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 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());
}
}
}
