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pymol-open-source/layer2/DistSet.cpp
Jarrett Johnson b52b6f2174 Port code changes from incentive (06/2023)
2025-01-04 12:09:32 -05:00

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/*
A* -------------------------------------------------------------------
B* This file contains source code for the PyMOL computer program
C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
D* -------------------------------------------------------------------
E* It is unlawful to modify or remove this copyright notice.
F* -------------------------------------------------------------------
G* Please see the accompanying LICENSE file for further information.
H* -------------------------------------------------------------------
I* Additional authors of this source file include:
-*
-*
-*
Z* -------------------------------------------------------------------
*/
#include"os_python.h"
#include"os_predef.h"
#include"os_std.h"
#include"Base.h"
#include"MemoryDebug.h"
#include"Err.h"
#include"DistSet.h"
#include"Scene.h"
#include"Color.h"
#include"RepDistDash.h"
#include"RepDistLabel.h"
#include"RepAngle.h"
#include"RepDihedral.h"
#include"PConv.h"
#include"ObjectDist.h"
#include"ObjectMolecule.h"
#include"ListMacros.h"
#include"Selector.h"
#include "PyMOL.h"
#include "Executive.h"
#include "Feedback.h"
int DistSetGetLabelVertex(DistSet * I, int at, float *v)
{
if (at >= 0 && at < I->LabCoord.size()) {
const auto& vv = I->LabCoord[at];
copy3f(vv.data(), v);
return true;
}
return false;
}
/**
* Retrieves label offset for given distance set
* @param atm atom index
*/
pymol::Result<pymol::Vec3> DistSet::getLabelOffset(int atm) const
{
std::array<float, 3> result;
if (atm < 0 || atm >= this->LabPos.size()) {
return pymol::make_error("Invalid index");
}
auto lp = &this->LabPos[atm];
if (lp->mode) {
std::copy_n(lp->offset, result.size(), result.data());
return result;
}
auto obj = this->Obj;
auto G = obj->G;
auto lab_pos =
SettingGet_3fv(G, nullptr, obj->Setting.get(), cSetting_label_position);
std::copy_n(lab_pos, result.size(), result.data());
return result;
}
/**
* Retrieves label offset for given distance set
* @param atm atom index
* @param pos offset to set the label at
*/
pymol::Result<> DistSet::setLabelOffset(int atm, const float* pos)
{
if (atm < 0) {
return pymol::make_error("Invalid index");
}
VecCheck(this->LabPos, atm);
auto& lp = this->LabPos[atm];
lp.mode = 1;
copy3f(pos, lp.offset);
return {};
}
int DistSetMoveLabel(DistSet * I, int a1, float *v, int mode)
{
if(a1 < 0) {
return 0;
}
VecCheck(I->LabPos, a1);
auto& lp = I->LabPos[a1];
if(!lp.mode) {
auto obj = I->Obj;
const float *lab_pos = SettingGet_3fv(obj->G, nullptr, obj->Setting.get(),
cSetting_label_position);
copy3f(lab_pos, lp.pos);
}
lp.mode = 1;
if(mode) {
add3f(v, lp.offset, lp.offset);
} else {
copy3f(v, lp.offset);
}
return 1;
}
/**
* @param I measurement set, must not be nullptr
* @param obj object molecule, can be nullptr so then all items in I will be updated
