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/dports/science/cdk/cdk-cdk-2.3/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/
H A DAbstractReactionTest.java41 reaction.addReactant(reaction.getBuilder().newInstance(IAtomContainer.class)); in testGetReactantCount()
49 reaction.addProduct(reaction.getBuilder().newInstance(IAtomContainer.class)); in testGetProductCount()
62 reaction.addReactant(water); in testAddReactant_IAtomContainer()
66 reaction.addReactant(acetate); in testAddReactant_IAtomContainer()
108 reaction.addProduct(water); in testAddProduct_IAtomContainer()
112 reaction.addProduct(acetate); in testAddProduct_IAtomContainer()
149 reaction.addAgent(proton); in testAddAgent_IAtomContainer()
256 reaction.addReactant(water); in testGetReactants()
268 reaction.addProduct(water); in testGetProducts()
276 reaction.addAgent(water); in testGetAgents()
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/dports/science/siconos/siconos-4.4.0/numerics/src/tools/test/
H A Dtest_projection.c17 ortho += (reaction_ori[i] - reaction[i])*(reaction[i]); in orthogonality()
73 reaction[0] = 1.0; in main()
74 reaction[1] = 0.0; in main()
75 reaction[2] = 0.0; in main()
76 reaction[3] = 0.0; in main()
77 reaction[4] = 0.0; in main()
85 reaction[1] = 0.5; in main()
86 reaction[2] = 0.0; in main()
87 reaction[3] = 0.5; in main()
88 reaction[4] = 0.0; in main()
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/c++/fbc/
H A Dfbc_example1.cpp139 reaction->setId("J0"); in main()
152 reaction->setId("J1"); in main()
165 reaction->setId("J2"); in main()
178 reaction->setId("J3"); in main()
191 reaction->setId("J4"); in main()
204 reaction->setId("J5"); in main()
217 reaction->setId("J6"); in main()
230 reaction->setId("J7"); in main()
243 reaction->setId("J8"); in main()
256 reaction->setId("J9"); in main()
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/csharp/fbc/
H A Dfbc_example1.cs140 reaction.setId("J0"); in Main()
153 reaction.setId("J1"); in Main()
166 reaction.setId("J2"); in Main()
179 reaction.setId("J3"); in Main()
192 reaction.setId("J4"); in Main()
205 reaction.setId("J5"); in Main()
218 reaction.setId("J6"); in Main()
231 reaction.setId("J7"); in Main()
244 reaction.setId("J8"); in Main()
257 reaction.setId("J9"); in Main()
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/java/fbc/
H A Dfbc_example1.java141 reaction.setId("J0"); in main()
154 reaction.setId("J1"); in main()
167 reaction.setId("J2"); in main()
180 reaction.setId("J3"); in main()
193 reaction.setId("J4"); in main()
206 reaction.setId("J5"); in main()
219 reaction.setId("J6"); in main()
232 reaction.setId("J7"); in main()
245 reaction.setId("J8"); in main()
258 reaction.setId("J9"); in main()
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/perl/fbc/
H A Dexample1.pl135 $reaction->setId("J0");
137 $reaction->setFast(0);
150 $reaction->setFast(0);
163 $reaction->setFast(0);
176 $reaction->setFast(0);
189 $reaction->setFast(0);
202 $reaction->setFast(0);
215 $reaction->setFast(0);
228 $reaction->setFast(0);
241 $reaction->setFast(0);
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/ruby/fbc/
H A Dexample1.rb141 reaction.setId("J0");
154 reaction.setId("J1");
167 reaction.setId("J2");
180 reaction.setId("J3");
193 reaction.setId("J4");
206 reaction.setId("J5");
219 reaction.setId("J6");
232 reaction.setId("J7");
245 reaction.setId("J8");
258 reaction.setId("J9");
