1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465
|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/STRUCTURE/residueChecker.h>
#include <BALL/KERNEL/forEach.h>
#include <BALL/KERNEL/bond.h>
#include <BALL/KERNEL/chain.h>
#include <BALL/KERNEL/PTE.h>
#include <BALL/DATATYPE/hashSet.h>
#include <BALL/STRUCTURE/fragmentDB.h>
#include <BALL/KERNEL/residue.h>
using namespace std;
namespace BALL
{
ResidueChecker::ResidueChecker()
: fragment_db_(0),
status_(true),
tests_(ResidueChecker::NUMBER_OF_TESTS),
selection_(false)
{
// Enable all tests by default except for overlapping atoms.
tests_.fill();
disable(OVERLAPPING_ATOMS);
}
ResidueChecker::ResidueChecker(FragmentDB& fragment_db)
: UnaryProcessor<Residue>(),
fragment_db_(&fragment_db),
status_(true),
tests_(ResidueChecker::NUMBER_OF_TESTS),
selection_(false)
{
// Enable all tests by default except for overlapping atoms.
tests_.fill();
disable(OVERLAPPING_ATOMS);
}
ResidueChecker::ResidueChecker(const ResidueChecker& residue_checker)
: UnaryProcessor<Residue>(),
fragment_db_(residue_checker.fragment_db_),
status_(residue_checker.status_),
tests_(residue_checker.tests_),
selection_(residue_checker.selection_)
{
}
bool ResidueChecker::isEnabled(ResidueChecker::TestType t) const
{
return tests_.getBit((Position)t);
}
void ResidueChecker::enable(ResidueChecker::TestType t, bool enable)
{
tests_.setBit((Position)t, enable);
}
void ResidueChecker::disable(ResidueChecker::TestType t)
{
tests_.setBit((Position)t, false);
}
ResidueChecker::~ResidueChecker()
{
}
bool ResidueChecker::getStatus() const
{
return status_;
}
bool ResidueChecker::start()
{
status_ = true;
return true;
}
bool ResidueChecker::finish()
{
return true;
}
Processor::Result ResidueChecker::operator () (Residue& residue)
{
String res_name;
if ((residue.getChain() != 0) && (residue.getChain()->getName() != BALL_CHAIN_DEFAULT_NAME))
{
res_name = residue.getChain()->getName() + ":";
}
res_name += residue.getName() + ":" + residue.getID();
// Check charges.
status_ &= checkCharge(residue, res_name);
// Check atom positions.
status_ &= checkAtomPositions(residue, res_name);
// if a fragment data base is defined, check for completeness
// of the residue
if (fragment_db_ != 0)
{
const Residue* reference = dynamic_cast<const Residue*>(fragment_db_->getReferenceFragment(residue));
if (reference == 0)
{
if (isEnabled(UNKNOWN_RESIDUES))
{
Log.warn() << "ResidueChecker: didn't find a reference fragment for " << res_name << endl;
status_ = false;
// If selection is enabled, mark the whol residue
if (selection_)
{
residue.select();
}
}
}
else
{
status_ &= checkCompleteness(residue, *reference, res_name);
status_ &= checkTemplate(residue, *reference, res_name);
}
}
return Processor::CONTINUE;
}
bool ResidueChecker::checkCharge(const Residue& residue, const String& res_name)
{
// Make sure we are suppose to do this.
if (!isEnabled(LARGE_NET_CHARGE) && !isEnabled(LARGE_CHARGES) && !isEnabled(NON_INTEGRAL_NET_CHARGE))
{
return true;
}
bool result = true;
// checking charge: charge should be integral and -2 <= charge <= 2
float total_charge = 0.0;
AtomConstIterator atom_it = residue.beginAtom();
for (; +atom_it; ++atom_it)
{
total_charge += atom_it->getCharge();
// warn for too large charges (above +/- 4 e0)
if (isEnabled(LARGE_CHARGES) && (fabs(atom_it->getCharge()) > 4.0))
{
Log.warn() << "ResidueChecker: suspect charge of " << atom_it->getCharge()
<< " for " << atom_it->getName() << " in " << res_name << std::endl;
result = false;
// If selection is enabled, mark the atom
if (selection_)
{
const_cast<Atom&>(*atom_it).select();
}
}
}
// check for very large absolute charges
if (isEnabled(LARGE_NET_CHARGE) && (total_charge < -2.0))
{
Log.warn() << "ResidueChecker: in residue " << res_name << ": total charge of "
<< total_charge << " is too negative." << endl;
result = false;
// If selection is enabled, mark the residue
if (selection_)
{
const_cast<Residue&>(residue).select();
}
}
if (isEnabled(LARGE_NET_CHARGE) && (total_charge > 2.0))
{
Log.warn() << "ResidueChecker: in residue " << res_name << ": total charge of "
<< total_charge << " is too positive." << endl;
result = false;
// If selection is enabled, mark the residue
if (selection_)
{
const_cast<Residue&>(residue).select();
}
}
// check for integrality of charges
float tmp = fabs(fabs(total_charge) - (float)((int)(fabs(total_charge) + 0.5)));
if (isEnabled(NON_INTEGRAL_NET_CHARGE) && (tmp > 0.05))
{
Log.warn() << "ResidueChecker: in residue " << res_name << ": residue total charge of "
<< total_charge << " is not integral." << endl;
result = false;
// If selection is enabled, mark the residue
if (selection_)
{
const_cast<Residue&>(residue).select();
}
}
return result;
}
bool ResidueChecker::checkCompleteness
(const Residue& residue, const Residue& reference, const String& res_name)
{
// Make sure we are suppose to do this.