* @return number of updated coordinates
*/
int DistSetMoveWithObject(DistSet * I, struct ObjectMolecule *obj)
{
PyMOLGlobals * G = I->G;
int i, N, rVal = 0;
float * varDst;
PRINTFD(G, FB_DistSet)
" DistSet: adjusting distance vertex\n" ENDFD;
for (auto& listitem : I->MeasureInfo) {
auto* memb = &listitem;
varDst = nullptr;
switch(memb->measureType) {
case cRepDash:
N = 2;
if(memb->offset < I->NIndex + 1)
varDst = I->Coord.data();
break;
case cRepAngle:
N = 3;
if(memb->offset < I->NAngleIndex + 2)
varDst = I->AngleCoord.data();
break;
case cRepDihedral:
N = 4;
if(memb->offset < I->NDihedralIndex + 3)
varDst = I->DihedralCoord.data();
break;
}
if(!varDst)
continue;
varDst += 3 * memb->offset;
for(i = 0; i < N; i++) {
auto eoo = ExecutiveUniqueIDAtomDictGet(G, memb->id[i]);
if(!eoo || (obj && obj != eoo->obj))
continue;
if(ObjectMoleculeGetAtomVertex(
eoo->obj, memb->state[i],
eoo->atm, varDst + i * 3))
rVal++;
}
}
if (rVal)
I->invalidateRep(cRepAll, cRepInvCoord);
PRINTFD(G, FB_DistSet)
" DistSet: done updating distance set's vertex\n" ENDFD;
return rVal;
}
static decltype(DistSet::MeasureInfo) MeasureInfoListFromPyList(
PyMOLGlobals* G, PyObject* list)
{
int i, ll, N;
decltype(DistSet::MeasureInfo) I;
CPythonVal *val, *tmp;
ok_assert(1, list && PyList_Check(list));
ll = PyList_Size(list);
for (i = 0; i < ll; i++) {
I.emplace_front();
auto* item = &I.front();
val = CPythonVal_PyList_GetItem(G, list, i);
if(val && PyList_Check(val) &&
PyList_Size(val) > 2) {
tmp = CPythonVal_PyList_GetItem(G, val, 1);
N = PyList_Size(tmp);
ok_assert(1, N < 5);
item->measureType = (N == 2) ? cRepDash :
(N == 3) ? cRepAngle : cRepDihedral;
CPythonVal_PConvPyIntToInt_From_List(G, val, 0, &item->offset);
CPythonVal_PConvPyListToIntArrayInPlace(G, tmp, item->id, N);
CPythonVal_PConvPyListToIntArrayInPlace_From_List(G, val, 2, item->state, N);
CPythonVal_Free(tmp);
for (int j = 0; j < N; ++j) {
item->id[j] = SettingUniqueConvertOldSessionID(G, item->id[j]);
}
}
CPythonVal_Free(val);
}
ok_except1:
return I;
}
static PyObject* MeasureInfoListAsPyList(
decltype(DistSet::MeasureInfo) const& list)
{
int N;
PyObject *item, *result = PyList_New(0);
ok_assert(1, result);
for (auto& listitem : list) {
auto const* I = &listitem;
switch(I->measureType) {
case cRepDash: N = 2; break;
case cRepAngle: N = 3; break;
default: N = 4;
}
ok_assert(1, item = PyList_New(3));
PyList_SetItem(item, 0, PyInt_FromLong(I->offset));
PyList_SetItem(item, 1, PConvIntArrayToPyList(I->id, N));
PyList_SetItem(item, 2, PConvIntArrayToPyList(I->state, N));
PyList_Append(result, item);
Py_DECREF(item);
}
ok_except1:
return PConvAutoNone(result);
}
DistSet* DistSetFromPyList(PyMOLGlobals * G, PyObject * list)
{
DistSet *I = nullptr;
int ll = 0;
CPythonVal *val;
if(CPythonVal_IsNone(list)) { /* allow None for CSet */
return nullptr;
}
ok_assert(1, list && PyList_Check(list));
ok_assert(1, I = DistSetNew(G));
ll = PyList_Size(list);
/* TO SUPPORT BACKWARDS COMPATIBILITY...
