| /dports/science/coordgenlibs/coordgenlibs-3.0.0/ |
| H A D | sketcherMinimizerMaths.h | 42 class sketcherMinimizerPointF
45 sketcherMinimizerPointF() = default;
47 sketcherMinimizerPointF(const sketcherMinimizerPointF& p) in sketcherMinimizerPointF() function
54 sketcherMinimizerPointF& operator=(const sketcherMinimizerPointF& p)
106 sketcherMinimizerPointF
125 sketcherMinimizerPointF& operator+=(const sketcherMinimizerPointF& p)
131 sketcherMinimizerPointF& operator-=(const sketcherMinimizerPointF& p)
302 sketcherMinimizerPointF v1 = p1 - p2; in signedAngle()
373 static sketcherMinimizerPointF
515 static sketcherMinimizerPointF
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| H A D | sketcherMinimizer.h | 39 std::vector<sketcherMinimizerPointF> additionVectors;
40 std::vector<sketcherMinimizerPointF> centers;
193 testAlignment(const sketcherMinimizerPointF& direction,
198 static sketcherMinimizerPointF scoreDirections(
200 const std::vector<std::pair<sketcherMinimizerPointF, float>>&
207 const sketcherMinimizerPointF& position,
229 static std::vector<std::pair<sketcherMinimizerPointF, float>>
255 alignmentMatrix(const std::vector<sketcherMinimizerPointF>& ref,
471 std::map<std::string, sketcherMinimizerPointF>
483 sketcherMinimizerPointF exploreGridAround(
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| H A D | sketcherMinimizer.cpp | 874 sketcherMinimizerPointF p = in bestRotation()
1230 sketcherMinimizerPointF p; in placeResiduesProteinOnlyModeLIDStyle()
1745 sketcherMinimizerPointF
1755 sketcherMinimizerPointF top = in exploreMolPosition()
1759 sketcherMinimizerPointF right = in exploreMolPosition()
1761 sketcherMinimizerPointF left = in exploreMolPosition()
1863 sketcherMinimizerPointF top = in exploreGridAround()
1869 sketcherMinimizerPointF left = in exploreGridAround()
2385 sketcherMinimizerPointF v(0, 0); in placeMolResidueLigandStyle()
2791 sketcherMinimizerPointF origin = in findDirectionsToAlignWith()
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| H A D | CoordgenFragmentBuilder.cpp | 73 vector<sketcherMinimizerPointF> v1, v2; in rotateMainFragment()
80 vector<sketcherMinimizerPointF> rotatedV2; in rotateMainFragment()
372 vector<sketcherMinimizerPointF> coords; in buildRing()
411 sketcherMinimizerPointF center = in buildRing()
473 sketcherMinimizerPointF newMean = in buildRing()
475 sketcherMinimizerPointF v = in buildRing()
483 sketcherMinimizerPointF newV = in buildRing()
543 vector<sketcherMinimizerPointF>
547 vector<sketcherMinimizerPointF> out; in listOfCoordinatesFromListofRingAtoms()
550 sketcherMinimizerPointF coords(0.f, 0.f); in listOfCoordinatesFromListofRingAtoms()
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| H A D | sketcherMinimizerEZConstrainInteraction.h | 48 sketcherMinimizerPointF projection1 =
51 sketcherMinimizerPointF projection2 =
56 sketcherMinimizerPointF projection = projection1;
65 sketcherMinimizerPointF force = projection - sideAtom->coordinates;
69 sideAtom->force = sketcherMinimizerPointF(0, 0);
70 doubleBondAtom->force = sketcherMinimizerPointF(0, 0);
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| H A D | sketcherMinimizerClashInteraction.h | 58 sketcherMinimizerPointF atomP = atom2->coordinates;
59 sketcherMinimizerPointF bondP1 = atom1->coordinates;
60 sketcherMinimizerPointF bondP2 = atom3->coordinates;
62 sketcherMinimizerPointF projection =
64 sketcherMinimizerPointF f = atomP - projection;
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| H A D | sketcherMinimizerFragment.cpp | 264 sketcherMinimizerPointF origin(-BONDLENGTH, 0); in apply()
265 sketcherMinimizerPointF coords = in apply()
303 sketcherMinimizerPointF pivot = m_pivotAtom->getCoordinates(); in apply()
305 sketcherMinimizerPointF normal(bondDir.y(), -bondDir.x()); in apply()
306 sketcherMinimizerPointF point1 = pivot + normal; in apply()
307 sketcherMinimizerPointF point2 = pivot - normal; in apply()
479 sketcherMinimizerPointF origin(0.f, 0.f); in storeCoordinateInformation()
495 sketcherMinimizerPointF c = at->coordinates - origin; in storeCoordinateInformation()
502 sketcherMinimizerPointF c = at->coordinates - origin; in storeCoordinateInformation()
