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/dports/science/smoldyn/smoldyn-2.67/source/BioNetGen/Perl2/
H A DSpeciesGraph.pm42 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 …]
H A DRxnRule.pm268 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 …]
H A DMap.pm45 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 );
H A DSpecies.pm76 …my $count = (scalar @{$spec->SpeciesGraph->Molecules}) - ($spec->SpeciesGraph->toString() =~ tr/@/…
82 …$radius = (scalar @{$spec->SpeciesGraph->Molecules} == 1) ? "Rsp" : "(".scalar @{$spec->SpeciesGra…
H A DRefineRule.pm71 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} )
/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smsd/algorithm/vflib/
H A DVFMapperTest.java92 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 …]
/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smsd/ring/
H A DHanserRingFinderTest.java33 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()
/dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/src/csgapps/part_dist/
H A Dpart_dist.cc179 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()
/dports/science/votca/votca-2021.2-18560-gfbe18d971/csg/csg-da5c1dc/src/csgapps/part_dist/
H A Dpart_dist.cc179 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()
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/GraphMol/FMCS/
H A DMaximumCommonSubgraph.h53 std::vector<const ROMol*> Molecules; variable
93 Molecules.clear(); in clear()
H A DMaximumCommonSubgraph.cpp60 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 …]
/dports/science/cdk/cdk-cdk-2.3/legacy/src/test/java/org/openscience/cdk/smsd/
H A DSMSDBondSensitiveTest.java37 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()
/dports/science/votca/votca-2021.2-18560-gfbe18d971/xtp/xtp-2a31d70/scripts/
H A Dxtp_update_mapfile.in119 Molecules = Root.find("molecules")
120 for molecule in Molecules.iter('molecule'):
/dports/science/votca/votca-2021.2-18560-gfbe18d971/xtp/scripts/
H A Dxtp_update_mapfile.in119 Molecules = Root.find("molecules")
120 for molecule in Molecules.iter('molecule'):
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/apbs/externals/pb_s_am/pb_wrap/src/
H A DPBSAMWrap.cpp209 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()
/dports/science/jmol/jmol-14.32.7/src/org/openscience/jmol/app/webexport/
H A DMolecules.java50 class Molecules extends JPanel {//implements ActionListener { class
/dports/science/lammps/lammps-stable_29Sep2021/examples/ASPHERE/box/
H A Ddata.box431 Molecules
/dports/science/lammps/lammps-stable_29Sep2021/examples/ASPHERE/dimer/
H A Ddata.dimer211 Molecules
/dports/science/lammps/lammps-stable_29Sep2021/examples/ASPHERE/star/
H A Ddata.star281 Molecules
/dports/science/jdftx/jdftx-1.6.0/jdftx/doc/tutorials/molecule/
H A Dindex.dox1 /** \page MoleculeTutorials Molecules
/dports/science/chemtool/chemtool-1.6.14/gnome/
H A Dchemtool.desktop3 Comment=Molecules 2D drawing
/dports/science/chemtool-devel/chemtool-1.7alpha15/gnome/
H A Dchemtool.desktop3 Comment=Molecules 2D drawing
/dports/science/chemtool-devel/chemtool-1.7alpha15/pld/
H A Dchemtool.desktop3 Comment=Molecules 2D drawing program
/dports/science/chemtool/chemtool-1.6.14/pld/
H A Dchemtool.desktop3 Comment=Molecules 2D drawing program
/dports/science/rdkit/rdkit-Release_2021_03_5/Contrib/SA_Score/
H A DREADME3 Estimation of Synthetic Accessibility Score of Drug-like Molecules based on Molecular Complexity an…

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