std::string _test_ifile(TextInput a) {
std::string read;
while (true) {
std::string cur;
a.get_stream() >> cur;
if (!a) break;
read = read + cur;
}
std::cout << read;
return read;
}
Hierarchy read_mol2(TextInput mol2_file, Model* model,
Mol2Selector* mol2sel) {
if (!mol2sel) {
mol2sel = new AllMol2Selector();
}
IMP::PointerMember<Mol2Selector> sel(mol2sel);
// create a map to save atom_index and atom particle pairs
boost::unordered_map<Int, Particle*> molecule_atoms;
// create root particle
Hierarchy root_d = root_particle(model, mol2_file.get_name());
std::string line;
Hierarchy molecule_d;
while (std::getline(mol2_file.get_stream(), line)) {
// check the line is the title line @<TRIPOS>MOLECULE
if (internal::is_MOLECULE_rec(line)) {
molecule_atoms.clear();
molecule_d = read_molecule_mol2(model, mol2_file, root_d);
}
// check the starting line of atom block @<TRIPOS>ATOM
else if (internal::is_MOL2ATOM_rec(line)) {
if (!molecule_d) {
IMP_THROW("Atom seen before molecule on line " << line, IOException);
}
read_atom_mol2(model, mol2_file, molecule_d, molecule_atoms, mol2sel);
}
// check the starting line of bond block @<TRIPOS>BOND
else if (internal::is_BOND_rec(line)) {
read_bond_mol2(model, mol2_file, molecule_d, molecule_atoms);
} else {
IMP_LOG_TERSE("Couldn't parse line " << line << std::endl);
}
}
// Hierarchies mps = get_by_type(root_d, RESIDUE_TYPE);
// std::cout << "check " << mps.size() << std::endl;
add_radii(root_d);
IMP_INTERNAL_CHECK(root_d.get_is_valid(true), "Invalid hierarchy produced");
return root_d;
}
void CHARMMParameters::read_parameter_file(TextInput input_file) {
IMP_OBJECT_LOG;
const String BONDS_LINE = "BOND";
const String ANGLES_LINE = "ANGL";
const String ANGLES_LINE2 = "THETA";
const String DIHEDRALS_LINE = "DIHE";
const String DIHEDRALS_LINE2 = "PHI";
const String IMPROPER_LINE = "IMPR";
const String IMPROPER_LINE2 = "IMPHI";
const String NONBONDED_LINE = "NONB";
const String NONBONDED_LINE2 = "NBON";
enum {
NONE,
BONDS,
ANGLES,
DIHEDRALS,
IMPROPERS,
NONBONDED
} section = NONE;
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;
if (line.substr(0, NONBONDED_LINE.length()) == NONBONDED_LINE ||
line.substr(0, NONBONDED_LINE2.length()) == NONBONDED_LINE2) {
section = NONBONDED;
getline(input_file.get_stream(), line); // remove second line of
// NONBONDED
} else if (line.substr(0, BONDS_LINE.length()) == BONDS_LINE) {
section = BONDS;
} else if (line.substr(0, ANGLES_LINE.length()) == ANGLES_LINE ||
line.substr(0, ANGLES_LINE2.length()) == ANGLES_LINE2) {
section = ANGLES;
} else if (line.substr(0, DIHEDRALS_LINE.length()) == DIHEDRALS_LINE ||
line.substr(0, DIHEDRALS_LINE2.length()) == DIHEDRALS_LINE2) {
section = DIHEDRALS;
} else if (line.substr(0, IMPROPER_LINE.length()) == IMPROPER_LINE ||
line.substr(0, IMPROPER_LINE2.length()) == IMPROPER_LINE2) {
section = IMPROPERS;
} else if (line.substr(0, 5) == "HBOND" || line.substr(0, 5) == "NBFIX") {
section = NONE;
} else if (line.substr(0, 3) == "END") {
break;
} else {
switch (section) {
case BONDS:
parse_bonds_parameters_line(line);
break;
case ANGLES:
parse_angles_parameters_line(line);
break;
case DIHEDRALS:
parse_dihedrals_parameters_line(line, dihedral_parameters_);
break;
case IMPROPERS:
parse_dihedrals_parameters_line(line, improper_parameters_);
break;
case NONBONDED:
parse_nonbonded_parameters_line(line);
break;
default:
break;
}
}
}
if (force_field_2_vdW_.size() == 0) {
IMP_FAILURE("NONBONDED params not found in CHARMM parameter file");
}
}
void CHARMMParameters::read_topology_file(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);
}
}