/** Sets the temporary charge array and makes sure that we have the necessary
* parameters in our topology to calculate nonbonded energy terms
*/
int Action_LIE::SetupParms(Topology const& ParmIn) {
if (!ParmIn.Nonbond().HasNonbond()) {
mprinterr("Error: Topology does not have LJ information.\n");
return 1;
}
// Store the charges
atom_charge_.clear();
atom_charge_.reserve( ParmIn.Natom() );
for (Topology::atom_iterator atom = ParmIn.begin();
atom != ParmIn.end(); ++atom)
atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER / sqrt(dielc_) );
return 0;
}
/** Sets the temporary charge array and makes sure that we have the necessary
* parameters in our topology to calculate nonbonded energy terms
*/
int Action_Spam::SetupParms(Topology* ParmIn) {
// Store the charges
atom_charge_.clear();
atom_charge_.reserve( ParmIn->Natom() );
for (Topology::atom_iterator atom = ParmIn->begin();
atom != ParmIn->end(); ++atom)
atom_charge_.push_back( atom->Charge() * Constants::ELECTOAMBER );
if (!ParmIn->Nonbond().HasNonbond()) {
mprinterr("Error: SPAM: Parm does not have LJ information.\n");
return 1;
}
return 0;
}
int Analysis_Matrix::NMWizOutput() const {
// Check # vecs
int nvecs;
if (nmwizvecs_ <= modes_->Nmodes())
nvecs = nmwizvecs_;
else {
mprintf("Warning: nmwizvecs > # eigenvectors, only writing %i vecs.\n",
modes_->Nmodes());
nvecs = modes_->Nmodes();
}
// Check # atoms
if (nmwizParm_.Natom() * 3 != modes_->VectorSize()) {
mprinterr("Error: nmwiz topology size %i does not match eigenvector size %i.\n",
nmwizParm_.Natom() * 3, modes_->VectorSize());
return 1;
}
nmwizfile_->Printf("nmwiz_load %s\n", nmwizfile_->Filename().full());
nmwizfile_->Printf("name default_name\n"); //TODO: get from optionally provided pdb file
nmwizfile_->Printf("atomnames ");
for (Topology::atom_iterator atom = nmwizParm_.begin(); atom != nmwizParm_.end(); ++atom)
nmwizfile_->Printf("%s ", atom->c_str());
nmwizfile_->Printf("\n");
nmwizfile_->Printf("resnames ");
for (Topology::atom_iterator atom = nmwizParm_.begin(); atom != nmwizParm_.end(); ++atom)
nmwizfile_->Printf("%s ", nmwizParm_.Res(atom->ResNum()).c_str());
nmwizfile_->Printf("\n");
nmwizfile_->Printf("resids ");
for (Topology::atom_iterator atom = nmwizParm_.begin(); atom != nmwizParm_.end(); ++atom)
nmwizfile_->Printf("%d ", atom->ResNum()+1);
nmwizfile_->Printf("\n");
nmwizfile_->Printf("chainids \n"); //TODO: get from optionally provided pdb file
nmwizfile_->Printf("bfactors \n"); //TODO: get from optionally provided pdb file
nmwizfile_->Printf("coordinates ");
for (int i = 0; i < modes_->NavgCrd(); ++i)
nmwizfile_->Printf("%8.3f ", modes_->AvgCrd()[i]);
nmwizfile_->Printf("\n");
for (int vec = 0; vec < nvecs; ++vec){
nmwizfile_->Printf("mode %i %12.10f ", vec+1, 1/modes_->Eigenvalue(vec));
const double* Vec = modes_->Eigenvector(vec);
for (int i = 0 ; i < modes_->VectorSize(); ++i)
nmwizfile_->Printf("%12.5f ", Vec[i]);
nmwizfile_->Printf("\n");
}
return 0;
}
int Parm_CharmmPsf::WriteParm(FileName const& fname, Topology const& parm) {
// TODO: CMAP etc info
CpptrajFile outfile;
if (outfile.OpenWrite(fname)) return 1;
// Write PSF
outfile.Printf("PSF\n\n");
// Write title
std::string titleOut = parm.ParmName();
titleOut.resize(78);
outfile.Printf("%8i !NTITLE\n* %-78s\n\n", 1, titleOut.c_str());
// Write NATOM section
outfile.Printf("%8i !NATOM\n", parm.Natom());
unsigned int idx = 1;
// Make fake segment ids for now.
