REAL computeSolvation(int size1, int size2, int * type1_m_aTypes, int * type2_m_aTypes, int type1, int type2,
REAL * dists,
int diff)
{
#pragma HLS INLINE recursive
//assert(diff >= 0);
REAL sum = 0.0;
for (int i = 0; i < size1; i++)
for (int j = 0; j < size2; j++)
{
int ex = isExcluded(diff, type1, i, type2, j);
if (ex != EXCLUDED)
{
REAL lambda1 = getLambda(type1, i, type1_m_aTypes[i]);
REAL lambda2 = getLambda(type2, j, type2_m_aTypes[j]);
REAL dists_param = dists[i*MAX_ROTAMER_SIZE + j];
sum += computeSolventEffect(type1_m_aTypes[i],
type2_m_aTypes[j],
dists_param, lambda1, lambda2, ex == PAIR1_4);
}
}
return sum;
}
bool AdcSearch::matchesFileLower(const string& aName, int64_t aSize, uint64_t aDate) {
if(!(aSize >= gt)) {
return false;
} else if(!(aSize <= lt)) {
return false;
} else if (!(aDate == 0 || (aDate >= minDate && aDate <= maxDate))) {
return false;
}
if (matchType == MATCH_EXACT) {
if (compare((*include->begin()).getPattern(), aName) != 0)
return false;
} else {
auto j = include->begin();
for(; j != include->end() && j->matchLower(aName); ++j)
; // Empty
if(j != include->end())
return false;
}
// Check file type...
if (!hasExt(aName))
return false;
if(isExcluded(aName))
return false;
return true;
}
REAL computeVdW(int size1, int size2, int type1, int type2, int * type1_m_aTypes, int * type2_m_aTypes, REAL * dists,int diff)
{
#pragma HLS INLINE recursive
//assert(diff >= 0);
REAL sum[1];
//#pragma HLS ARRAY_PARTITION variable=sum complete dim=1
//#pragma HLS ARRAY_PARTITION variable=type1_m_aTypes complete dim=1
//#pragma HLS ARRAY_PARTITION variable=type2_m_aTypes complete dim=1
//#pragma HLS ARRAY_PARTITION variable=dists complete dim=1
sum[0] = 0.0;
compute_vdw_outer:for (int i = 0; i < 12; i++)
{
#pragma HLS PIPELINE
if(i < size1){
compute_vdw_inner:for (int j = 0; j < 12; j++)
{
#pragma HLS PIPELINE
if(j < size2){
int ex = isExcluded(diff, type1, i, type2, j);
if (ex != EXCLUDED)
{
sum[0] += compute_vdW(type1_m_aTypes[i],
type2_m_aTypes[j],
dists[i*MAX_ROTAMER_SIZE + j], ex == PAIR1_4);
}
}
}
}
}
return sum[0];
}
Exclude&
Exclude::excludeOne(const name::Component& comp)
{
if (!isExcluded(comp)) {
m_exclude.insert(std::make_pair(comp, false));
m_wire.reset();
}
return *this;
}
Exclude&
Exclude::excludeOne(const name::Component& comp)
{
if (!isExcluded(comp)) {
this->appendEntry(comp, false);
m_wire.reset();
}
return *this;
}
bool AdcSearch::matchesDirectory(const string& aName) {
if (itemType == TYPE_FILE)
return false;
bool hasMatch = false;
for(const auto& k: *include) {
if(k.match(aName) && !isExcluded(aName))
hasMatch = true;
else {
hasMatch = false;
break;
}
}
//bool sizeOk = (aStrings.gt == 0);
if(hasMatch && ext.empty()) {
return true;
}
return false;
}
REAL computeVdW(int size1, int size2, int type1, int type2, int * type1_m_aTypes, int * type2_m_aTypes, REAL * dists,int diff)
{
#pragma HLS INLINE recursive
//assert(diff >= 0);
REAL sum = 0.0;
compute_vdw_outer:for (int i = 0; i < size1; i++)
{
#pragma HLS PIPELINE
compute_vdw_inner:for (int j = 0; j < size2; j++)
{
int ex = isExcluded(diff, type1, i, type2, j);
if (ex != EXCLUDED)
{
sum += compute_vdW(type1_m_aTypes[i],
type2_m_aTypes[j],
dists[i*MAX_ROTAMER_SIZE + j], ex == PAIR1_4);
}
}
}
return sum;
}
/**
* Check if the library should be loaded
* @param filename The filename of the library, i.e no directory
* @param excludes If not empty then each string is considered as a substring
* to search within each library to be opened. If the substring is found then
* the library is not opened.
* @return True if loading should be attempted
*/
bool LibraryManagerImpl::shouldBeLoaded(
const std::string &filename,
const std::vector<std::string> &excludes) const {
return !isLoaded(filename) && DllOpen::isValidFilename(filename) &&
!isExcluded(filename, excludes);
}
REAL computeElectrostatics(int size1, int size2, int type1_m_nGroups, int type2_m_nGroups, int * type1_m_groups, int * type2_m_groups, REAL * type1_m_charges, REAL * type2_m_charges, int type1, int type2,
REAL * dists,
int diff)
{
#pragma HLS INLINE recursive
//assert(diff >= 0);
// Proline is treated differently because the Cd atom is in a group
// with the Ca atom which is in a different leaf node.
if (type1 == BBP)
size1++;
else if (type1 == PRO)
size1--;
if (type2 == BBP)
size2++;
else if (type2 == PRO)
size2--;
int ngr1 = type1_m_nGroups;
int ngr2 = type2_m_nGroups;
REAL sum = 0.0;
for (int g1 = 0; g1 < ngr1; g1++)
for (int g2 = 0; g2 < ngr2; g2++)
{
int end1, end2, start1, start2;
start1 = type1_m_groups[g1];
start2 = type2_m_groups[g2];
if (g1 == ngr1 - 1)
end1 = size1;
else
end1 = type1_m_groups[g1 + 1];
if (g2 == ngr2 - 1)
end2 = size2;
else
end2 = type2_m_groups[g2 + 1];
// Decide whether the two groups are close enough to interact.
// They are close enough if they contain an interacting pair
// of atoms.
bool bCompute = false;
for (int i = start1; i < end1; i++)
for(int j = start2; j < end2; j++)
{
if (dists[i*MAX_ROTAMER_SIZE + j] < CUTOFF_DISTANCE_2)
{
bCompute = true;
i = 1000;
break;
}
}
// If the groups are interacting, compute their contribution.
if (bCompute)
{
for (int i = start1; i < end1; i++)
for(int j = start2; j < end2; j++)
{
int ex = isExcluded(diff, type1, i, type2, j);
if (ex != EXCLUDED)
{
REAL w = compute_ES(type1_m_charges[i], type2_m_charges[j],
dists[i*MAX_ROTAMER_SIZE + j]);
if (ex == PAIR1_4)
w *= 0.4;
sum += w;
}
}
}
}
return sum;
}
