int main (void)
{
linkedList* memoryMap = new linkedList(); // instantiate linkedList
memoryMap->create(); // create memory map (add Node)
displayMenu(); // print menu to screen
do {
input = parseUser(); // make sure user is inputting number
switch (input) {
case 1:
addProgram(memoryMap); // add program in MM
break;
case 2:
killProgram(memoryMap); // kill progam in MM
break;
case 3:
getFragments(memoryMap); // get fragements in MM
break;
case 4:
memoryMap -> display(); // display MM
break;
}
while (input != 1 && input != 2 && input != 3 && input != 4 && input != 5) {
input = parseUser(); // make sure user is inputting numbers
}
} while (input == 1 || input == 2 || input == 3 || input == 4); // if input = 5 -> exit Program
}
void fingerprint2::getFragments(vector<int> levels, vector<int> curfrag,
int level, OBAtom* patom, OBBond* pbond)
{
//Recursive routine to analyse schemical structure and populate fragset and ringset
//Hydrogens,charges(except dative bonds), spinMultiplicity ignored
const int Max_Fragment_Size = 7;
int bo=0;
if(pbond)
{
bo = pbond->IsAromatic() ? 5 : pbond->GetBO();
// OBAtom* pprevat = pbond->GetNbrAtom(patom);
// if(patom->GetFormalCharge() && (patom->GetFormalCharge() == -pprevat->GetFormalCharge()))
// ++bo; //coordinate (dative) bond eg C[N+]([O-])=O is seen as CN(=O)=O
}
curfrag.push_back(bo);
curfrag.push_back(patom->GetAtomicNum());
levels[patom->GetIdx()-1] = level;
vector<OBEdgeBase*>::iterator itr;
OBBond *pnewbond;
// PrintFpt(curfrag,(int)patom);
for (pnewbond = patom->BeginBond(itr);pnewbond;pnewbond = patom->NextBond(itr))
{
if(pnewbond==pbond) continue; //don't retrace steps
OBAtom* pnxtat = pnewbond->GetNbrAtom(patom);
if(pnxtat->GetAtomicNum() == OBElements::Hydrogen) continue;
int atlevel = levels[pnxtat->GetIdx()-1];
if(atlevel) //ring
{
if(atlevel==1)
{
//If complete ring (last bond is back to starting atom) add bond at front
//and save in ringset
curfrag[0] = pnewbond->IsAromatic() ? 5 : pnewbond->GetBO();
ringset.insert(curfrag);
curfrag[0] = 0;
}
}
else //no ring
{
if(level<Max_Fragment_Size)
{
// TRACE("level=%d size=%d %p frag[0]=%p\n",level, curfrag.size(),&curfrag, &(curfrag[0]));
//Do the next atom; levels, curfrag are passed by value and hence copied
getFragments(levels, curfrag, level+1, pnxtat, pnewbond);
}
}
}
//do not save C,N,O single atom fragments
if(curfrag[0]==0 &&
(level>1 || patom->GetAtomicNum()>8 || patom->GetAtomicNum()<6))
{
fragset.insert(curfrag); //curfrag ignored if an identical fragment already present
// PrintFpt(curfrag,level);
}
}
FastServer(
std::vector<std::string> const & rfilenames,
std::vector< ::libmaus::fastx::FastInterval > const & rintervals,
std::string const & shostname,
unsigned short rport = 4444,
unsigned int const backlog = 128)
: filenames(rfilenames), fragments(getFragments(filenames)), intervals(rintervals), port(rport),
seso(UNIQUE_PTR_MOVE(server_socket_type::allocateServerSocket(port,backlog,shostname.c_str(),32*1024))),
intervalserver(false)
{
}
Node* CylinderSurfaceModule::evaluate(Context* ctx)
{
NumberValue* heightValue = dynamic_cast<NumberValue*>(getParameterArgument(ctx,0));
double h=1.0;
if(heightValue)
h=heightValue->getNumber();
NumberValue* rValue = dynamic_cast<NumberValue*>(getParameterArgument(ctx,1));
double r=1.0;
if(rValue)
r=rValue->getNumber();
Value* centerValue=getParameterArgument(ctx,2);
