| /dports/biology/protomol/protomol/framework/topology/ |
| H A D | topologyutilities.h | 24 class GenericTopology; variable
123 const GenericTopology *topo);
127 const GenericTopology *topo);
132 const GenericTopology *topo);
137 const GenericTopology *topo,
147 const GenericTopology *topo);
152 const GenericTopology *topo);
182 const GenericTopology * );
187 const GenericTopology * );
191 GenericTopology * topo);
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| H A D | GenericTopology.cpp | 7 const string GenericTopology::scope("Topology");
8 const string GenericTopology::keyword("Topology");
10 GenericTopology::GenericTopology():Makeable(), in GenericTopology() function in ProtoMol::GenericTopology
18 GenericTopology::GenericTopology(Real c, const ExclusionType& e):Makeable(), in GenericTopology() function in ProtoMol::GenericTopology
29 GenericTopology* GenericTopology::make(string& errMsg, const vector<Value>& values)const{ in make()
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| H A D | GenericTopology.h | 47 class GenericTopology : public Makeable{
53 GenericTopology();
54 GenericTopology(Real c, const ExclusionType& e);
55 virtual ~GenericTopology(){}; in ~GenericTopology()
96 GenericTopology* make(std::string& errMsg, const std::vector<Value>& values)const;
101 virtual GenericTopology* doMake(std::string& errMsg, std::vector<Value> values)const=0;
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| H A D | topologyutilities.cpp | 25 const GenericTopology* topology, in randomVelocity()
58 const GenericTopology* topology, in randomVelocity()
291 const GenericTopology* topology, in addVelocityVirial()
340 const GenericTopology *topo){ in linearMomentum()
362 const GenericTopology *topo){ in removeLinearMomentum()
377 const GenericTopology *topo){ in centerOfMass()
409 const GenericTopology *topo){ in angularMomentum()
420 const GenericTopology *topo, in angularMomentum()
465 const GenericTopology *topo){ in removeAngularMomentum()
574 GenericTopology *topo ) { in buildMolecularCenterOfMass()
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| /dports/biology/protomol/protomol/framework/forces/ |
| H A D | oneAtomContraints.h | 23 static bool check(const GenericTopology*, int, int){return true;} in check()
24 static bool check(const GenericTopology*, int){return true;} in check()
27 static void check(const GenericTopology*, int, int, const Vector3D&, Real, const Vector3D&){} in check()
38 static void check(const GenericTopology*, int, int, const Vector3D&, Real, const Vector3D&){} in check()
49 static void check(const GenericTopology*, int, int, const Vector3D&, Real, const Vector3D&){} in check()
60 static void check(const GenericTopology*, int, int, const Vector3D&, Real, const Vector3D&){} in check()
68 static bool check(const GenericTopology*, int i, int j){ in check()
72 static bool check(const GenericTopology*, int){return true;} in check()
75 static void check(const GenericTopology*, int, int, const Vector3D&, Real, const Vector3D&){} in check()
80 static bool check(const GenericTopology*, int, int){return true;} in check()
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| H A D | ExternalGravitationSystemForce.h | 10 class GenericTopology; variable
25 void doEvaluate(const GenericTopology* topo,
34 virtual void evaluate(const GenericTopology* topo,
39 virtual void parallelEvaluate(const GenericTopology* topo,
48 virtual unsigned int numberOfBlocks(const GenericTopology* topo,
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| H A D | ExternalMagneticFieldExtendedForce.h | 10 class GenericTopology; variable
25 void doEvaluate(const GenericTopology* topo,
35 virtual void evaluate(const GenericTopology* topo,
41 virtual void parallelEvaluate(const GenericTopology* topo,
51 virtual unsigned int numberOfBlocks(const GenericTopology* topo,
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| H A D | FrictionExtendedForce.h | 10 class GenericTopology; variable
25 void doEvaluate(const GenericTopology* topo,
35 virtual void evaluate(const GenericTopology* topo,
41 virtual void parallelEvaluate(const GenericTopology* topo,
51 virtual unsigned int numberOfBlocks(const GenericTopology* topo,
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| H A D | SphericalSystemForce.h | 23 void doEvaluate(const GenericTopology* topo,
32 virtual void evaluate(const GenericTopology* topo,
37 virtual void parallelEvaluate(const GenericTopology* topo,
47 virtual unsigned int numberOfBlocks(const GenericTopology* topo,