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/c/fbc/
H A Dfbc_example1.c68 Reaction_t * reaction; in main() local
183 Reaction_setFast(reaction, 0); in main()
196 Reaction_setFast(reaction, 0); in main()
209 Reaction_setFast(reaction, 0); in main()
222 Reaction_setFast(reaction, 0); in main()
235 Reaction_setFast(reaction, 0); in main()
248 Reaction_setFast(reaction, 0); in main()
261 Reaction_setFast(reaction, 0); in main()
274 Reaction_setFast(reaction, 0); in main()
287 Reaction_setFast(reaction, 0); in main()
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H A Dfbc_example1_v2.c68 Reaction_t * reaction; in main() local
205 Reaction_setFast(reaction, 0); in main()
227 Reaction_setFast(reaction, 0); in main()
240 Reaction_setFast(reaction, 0); in main()
253 Reaction_setFast(reaction, 0); in main()
266 Reaction_setFast(reaction, 0); in main()
279 Reaction_setFast(reaction, 0); in main()
292 Reaction_setFast(reaction, 0); in main()
305 Reaction_setFast(reaction, 0); in main()
318 Reaction_setFast(reaction, 0); in main()
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/dports/science/siconos/siconos-4.4.0/numerics/src/FrictionContact/
H A Drolling_fc3d_projection.c214 double * reaction, in rolling_fc3d_check_trivial_solution() argument
220 reaction[0]=0.0; in rolling_fc3d_check_trivial_solution()
273 double normT = sqrt(reaction[1] * reaction[1] + reaction[2] * reaction[2]); in rolling_fc3d_check_trivial_solution()
274 double normMT = sqrt(reaction[3] * reaction[3] + reaction[4] * reaction[4]); in rolling_fc3d_check_trivial_solution()
276 if((normT <= mu * -reaction [0]) && (normMT <= mur * -reaction[0])) in rolling_fc3d_check_trivial_solution()
278 reaction[0]=-reaction[0]; in rolling_fc3d_check_trivial_solution()
279 reaction[1]=-reaction[1]; in rolling_fc3d_check_trivial_solution()
280 reaction[2]=-reaction[2]; in rolling_fc3d_check_trivial_solution()
281 reaction[3]=-reaction[3]; in rolling_fc3d_check_trivial_solution()
282 reaction[4]=-reaction[4]; in rolling_fc3d_check_trivial_solution()
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H A Dfc3d_projection.c229 reaction[0] = 0.; in fc3d_projectionWithDiagonalization_solve()
230 reaction[1] = 0.; in fc3d_projectionWithDiagonalization_solve()
231 reaction[2] = 0.; in fc3d_projectionWithDiagonalization_solve()
245 mrn = reaction[1] * reaction[1] + reaction[2] * reaction[2]; in fc3d_projectionWithDiagonalization_solve()
247 if(mrn > mu2 * reaction[0]*reaction[0]) in fc3d_projectionWithDiagonalization_solve()
250 reaction[1] = reaction[1] * num; in fc3d_projectionWithDiagonalization_solve()
251 reaction[2] = reaction[2] * num; in fc3d_projectionWithDiagonalization_solve()
407 a2 = sqrt((reaction_k[0] - reaction[0]) * (reaction_k[0] - reaction[0]) + in fc3d_projectionOnConeWithLocalIteration_solve()
419 sqrt(reaction[0] * reaction[0] + in fc3d_projectionOnConeWithLocalIteration_solve()
420 reaction[1] * reaction[1] + in fc3d_projectionOnConeWithLocalIteration_solve()
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H A Drolling_fc2d_projection.c206 double * reaction, in rolling_fc2d_check_trivial_solution() argument
212 reaction[0]=0.0; in rolling_fc2d_check_trivial_solution()
213 reaction[1]=0.0; in rolling_fc2d_check_trivial_solution()
214 reaction[2]=0.0; in rolling_fc2d_check_trivial_solution()
266 if((normT <= mu * -reaction [0]) && (normMT <= mur * -reaction[0])) in rolling_fc2d_check_trivial_solution()
