csg_dlptopol.cc

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/*
 * Copyright 2009-2023 The VOTCA Development Team (http://www.votca.org)
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */
 
// Standard includes
#include <fstream>
#include <iostream>
 
// Third party includes
#include <boost/format.hpp>
 
// Local VOTCA includes
#include "votca/csg/csgapplication.h"
 
using namespace votca::csg;
using namespace std;

 
class DLPTopolApp : public CsgApplication {
 public:
  string ProgramName() override { return "csg_dlptopol"; }
  void HelpText(ostream &out) override {
    out << "Create a dlpoly topology template based on an existing (atomistic) "
           "topology and \n"
        << "a mapping xml-file. The created template file needs to be "
           "inspected and amended by the user!\n\n"
        << "Examples:\n"
        << "* csg_dlptopol --top .dlpf --out .dlpf --cg cg-map.xml\n  convert "
           "FIELD to FIELD_CGV using cg-map.xml\n"
        << "* csg_dlptopol --top FA-dlpoly.dlpf --out CG-dlpoly.dlpf --cg "
           "cg-map.xml\n"
        << "* csg_dlptopol --top FA-gromacs.tpr --out FA-dlpoly.dlpf "
           "--no-map\n";
  }
 
  bool DoMapping(void) override { return true; }
 
  void Initialize(void) override;
  bool EvaluateOptions(void) override {
    CsgApplication::EvaluateOptions();
    CheckRequired("out", "no output topology specified");
    return true;
  }
  bool EvaluateTopology(Topology *top, Topology *top_ref) override;
 
 protected:
  void WriteMoleculeAtoms(ostream &out, const Molecule &cg);
  void WriteMoleculeInteractions(ostream &out, const Molecule &cg);
  void WriteVDWInteractions(ostream &out, const Molecule &cg);
  void WriteMolecularType(ostream &out, const Molecule &cg,
                          votca::Index nummol);
};
 
void DLPTopolApp::Initialize(void) {
  CsgApplication::Initialize();
  // AddProgramOptions()
  //("top", boost::program_options::value<string>(),
  //"  input topology in any known format:\n  <name>.dlpf for dlpoly, <name>.tpr
  // for gromacs\n  (convention: '.dlpf'='use FIELD')");
  AddProgramOptions()("out", boost::program_options::value<string>(),
                      "  output topology in dlpoly format");
}
 
bool DLPTopolApp::EvaluateTopology(Topology *top, Topology *) {
  // check the file names from options
 
  string fname = OptionsMap()["top"].as<string>();
 
  if (fname == ".dlpf") {
    fname = "FIELD";
  }
 
  cout << "input  file-name: " << fname << endl;
 
  fname = OptionsMap()["out"].as<string>();
 
#ifndef NDEBUG
  cout << "output file-name given: " << fname << endl;
#endif
 
  if (fname == ".dlpf") {
    fname = "FIELD_CGV";
  }
 
#ifndef NDEBUG
  cout << "output file-name actual: " << fname << endl;
#else
  cout << "output file-name: " << fname << endl;
#endif
 
  // do CG mapping
 
  MoleculeContainer &mols = top->Molecules();
  std::vector<const Molecule *> MolecularTypes;
 
  votca::Index prv_mol_number = 1;
  string prv_mol_name;
  vector<votca::Index> nummols;
 
  vector<string> vdw_pairs;
 
  // find all unique molecular types
 
  for (const auto &mol : mols) {
    // molecules are ignored during the mapping stage
    // i.e. the ignored ones do not enter the CG topology (*top) - ?
    // if( IsIgnored(mol->getName()) ) continue;
 
    if (mol.getName() == prv_mol_name) {
      prv_mol_number++;
      continue;
    }
 
    nummols.push_back(prv_mol_number);
    prv_mol_number = 1;
    prv_mol_name = mol.getName();
 
    cout << "'" << mol.getName() << "' added to CG molecular types" << endl;
 
    MolecularTypes.push_back(&mol);
 
    // collect unique bead pairs over all molecular types found
 
    for (votca::Index ib1 = 0; ib1 < mol.BeadCount(); ib1++) {
      string bead_name1 = mol.getBead(ib1)->getType();
      bead_name1 = bead_name1.substr(
          0,
          bead_name1.find_first_of("#"));  // skip #index of atom from its name
 
      for (const auto &MolecularType : MolecularTypes) {
 
        for (votca::Index ib2 = 0; ib2 < MolecularType->BeadCount(); ib2++) {
 
          string bead_name2 = MolecularType->getBead(ib2)->getType();
          bead_name2 = bead_name2.substr(
              0, bead_name2.find_first_of("#"));  // skip #index of atom from
                                                  // its name
 
          stringstream ss_bp1, ss_bp2;
 
          ss_bp1 << boost::format("%8s%8s") % bead_name1 % bead_name2;
          ss_bp2 << boost::format("%8s%8s") % bead_name2 % bead_name1;
 
