/dports/science/smoldyn/smoldyn-2.67/source/BioNetGen/Perl2/ |
H A D | SpeciesGraph.pm | 42 Molecules => '@', 290 unless ( @{$sg->Molecules} ) 543 ( 0 .. $#{ $sg->Molecules } ); 586 @{$sg->Molecules} = sort by_molecule @{$sg->Molecules}; 1013 $sg_copy->Molecules($mol_copy); 1079 if ( @{$sg->Molecules} ) 1081 $sg_copy->Molecules( [map {$_->copy($copy_labels)} @{$sg->Molecules}] ); 1944 if ( @{$sg->Molecules} ) 2243 push @{$sgs->[$ipatt]->Molecules}, $sg->Molecules->[$imol2]; 2250 @{$sg->Molecules} = (); [all …]
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H A D | RxnRule.pm | 268 foreach my $mol ( @{$g->Molecules} ) 1563 for my $mol ( @{ $g->Molecules } ) { 2081 my @pused = (0) x @{$pg->Molecules}; 2209 my $mol = $pg->Molecules->[$imP]; 3523 my $mol = $g->Molecules; 3634 my $nmol = @{$g->Molecules}; 3644 push @{$g->Molecules}, $newMol; 3974 $g->Molecules->[$im_targ] = undef; 3990 $g->Molecules->[$im_targ] = undef; 4001 while ( $im < @{$g->Molecules} ) [all …]
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H A D | Map.pm | 45 my $molecules = $map->Source->Molecules; 257 for ( my $imol = 0; $imol < @{$source->Molecules}; ++$imol ) 259 my $mol = $source->Molecules->[$imol]; 264 $target->Molecules->[$imol_targ]->Label( $mol->Label ); 275 … $target->Molecules->[$imol_targ]->Components->[$icomp_targ]->Label( $comp->Label );
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H A D | Species.pm | 76 …my $count = (scalar @{$spec->SpeciesGraph->Molecules}) - ($spec->SpeciesGraph->toString() =~ tr/@/… 82 …$radius = (scalar @{$spec->SpeciesGraph->Molecules} == 1) ? "Rsp" : "(".scalar @{$spec->SpeciesGra…
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H A D | RefineRule.pm | 71 foreach my $mol ( @{ $g->Molecules } ) 141 unless ( @{$g->Molecules} == 1 ) 146 if ( defined $model->MoleculeTypesList->findMoleculeType($g->Molecules->[0]->Name) ) 151 unless ( @{$g->Molecules->[0]->Components} == 0 ) 165 foreach my $mol ( @{$g->Molecules} ) 528 if ( @{$p->Molecules} > $params->{max_agg} )
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/ |
H A D | VFMapperTest.java | 92 hexane = Molecules.createHexane(); in setUp() 93 benzene = Molecules.createBenzene(); in setUp() 94 pyridine = Molecules.createPyridine(); in setUp() 95 toluene4 = Molecules.create4Toluene(); in setUp() 96 pyridazine = Molecules.createPyridazine(); in setUp() 99 naphthalene = Molecules.createNaphthalene(); in setUp() 100 toluene = Molecules.createToluene(); in setUp() 101 phenol = Molecules.createPhenol(); in setUp() 102 acetone = Molecules.createAcetone(); in setUp() 103 propane = Molecules.createPropane(); in setUp() [all …]
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smsd/ring/ |
H A D | HanserRingFinderTest.java | 33 import org.openscience.cdk.smsd.algorithm.vflib.Molecules; 66 IAtomContainer benzene = Molecules.createBenzene(); in testItShoudFindOneRingInBenzene() 73 IAtomContainer naphthalene = Molecules.createNaphthalene(); in testItShouldFindThreeRingsInNaphthalene() 80 IAtomContainer cubane = Molecules.createCubane(); in testItShouldFind28RingsInCubane()
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/dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/src/csgapps/part_dist/ |
H A D | part_dist.cc | 179 for (const auto &mol : top.Molecules()) { in main() 202 for (const auto &mol : top.Molecules()) { in main() 251 for (const auto &mol : top.Molecules()) { in main() 274 for (const auto &mol : top.Molecules()) { in main()
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/dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/csg-da5c1dc/src/csgapps/part_dist/ |
H A D | part_dist.cc | 179 for (const auto &mol : top.Molecules()) { in main() 202 for (const auto &mol : top.Molecules()) { in main() 251 for (const auto &mol : top.Molecules()) { in main() 274 for (const auto &mol : top.Molecules()) { in main()
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/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FMCS/ |