75 inline void SphericalSystemForce::evaluate(const GenericTopology* topo, in evaluate()
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| H A D | DihedralSystemForce.h | 26 virtual void evaluate(const GenericTopology* topo,
31 virtual void parallelEvaluate(const GenericTopology* topo,
41 virtual unsigned int numberOfBlocks(const GenericTopology* topo,
67 inline void DihedralSystemForce<TBoundaryConditions>::evaluate(const GenericTopology* topo, in evaluate()
78 …inline void DihedralSystemForce<TBoundaryConditions>::parallelEvaluate(const GenericTopology* topo, in parallelEvaluate()
102 …unsigned int DihedralSystemForce<TBoundaryConditions>::numberOfBlocks(const GenericTopology* topo, in numberOfBlocks()
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| H A D | ImproperSystemForce.h | 25 virtual void evaluate(const GenericTopology* topo,
30 virtual void parallelEvaluate(const GenericTopology* topo,
39 virtual unsigned int numberOfBlocks(const GenericTopology* topo,
64 inline void ImproperSystemForce<TBoundaryConditions>::evaluate(const GenericTopology* topo, in evaluate()
75 …inline void ImproperSystemForce<TBoundaryConditions>::parallelEvaluate(const GenericTopology* topo, in parallelEvaluate()
99 …unsigned int ImproperSystemForce<TBoundaryConditions>::numberOfBlocks(const GenericTopology* topo, in numberOfBlocks()
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| H A D | MollyForce.h | 11 class GenericTopology; variable
33 virtual void evaluate(const GenericTopology*,
39 virtual void parallelEvaluate(const GenericTopology*,
63 inline void MollyForce::parallelEvaluate(const GenericTopology* topo, in parallelEvaluate()
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| H A D | SystemForce.h | 10 class GenericTopology; variable
32 virtual void evaluate(const GenericTopology* topo,
39 virtual void parallelEvaluate(const GenericTopology* topo,
67 inline void SystemForce::parallelEvaluate(const GenericTopology* topo, in parallelEvaluate()
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| H A D | ExtendedForce.h | 11 class GenericTopology; variable
33 virtual void evaluate(const GenericTopology* topo,
40 virtual void parallelEvaluate(const GenericTopology* topo,
54 inline void ExtendedForce::parallelEvaluate(const GenericTopology* topo, in parallelEvaluate()
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| H A D | ElectricFieldSystemForce.h | 31 void doEvaluate(const GenericTopology* topo,
40 virtual void evaluate(const GenericTopology* topo,
45 virtual void parallelEvaluate(const GenericTopology* topo,
55 virtual unsigned int numberOfBlocks(const GenericTopology* topo,
119 …temForce<TBoundaryConditions,TSwitchingFunction,TConstraint>::evaluate(const GenericTopology* topo, in evaluate()
129 …<TBoundaryConditions,TSwitchingFunction,TConstraint>::parallelEvaluate(const GenericTopology* topo, in parallelEvaluate()
150 …mForce<TBoundaryConditions,TSwitchingFunction,TConstraint>::doEvaluate(const GenericTopology* topo, in doEvaluate()
201 …emForce<TBoundaryConditions,TSwitchingFunction,TConstraint>::numberOfBlocks(const GenericTopology*, in numberOfBlocks() argument
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| H A D | BondSystemForce.h | 39 virtual void evaluate(const GenericTopology* topo,
44 virtual void parallelEvaluate(const GenericTopology* topo,
53 virtual unsigned int numberOfBlocks(const GenericTopology* topo,
80 inline void BondSystemForce<TBoundaryConditions>::evaluate(const GenericTopology* topo, in evaluate()
153 inline void BondSystemForce<TBoundaryConditions>::parallelEvaluate(const GenericTopology* topo, in parallelEvaluate()
177 …inline unsigned int BondSystemForce<TBoundaryConditions>::numberOfBlocks(const GenericTopology* to… in numberOfBlocks()
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| H A D | ForceGroup.h | 15 class GenericTopology; variable
40 void evaluateSystemForces(GenericTopology* topo,
46 void evaluateExtendedForces(GenericTopology* topo,
53 void evaluateMollyForces(GenericTopology* topo,
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| H A D | ExternalGravitationSystemForce.cpp | 34 void ExternalGravitationSystemForce::evaluate(const GenericTopology* topo, in evaluate()
42 void ExternalGravitationSystemForce::parallelEvaluate(const GenericTopology* topo, in parallelEvaluate()
61 void ExternalGravitationSystemForce::doEvaluate(const GenericTopology* topo, in doEvaluate()