268 reaction[0]=-reaction[0]; in rolling_fc2d_check_trivial_solution()
269 reaction[1]=-reaction[1]; in rolling_fc2d_check_trivial_solution()
270 reaction[2]=-reaction[2]; in rolling_fc2d_check_trivial_solution()
280 double* reaction, in rolling_fc2d_projectionOnConeWithLocalIteration_solve() argument
450 (reaction_k[0] - reaction[0]) * (reaction_k[0] - reaction[0]) + in rolling_fc2d_projectionOnConeWithLocalIteration_solve()
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H A Dfc3d_driver.c80 double *reaction, double *velocity, in fc3d_driver() argument
97 info = fc3d_checkTrivialCase(problem, velocity, reaction, options); in fc3d_driver()
115 fc3d_nsgs(problem, reaction, velocity, &info, options); in fc3d_driver()
121 fc3d_nsgs_velocity(problem, reaction, velocity, &info, options); in fc3d_driver()
128 fc3d_admm(problem, reaction, velocity, &info, options); in fc3d_driver()
135 fc3d_proximal(problem, reaction, velocity, &info, options); in fc3d_driver()
163 fc3d_SOCLCP(problem, reaction, velocity, &info, options); in fc3d_driver()
185 fc3d_ExtraGradient(problem, reaction, velocity, &info, options); in fc3d_driver()
264 fc3d_AVI_gams_path(problem, reaction, velocity, &info, options); in fc3d_driver()
303 double* reaction, SolverOptions* options) in fc3d_checkTrivialCase() argument
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H A Dgfc3d_solvers_wr.c59 fc3d_nsgs(localproblem, reaction, velocity, info, options); in gfc3d_nsgs_wr()
61 globalFrictionContact_computeGlobalVelocity(problem, reaction, globalVelocity); in gfc3d_nsgs_wr()
77 globalFrictionContact_computeGlobalVelocity(problem, reaction, globalVelocity); in gfc3d_nsgs_wr()
101 fc3d_admm(localproblem, reaction, velocity, info, options); in gfc3d_admm_wr()
102 globalFrictionContact_computeGlobalVelocity(problem, reaction, globalVelocity); in gfc3d_admm_wr()
108 globalFrictionContact_computeGlobalVelocity(problem, reaction, globalVelocity); in gfc3d_admm_wr()
132 globalFrictionContact_computeGlobalVelocity(problem, reaction, globalVelocity); in gfc3d_nonsmooth_Newton_AlartCurnier_wr()
162 fc3d_nsgs_velocity(localproblem, reaction, velocity, info, options); in gfc3d_nsgs_velocity_wr()
191 fc3d_proximal(localproblem, reaction, velocity, info, options); in gfc3d_proximal_wr()
220 fc3d_DeSaxceFixedPoint(localproblem, reaction, velocity, info, options); in gfc3d_DeSaxceFixedPoint_wr()
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/python/fbc/
H A Dfbc_example1.py148 reaction.setId("J0")
161 reaction.setId("J1")
174 reaction.setId("J2")
187 reaction.setId("J3")
200 reaction.setId("J4")
213 reaction.setId("J5")
226 reaction.setId("J6")
239 reaction.setId("J7")
252 reaction.setId("J8")
265 reaction.setId("J9")
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/dports/science/thermofun/thermofun-0.3.8/ThermoFun/
H A DThermoModelsReaction.cpp18 Reaction reaction; member
24 : reaction(reaction) in Impl()
49 Reaction reaction; member
55 : reaction(reaction) in Impl()
80 Reaction reaction; member
86 : reaction(reaction) in Impl()
111 Reaction reaction; member
117 : reaction(reaction) in Impl()
142 Reaction reaction; member
148 : reaction(reaction) in Impl()
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/dports/science/cdk/cdk-cdk-2.3/base/reaction/src/main/resources/
H A Dreaction-types.set1 org.openscience.cdk.reaction.ReactionEngine
