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pymol-open-source/layer2/ObjectDist.cpp
Jarrett Johnson 83f11bc317 More Replace NULL with nullptr
2024-06-02 20:44:43 -04:00

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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"Vector.h"
#include"MemoryDebug.h"
#include"Err.h"
#include"Setting.h"
#include"Scene.h"
#include"Ray.h"
#include"ObjectDist.h"
#include"Selector.h"
#include"PConv.h"
#include"ObjectMolecule.h"
#include"Feedback.h"
#include"DistSet.h"
#include"ListMacros.h"
#include "Interactions.h"
#ifdef _PYMOL_INCENTIVE
#endif
static void ObjectDistUpdateExtents(ObjectDist * I);
int ObjectDistGetLabelTxfVertex(ObjectDist * I, int state, int index, float *v)
{
int result = 0;
if(!I->DSet.empty()) {
if(state < 0)
state = SettingGet_i(I->G, nullptr, I->Setting.get(), cSetting_state) - 1;
if(state < 0)
state = SceneGetState(I->G);
if(I->DSet.size() == 1)
state = 0; /* static singletons always active here it seems */
state = state % I->DSet.size();
{
DistSet *ds = I->DSet[state].get();
if((!ds) && (SettingGet_b(I->G, I->Setting.get(), nullptr, cSetting_all_states))) {
state = 0;
ds = I->DSet[state].get();
}
if(ds) {
result = DistSetGetLabelVertex(ds, index, v);
}
}
}
return (result);
}
int ObjectDistMoveLabel(ObjectDist * I, int state, int index, float *v, int mode, int log)
{
int result = 0;
/* determine which state we're using */
if(state < 0)
state = 0;
if(I->DSet.size() == 1)
state = 0;
state = state % I->DSet.size();
if((!I->DSet[state])
&& (SettingGet_b(I->G, I->Setting.get(), nullptr, cSetting_all_states)))
state = 0;
/* find the corresponding distance set, for this state */
auto ds = I->DSet[state].get();
if(ds) {
result = DistSetMoveLabel(I->DSet[state].get(), index, v, mode);
/* force this object to redraw itself; invalidate the Label's coordinates
* with the new data set, ds */
ds->invalidateRep(cRepLabel, cRepInvCoord);
/* ExecutiveUpdateCoordDepends(I->G,I); */
}
return (result);
}
/* ObjectDistMoveWithObject -- updates the vertex positions of a distance measure
*
* PARAMS
* (ObjectDist*) I
* the object to update
* (ObjectMolecule*) O
* the object that moved, causing this function to be called
* RETURNS
* (integer) 0=nothing moved; 1=something moved
*/
int ObjectDistMoveWithObject(ObjectDist * I, struct ObjectMolecule * O) {
int result = 0, curResult = 0;
/* bail if the distance object is empty, or it doesn't have any distances */
if (!I || I->DSet.empty() ) {
return 0;
}
/* ask each DistSet to move itself, if required */
for (int i=0; i<I->DSet.size(); i++) {
auto ds = I->DSet[i].get();
if (ds) {
curResult = DistSetMoveWithObject(ds, O);
result |= curResult;
}
}
PRINTFD(I->G, FB_ObjectDist) " ObjectDist-Move: Out of Move\n" ENDFD;
return result;
}
/* -- JV end */
/*========================================================================*/
void ObjectDistUpdateExtents(ObjectDist * I)
{
float maxv[3] = { FLT_MAX, FLT_MAX, FLT_MAX };
float minv[3] = { -FLT_MAX, -FLT_MAX, -FLT_MAX };
/* update extents */
copy3f(maxv, I->ExtentMin);
copy3f(minv, I->ExtentMax);
I->ExtentFlag = false;
for(int a = 0; a < I->DSet.size(); a++) {
auto ds = I->DSet[a].get();
