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/*
* Atom iterators
*
* (c) 2014 Schrodinger, Inc.
*/
#ifndef _H_ATOMITERATORS
#define _H_ATOMITERATORS
#include "PyMOLGlobals.h"
#include "ObjectMolecule.h"
#include "CoordSet.h"
#include "AtomInfo.h"
/*
* Atom iterator base class
*/
class AbstractAtomIterator {
protected:
int atm; // atom index in object molecule
int idx; // atom index in coordset
public:
ObjectMolecule * obj;
CoordSet * cs;
// virtual destructor for dynamic types
virtual ~AbstractAtomIterator() {}
// resets the internal state to start over
virtual void reset() = 0;
// advance the internal state to the next atom, return false if there is no
// next atom
virtual bool next() = 0;
// get current atom
AtomInfoType * getAtomInfo() {
return obj->AtomInfo + atm;
};
// get current atom's coordinates
float * getCoord() {
return cs->Coord + (3 * idx);
};
// get current atom index in object molecule
int getAtm() {
return atm;
}
// get current coordinate index (atom index in coordset)
int getIdx() {
return idx;
}
};
/*
* State specific iterator over an atom selection. Similar to cmd.iterate_state.
* If state is -1 then iterate over all states.
*
* SeleCoordIterator iter(G, sele, state);
* while(iter.next()) {
* dump3f(iter.getCoord(), "coords");
* }
*/
class SeleCoordIterator : public AbstractAtomIterator {
PyMOLGlobals * G;
int statearg; // state argument, can be -1 (all), -2 (current), -3 (effective)
int statemax; // largest state in selection
bool per_object; // whether to iterate over object states or global states
ObjectMolecule * prev_obj; // for per_object=true
public:
int a; // index in selection
int state; // current state
void init(PyMOLGlobals * G_, int sele_, int state_);
SeleCoordIterator() {} // undefined state until "init()" called
SeleCoordIterator(PyMOLGlobals * G_, int sele_, int state_) {
init(G_, sele_, state_);
};
void reset();
bool next();
// return true if iterating over all states
bool isMultistate() const {
return statearg == -1;
}
// return true if iterating over all states of an object before advancing
// to the next object, rather than iterating over global states
bool isPerObject() const {
return per_object;
}
void setPerObject(bool per_object_) {
per_object = per_object_ && isMultistate();
}
private:
bool nextStateInPrevObject() {
if (prev_obj && (++state) < prev_obj->NCSet) {
a = prev_obj->SeleBase - 1;
return true;
}
return false;
}
};
/*
* Iterator over an atom selection. Similar to cmd.iterate.
*
* Does NOT provide coord or coordset access
*
* SeleAtomIterator iter(G, sele);
* while(iter.next()) {
* ai = iter.getAtomInfo();
* }
*/
class SeleAtomIterator : public AbstractAtomIterator {
PyMOLGlobals * G;
int sele; // selection
char * stmp; // temporary named selection
public:
int a; // index in selection
SeleAtomIterator(PyMOLGlobals * G_, int sele_) {
G = G_;
sele = sele_;
stmp = NULL;
reset();
};
SeleAtomIterator(PyMOLGlobals * G_, const char * sele_);
~SeleAtomIterator();
void reset();
bool next();
};
/*
* CoordSet atom iterator, iterates over sorted atoms
*
* CoordSetAtomIterator iter(G, cs);
* while(iter.next()) {
* dump3f(iter.getCoord(), "coords");
* }
*/
class CoordSetAtomIterator : public AbstractAtomIterator {
public:
CoordSetAtomIterator(CoordSet * cs_) {
cs = cs_;
obj = cs->Obj;
reset();
}
void reset() {
atm = -1;
}
bool next();
};
#endif
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