mirror of
https://github.com/schrodinger/pymol-open-source.git
synced 2026-06-04 20:04:21 +08:00
dc2aff4133
- Use proper doxygen syntax for all function comments - ObjectMoleculeUpdateNeighbors allow const argument - Remove obsolete ObjectMolecule::BondCounter
73 lines
1.5 KiB
C++
73 lines
1.5 KiB
C++
/*
|
|
* 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->setNIndex(idxmap.size());
|
|
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)
|
|
delete I->CSet[i];
|
|
|
|
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);
|
|
}
|
|
}
|