509 const sketcherMinimizerPointF& position, float angle) in setCoordinates()
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| H A D | sketcherMinimizerAtom.h | 148 void setCoordinates(sketcherMinimizerPointF coords);
154 const sketcherMinimizerPointF& getCoordinates() const in getCoordinates()
169 sketcherMinimizerPointF coordinates;
170 sketcherMinimizerPointF templateCoordinates;
171 sketcherMinimizerPointF force;
260 sketcherMinimizerPointF getSingleAdditionVector() const;
262 static sketcherMinimizerPointF
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| H A D | sketcherMinimizerMolecule.h | 19 class sketcherMinimizerPointF; variable
82 void boundingBox(sketcherMinimizerPointF& min,
83 sketcherMinimizerPointF& max);
86 sketcherMinimizerPointF center();
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| H A D | sketcherMinimizerResidue.h | 24 sketcherMinimizerPointF computeStartingCoordinates(float d = 2.f)
26 sketcherMinimizerPointF out = templateCoordinates;
33 sketcherMinimizerPointF coords(0.f, 0.f);
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| H A D | CoordgenMinimizer.cpp | 84 all_coordinates.push_back({sketcherMinimizerPointF(0,0)}); in run()
136 displacement = sketcherMinimizerPointF(0.f, 0.f); in applyForces()
148 atom->force = sketcherMinimizerPointF(0, 0); in applyForces()
932 sketcherMinimizerPointF c = r->findCenter(); in scoreAtomsInsideRings()
972 sketcherMinimizerPointF v1, v2; in scoreProximityRelationsOnOppositeSides()
1340 sketcherMinimizerPointF vec = in avoidInternalClashes()
1466 sketcherMinimizerPointF position(0.f, 0.f); in buildMoleculeFromFragments()
1468 sketcherMinimizerPointF p1 = in buildMoleculeFromFragments()
1470 sketcherMinimizerPointF p2 = in buildMoleculeFromFragments()
1472 sketcherMinimizerPointF p = p2 - p1; in buildMoleculeFromFragments()
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| H A D | sketcherMinimizerRing.h | 18 class sketcherMinimizerPointF; variable
44 sketcherMinimizerPointF findCenter();
50 bool contains(const sketcherMinimizerPointF& p);
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| H A D | CoordgenFragmentBuilder.h | 21 class sketcherMinimizerPointF; variable
52 static std::vector<sketcherMinimizerPointF>
169 sketcherMinimizerPointF& startCoordinates,
177 sketcherMinimizerPointF& startCoordinates,
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| H A D | sketcherMinimizerRing.cpp | 26 sketcherMinimizerPointF sketcherMinimizerRing::findCenter() in findCenter()
28 sketcherMinimizerPointF o(0.f, 0.f); in findCenter()
149 bool sketcherMinimizerRing::contains(const sketcherMinimizerPointF& p) in contains()
158 sketcherMinimizerPointF v = in contains()
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| /dports/science/openbabel/openbabel-3.1.1/external/coordgen-master/coordgen/ |
| H A D | sketcherMinimizerMaths.h | 47 class sketcherMinimizerPointF
50 sketcherMinimizerPointF() = default;
52 sketcherMinimizerPointF(const sketcherMinimizerPointF& p) in sketcherMinimizerPointF() function
59 sketcherMinimizerPointF& operator=(const sketcherMinimizerPointF& p)
111 sketcherMinimizerPointF
130 sketcherMinimizerPointF& operator+=(const sketcherMinimizerPointF& p)
136 sketcherMinimizerPointF& operator-=(const sketcherMinimizerPointF& p)
307 sketcherMinimizerPointF v1 = p1 - p2; in signedAngle()
378 static sketcherMinimizerPointF
520 static sketcherMinimizerPointF
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| H A D | sketcherMinimizer.h | 48 std::vector<sketcherMinimizerPointF> additionVectors;
49 std::vector<sketcherMinimizerPointF> centers;
181 std::map<sketcherMinimizerMolecule*, sketcherMinimizerPointF>&
197 const std::vector<sketcherMinimizerPointF>& shape,
285 std::map<std::string, sketcherMinimizerPointF>
297 sketcherMinimizerPointF exploreGridAround(
302 const sketcherMinimizerPointF& direction = sketcherMinimizerPointF(0,
317 testAlignment(const sketcherMinimizerPointF& direction,
322 static sketcherMinimizerPointF scoreDirections(
353 static std::vector<std::pair<sketcherMinimizerPointF, float>>
