/**
* Calculates thecontacts in a structure.
*
* @param structure The structure.
* @param distanceCutoff The maximum distance between two residues from them to be considered in contact.
* @param minSequenceDistance The minimum separation in the sequence for two residues to be considered contacts.
* @param maxSequenceDistance The maximum separation in the sequence for two residues to be considered contacts.
* @return The contacts present in the structure.
*/
ContactList* ContactTools::getContacts(Structure* structure, double distanceCutoff, int minSequenceDistance, int maxSequenceDistance)
{
// Find all of the contacts within the cutoff distance.
ContactList* contacts = new ContactList;
int length = structure->getSize();
int i, j, k, l;
for (i=0; i<length-minSequenceDistance; i++)
{
int maxJ = length;
if (maxSequenceDistance >= 0)
{
maxJ = i+maxSequenceDistance+1;
if (maxJ > length) maxJ = length;
}
for (j=i+minSequenceDistance; j<maxJ; j++)
{
Residue* residue1 = structure->getResidue(i);
Residue* residue2 = structure->getResidue(j);
// If this is the same residue, process each atom pair only once.
if (i == j)
{
for (k=0; k<residue1->getNumberAtoms()-1; k++)
{
Atom* atom1 = residue1->getAtom(k);
for (l=k+1; l<residue2->getNumberAtoms(); l++)
{
Atom* atom2 = residue2->getAtom(l);
if (atom1->getDistanceTo(*atom2) <= distanceCutoff)
{
contacts->addContact(new Contact(structure, i, k, j, l));
}
}
}
}
// Otherwise, process each atom pair.
else
{
for (k=0; k<residue1->getNumberAtoms(); k++)
{
Atom* atom1 = residue1->getAtom(k);
for (l=0; l<residue2->getNumberAtoms(); l++)
{
Atom* atom2 = residue2->getAtom(l);
if (atom1->getDistanceTo(*atom2) <= distanceCutoff)
{
contacts->addContact(new Contact(structure, i, k, j, l));
}
}
}
}
}
}
return contacts;
}
ContactList* ContactTools::getFormedNativeContacts(ContactList* nativeContacts, Structure* comparisonStructure, double maxDistanceDeviation)
{
// Get the sequence distance for each formed native contact.
ContactList* formedNativeContacts = new ContactList;
int i;
for (i=0; i<nativeContacts->getNumberContacts(); i++)
{
Contact* nativeContact = nativeContacts->getContact(i);
double nativeDistance = nativeContact->getContactDistance();
// Find the contact in the comparison structure.
Contact* comparisonContact = new Contact(comparisonStructure, nativeContact->getResidue1Index(), nativeContact->getAtom1Index(), nativeContact->getResidue2Index(), nativeContact->getAtom2Index());
double comparisonDistance = comparisonContact->getContactDistance();
if (nativeDistance-maxDistanceDeviation <= comparisonDistance && comparisonDistance <= nativeDistance+maxDistanceDeviation)
{
formedNativeContacts->addContact(comparisonContact);
}
else
{
// Otherwise delete the contact.
delete comparisonContact;
comparisonContact = NULL;
}
}
return formedNativeContacts;
}
ContactList* ContactList::getSubsetExcluding(ContactList* excludeList)
{
int i, j;
ContactList* newList = new ContactList();
for (i=0; i<getNumberContacts(); i++)
{
bool include = true;
Contact* contact = getContact(i);
for (j=0; j<excludeList->getNumberContacts(); j++)
{
if (*contact == *excludeList->getContact(j))
{
include = false;
break;
}
}
// If this contact should be included, add it to the list.
if (include)
{
newList->addContact(new Contact(*contact));
}
}
return newList;
}