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);
}
}