if(ds) {
if(DistSetGetExtent(ds, I->ExtentMin, I->ExtentMax))
I->ExtentFlag = true;
}
}
}
static PyObject *ObjectDistDSetAsPyList(ObjectDist * I)
{
auto result = PyList_New(I->DSet.size());
for(int a = 0; a < I->DSet.size(); a++) {
if(I->DSet[a]) {
PyList_SetItem(result, a, DistSetAsPyList(I->DSet[a].get()));
} else {
PyList_SetItem(result, a, PConvAutoNone(Py_None));
}
}
return (PConvAutoNone(result));
}
static int ObjectDistDSetFromPyList(ObjectDist * I, PyObject * list)
{
int ok = true;
if(ok)
ok = PyList_Check(list);
if(ok) {
I->DSet.resize(PyList_Size(list));
for(int a = 0; a < I->DSet.size(); a++) {
if(ok){
CPythonVal *val = CPythonVal_PyList_GetItem(I->G, list, a);
I->DSet[a].reset(DistSetFromPyList(I->G, val));
CPythonVal_Free(val);
}
if(ok && I->DSet[a])
I->DSet[a]->Obj = I;
}
}
return (ok);
}
/*========================================================================*/
PyObject *ObjectDistAsPyList(ObjectDist * I)
{
PyObject *result = nullptr;
/* first, dump the atoms */
result = PyList_New(4);
PyList_SetItem(result, 0, ObjectAsPyList(I));
// for backwards compatibility
PyList_SetItem(result, 1, PyInt_FromLong(I->DSet.size()));
PyList_SetItem(result, 2, ObjectDistDSetAsPyList(I));
PyList_SetItem(result, 3, PyInt_FromLong(0));
return (PConvAutoNone(result));
}
int ObjectDistNewFromPyList(PyMOLGlobals * G, PyObject * list, ObjectDist ** result)
{
int ok = true;
ObjectDist *I = nullptr;
(*result) = nullptr;
if(ok)
ok = PyList_Check(list);
I = new ObjectDist(G);
if(ok)
ok = (I != nullptr);
if(ok){
auto *val = PyList_GetItem(list, 0);
ok = ObjectFromPyList(G, val, I);
}
if(ok){
CPythonVal *val = CPythonVal_PyList_GetItem(G, list, 2);
ok = ObjectDistDSetFromPyList(I, val);
CPythonVal_Free(val);
}
ObjectDistInvalidateRep(I, cRepAll);
if(ok) {
(*result) = I;
ObjectDistUpdateExtents(I);
} else {
/* cleanup? */
}
return (ok);
}
/*========================================================================*/
int ObjectDist::getNFrame() const
{
return DSet.size();
}
/*========================================================================*/
void ObjectDist::update()
{
auto I = this;
OrthoBusyPrime(I->G);
for(int a = 0; a < I->DSet.size(); a++)
if(I->DSet[a]) {
OrthoBusySlow(I->G, a, I->DSet.size());
/* printf(" ObjectDist: updating state %d of \"%s\".\n" , a+1, I->Name); */
I->DSet[a]->update(a);
}
}
/*========================================================================*/
void ObjectDistInvalidateRep(ObjectDist * I, cRep_t rep)
{
int a;
PRINTFD(I->G, FB_ObjectDist)
" ObjectDistInvalidateRep: entered.\n" ENDFD;
for(a = 0; a < I->DSet.size(); a++)
if(I->DSet[a]) {
I->DSet[a]->invalidateRep(rep, cRepInvAll);
}
}
/*========================================================================*/
void ObjectDist::render(RenderInfo * info)
{
auto I = this;
int state = info->state;
const RenderPass pass = info->pass;
CRay *ray = info->ray;
auto pick = info->pick;
bool shouldRender = false;
if(ray || pick) {
shouldRender = true;
} else {
shouldRender = pass != RenderPass::Antialias;
// distance measurements should render
// both in opaque and transparency loop,
// the rep decides based on transparency
// whether it renders in that loop.