          bool is_new_pair = true;
 
          for (const auto &vdw_pair : vdw_pairs) {
            if (ss_bp1.str() == vdw_pair || ss_bp2.str() == vdw_pair) {
              is_new_pair = false;
              break;
            }
          }
          if (is_new_pair) {
            vdw_pairs.push_back(ss_bp1.str());
#ifndef NDEBUG
            cout << "'" << ss_bp1.str() << "' added to CG vdw pairs" << endl;
#endif
          }
        }
      }
    }
  }
  nummols.push_back(prv_mol_number);
 
  if (MolecularTypes.size() > 1) {
    cout << "WARNING: creation of topology for multiple molecular types "
            "is experimental at this stage\n";
  }
 
  ofstream fl;
  fl.open(fname);
 
  fl << "From VOTCA with love"
     << " # check/amend this file if needed!\n";
  fl << "units kJ\n";
  fl << "molecular types " << MolecularTypes.size() << endl;
 
  for (votca::Index i = 0; i < votca::Index(MolecularTypes.size()); i++) {
    WriteMolecularType(fl, *(MolecularTypes[i]), nummols[i + 1]);
  }
 
  // vdw seciton (pairwise vdw/CG interactions)
 
  if (vdw_pairs.size() > 0) {
 
    fl << "vdw " << vdw_pairs.size() << endl;
 
    for (const auto &vdw_pair : vdw_pairs) {
      fl << vdw_pair << " tab   1.00000  0.00000\n";
    }
  }
 
  fl << "close" << endl;
 
  cout << "Created template for dlpoly topology - please, check & amend if "
          "needed!"
       << endl;
 
  fl.close();
  return true;
}
 
void DLPTopolApp::WriteMoleculeAtoms(ostream &out, const Molecule &cg) {
  out << "atoms " << cg.BeadCount() << endl;
  out << "# name  mass  charge  nrept  ifrozen (optional: ngroup, index, "
         "name/type, type/residue, index/res-ID) \n";
  for (votca::Index i = 0; i < cg.BeadCount(); ++i) {
    const Bead *b = cg.getBead(i);
 
    string bname = b->getName();
    string btype = b->getType();
 
    bname = bname.substr(
        0, bname.find_first_of("#"));  // skip #index of atom from its name
    btype = btype.substr(
        0, btype.find_first_of("#"));  // skip #index of atom from its type
 
    out << boost::format("%8s  %10f  %10f     1     0     1 %10d  %8s  %8s %10d \n") %
               btype % b->getMass() % b->getQ() % (i + 1) % btype % bname %
               (i + 1);
    //% b->getType()->getName() % b->getMass() % b->getQ() % (i+1) %
    // b->getType()->getName() % b->getName() % (i+1);
  }
}
 
void DLPTopolApp::WriteMoleculeInteractions(ostream &out, const Molecule &cg) {
 
  stringstream sout;
 
  votca::Index n_entries = 0;
  votca::Index nb = -1;
 
  for (const Interaction *ic : cg.Interactions()) {
    if (nb != ic->BeadCount()) {
 
      if (sout.str() != "") {
        out << n_entries << endl << sout.str();
      }
 
      sout.str("");
      n_entries = 0;
 
      nb = ic->BeadCount();
      switch (nb) {
        case 2:
          out << "bonds ";
          break;
        case 3:
          out << "angles ";
          break;
        case 4:
          out << "dihedrals ";
          break;
        default:
          string err = "cannot handle number of beads in interaction:";
          err += to_string(ic->getMolecule() + 1) + ":" + ic->getGroup();
          err += ":" + to_string(ic->getIndex() + 1);
          throw runtime_error(err);
      }
    }
    n_entries++;
    // to do: is it possible to use bond/angle/dihedral function types for 1:1
    // mapping? (CG map overwrites ic->Group anyway)
    // sout << ic->getInteractionFunc(); // something like that (only for 1:1
    // mapping!)
    sout << " tab ";
    for (votca::Index i = 0; i < nb; ++i) {
      sout << ic->getBeadId(i) + 1 << " ";
    }
    sout << "   1.00000  0.00000"
         << " # ";
    sout << to_string(ic->getMolecule() + 1);
    sout << ":" + ic->getGroup();
    sout << ":" + to_string(ic->getIndex() + 1) << endl;
  }
  if (sout.str() != "") {
    out << n_entries << endl << sout.str();
  }
}
 
void DLPTopolApp::WriteMolecularType(ostream &out, const Molecule &cg,
                                     votca::Index nummol) {
  out << cg.getName() << endl;
  out << "nummols " << nummol << endl;
 
  WriteMoleculeAtoms(out, cg);
  WriteMoleculeInteractions(out, cg);
 
  out << "finish" << endl;
}
 
int main(int argc, char **argv) {
  DLPTopolApp app;
  return app.Exec(argc, argv);
}