2 org.openscience.cdk.reaction.type.AdductionProtonLPReaction
3 org.openscience.cdk.reaction.type.AdductionProtonPBReaction
4 org.openscience.cdk.reaction.type.AdductionSodiumLPReaction
5 org.openscience.cdk.reaction.type.CarbonylEliminationReaction
6 org.openscience.cdk.reaction.type.ElectronImpactNBEReaction
7 org.openscience.cdk.reaction.type.ElectronImpactPDBReaction
8 org.openscience.cdk.reaction.type.ElectronImpactSDBReaction
11 org.openscience.cdk.reaction.type.HomolyticCleavageReaction
12 org.openscience.cdk.reaction.type.HyperconjugationReaction
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/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/
H A DReactionManipulatorTest.java73 reaction = set.getReaction(0); in setUp()
96 reaction.setID("r1"); in testGetAllIDs_IReaction()
102 reaction.addReactant(water); in testGetAllIDs_IReaction()
103 reaction.addProduct(water); in testGetAllIDs_IReaction()
122 reaction.addMapping(mapping); in testGetMappedChemObject_IReaction_IAtom()
124 reaction.addMapping(mapping); in testGetMappedChemObject_IReaction_IAtom()
126 reaction.addMapping(mapping); in testGetMappedChemObject_IReaction_IAtom()
129 reaction.addProduct(product); in testGetMappedChemObject_IReaction_IAtom()
152 reaction.addMapping(mapping); in testGetMappedChemObject_IReaction_IBond()
235 reaction.addReactant(mol); in testRemoveElectronContainer_IReaction_IElectronContainer()
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/dports/science/cantera/cantera-2.5.1-611-gc4d6ecc15/data/inputs/
H A DnDodecane_Reitz.cti1842 reaction('c4h9 + o2 => c4h9o2', [5.050000e+12, 0.0, 0.0])
1917 reaction('c3h5 + ch3 => c4h8', [5.000000e+12, 0.0, 0.0])
2020 reaction('h + c3h6 => c3h7', [1.000000e+13, 0.0, 2500.0])
2053 reaction('c3h7 + o2 => c3h7o2', [4.520000e+12, 0.0, 0.0])
2188 reaction('c2h5 + h <=> 2 ch3', [3.610000e+13, 0.0, 0.0])
2351 reaction('hcco + oh => 2 hco', [1.000000e+13, 0.0, 0.0])
2888 reaction('2 c3h3 <=> A1', [1.000000e+36, -7.18, 8413.0])
2894 reaction('c4h3 + c2h3 <=> A1', [3.000000e+13, 0.0, 0.0])
2915 reaction('c4h5 + c2h <=> A1', [1.000000e+13, 0.0, 0.0])
3057 reaction('A2- + h <=> A2', [7.800000e+13, 0.0, 0.0])
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H A Dgri30_highT.cti1028 reaction( "O + HO2 <=> OH + O2", [2.00000E+13, 0, 0])
1034 reaction( "O + CH <=> H + CO", [5.70000E+13, 0, 0])
1160 reaction( "H + HO2 <=> 2 OH", [8.40000E+13, 0, 635])
1169 reaction( "H + CH <=> C + H2", [1.65000E+14, 0, 0])
1351 reaction( "OH + C <=> H + CO", [5.00000E+13, 0, 0])
1682 reaction( "NH + O <=> NO + H", [4.00000E+13, 0, 0])
1700 reaction( "NH + N <=> N2 + H", [1.50000E+13, 0, 0])
1724 reaction( "NNH <=> N2 + H", [3.30000E+08, 0, 0])
1765 reaction( "CN + O <=> CO + N", [7.70000E+13, 0, 0])
1855 reaction( "C + NO <=> CN + O", [1.90000E+13, 0, 0])
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H A Dgri30.cti1028 reaction( "O + HO2 <=> OH + O2", [2.00000E+13, 0, 0])
1034 reaction( "O + CH <=> H + CO", [5.70000E+13, 0, 0])
1160 reaction( "H + HO2 <=> 2 OH", [8.40000E+13, 0, 635])
1169 reaction( "H + CH <=> C + H2", [1.65000E+14, 0, 0])
1351 reaction( "OH + C <=> H + CO", [5.00000E+13, 0, 0])
1682 reaction( "NH + O <=> NO + H", [4.00000E+13, 0, 0])
1700 reaction( "NH + N <=> N2 + H", [1.50000E+13, 0, 0])
1724 reaction( "NNH <=> N2 + H", [3.30000E+08, 0, 0])
1765 reaction( "CN + O <=> CO + N", [7.70000E+13, 0, 0])