Always check ll when adding new PyList_GetItem's */
ok_assert(1, CPythonVal_PConvPyIntToInt_From_List(G, list, 0, &I->NIndex));
ok_assert(1, CPythonVal_PConvPyListToFloatVLANoneOkay_From_List(G, list, 1, &I->Coord));
ok_assert(2, ll > 2);
ok_assert(1, CPythonVal_PConvPyIntToInt_From_List(G, list, 3, &I->NAngleIndex));
ok_assert(1, CPythonVal_PConvPyListToFloatVLANoneOkay_From_List(G, list, 4, &I->AngleCoord));
ok_assert(1, CPythonVal_PConvPyIntToInt_From_List(G, list, 5, &I->NDihedralIndex));
ok_assert(1, CPythonVal_PConvPyListToFloatVLANoneOkay_From_List(G, list, 6, &I->DihedralCoord));
ok_assert(2, ll > 7);
// DistSet->Setting never gets set (removed BB 11/14), was state settings?
/* val = CPythonVal_PyList_GetItem(G, list, 7);
I->Setting = SettingNewFromPyList(G, val);
CPythonVal_Free(val); */
ok_assert(2, ll > 8);
val = CPythonVal_PyList_GetItem(G, list, 8);
{
auto labPosRes = CPythonVal_PConvPyListToLabPosVec(G, val);
ok_assert(1, (bool)labPosRes);
I->LabPos = std::move(*labPosRes);
}
CPythonVal_Free(val);
ok_assert(2, ll > 9);
val = CPythonVal_PyList_GetItem(G, list, 9);
I->MeasureInfo = MeasureInfoListFromPyList(G, val);
CPythonVal_Free(val);
ok_except2:
return I;
ok_except1:
delete I;
return nullptr;
}
PyObject *DistSetAsPyList(DistSet * I)
{
PyObject *result = nullptr;
if(I) {
result = PyList_New(10);
PyList_SetItem(result, 0, PyInt_FromLong(I->NIndex));
PyList_SetItem(result, 1, PConvFloatArrayToPyListNullOkay(I->Coord, I->NIndex * 3));
PyList_SetItem(result, 2, PConvAutoNone(nullptr)); // I->LabCoord recalculated in RepDistLabelNew
PyList_SetItem(result, 3, PyInt_FromLong(I->NAngleIndex));
PyList_SetItem(result, 4,
PConvFloatArrayToPyListNullOkay(I->AngleCoord, I->NAngleIndex * 3));
PyList_SetItem(result, 5, PyInt_FromLong(I->NDihedralIndex));
PyList_SetItem(result, 6,
PConvFloatArrayToPyListNullOkay(I->DihedralCoord,
I->NDihedralIndex * 3));
// DistSet->Setting never gets set (removed BB 11/14), was state settings?
PyList_SetItem(result, 7, PConvAutoNone(nullptr) /* SettingAsPyList(I->Setting) */);
if(!I->LabPos.empty()) {
PyList_SetItem(result, 8, PConvLabPosVecToPyList(I->LabPos));
} else {
PyList_SetItem(result, 8, PConvAutoNone(nullptr));
}
PyList_SetItem(result, 9, MeasureInfoListAsPyList(I->MeasureInfo));
/* TODO setting ... */
}
return (PConvAutoNone(result));
}
/*========================================================================*/
int DistSetGetExtent(DistSet * I, float *mn, float *mx)
{
int a;
int c;
const float* v = I->Coord.data();
for(a = 0; a < I->NIndex; a++) {
min3f(v, mn, mn);
max3f(v, mx, mx);
v += 3;
}
v = I->AngleCoord;
c = I->NAngleIndex / 5;
for(a = 0; a < c; a++) {
min3f(v, mn, mn);
max3f(v, mx, mx);
v += 3;
min3f(v, mn, mn);
max3f(v, mx, mx);
v += 3;
min3f(v, mn, mn);
max3f(v, mx, mx);
v += 9;
}
v = I->DihedralCoord;
c = I->NDihedralIndex / 6;
for(a = 0; a < c; a++) {
min3f(v, mn, mn);
max3f(v, mx, mx);
v += 3;
min3f(v, mn, mn);
max3f(v, mx, mx);
v += 3;
min3f(v, mn, mn);
max3f(v, mx, mx);
v += 3;
min3f(v, mn, mn);
max3f(v, mx, mx);
v += 9;
}
return (I->NIndex + I->NAngleIndex + I->NDihedralIndex);
}