if (!isEnabled(EXTRA_ATOMS) && !isEnabled(MISSING_ATOMS))
{
return true;
}
bool result = true;
// First, check for completeness
HashSet<String> reference_names;
AtomConstIterator atom_it;
for (atom_it = reference.beginAtom(); +atom_it; ++atom_it)
{
reference_names.insert(atom_it->getName());
}
// Check for extra atoms in the residue.
for (atom_it = residue.beginAtom(); +atom_it; ++atom_it)
{
if (reference_names.has(atom_it->getName()))
{
reference_names.erase(atom_it->getName());
}
else if (isEnabled(EXTRA_ATOMS))
{
Log.warn() << "ResidueChecker: did not find atom " << atom_it->getName() << " of "
<< res_name << " in the reference residue " << reference.getName() << endl;
result = false;
// If selection is enabled, mark the residue
if (selection_)
{
const_cast<Residue&>(residue).select();
}
}
}
// Check for missing atoms in the residue.
if (isEnabled(MISSING_ATOMS) && (reference_names.size() > 0))
{
Log.warn() << "ResidueChecker: did not find the following atoms in " << res_name << " : ";
HashSet<String>::Iterator set_it = reference_names.begin();
for (; set_it != reference_names.end(); ++set_it)
{
Log.warn() << *set_it << " ";
}
Log.warn() << " (template was " << reference.getName() << ")" << endl;
result = false;
// If selection is enabled, mark the residue
if (selection_)
{
const_cast<Residue&>(residue).select();
}
}
return result;
}
bool ResidueChecker::checkAtomPositions(const Residue& res, const String& res_name)
{
// Make sure we are suppose to do this.
if (!isEnabled(NAN_POSITIONS) && !isEnabled(STRONGLY_OVERLAPPING_ATOMS)
&& !isEnabled(OVERLAPPING_ATOMS) && !isEnabled(DUPLICATE_ATOM_NAMES))
{
return true;
}
bool result = true;
AtomConstIterator atom_it;
for (atom_it = res.beginAtom(); +atom_it; ++atom_it)
{
// Check for illegal atom positions (NaNs in any of the coordinates).
if (isEnabled(NAN_POSITIONS)
&& (Maths::isNan(atom_it->getPosition().x)
|| Maths::isNan(atom_it->getPosition().y)
|| Maths::isNan(atom_it->getPosition().z)))
{
Log.warn() << "ResidueChecker: illegal atom position (not a number) for atom "
<< atom_it->getName() << " of " << res_name << endl;
// Mark the atoms affected
if (selection_)
{
const_cast<Atom&>(*atom_it).select();
}
result = false;
}
Vector3 pos(atom_it->getPosition());
AtomConstIterator atom_it2;
for (atom_it2 = atom_it, ++atom_it2; +atom_it2; ++atom_it2)
{
// Check for strongly overlapping atoms (closer than 0.2 Angstrom)
if (isEnabled(STRONGLY_OVERLAPPING_ATOMS)
&& (pos.getSquareDistance(atom_it2->getPosition()) < 0.04))
{
Log.warn() << "ResidueChecker: atoms far too close -- distance between "
<< atom_it->getName() << " and " << atom_it2->getName()
<< " in " << res_name << " is " << pos.getDistance(atom_it2->getPosition())
<< " A." << std::endl;
// Mark the atoms affected
if (selection_)
{
const_cast<Atom&>(*atom_it).select();
const_cast<Atom&>(*atom_it2).select();
}
result = false;
}
// Check for overlapping atoms (closer than vdW radii minus 0.5 Angstrom)
if (isEnabled(OVERLAPPING_ATOMS) && (!atom_it->isBoundTo(*atom_it2)))
{
double radius1 = atom_it->getElement().getVanDerWaalsRadius();
if (radius1 == 0.0)
{
radius1 = atom_it->getElement().getAtomicRadius();
}
double radius2 = atom_it2->getElement().getVanDerWaalsRadius();
if (radius2 == 0.0)
{
radius2 = atom_it2->getElement().getAtomicRadius();
}
// Compute the square of the sum of the vdw radii minus 0.6 Angstrom
// overlap.
