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/*
* Biological Assembly Helpers
*
* (c) 2017 Schrodinger, Inc.
*/
#include <vector>
#include "os_std.h"
#include "AssemblyHelpers.h"
#include "MemoryDebug.h"
/*
* Create a coordset for a segi (chain) selection
*/
CoordSet * CoordSetCopyFilterChains(
const CoordSet * other,
const AtomInfoType * atInfo,
const std::set<lexborrow_t> & chains_set)
{
std::vector<int> idxmap;
idxmap.reserve(other->NIndex);
for (int idx = 0; idx < other->NIndex; ++idx)
if (chains_set.count(atInfo[other->IdxToAtm[idx]].segi) > 0)
idxmap.push_back(idx);
CoordSet* cset = new CoordSet(other->G);
cset->NIndex = idxmap.size();
cset->Coord = pymol::vla<float>(cset->NIndex * 3);
cset->IdxToAtm = pymol::vla<int>(cset->NIndex);
cset->Obj = other->Obj;
for (int idx = 0; idx < cset->NIndex; ++idx) {
cset->IdxToAtm[idx] = other->IdxToAtm[idxmap[idx]];
copy3f(other->coordPtr(idxmap[idx]), cset->coordPtr(idx));
}
return cset;
}
/*
* Replace coordinate sets and set all_states
*/
void ObjectMoleculeSetAssemblyCSets(
ObjectMolecule * I,
CoordSet ** assembly_csets)
{
if (!assembly_csets)
return;
if (I->DiscreteFlag) {
printf("error/TODO: can't make discrete assembly\n");
return;
}
// remove asymetric unit coordinate sets
for (int i = 0; i < I->NCSet; ++i)
if (I->CSet[i])
I->CSet[i]->fFree();
VLAFreeP(I->CSet);
// get assembly coordinate sets into ObjectMolecule
I->CSet = pymol::vla_take_ownership(assembly_csets);
I->NCSet = VLAGetSize(assembly_csets);
I->updateAtmToIdx();
// all_states for multi-model assembly
if (I->NCSet > 1) {
SettingSet(cSetting_all_states, true, I);
}
}
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