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| H A D | sketcherMinimizer.cpp | 858 sketcherMinimizerPointF p = in bestRotation()
1182 sketcherMinimizerPointF p; in placeResiduesProteinOnlyModeLIDStyle()
1698 sketcherMinimizerPointF
1708 sketcherMinimizerPointF top = in exploreMolPosition()
1712 sketcherMinimizerPointF right = in exploreMolPosition()
1714 sketcherMinimizerPointF left = in exploreMolPosition()
1816 sketcherMinimizerPointF top = in exploreGridAround()
1822 sketcherMinimizerPointF left = in exploreGridAround()
2339 sketcherMinimizerPointF v(0, 0); in placeMolResidueLigandStyle()
2745 sketcherMinimizerPointF origin = in findDirectionsToAlignWith()
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| H A D | CoordgenFragmentBuilder.cpp | 66 vector<sketcherMinimizerPointF> v1, v2; in rotateMainFragment()
73 vector<sketcherMinimizerPointF> rotatedV2; in rotateMainFragment()
359 vector<sketcherMinimizerPointF> coords; in buildRing()
398 sketcherMinimizerPointF center = in buildRing()
460 sketcherMinimizerPointF newMean = in buildRing()
462 sketcherMinimizerPointF v = in buildRing()
470 sketcherMinimizerPointF newV = in buildRing()
538 vector<sketcherMinimizerPointF>
542 vector<sketcherMinimizerPointF> out; in listOfCoordinatesFromListofRingAtoms()
545 sketcherMinimizerPointF coords(0.f, 0.f); in listOfCoordinatesFromListofRingAtoms()
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| H A D | sketcherMinimizerEZConstrainInteraction.h | 48 sketcherMinimizerPointF projection1 =
51 sketcherMinimizerPointF projection2 =
56 sketcherMinimizerPointF projection = projection1;
65 sketcherMinimizerPointF force = projection - sideAtom->coordinates;
69 sideAtom->force = sketcherMinimizerPointF(0, 0);
70 doubleBondAtom->force = sketcherMinimizerPointF(0, 0);
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| H A D | sketcherMinimizerClashInteraction.h | 58 sketcherMinimizerPointF atomP = atom2->coordinates;
59 sketcherMinimizerPointF bondP1 = atom1->coordinates;
60 sketcherMinimizerPointF bondP2 = atom3->coordinates;
62 sketcherMinimizerPointF projection =
64 sketcherMinimizerPointF f = atomP - projection;
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| H A D | sketcherMinimizerFragment.cpp | 259 sketcherMinimizerPointF origin(-BONDLENGTH, 0); in apply()
260 sketcherMinimizerPointF coords = in apply()
298 sketcherMinimizerPointF pivot = m_pivotAtom->getCoordinates(); in apply()
300 sketcherMinimizerPointF normal(bondDir.y(), -bondDir.x()); in apply()
301 sketcherMinimizerPointF point1 = pivot + normal; in apply()
302 sketcherMinimizerPointF point2 = pivot - normal; in apply()
474 sketcherMinimizerPointF origin(0.f, 0.f); in storeCoordinateInformation()
490 sketcherMinimizerPointF c = at->coordinates - origin; in storeCoordinateInformation()
497 sketcherMinimizerPointF c = at->coordinates - origin; in storeCoordinateInformation()
504 const sketcherMinimizerPointF& position, float angle) in setCoordinates()
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| H A D | sketcherMinimizerAtom.h | 148 void setCoordinates(sketcherMinimizerPointF coords);
154 const sketcherMinimizerPointF& getCoordinates() const in getCoordinates()
169 sketcherMinimizerPointF coordinates;
170 sketcherMinimizerPointF templateCoordinates;
171 sketcherMinimizerPointF force;
260 sketcherMinimizerPointF getSingleAdditionVector() const;
262 static sketcherMinimizerPointF
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| H A D | sketcherMinimizerMolecule.h | 19 class sketcherMinimizerPointF; variable
82 void boundingBox(sketcherMinimizerPointF& min,
83 sketcherMinimizerPointF& max);
86 sketcherMinimizerPointF center();
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| H A D | sketcherMinimizerResidue.h | 24 sketcherMinimizerPointF computeStartingCoordinates(float d = 2.f)
26 sketcherMinimizerPointF out = templateCoordinates;
33 sketcherMinimizerPointF coords(0.f, 0.f);
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| H A D | sketcherMinimizerRing.h | 18 class sketcherMinimizerPointF; variable
44 sketcherMinimizerPointF findCenter();
50 bool contains(const sketcherMinimizerPointF& p);
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