double min_dist = std::max(radius1 + radius2 - 0.6, 0.0);
if (atom_it->isGeminal(*atom_it2))
{
min_dist = std::max(min_dist - 1.0, 0.0);
}
min_dist *= min_dist;
// If the atoms are further apart, skip them.
if (pos.getSquareDistance(atom_it2->getPosition()) > min_dist)
{
continue;
}
// Complain about the overlap and mark the two atoms.
Log.warn() << "ResidueChecker: atoms too close -- distance between "
<< atom_it->getName() << " and " << atom_it2->getName()
<< " in " << res_name << " is " << pos.getDistance(atom_it2->getPosition())
<< " A (min: " << sqrt(min_dist) << ")." << std::endl;
// Mark the atoms affected
if (selection_)
{
const_cast<Atom&>(*atom_it).select();
const_cast<Atom&>(*atom_it2).select();
}
result = false;
}
// Check for identical names (OK, a bad place, but why not...)
if (isEnabled(DUPLICATE_ATOM_NAMES)
&& (atom_it->getName() == atom_it2->getName()))
{
Log.warn() << "ResidueChecker: duplicate atom name " << atom_it->getName()
<< " in " << res_name << "." << std::endl;
result = false;
const_cast<Atom&>(*atom_it).select();
const_cast<Atom&>(*atom_it2).select();
}
}
}
return result;
}
bool ResidueChecker::checkTemplate(const Residue& residue, const Residue& reference, const String& res_name)
{
// Make sure there's something to be done at all.
if (!isEnabled(SUSPECT_BOND_LENGTHS) && !isEnabled(ELEMENTS))
{
return true;
}
bool result = true;
// Check bond lengths (should be within +/- 15% of reference values).
Atom::BondConstIterator bond_it;
AtomConstIterator bond_atom_it;
AtomConstIterator atom_it;
BALL_FOREACH_BOND(reference, bond_atom_it, bond_it)
{
const Atom* first = 0;
const Atom* second = 0;
for (atom_it = residue.beginAtom(); +atom_it && (first == 0 || second == 0); ++atom_it)
{
if (atom_it->getName() == bond_it->getFirstAtom()->getName())
{
first = &*atom_it;
}
if (atom_it->getName() == bond_it->getSecondAtom()->getName())
{
second = &*atom_it;
}
}
// if we found the bond atoms in residue, check the atom distance
if ((first != 0) && (second != 0))
{
float distance = first->getPosition().getDistance(second->getPosition());
float deviation = fabs(distance - bond_it->getLength()) / bond_it->getLength();
if (isEnabled(SUSPECT_BOND_LENGTHS) && (deviation > 0.15))
{
Log.warn() << "ResidueChecker: in residue " << res_name << ": atom distance "
<< "between " << first->getName() << " and " << second->getName() << " suspect: "
<< distance << " A instead of " << bond_it->getLength() << " A" << endl;
result = false;
// If selection is enabled, mark the two atoms
if (selection_)
{
const_cast<Atom*>(first)->select();
const_cast<Atom*>(second)->select();
}
}
// Check for the element type of each atom
if (isEnabled(ELEMENTS)
&& (first->getElement() != bond_it->getFirstAtom()->getElement()))
{
Log.warn() << "ResidueChecker: in residue " << res_name << ": atom "
<< first->getName() << " is "
<< first->getElement().getSymbol() << " should be "
<< bond_it->getFirstAtom()->getElement().getSymbol() << endl;
// This could be the anchor of a ResidueRectfifier...
// (const_cast<Atom*> (first))->setElement(bond_it->getFirstAtom()->getElement());
result = false;
// If selection is enabled, mark the atom
if (selection_)
{
const_cast<Atom*>(first)->select();
}
}
if (isEnabled(ELEMENTS)
&& (second->getElement() != bond_it->getSecondAtom()->getElement()))
{
Log.warn() << "ResidueChecker: in residue " << res_name << ": atom "
<< second->getName() << " is "
<< second->getElement().getSymbol() << " should be "
<< bond_it->getSecondAtom()->getElement().getSymbol() << endl;
result = false;
// If selection is enabled, mark the atom
if (selection_)
{
const_cast<Atom*>(second)->select();
}
}
}
}
return result;
}
} // namespace BALL
|