/dports/science/cdk/cdk-cdk-2.3/base/test-interfaces/src/test/java/org/openscience/cdk/interfaces/ |
H A D | AbstractReactionTest.java | 41 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() [all …]
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/dports/science/siconos/siconos-4.4.0/numerics/src/tools/test/ |
H A D | test_projection.c | 17 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() [all …]
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/c++/fbc/ |
H A D | fbc_example1.cpp | 139 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() [all …]
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/csharp/fbc/ |
H A D | fbc_example1.cs | 140 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() [all …]
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/java/fbc/ |
H A D | fbc_example1.java | 141 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() [all …]
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/perl/fbc/ |
H A D | example1.pl | 135 $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); [all …]
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/ruby/fbc/ |
H A D | example1.rb | 141 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"); [all …]
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/c/fbc/ |
H A D | fbc_example1.c | 68 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() [all …]
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H A D | fbc_example1_v2.c | 68 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() [all …]
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/dports/science/siconos/siconos-4.4.0/numerics/src/FrictionContact/ |
H A D | rolling_fc3d_projection.c | 214 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() [all …]
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H A D | fc3d_projection.c | 229 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() [all …]
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H A D | rolling_fc2d_projection.c | 206 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() [all …]
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H A D | fc3d_driver.c | 80 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 [all …]
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H A D | gfc3d_solvers_wr.c | 59 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() [all …]
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/examples/python/fbc/ |
H A D | fbc_example1.py | 148 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") [all …]
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/dports/science/thermofun/thermofun-0.3.8/ThermoFun/ |
H A D | ThermoModelsReaction.cpp | 18 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() [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/reaction/src/main/resources/ |
H A D | reaction-types.set | 1 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 [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/test-standard/src/test/java/org/openscience/cdk/tools/manipulator/ |
H A D | ReactionManipulatorTest.java | 73 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() [all …]
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/dports/science/cantera/cantera-2.5.1-611-gc4d6ecc15/data/inputs/ |
H A D | nDodecane_Reitz.cti | 1842 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]) [all …]
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H A D | gri30_highT.cti | 1028 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]) [all …]
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H A D | gri30.cti | 1028 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]) [all …]
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/dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ |
H A D | ReactionSetManipulator.java | 62 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() [all …]
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/dports/biology/py-python-libsbml/python-libsbml-5.19.0/libsbml_source/src/bindings/matlab/test/ |
H A D | testReadFromFile1.m | 8 '<p>The reaction looks like this:</p>', ... 9 '<p>reaction-1: X0 -> S1; k1*X0;</p>', ... 10 '<p>reaction-2: S1 -> X1; k2*S1;</p>', ... 11 '<p>reaction-3: S1 -> 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> [all …]
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/dports/biology/libsbml/libsbml-5.19.0/src/bindings/matlab/test/ |
H A D | testReadFromFile1.m | 8 '<p>The reaction looks like this:</p>', ... 9 '<p>reaction-1: X0 -> S1; k1*X0;</p>', ... 10 '<p>reaction-2: S1 -> X1; k2*S1;</p>', ... 11 '<p>reaction-3: S1 -> 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> [all …]
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/dports/www/firefox-legacy/firefox-52.8.0esr/testing/web-platform/meta/custom-elements/reactions/ |
H A D | Element.html.ini | 3 [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] [all …]
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