73 unsigned int ExternalGravitationSystemForce::numberOfBlocks(const GenericTopology*, in numberOfBlocks() argument
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| /dports/biology/protomol/protomol/framework/frontend/ |
| H A D | TopologyFactoryDetails.cpp | 14 TopologyFactoryDetails::TopologyFactoryDetails():FactoryBase<GenericTopology>(){ in TopologyFactoryDetails()
30 GenericTopology* TopologyFactoryDetails::make(string& errMsg, const Configuration* config){ in make()
31 string id = config->get(GenericTopology::getKeyword()).getString(); in make()
32 const GenericTopology* prototype = TFactory::instance().getPrototype(id); in make()
37 …GenericTopology* TopologyFactoryDetails::make(string& errMsg, const string& id, const vector<Value… in make()
41 …GenericTopology* TopologyFactoryDetails::doMake(string& errMsg, const string& id, const vector<Val… in doMake()
43 const GenericTopology* prototype = getPrototype(id); in doMake()
51 GenericTopology* newObj = prototype->make(errMsg,values); in doMake()
62 for(set<const GenericTopology*>::const_iterator i=myPointers.begin();i != myPointers.end();++i){ in doRegisterAllExemplarsConfiguration()
67 …config->registerKeyword(GenericTopology::getKeyword(),Value(string(""),ConstraintValueType::NotEmp… in doRegisterAllExemplarsConfiguration()
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| H A D | TopologyFactoryDetails.h | 15 class FactoryTraits<GenericTopology> {
21 class TopologyFactoryDetails : public FactoryBase <GenericTopology> {
26 typedef Factory<GenericTopology> TFactory;
48 static GenericTopology* make(std::string& errMsg, const Configuration* config);
49 …static GenericTopology* make(std::string& errMsg, const std::string& id, const std::vector<Value>&…
53 …GenericTopology* doMake(std::string& errMsg, const std::string& id, const std::vector<Value>& valu…
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| H A D | buildTopology.h | 6 class GenericTopology; variable
12 void buildTopology(GenericTopology* topo,const PSF& psf, const PAR& par, bool dihedralMultPSF);
14 void buildMoleculeTable(GenericTopology *topo);
15 void buildExclusionTable(GenericTopology* topo, const ExclusionType& exclusionType);
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| /dports/biology/protomol/protomol/applications/iSGProtomol-app/frontend/ |
| H A D | buildISGTopology.h | 5 class GenericTopology; variable
11 void buildISGTopology(GenericTopology* topo,const PSF& psf, const iSGPAR& par);
13 void buildMoleculeTable(GenericTopology *topo);
14 void buildExclusionTable(GenericTopology* topo, const ExclusionType& exclusionType);
15 void buildMoleculeBondingLists(GenericTopology* topo);
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| /dports/biology/protomol/protomol/applications/iSGProtomol-app/integrators/ |
| H A D | ModifierISG.h | 16 class GenericTopology; variable
38 void setForcesAfterTransformation(GenericTopology *topo);
39 void pickNewMolecule(GenericTopology *topo, ScalarStructure *myEnergies);
43 virtual void readXSCs(const std::string myFile, GenericTopology *topo);
45 void indexBonds(GenericTopology *topo, const TRANS &trans);
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| /dports/biology/protomol/protomol/applications/iSGProtomol-app/forces/ |
| H A D | iSGDihedralSystemForce.h | 26 virtual void evaluate(const GenericTopology* topo,
31 virtual void parallelEvaluate(const GenericTopology* topo,
41 virtual unsigned int numberOfBlocks(const GenericTopology* topo,
65 inline void iSGDihedralSystemForce<TBoundaryConditions>::evaluate(const GenericTopology* topo, in evaluate()
80 …inline void iSGDihedralSystemForce<TBoundaryConditions>::parallelEvaluate(const GenericTopology* t… in parallelEvaluate()
107 …signed int iSGDihedralSystemForce<TBoundaryConditions>::numberOfBlocks(const GenericTopology* topo, in numberOfBlocks()
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| H A D | iSGImproperSystemForce.h | 25 virtual void evaluate(const GenericTopology* topo,
30 virtual void parallelEvaluate(const GenericTopology* topo,
39 virtual unsigned int numberOfBlocks(const GenericTopology* topo,
62 inline void iSGImproperSystemForce<TBoundaryConditions>::evaluate(const GenericTopology* topo, in evaluate()
76 …inline void iSGImproperSystemForce<TBoundaryConditions>::parallelEvaluate(const GenericTopology* t… in parallelEvaluate()
103 …signed int iSGImproperSystemForce<TBoundaryConditions>::numberOfBlocks(const GenericTopology* topo, in numberOfBlocks()
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