}
if (!shouldRender)
return;
ObjectPrepareContext(I, info);
for(StateIterator iter(I->G, I->Setting.get(), state, I->DSet.size());
iter.next();) {
DistSet * ds = I->DSet[iter.state].get();
if(ds)
ds->render(info);
}
}
#if 0
static CSetting **ObjectDistGetSettingHandle(ObjectDist * I, int state)
{
if(state < 0) {
return (&I->Setting.get());
} else {
return (nullptr);
}
}
#endif
void ObjectDist::invalidate(cRep_t rep, cRepInv_t level, int state){
auto I = this;
for(StateIterator iter(I->G, I->Setting.get(), state, I->DSet.size());
iter.next();) {
DistSet * ds = I->DSet[iter.state].get();
if(ds)
ds->invalidateRep(rep, level);
}
}
/*========================================================================*/
ObjectDist::ObjectDist(PyMOLGlobals * G) : pymol::CObject(G)
{
auto I = this;
I->type = cObjectMeasurement;
I->DSet.reserve(10); /* auto-zero */
I->Color = ColorGetIndex(G, "dash");
}
ObjectDist::ObjectDist(const ObjectDist& other)
: pymol::CObject(other)
, DSet(other.DSet)
{
for (auto& d : DSet) {
if (d) {
d->Obj = this;
}
}
}
ObjectDist& ObjectDist::operator=(const ObjectDist& other)
{
pymol::CObject::operator=(other);
DSet = other.DSet;
for (auto& d : DSet) {
if (d) {
d->Obj = this;
}
}
return *this;
}
/*========================================================================*/
static void ObjectDistReset(PyMOLGlobals * G, ObjectDist * I)
{
/* This wipes out all the distance sets and clears the state */
I->DSet.clear();
}
/*========================================================================*/
static bool checkFrozenState(PyMOLGlobals * G, int sele, int &state) {
if (state >= 0)
return true;
if (sele < 0)
return false;
auto obj = (const pymol::CObject*) SelectorGetSingleObjectMolecule(G, sele);
if(!obj ||
!SettingGetIfDefined_i(G, obj->Setting.get(), cSetting_state, &state))
return false;
--state;
return true;
}
/*========================================================================*/
ObjectDist *ObjectDistNewFromSele(PyMOLGlobals * G, ObjectDist * oldObj,
int sele1, int sele2, int mode, float cutoff,
int labels, int reset, float *result, int state,
int state1, int state2)
{
int a, mn;
float dist_sum = 0.0, dist;
int dist_cnt = 0;
int n_state1, n_state2;
int frozen1 = -1, frozen2 = -1;
ObjectDist *I;
/* if the distance name we presented exists and is an object, just
* overwrite it by resetting it; otherwise intialize the
* objectDistance and its base class */
if(!oldObj)
I = new ObjectDist(G);
else {
I = oldObj;
if(reset)
ObjectDistReset(G, I);
}
*result = 0.0;
/* max number of states */
mn = 0;
SelectorUpdateTable(G, state, -1);
/* here we determine the highest number of states with which we need to concern ourselves */
n_state1 = SelectorGetSeleNCSet(G, sele1);
n_state2 = SelectorGetSeleNCSet(G, sele2);
/* take the larger state count */
mn = (n_state2>n_state1) ? n_state2 : n_state1;
/* updated state handling */
frozen1 = checkFrozenState(G, sele1, state1);
frozen2 = checkFrozenState(G, sele2, state2);
/* FIX for incorrectly handling state=-1 for multi-molecule selections */
if(state1<0) state1=0;
if(state2<0) state2=0;
if(mn) {
/* loop over the max number of states */
