/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/analysis/ |
H A D | test_hydrogenbondautocorrel.py | 58 hydrogens=hydrogens, 75 hydrogens=hydrogens, 95 hydrogens=hydrogens, 113 hydrogens=hydrogens, 131 hydrogens=hydrogens, 152 hydrogens=hydrogens, 177 hydrogens=hydrogens, 204 hydrogens=hydrogens, 239 hydrogens=hydrogens, 250 hydrogens=hydrogens, [all …]
|
/dports/science/p5-Chemistry-Mol/Chemistry-Mol-0.38/t/ |
H A D | Atom.t | 40 # default hydrogens 41 ok( ! $atom->hydrogens, 'hydrogens default' ); 45 # set hydrogens 46 $atom->hydrogens(1); 47 is( $atom->hydrogens, 1, 'hydrogens' ); 53 is( $atom->hydrogens, 2, 'hydrogens' ); 64 is( $atom->hydrogens, 0, 'hydrogens' ); 72 is( $atom->hydrogens, 2, 'hydrogens' );
|
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-Mol-0.35/t/ |
H A D | Atom.t | 40 # default hydrogens 41 ok( ! $atom->hydrogens, 'hydrogens default' ); 45 # set hydrogens 46 $atom->hydrogens(1); 47 is( $atom->hydrogens, 1, 'hydrogens' ); 53 is( $atom->hydrogens, 2, 'hydrogens' ); 64 is( $atom->hydrogens, 0, 'hydrogens' ); 72 is( $atom->hydrogens, 2, 'hydrogens' );
|
/dports/science/cdk/cdk-cdk-2.3/tool/hash/src/main/java/org/openscience/cdk/hash/ |
H A D | AtomSuppression.java | 69 BitSet hydrogens = new BitSet(); in suppress() local 72 hydrogens.set(i, "H".equals(atom.getSymbol())); in suppress() 74 return Suppressed.fromBitSet(hydrogens); in suppress() 84 BitSet hydrogens = new BitSet(); in suppress() local 87 hydrogens.set(i, atom instanceof IPseudoAtom); in suppress() 89 return Suppressed.fromBitSet(hydrogens); in suppress()
|
/dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/graph/invariant/ |
H A D | Canon.java | 98 private Canon(int[][] g, long[] partition, boolean[] hydrogens, boolean symOnly) { in Canon() argument 102 symmetry = refine(labelling, hydrogens); in Canon() 201 private long[] refine(long[] invariants, boolean[] hydrogens) { in refine() argument 239 curr[v] = hydrogens[v] ? prev[v] : primeProduct(g[v], prev, hydrogens); in refine() 252 if (hydrogens[i]) { in refine() 254 hydrogens[i] = false; in refine() 294 private long primeProduct(int[] ws, long[] ranks, boolean[] hydrogens) { in primeProduct() argument 297 if (!hydrogens[w]) { in primeProduct() 418 final boolean[] hydrogens = new boolean[ac.getAtomCount()]; in terminalHydrogens() 424 hydrogens[i] = atom.getAtomicNumber() == 1 && in terminalHydrogens() [all …]
|
/dports/science/openbabel/openbabel-3.1.1/test/ |
H A D | README | 22 // Add hydrogens 30 // Delete hydrogens 31 // Add polar hydrogens 32 // Add pH hydrogens
|
/dports/science/cdk/cdk-cdk-2.3/display/renderbasic/src/main/java/org/openscience/cdk/renderer/generators/standard/ |
H A D | StandardAtomGenerator.java | 374 …AtomSymbol generatePeriodicSymbol(final int number, final int hydrogens, final int mass, final int… in generatePeriodicSymbol() argument 382 …TextOutline hydrogenCount = new TextOutline(Integer.toString(hydrogens), font).resize(scriptSize, … in generatePeriodicSymbol() 390 … chargeAdjunct = positionChargeLabel(hydrogens, position, chargeAdjunct, element, hydrogenAdjunct); in generatePeriodicSymbol() 404 if (hydrogens > 0) adjuncts.add(hydrogenAdjunct); in generatePeriodicSymbol() 405 if (hydrogens > 1) adjuncts.add(hydrogenCount); in generatePeriodicSymbol() 489 if (hydrogens > 0 && position == Right) in positionChargeLabel() 491 else if (hydrogens > 1 && position == Above) referenceBounds = hydrogen.getBounds(); in positionChargeLabel() 526 …private double hydrogenXDodge(int hydrogens, int mass, TextOutline elementLabel, TextOutline hydro… in hydrogenXDodge() argument 528 if (mass < 0 && hydrogens > 1) { in hydrogenXDodge() 531 if (hydrogens > 1) { in hydrogenXDodge() [all …]
