Hierarchy get_previous_residue(Residue rd) {
// only handle simple case so far
Hierarchy p = rd.get_parent();
Chain c = p.get_as_chain();
Hierarchy r = get_residue(c, rd.get_index() - 1);
return r;
}
Hierarchy get_next_residue(Residue rd) {
// only handle simple case so far
Hierarchy p = rd.get_parent();
/*if (!p.get_as_chain()) {
IMP_NOT_IMPLEMENTED("get_next_residue() only handles the simple case"
<< " so far. Complain about it.");
}*/
IMP_USAGE_CHECK(Chain::get_is_setup(p),
"Parent of residue must be a chain. It is not.");
Hierarchy r = get_residue(Chain(p), rd.get_index() + 1);
return r;
}
void CHARMMSegmentTopology::apply_default_patches(const CHARMMParameters *ff) {
if (get_number_of_residues() == 0) return;
CHARMMResidueTopology *first = get_residue(0);
CHARMMResidueTopology *last = get_residue(get_number_of_residues() - 1);
if (first->get_default_first_patch() != "") {
ff->get_patch(first->get_default_first_patch())->apply(first);
}
if (last->get_default_last_patch() != "") {
// If chain contains only a single residue, allow both the first and last
// patch to be applied to it
if (get_number_of_residues() == 1 &&
first->get_default_first_patch() != "") {
first->set_patched(false);
}
ff->get_patch(last->get_default_last_patch())->apply(last);
}
}
void get_atom_2_residue_map(const IMP::Particles& atom_particles,
const IMP::Particles& residue_particles,
std::vector<int>& atom_2_residue_map) {
atom_2_residue_map.resize(atom_particles.size());
unsigned int residue_index=0;
for(unsigned int atom_index=0; atom_index<atom_particles.size(); ) {
if(get_residue(IMP::atom::Atom(atom_particles[atom_index])).get_particle()
== residue_particles[residue_index]) {
atom_2_residue_map[atom_index] = residue_index;
atom_index++;
} else {
residue_index++;
}
}
}
void write_pdb(const ParticlesTemp& ps, TextOutput out) {
IMP_FUNCTION_LOG;
int last_index = 0;
bool use_input_index = true;
for (unsigned int i = 0; i < ps.size(); ++i) {
if (Atom(ps[i]).get_input_index() != last_index + 1) {
use_input_index = false;
break;
} else {
++last_index;
}
}
for (unsigned int i = 0; i < ps.size(); ++i) {
if (Atom::get_is_setup(ps[i])) {
Atom ad(ps[i]);
Residue rd = get_residue(ad);
// really dumb and slow, fix later
char chain;
Chain c = get_chain(rd);
if (c) {
chain = c.get_id()[0];
} else {
chain = ' ';
}
int inum = i+1;
if (i>=99999) inum=99999;
out.get_stream() << get_pdb_string(
core::XYZ(ps[i]).get_coordinates(),
use_input_index ? ad.get_input_index()
: static_cast<int>(inum),
ad.get_atom_type(), rd.get_residue_type(), chain,
rd.get_index(), rd.get_insertion_code(),
ad.get_occupancy(), ad.get_temperature_factor(),
ad.get_element());
if (!out) {
IMP_THROW("Error writing to file in write_pdb", IOException);
}
}
else if (Residue::get_is_setup(ps[i])) { // if C-alpha residue is available
Residue rd = IMP::atom::Residue(ps[i]);
// comment 1 by SJ - TODO: How to retrieve the correct chain information without an hierarchy?
char chain;
Chain c = get_chain(rd);
if (c) {
chain = c.get_id()[0];
} else {
chain = ' ';
}
// comment 2 by SJ - TODO: The C-alpha residues are not sorted yet. We need to sort the residues similarly to what PMI does.
out.get_stream() << get_pdb_string(
core::XYZ(ps[i]).get_coordinates(),
static_cast<int>(i + 1),
IMP::atom::AT_CA, rd.get_residue_type(), chain,
rd.get_index(), ' ',
1.0, IMP::core::XYZR(ps[i]).get_radius());
}
else { // if a coarse-grained BEAD is available
Ints resindexes = IMP::atom::Fragment(ps[i]).get_residue_indexes();
int resindex = (int)resindexes.front() + (int)(resindexes.size()/2);
// comment 1 by SJ - TODO: How to retrieve the correct chain information without an hierarchy?
char chain = ' ';
// comment 3 by SJ - TODO: The BEADs are not sorted yet. We need to sort the residues similarly to what PMI does.
// comment 4 by SJ - TODO: currently IMP does not allow "BEA" as a residue name, while PMI allows it. Thus "UNK" was used instead.
out.get_stream() << get_pdb_string(
core::XYZ(ps[i]).get_coordinates(),
static_cast<int>(i + 1),
IMP::atom::AT_CA, IMP::atom::UNK, chain,
(int)resindex, ' ',
1.0, IMP::core::XYZR(ps[i]).get_radius());
}
}
}
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);
}
}