for(a = 0; a < mn; a++) {
/* the state param is valid, set it */
if(state >= 0) {
if(state >= mn) /* bail */
break;
a = state; /* otherwise, set a to state */
}
PRINTFB(G, FB_ObjectDist, FB_Blather)
" ObjectDistNewFromSele: obj1 is frozen = %d into state %d+1\n", frozen1, state1
ENDFB(G);
PRINTFB(G, FB_ObjectDist, FB_Blather)
" ObjectDistNewFromSele: obj1 is frozen = %d into state %d+1\n", frozen2, state2
ENDFB(G);
VecCheck(I->DSet, a);
if(!frozen1)
state1 = (n_state1>1) ? a : 0;
if(!frozen2)
state2 = (n_state2>1) ? a : 0;
/* this does the actual work of creating the distances for this state */
/* I->DSet[a] = new DistSet(G, selections, states, etc) -- created this new DistSet */
if (5 <= mode && mode <= 7) {
#ifdef _PYMOL_INCENTIVE
#else
PRINTFB(G, FB_ObjectDist, FB_Errors)
" ObjectDist-Error: modes 5-7 only available in Incentive PyMOL\n"
ENDFB(G);
I->DSet[a] = nullptr;
#endif
} else if (mode == 9) { // 9: halogen-bond interaction
I->DSet[a].reset(pymol::FindHalogenBondInteractions(G,
I->DSet[a].release(), sele1, state1, sele2, state2, cutoff, &dist));
} else if (mode == 10) { // 10: salt-bridge interaction
I->DSet[a].reset(pymol::FindSaltBridgeInteractions(G,
I->DSet[a].release(), sele1, state1, sele2, state2, cutoff, &dist));
} else {
I->DSet[a].reset(SelectorGetDistSet(
G, I->DSet[a].release(), sele1, state1, sele2, state2, mode, cutoff, &dist));
}
/* if the distances are valid, then tally the total and set the ObjectMolecule pointer as necessary */
if(I->DSet[a]) {
dist_sum += dist; /* average distance over N states */
dist_cnt++;
I->DSet[a]->Obj = I; /* point to the ObjectMolecule for this state's DistanceSet */
}
if(state >= 0 || (frozen1 && frozen2))
break;
}
}
/* set the object's bounds and redraw */
ObjectDistUpdateExtents(I);
ObjectDistInvalidateRep(I, cRepAll);
/* return the avg dist */
if(dist_cnt)
(*result) = dist_sum / dist_cnt;
SceneChanged(G);
return (I);
}
ObjectDist *ObjectDistNewFromAngleSele(PyMOLGlobals * G, ObjectDist * oldObj,
int sele1, int sele2, int sele3, int mode,
int labels, float *result, int reset, int state,
int state1, int state2, int state3)
{
int a, mn;
float angle_sum = 0.0;
int angle_cnt = 0;
int n_state1, n_state2, n_state3;
ObjectDist *I;
int frozen1=-1, frozen2=-1, frozen3=-1;
if(!oldObj) /* create object if new */
I = new ObjectDist(G);
else { /* otherwise, use existing object */
I = oldObj;
if(reset) { /* if reseting, then clear out all existing coordinate sets */
ObjectDistReset(G, I);
}
}
*result = 0.0;
/* count number of states in each selection */
SelectorUpdateTable(G, state, -1);
n_state1 = SelectorGetSeleNCSet(G, sele1);
n_state2 = SelectorGetSeleNCSet(G, sele2);
n_state3 = SelectorGetSeleNCSet(G, sele3);
/* figure out the total number of states */
mn = std::max({n_state1, n_state2, n_state3});
/* updated state handling */
frozen1 = checkFrozenState(G, sele1, state1);
frozen2 = checkFrozenState(G, sele2, state2);
frozen3 = checkFrozenState(G, sele3, state3);
if(mn) {
for(a = 0; a < mn; a++) {
if(state >= 0) {
if(state > mn)
break;
a = state;
}
/* treat selections with one state as static singletons */
PRINTFB(G, FB_ObjectDist, FB_Blather)
