Hierarchy create_protein(Model *m, std::string name, double resolution,
int number_of_residues, int first_residue_index,
double volume, bool ismol) {
double mass =
atom::get_mass_from_number_of_residues(number_of_residues) / 1000;
if (volume < 0) {
volume = atom::get_volume_from_mass(mass * 1000);
}
// assume a 20% overlap in the beads to make the protein not too bumpy
double overlap_frac = .2;
std::pair<int, double> nr = compute_n(volume, resolution, overlap_frac);
Hierarchy pd = Hierarchy::setup_particle(new Particle(m));
Ints residues;
for (int i = 0; i < number_of_residues; ++i) {
residues.push_back(i + first_residue_index);
}
atom::Fragment::setup_particle(pd, residues);
if (ismol) Molecule::setup_particle(pd);
pd->set_name(name);
for (int i = 0; i < nr.first; ++i) {
Particle *pc;
if (nr.first > 1) {
pc = new Particle(m);
std::ostringstream oss;
oss << name << "-" << i;
pc->set_name(oss.str());
atom::Fragment pcd = atom::Fragment::setup_particle(pc);
Ints indexes;
for (int j = i * (number_of_residues / nr.first) + first_residue_index;
j < (i + 1) * (number_of_residues / nr.first) + first_residue_index;
++j) {
indexes.push_back(j);
}
pcd.set_residue_indexes(indexes);
pd.add_child(pcd);
} else {
pc = pd;
}
core::XYZR xyzd = core::XYZR::setup_particle(pc);
xyzd.set_radius(nr.second);
atom::Mass::setup_particle(pc, mass / nr.first);
}
IMP_INTERNAL_CHECK(pd.get_is_valid(true), "Invalid hierarchy produced "
<< pd);
return pd;
}
cmsHANDLE CMSEXPORT cmsCIECAM02Init(cmsContext ContextID, const cmsViewingConditions* pVC)
{
cmsCIECAM02* lpMod;
_cmsAssert(pVC != NULL);
if((lpMod = (cmsCIECAM02*) _cmsMallocZero(ContextID, sizeof(cmsCIECAM02))) == NULL) {
return NULL;
}
lpMod ->ContextID = ContextID;
lpMod ->adoptedWhite.XYZ[0] = pVC ->whitePoint.X;
lpMod ->adoptedWhite.XYZ[1] = pVC ->whitePoint.Y;
lpMod ->adoptedWhite.XYZ[2] = pVC ->whitePoint.Z;
lpMod -> LA = pVC ->La;
lpMod -> Yb = pVC ->Yb;
lpMod -> D = pVC ->D_value;
lpMod -> surround = pVC ->surround;
switch (lpMod -> surround) {
case CUTSHEET_SURROUND:
lpMod->F = 0.8;
lpMod->c = 0.41;
lpMod->Nc = 0.8;
break;
case DARK_SURROUND:
lpMod -> F = 0.8;
lpMod -> c = 0.525;
lpMod -> Nc = 0.8;
break;
case DIM_SURROUND:
lpMod -> F = 0.9;
lpMod -> c = 0.59;
lpMod -> Nc = 0.95;
break;
default:
// Average surround
lpMod -> F = 1.0;
lpMod -> c = 0.69;
lpMod -> Nc = 1.0;
}
lpMod -> n = compute_n(lpMod);
lpMod -> z = compute_z(lpMod);
lpMod -> Nbb = computeNbb(lpMod);
lpMod -> FL = computeFL(lpMod);
if (lpMod -> D == D_CALCULATE) {
lpMod -> D = computeD(lpMod);
}
lpMod -> Ncb = lpMod -> Nbb;
lpMod -> adoptedWhite = XYZtoCAT02(lpMod -> adoptedWhite);
lpMod -> adoptedWhite = ChromaticAdaptation(lpMod -> adoptedWhite, lpMod);
lpMod -> adoptedWhite = CAT02toHPE(lpMod -> adoptedWhite);
lpMod -> adoptedWhite = NonlinearCompression(lpMod -> adoptedWhite, lpMod);
return (cmsHANDLE) lpMod;
}
LCMSHANDLE LCMSEXPORT cmsCIECAM02Init(LPcmsViewingConditions pVC)
{
LPcmsCIECAM02 lpMod;
if((lpMod = (LPcmsCIECAM02) malloc(sizeof(cmsCIECAM02))) == NULL) {
return (LCMSHANDLE) NULL;
}
ZeroMemory(lpMod, sizeof(cmsCIECAM02));
lpMod ->adoptedWhite.XYZ[0] = pVC ->whitePoint.X;
lpMod ->adoptedWhite.XYZ[1] = pVC ->whitePoint.Y;
lpMod ->adoptedWhite.XYZ[2] = pVC ->whitePoint.Z;
lpMod -> LA = pVC ->La;
lpMod -> Yb = pVC ->Yb;
lpMod -> D = pVC ->D_value;
lpMod -> surround = pVC ->surround;
switch (lpMod -> surround) {
case AVG_SURROUND_4:
lpMod->F = 1.0; // Not included in CAM02
lpMod->c = 0.69;
lpMod->Nc = 1.0;
break;
case CUTSHEET_SURROUND:
lpMod->F = 0.8;
lpMod->c = 0.41;
lpMod->Nc = 0.8;
break;
case DARK_SURROUND:
lpMod -> F = 0.8;
lpMod -> c = 0.525;
lpMod -> Nc = 0.8;
break;
case DIM_SURROUND:
lpMod -> F = 0.9;
lpMod -> c = 0.59;
lpMod -> Nc = 0.95;
break;
default:
// Average surround
lpMod -> F = 1.0;
lpMod -> c = 0.69;
lpMod -> Nc = 1.0;
}
lpMod -> n = compute_n(lpMod);
lpMod -> z = compute_z(lpMod);
lpMod -> Nbb = computeNbb(lpMod);
lpMod -> FL = computeFL(lpMod);
lpMod -> D = computeD(lpMod);
lpMod -> Ncb = lpMod -> Nbb;
lpMod -> adoptedWhite = XYZtoCAT02(lpMod -> adoptedWhite);
lpMod -> adoptedWhite = ChromaticAdaptation(lpMod -> adoptedWhite, lpMod);
lpMod -> adoptedWhite = CAT02toHPE(lpMod -> adoptedWhite);
lpMod -> adoptedWhite = NonlinearCompression(lpMod -> adoptedWhite, lpMod);
lpMod -> adoptedWhite = ComputeCorrelates(lpMod -> adoptedWhite, lpMod);
return (LCMSHANDLE) lpMod;
}
