/** 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; }