char segid[2];
segid[0] = 'A';
segid[1] = '\0';
mprintf("Warning: Assigning single letter segment IDs.\n");
int currentMol = 0;
bool inSolvent = false;
for (Topology::atom_iterator atom = parm.begin(); atom != parm.end(); ++atom, ++idx) {
int resnum = atom->ResNum();
if (atom->MolNum() != currentMol) {
if (!inSolvent) {
inSolvent = parm.Mol(atom->MolNum()).IsSolvent();
currentMol = atom->MolNum();
segid[0]++;
} else
inSolvent = parm.Mol(atom->MolNum()).IsSolvent();
}
// TODO: Print type name for xplor-like PSF
int typeindex = atom->TypeIndex() + 1;
// If type begins with digit, assume charmm numbers were read as
// type. Currently Amber types all begin with letters.
if (isdigit(atom->Type()[0]))
typeindex = convertToInteger( *(atom->Type()) );
// ATOM# SEGID RES# RES ATNAME ATTYPE CHRG MASS (REST OF COLUMNS ARE LIKELY FOR CMAP AND CHEQ)
outfile.Printf("%8i %-4s %-4i %-4s %-4s %4i %14.6G %9g %10i\n", idx, segid,
parm.Res(resnum).OriginalResNum(), parm.Res(resnum).c_str(),
atom->c_str(), typeindex, atom->Charge(),
atom->Mass(), 0);
}
outfile.Printf("\n");
// Write NBOND section
outfile.Printf("%8u !NBOND: bonds\n", parm.Bonds().size() + parm.BondsH().size());
idx = 1;
for (BondArray::const_iterator bond = parm.BondsH().begin();
bond != parm.BondsH().end(); ++bond, ++idx)
{
outfile.Printf("%8i%8i", bond->A1()+1, bond->A2()+1);
if ((idx % 4)==0) outfile.Printf("\n");
}
for (BondArray::const_iterator bond = parm.Bonds().begin();
bond != parm.Bonds().end(); ++bond, ++idx)
{
outfile.Printf("%8i%8i", bond->A1()+1, bond->A2()+1);
if ((idx % 4)==0) outfile.Printf("\n");
}
if ((idx % 4)!=0) outfile.Printf("\n");
outfile.Printf("\n");
// Write NTHETA section
outfile.Printf("%8u !NTHETA: angles\n", parm.Angles().size() + parm.AnglesH().size());
idx = 1;
for (AngleArray::const_iterator ang = parm.AnglesH().begin();
ang != parm.AnglesH().end(); ++ang, ++idx)
{
outfile.Printf("%8i%8i%8i", ang->A1()+1, ang->A2()+1, ang->A3()+1);
if ((idx % 3)==0) outfile.Printf("\n");
}
for (AngleArray::const_iterator ang = parm.Angles().begin();
ang != parm.Angles().end(); ++ang, ++idx)
{
outfile.Printf("%8i%8i%8i", ang->A1()+1, ang->A2()+1, ang->A3()+1);
if ((idx % 3)==0) outfile.Printf("\n");
}
if ((idx % 3)==0) outfile.Printf("\n");
outfile.Printf("\n");
// Write out NPHI section
outfile.Printf("%8u !NPHI: dihedrals\n", parm.Dihedrals().size() + parm.DihedralsH().size());
idx = 1;
for (DihedralArray::const_iterator dih = parm.DihedralsH().begin();
dih != parm.DihedralsH().end(); ++dih, ++idx)
{
outfile.Printf("%8i%8i%8i%8i", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1);
if ((idx % 2)==0) outfile.Printf("\n");
}
for (DihedralArray::const_iterator dih = parm.Dihedrals().begin();
dih != parm.Dihedrals().end(); ++dih, ++idx)
{
outfile.Printf("%8i%8i%8i%8i", dih->A1()+1, dih->A2()+1, dih->A3()+1, dih->A4()+1);
if ((idx % 2)==0) outfile.Printf("\n");
}
if ((idx % 2)==0) outfile.Printf("\n");
outfile.Printf("\n");
outfile.CloseFile();
return 0;
}