1855 reaction( "C + NO <=> CN + O", [1.90000E+13, 0, 0])
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/dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/
H A DReactionSetManipulator.java62 for (IReaction reaction : set.reactions()) { in removeAtomAndConnectedElectronContainers()
68 for (IReaction reaction : set.reactions()) { in removeElectronContainer()
121 return reaction; in getRelevantReaction()
131 return reaction; in getRelevantReaction()
148 newReactSet.addReaction(reaction); in getRelevantReactions()
151 newReactSet.addReaction(reaction); in getRelevantReactions()
234 … if (AtomContainerSetManipulator.containsByID(reaction.getProducts(), id)) return reaction; in getReactionByAtomContainerID()
237 … if (AtomContainerSetManipulator.containsByID(reaction.getReactants(), id)) return reaction; in getReactionByAtomContainerID()
252 for (IReaction reaction : reactionIter) { in getReactionByReactionID()
253 if (reaction.getID() != null && reaction.getID().equals(id)) { in getReactionByReactionID()
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/src/bindings/matlab/test/
H A DtestReadFromFile1.m8 '<p>The reaction looks like this:</p>', ...
9 '<p>reaction-1: X0 -&gt; S1; k1*X0;</p>', ...
10 '<p>reaction-2: S1 -&gt; X1; k2*S1;</p>', ...
11 '<p>reaction-3: S1 -&gt; X2; k3*S1;</p>', ...
78 % * <reaction name="reaction_1" reversible="false"> ... </reaction>
79 % * <reaction name="reaction_2" reversible="false"> ... </reaction>
80 % * <reaction name="reaction_3" reversible="false"> ... </reaction>
98 % * <reaction name="reaction_1" reversible="false">
110 % * </reaction>
144 % * </reaction>
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/dports/biology/libsbml/libsbml-5.19.0/src/bindings/matlab/test/
H A DtestReadFromFile1.m8 '<p>The reaction looks like this:</p>', ...
9 '<p>reaction-1: X0 -&gt; S1; k1*X0;</p>', ...
10 '<p>reaction-2: S1 -&gt; X1; k2*S1;</p>', ...
11 '<p>reaction-3: S1 -&gt; X2; k3*S1;</p>', ...
78 % * <reaction name="reaction_1" reversible="false"> ... </reaction>
79 % * <reaction name="reaction_2" reversible="false"> ... </reaction>
80 % * <reaction name="reaction_3" reversible="false"> ... </reaction>
98 % * <reaction name="reaction_1" reversible="false">
110 % * </reaction>
144 % * </reaction>
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/dports/www/firefox-legacy/firefox-52.8.0esr/testing/web-platform/meta/custom-elements/reactions/
H A DElement.html.ini3 [id on Element must enqueue an attributeChanged reaction when adding id content attribute]
6 [id on Element must enqueue an attributeChanged reaction when replacing an existing attribute]
9 …[className on Element must enqueue an attributeChanged reaction when adding class content attribut…
12 …[className on Element must enqueue an attributeChanged reaction when replacing an existing attribu…
15 [slot on Element must enqueue an attributeChanged reaction when adding slot content attribute]
18 [slot on Element must enqueue an attributeChanged reaction when replacing an existing attribute]
21 [setAttribute on Element must enqueue an attributeChanged reaction when adding an attribute]
33 [setAttributeNS on Element must enqueue an attributeChanged reaction when adding an attribute]
69 [setAttributeNode on Element must enqueue an attributeChanged reaction when adding an attribute]
105 [undefined must enqueue a connected reaction]
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