H A D | MaximumCommonSubgraph.h | 53 std::vector<const ROMol*> Molecules; variable 93 Molecules.clear(); in clear()
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H A D | MaximumCommonSubgraph.cpp | 60 QueryMolecule = Molecules.front(); in init() 211 Targets.resize(Molecules.size() - 1); in init() 213 for (auto it = Molecules.begin() + 1; it != Molecules.end(); it++, i++) { in init() 964 Molecules.push_back(src_mol.get()); in find() 965 if (!Molecules.back()->getRingInfo()->isInitialized()) { in find() 966 Molecules.back()->getRingInfo()->initialize(); // but do not fill out !!! in find() 972 std::stable_sort(Molecules.begin(), Molecules.end(), molPtr_NumBondLess); in find() 976 i < Molecules.size() - ThresholdCount && !areSeedsEmpty && !res.Canceled; in find() 1028 } else if (i + 1 < Molecules.size() - ThresholdCount) { in find() 1033 std::swap(Molecules[0], in find() [all …]
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/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smsd/ |
H A D | SMSDBondSensitiveTest.java | 37 import org.openscience.cdk.smsd.algorithm.vflib.Molecules; 56 Napthalene = Molecules.createNaphthalene(); in setUp() 57 Cyclohexane = Molecules.createCyclohexane(); in setUp() 58 Benzene = Molecules.createBenzene(); in setUp()
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/dports/science/votca/votca-2021.2-18560-gfbe18d971/xtp/xtp-2a31d70/scripts/ |
H A D | xtp_update_mapfile.in | 119 Molecules = Root.find("molecules") 120 for molecule in Molecules.iter('molecule'):
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/dports/science/votca/votca-2021.2-18560-gfbe18d971/xtp/scripts/ |
H A D | xtp_update_mapfile.in | 119 Molecules = Root.find("molecules") 120 for molecule in Molecules.iter('molecule'):
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/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/pb_wrap/src/ |
H A D | PBSAMWrap.cpp | 209 Valist* Molecules[], int nmls ) in runPBSAMWrapAPBS() argument 218 unsigned int natoms = Valist_getNumberAtoms(Molecules[mol]); in runPBSAMWrapAPBS() 245 atom = Valist_getAtom(Molecules[mol], i); in runPBSAMWrapAPBS()
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/dports/science/jmol/jmol-14.32.7/src/org/openscience/jmol/app/webexport/ |
H A D | Molecules.java | 50 class Molecules extends JPanel {//implements ActionListener { class
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/dports/science/lammps/lammps-stable_29Sep2021/examples/ASPHERE/box/ |
H A D | data.box | 431 Molecules
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/dports/science/lammps/lammps-stable_29Sep2021/examples/ASPHERE/dimer/ |
H A D | data.dimer | 211 Molecules
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/dports/science/lammps/lammps-stable_29Sep2021/examples/ASPHERE/star/ |
H A D | data.star | 281 Molecules
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/dports/science/jdftx/jdftx-1.6.0/jdftx/doc/tutorials/molecule/ |
H A D | index.dox | 1 /** \page MoleculeTutorials Molecules
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/dports/science/chemtool/chemtool-1.6.14/gnome/ |
H A D | chemtool.desktop | 3 Comment=Molecules 2D drawing
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/dports/science/chemtool-devel/chemtool-1.7alpha15/gnome/ |
H A D | chemtool.desktop | 3 Comment=Molecules 2D drawing
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/dports/science/chemtool-devel/chemtool-1.7alpha15/pld/ |
H A D | chemtool.desktop | 3 Comment=Molecules 2D drawing program
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/dports/science/chemtool/chemtool-1.6.14/pld/ |
H A D | chemtool.desktop | 3 Comment=Molecules 2D drawing program
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/dports/science/rdkit/rdkit-Release_2021_03_5/Contrib/SA_Score/ |
H A D | README | 3 Estimation of Synthetic Accessibility Score of Drug-like Molecules based on Molecular Complexity an…
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