
mprinterr("Error: Solvent molecules in '%s' are not of uniform size.\n"
"Error: First solvent mol = %i atoms, solvent mol %i = %i atoms.\n",
topIn.c_str(), NsolventAtoms, molnum, (*Mol).NumAtoms());
return Action_Closest::ERR;
}
// mol here is the output molecule number which is why it starts from 1.
mdist->mol = molnum;
// Solvent molecule mask
mdist->mask.AddAtomRange( Mol->BeginAtom(), Mol->EndAtom() );
// Atoms in the solvent molecule to actually calculate distances to.
if (firstAtom_) {
mdist->solventAtoms.assign(1, Mol->BeginAtom() );
} else {
mdist->solventAtoms.clear();
mdist->solventAtoms.reserve( Mol->NumAtoms() );
for (int svatom = Mol->BeginAtom(); svatom < Mol->EndAtom(); svatom++)
mdist->solventAtoms.push_back( svatom );
}
if (debug_ > 0) {
mprintf("DEBUG:\tSet up mol %i:", mdist->mol); // DEBUG
mdist->mask.PrintMaskAtoms("solvent"); // DEBUG
mprintf("\n"); // DEBUG
}
++mdist;
}
++molnum;
}
// Setup distance atom mask
// NOTE: Should ensure that no solvent atoms are selected!
if ( topIn.SetupIntegerMask(distanceMask_) ) return Action_Closest::ERR;
if (distanceMask_.None()) {
mprintf("Warning: Distance mask '%s' contains no atoms.\n",
distanceMask_.MaskString());
return Action_Closest::SKIP;
}
distanceMask_.MaskInfo();
// Check the total number of solvent atoms to be kept.
NsolventAtoms *= closestWaters_;
mprintf("\tKeeping %i solvent atoms.\n",NsolventAtoms);
if (NsolventAtoms < 1) {
mprintf("Warning: # of solvent atoms to be kept is < 1.\n");
return Action_Closest::SKIP;
}
NsolventMolecules_ = (int)SolventMols_.size();
return Action_Closest::OK;
}
// Action_RandomizeIons::Setup()
Action::RetType Action_RandomizeIons::Setup(ActionSetup& setup) {
n_solvent_ = setup.Top().Nsolvent();
if (n_solvent_ < 1) {
mprinterr("Error: This command only works if solvent information has been specified.\n");
return Action::ERR;
}
// Set up ion mask
if (setup.Top().SetupIntegerMask( ions_ )) return Action::ERR;
if ( ions_.None() ) {
mprintf("Warning: Ion mask '%s' has no atoms.\n", ions_.MaskString());
return Action::SKIP;
}
mprintf("\tIon mask is '%s' (%i atoms)\n", ions_.MaskString(), ions_.Nselected());
// Set up the around mask if necessary
if (around_.MaskStringSet()) {
if (setup.Top().SetupIntegerMask( around_ )) return Action::ERR;
if ( around_.None() ) {
mprintf("Warning: Around mask '%s' has no atoms.\n", around_.MaskString());
} else {
mprintf("\tAround mask is '%s' (%i atoms)\n", around_.MaskString(),
around_.Nselected());
}
}
// Check that each ion is only a single atom residue.
// NOTE: Should this be a molecule check instead? If so can then get rid of ResSize
for (AtomMask::const_iterator ion = ions_.begin(); ion != ions_.end(); ++ion)
{
int res = setup.Top()[*ion].ResNum();
if (debug_ > 0)
mprintf("\tAtom %i is in residue %i which is %i atoms\n",
*ion+1, res+1, setup.Top().Res( res ).NumAtoms() );
if ( setup.Top().Res( res ).NumAtoms() > 1 ) {
mprintf("Warning: randomizeions: Ion atom %i belongs to residue %i which\n",
*ion + 1, res + 1);
mprintf("Warning: contains more than 1 atom (%i)!\n",
setup.Top().Res( res ).NumAtoms());
}
}
// Check the solvent information to make sure that each solvent listed has the
// same number of atoms in each molecule; otherwise a uniform trajectory is not
// possible and therefore this command will be ignored.
// Also save the start and end atom of each solvent molecule.
int NsolventAtoms = -1;
solventStart_.clear();
solventEnd_.clear();
solventStart_.reserve( n_solvent_ );
solventEnd_.reserve( n_solvent_ );
for (Topology::mol_iterator Mol = setup.Top().MolStart();
Mol != setup.Top().MolEnd(); ++Mol)
{
if ( Mol->IsSolvent() ) {
if (NsolventAtoms == -1)
NsolventAtoms = Mol->NumAtoms();
else if ( NsolventAtoms != Mol->NumAtoms() ) {
mprinterr("Error: Solvent molecules in %s are not of uniform size.\n",
setup.Top().c_str());
mprinterr("Error: First solvent mol = %i atoms, this solvent mol = %i atoms.\n",
NsolventAtoms, Mol->NumAtoms());
return Action::ERR;
}
solventStart_.push_back( Mol->BeginAtom() );
solventEnd_.push_back( Mol->EndAtom() );
}
}
image_.SetupImaging( setup.CoordInfo().TrajBox().Type() );
// Allocate solvent molecule mask
solvent_.resize( n_solvent_ );
return Action::OK;
}