" ObjectDistNewFromAngleSele: obj1 is frozen = %d into state %d+1\n", frozen1, state1
ENDFB(G);
PRINTFB(G, FB_ObjectDist, FB_Blather)
" ObjectDistNewFromAngleSele: obj2 is frozen = %d into state %d+1\n", frozen2, state2
ENDFB(G);
PRINTFB(G, FB_ObjectDist, FB_Blather)
" ObjectDistNewFromAngleSele: obj3 is frozen = %d into state %d+1\n", frozen3, state3
ENDFB(G);
if(!frozen1)
state1 = (n_state1>1) ? a : 0;
if(!frozen2)
state2 = (n_state2>1) ? a : 0;
if(!frozen3)
state3 = (n_state3>1) ? a : 0;
VecCheck(I->DSet, a);
I->DSet[a].reset(SelectorGetAngleSet(G, I->DSet[a].release(), sele1, state1, sele2,
state2, sele3, state3, mode, &angle_sum,
&angle_cnt));
if(I->DSet[a]) {
I->DSet[a]->Obj = I;
}
if(state >= 0 || (frozen1 && frozen2 && frozen3))
break;
}
}
/* else {
VLAFreeP(I->DSet);
DeleteP(I);
}
*/
ObjectDistUpdateExtents(I);
ObjectDistInvalidateRep(I, cRepAll);
if(angle_cnt)
(*result) = angle_sum / angle_cnt;
SceneChanged(G);
return (I);
}
ObjectDist *ObjectDistNewFromDihedralSele(PyMOLGlobals * G, ObjectDist * oldObj,
int sele1, int sele2, int sele3, int sele4,
int mode, int labels, float *result,
int reset, int state)
{
int a, mn;
float angle_sum = 0.0;
int angle_cnt = 0;
int n_state1, n_state2, n_state3, n_state4;
int state1 = -1, state2 = -1, state3 = -1, state4 = -1;
ObjectDist *I;
int frozen1=-1, frozen2=-1, frozen3=-1, frozen4=-1;
if(!oldObj) /* create object if new */
I = new ObjectDist(G);
else { /* otherwise, use existing object */
I = oldObj;
if(reset) { /* if reseting, then clear out all existing coordinate sets */
ObjectDistReset(G, I);
}
}
*result = 0.0;
/* count number of states in each selection */
SelectorUpdateTable(G, state, -1);
n_state1 = SelectorGetSeleNCSet(G, sele1);
n_state2 = SelectorGetSeleNCSet(G, sele2);
n_state3 = SelectorGetSeleNCSet(G, sele3);
n_state4 = SelectorGetSeleNCSet(G, sele4);
/* figure out the total number of states */
mn = n_state1;
if(n_state2 > mn)
mn = n_state2;
if(n_state3 > mn)
mn = n_state3;
if(n_state4 > mn)
mn = n_state4;
/* updated state handling */
frozen1 = checkFrozenState(G, sele1, state1);
frozen2 = checkFrozenState(G, sele2, state2);
frozen3 = checkFrozenState(G, sele3, state3);
frozen4 = checkFrozenState(G, sele4, state4);
if(mn) {
for(a = 0; a < mn; a++) {
if(state >= 0) {
if(state > mn)
break;
a = state;
}
/* treat selections with one state as static singletons */
if(!frozen1)
state1 = (n_state1>1) ? a : 0;
if(!frozen2)
state2 = (n_state2>1) ? a : 0;
if(!frozen3)
state3 = (n_state3>1) ? a : 0;
if(!frozen4)
state4 = (n_state4>1) ? a : 0;
VecCheck(I->DSet, a);
I->DSet[a].reset(SelectorGetDihedralSet(G, I->DSet[a].release(), sele1, state1, sele2,
state2, sele3, state3, sele4, state4,
mode, &angle_sum, &angle_cnt));
if(I->DSet[a]) {
I->DSet[a]->Obj = I;
}
if(state >= 0 || (frozen1 && frozen2 && frozen3 && frozen4))
break;
}
}
/* else {
VLAFreeP(I->DSet);
DeleteP(I);
}
*/
ObjectDistUpdateExtents(I);
ObjectDistInvalidateRep(I, cRepAll);
if(angle_cnt)
(*result) = angle_sum / angle_cnt;
SceneChanged(G);
return (I);
}
pymol::CObject* ObjectDist::clone() const
{
return new ObjectDist(*this);
}
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