bool center=false;
if(centerValue)
center=centerValue->isTrue();
double z1,z2;
if(center) {
z1 = -h/2;
z2 = +h/2;
} else {
z1 = 0.0;
z2 = h;
}
int f = getFragments(r,ctx);
Polygon c1 = getCircle(r,f,z1);
Polygon c2 = getCircle(r,f,z2);
PrimitiveNode* p = new PrimitiveNode();
for(int i=0; i<f; i++) {
int j=(i+1)%f;
p->createPolygon();
p->appendVertex(c1.at(i));
p->appendVertex(c2.at(i));
p->appendVertex(c2.at(j));
p->appendVertex(c1.at(j));
}
return p;
}
bool fingerprint2::GetFingerprint(OBBase* pOb, vector<unsigned int>&fp, int nbits)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(!pmol) return false;
fp.resize(1024/Getbitsperint());
fragset.clear();//needed because now only one instance of fp class
ringset.clear();
//identify fragments starting at every atom
OBAtom *patom;
vector<OBNodeBase*>::iterator i;
for (patom = pmol->BeginAtom(i);patom;patom = pmol->NextAtom(i))
{
if(patom->GetAtomicNum() == OBElements::Hydrogen) continue;
vector<int> curfrag;
vector<int> levels(pmol->NumAtoms());
getFragments(levels, curfrag, 1, patom, NULL);
}
// TRACE("%s %d frags before; ",pmol->GetTitle(),fragset.size());
//Ensure that each chemically identical fragment is present only in a single
DoRings();
DoReverses();
SetItr itr;
_ss.str("");
for(itr=fragset.begin();itr!=fragset.end();++itr)
{
//Use hash of fragment to set a bit in the fingerprint
int hash = CalcHash(*itr);
SetBit(fp,hash);
if(!(Flags() & FPT_NOINFO))
PrintFpt(*itr,hash);
}
if(nbits)
Fold(fp, nbits);
// TRACE("%d after\n",fragset.size());
return true;
}
Node* CircleModule::evaluate(Context* ctx)
{
NumberValue* rValue=dynamic_cast<NumberValue*>(getParameterArgument(ctx,0));
double r=1;
if(rValue) {
r=rValue->getNumber();
}
int f = getFragments(r,ctx);
Polygon c = getCircle(r,f,0);
PrimitiveNode* p = new PrimitiveNode();
if(r > 0) {
p->createPolygon();
for(int i=0; i<f; i++)
p->appendVertex(c.at(i));
}
return p;
}
Node* SphereModule::evaluate(Context* ctx)
{
NumberValue* rValue=dynamic_cast<NumberValue*>(getParameterArgument(ctx,0));
Value* centerValue=getParameterArgument(ctx,1);
bool center=true;
if(centerValue)
center=centerValue->isTrue();
double r=1.0;
if(rValue) {
r=rValue->getNumber();
} else {
NumberValue* dValue = dynamic_cast<NumberValue*>(ctx->getArgument(0,"diameter"));
if(dValue)
r=(dValue->getNumber()/2.0);
}
int f = getFragments(r,ctx);
int ringCount=f/2;
QList<Polygon> rings;
for(int i=0; i<ringCount; i++) {
double phi = (M_PI*(i+0.5)) / ringCount;
double r2 = r*sin(phi);
double z = r*cos(phi)+!center*r;
Polygon c = getCircle(r2,f,z);
rings.append(c);
}
PrimitiveNode* p = new PrimitiveNode();
p->createPolygon();
for(int i=0; i<f; i++)
p->appendVertex(rings.at(0).at(i));
for(int i = 0; i < ringCount-1; i++) {
Polygon r1 = rings.at(i);
Polygon r2 = rings.at(i+1);
int r1i = 0, r2i = 0;
while(r1i < f || r2i < f) {
if(r1i >= f)
goto next_r2;
if(r2i >= f)
goto next_r1;
if((double)r1i / f <
(double)r2i / f) {
next_r1:
p->createPolygon();
int r1j = (r1i+1) % f;
p->prependVertex(r1.at(r1i));
p->prependVertex(r1.at(r1j));
p->prependVertex(r2.at(r2i % f));
r1i++;
} else {
next_r2:
p->createPolygon();
int r2j = (r2i+1) % f;
p->appendVertex(r2.at(r2i));
p->appendVertex(r2.at(r2j));
p->appendVertex(r1.at(r1i % f));
r2i++;
}
}
}
p->createPolygon();
for(int i=0; i<f; i++)
p->prependVertex(rings.at(ringCount-1).at(i));
return p;
}
