ResidueType CHARMMParameters::parse_residue_line(const String &line, bool translate_names_to_pdb) { Strings split_results; boost::split(split_results, line, boost::is_any_of(" \t"), boost::token_compress_on); if (split_results.size() < 3) { IMP_THROW("Invalid RESI line: " << line, ValueException); } String curr_residue = get_residue_name(split_results[1], translate_names_to_pdb); if (ResidueType::get_key_exists(curr_residue)) { return ResidueType(curr_residue); } else { // assume charmm is correct return ResidueType(ResidueType::add_key(curr_residue)); } }
void CHARMMParameters::read_topology_file(base::TextInput input_file, bool translate_names_to_pdb) { IMP_OBJECT_LOG; const String MASS_LINE = "MASS"; const String DEFA_LINE = "DEFA"; const String PATC_LINE = "PATC"; const String RESI_LINE = "RESI"; const String PRES_LINE = "PRES"; const String ATOM_LINE = "ATOM"; const String DELE_LINE = "DELE"; const String BOND_LINE = "BOND"; const String BOND_LINE2 = "DOUBLE"; const String ANGLE_LINE = "ANGL"; const String ANGLE_LINE2 = "THET"; const String DIHEDRAL_LINE = "DIHE"; const String DIHEDRAL_LINE2 = "PHI"; const String IMPROPER_LINE = "IMPR"; const String IMPROPER_LINE2 = "IMPH"; const String IC_LINE = "IC"; std::string first_patch = "", last_patch = ""; Pointer<CHARMMIdealResidueTopology> residue; Pointer<CHARMMPatch> patch; ResidueType curr_res_type; while (!input_file.get_stream().eof()) { String line; getline(input_file.get_stream(), line); boost::trim(line); // remove all spaces // skip comments or empty lines if (line[0] == '!' || line[0] == '*' || line.length() == 0) continue; // read residue line if(line.substr(0, RESI_LINE.length()) == RESI_LINE) { if (residue) { add_residue_topology(residue.release()); } else if (patch) { add_patch(patch.release()); } curr_res_type = parse_residue_line(line, translate_names_to_pdb); ResidueType rt(curr_res_type.get_string()); residue = new CHARMMIdealResidueTopology(rt); residue->set_default_first_patch(first_patch); residue->set_default_last_patch(last_patch); // handle patch residues } else if (line.substr(0, PRES_LINE.length()) == PRES_LINE) { if (residue) { add_residue_topology(residue.release()); } else if (patch) { add_patch(patch.release()); } Strings split_results; boost::split(split_results, line, boost::is_any_of(" \t"), boost::token_compress_on); if (split_results.size() < 3) { IMP_THROW("Invalid PRES line: " << line, ValueException); } patch = new CHARMMPatch(get_residue_name(split_results[1], translate_names_to_pdb)); // handle MASS line } else if (line.substr(0, MASS_LINE.length()) == MASS_LINE) { parse_mass_line(line, atom_type_to_element_); // handle DEFA line } else if (line.substr(0, DEFA_LINE.length()) == DEFA_LINE) { parse_patch_line(line, first_patch, last_patch, translate_names_to_pdb); // handle PATC line } else if (line.substr(0, PATC_LINE.length()) == PATC_LINE && residue) { std::string first = residue->get_default_first_patch(); std::string last = residue->get_default_last_patch(); parse_patch_line(line, first, last, translate_names_to_pdb); residue->set_default_first_patch(first); residue->set_default_last_patch(last); // read DELE line } else if (line.substr(0, DELE_LINE.length()) == DELE_LINE && patch) { parse_dele_line(line, patch, translate_names_to_pdb); // read atom line } else if (line.substr(0, ATOM_LINE.length()) == ATOM_LINE && (residue || patch)) { parse_atom_line(line, curr_res_type, get_residue(residue, patch), translate_names_to_pdb); // read bond line } else if ((line.substr(0, BOND_LINE.length()) == BOND_LINE || line.substr(0, BOND_LINE2.length()) == BOND_LINE2) && (residue || patch)) { parse_bond_line(line, curr_res_type, get_residue(residue, patch), translate_names_to_pdb); // read angle line } else if ((line.substr(0, ANGLE_LINE.length()) == ANGLE_LINE || line.substr(0, ANGLE_LINE2.length()) == ANGLE_LINE2) && (residue || patch)) { parse_angle_line(line, get_residue(residue, patch), translate_names_to_pdb); // read dihedral line } else if ((line.substr(0, DIHEDRAL_LINE.length()) == DIHEDRAL_LINE || line.substr(0, DIHEDRAL_LINE2.length()) == DIHEDRAL_LINE2) && (residue || patch)) { parse_dihedral_line(line, get_residue(residue, patch), translate_names_to_pdb); // read improper line } else if ((line.substr(0, IMPROPER_LINE.length()) == IMPROPER_LINE || line.substr(0, IMPROPER_LINE2.length()) == IMPROPER_LINE2) && (residue || patch)) { parse_improper_line(line, get_residue(residue, patch), translate_names_to_pdb); // read internal coordinate line } else if (line.substr(0, IC_LINE.length()) == IC_LINE && (residue || patch)) { parse_internal_coordinate_line(line, get_residue(residue, patch), translate_names_to_pdb); } } if (residue) { add_residue_topology(residue); } else if (patch) { add_patch(patch); } }