/*========================================================================*/
/**
* Invalidate reps
*
* type: rep enum, e.g. cRepDash
* level: e.g. cRepInvColor
*/
void DistSet::invalidateRep(cRep_t type, cRepInv_t level)
{
int a = 0, a_stop = getNRep();
bool changed = false;
/* if representation type is specified, adjust it */
if(type >= 0) {
if(type >= getNRep())
return;
a = type;
a_stop = a + 1;
}
for(; a < a_stop; a++) {
if(Rep[a]) {
changed = true;
Rep[a].reset();
}
}
if (changed)
SceneChanged(G);
}
/*========================================================================*/
void DistSet::update(int state)
{
DistSet * I = this;
/* status bar 0% */
OrthoBusyFast(G, 0, I->getNRep());
if(!I->Rep[cRepDash]) {
/* query the dist set looking for the selected atoms for this distance,
* then update the *coords */
I->Rep[cRepDash].reset(RepDistDashNew(I,state));
SceneInvalidate(G);
}
if(!I->Rep[cRepLabel]) {
/* query the dist set looking for the selected atoms for this distance,
* then update the *coords */
I->Rep[cRepLabel].reset(RepDistLabelNew(I, state));
SceneInvalidate(G);
}
if(!I->Rep[cRepAngle]) {
/* query the angle set looking for the selected atoms for this distance,
* then update the *coords */
I->Rep[cRepAngle].reset(RepAngleNew(I, state));
SceneInvalidate(G);
}
if(!I->Rep[cRepDihedral]) {
/* query the dihedral set looking for the selected atoms for this distance,
* then update the *coords */
I->Rep[cRepDihedral].reset(RepDihedralNew(I, state));
SceneInvalidate(G);
}
/* status bar 100% */
OrthoBusyFast(G, 1, 1);
}
/*========================================================================*/
void DistSet::render(RenderInfo * info)
{
DistSet * I = this;
CRay *ray = info->ray;
auto pick = info->pick;
for (int a = 0; a < I->getNRep(); a++) {
if(!GET_BIT(I->Obj->visRep, a))
continue;
if(!I->Rep[a]) {
switch(a) {
case cRepDash:
I->Rep[a].reset(RepDistDashNew(I, -1));
break;
case cRepLabel:
I->Rep[a].reset(RepDistLabelNew(I, -1));
break;
case cRepAngle:
I->Rep[a].reset(RepAngleNew(I, -1));
break;
case cRepDihedral:
I->Rep[a].reset(RepDihedralNew(I, -1));
break;
}
}
if(I->Rep[a])
{
if(ray) {
ray->color3fv(ColorGet(G, I->Obj->Color));
} else if (!pick) {
ObjectUseColor(I->Obj);
}
Rep[a]->render(info);
}
}
}
/*========================================================================*/
DistSet::DistSet(PyMOLGlobals* G)
: CObjectState(G)
{
}
/**
+ * Get the number of atoms in a measurement
+ * @param measureType cRepDash, cRepAngle, cRepDihedral
+ */
static int DistSetGetMemberN(cRep_t measureType)
{
switch (measureType) {
case cRepDash:
return 2;
case cRepAngle:
return 3;
case cRepDihedral:
default:
return 4;
}
}
std::unordered_set<const pymol::CObject*> DistSet::getDependentObjects() const
{
std::unordered_set<const pymol::CObject*> deps;
for (const auto& listitem : this->MeasureInfo) {
auto* memb = &listitem;
auto N = DistSetGetMemberN(static_cast<cRep_t>(memb->measureType));
for (auto i = 0; i < N; ++i) {
auto eoo = ExecutiveUniqueIDAtomDictGet(G, memb->id[i]);
deps.insert(eoo->obj);
}
}
return deps;
}
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