|
/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/Features/ |
H A D | FeatDirUtilsRD.py | 138 hydrogens = [] 143 hydrogens.append(nbr) 272 hydrogens = [] 276 hydrogens.append(nbr) 282 assert len(hydrogens) == 0 289 assert len(hydrogens) == 1 294 hid = hydrogens[0].GetIdx() 314 for hid in hydrogens:
|
/dports/science/cdk/cdk-cdk-2.3/base/standard/src/main/java/org/openscience/cdk/tools/manipulator/ |
H A D | AtomContainerManipulator.java | 538 int hydrogens = 0; in getTotalHydrogenCount() local 542 hydrogens++; in getTotalHydrogenCount() 548 hydrogens += implicit; in getTotalHydrogenCount() 552 return hydrogens; in getTotalHydrogenCount() 640 for (IAtom atom : hydrogens) in convertImplicitToExplicitHydrogens() 922 hydrogens.add(atom); in suppressHydrogens() 930 if (hydrogens.isEmpty()) return org; in suppressHydrogens() 935 int remaining = hydrogens.size(); in suppressHydrogens() 938 … if (remaining > 0 && (hydrogens.contains(bond.getBegin()) || hydrogens.contains(bond.getEnd()))) { in suppressHydrogens() 1017 if (hydrogens.contains(x)) { in suppressHydrogens() [all …]
|
/dports/science/openbabel/openbabel-3.1.1/tools/ |
H A D | obenergy.cpp | 60 bool hydrogens = false; in main() local 73 hydrogens = true; in main() 124 if (hydrogens) in main()
|
H A D | obminimize.cpp | 47 bool hydrogens = false; in main() local 138 hydrogens = true; in main() 209 if (hydrogens) in main()
|
/dports/science/py-MDAnalysis/MDAnalysis-0.19.2/MDAnalysis/analysis/hbonds/ |
H A D | hbond_analysis.py | 788 hydrogens = [ 794 hydrogens = [] # weird corner case that atom is the last one in universe 795 return hydrogens 1376 def _make_dict(donors, hydrogens): argument 1378 d = dict((donors[k].resid, {}) for k in range(len(donors)) if k in hydrogens) 1380 if k in hydrogens: 1381 … d[donors[k].resid].update(dict((atom.name, donors[k].name) for atom in hydrogens[k])) 1414 def _make_dict(donors, hydrogens): argument 1419 if k in hydrogens: 1420 x.extend([(atom.index, donors[k].name) for atom in hydrogens[k]])
|
/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/ |
H A D | functional_groups.py | 213 hydrogens = {n for n in self.molgraph.graph.nodes if str(self.species[n]) == "H"} 225 if neighbor in hydrogens: 250 hydrogens = {n for n in self.molgraph.graph.nodes if str(self.species[n]) == "H"} 262 hs = {n["site_index"] for n in neighbors if n["site_index"] in hydrogens} 290 if neighbor in hydrogens:
|
/dports/science/nwchem-data/nwchem-7.0.2-release/src/data/amber_q/ |
H A D | ions.par | 74 # 2000 two non-hydrogens 75 # 3000 three non-hydrogens 76 # 4000 four non-hydrogens 78 # Atom number 3500 would signify any unprotonated atom with three non-hydrogens
|
/dports/science/nwchem/nwchem-7b21660b82ebd85ef659f6fba7e1e73433b0bd0a/src/data/amber_q/ |
H A D | ions.par | 74 # 2000 two non-hydrogens 75 # 3000 three non-hydrogens 76 # 4000 four non-hydrogens 78 # Atom number 3500 would signify any unprotonated atom with three non-hydrogens
|
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/doc/examples/ |
H A D | adding-hydrogens.rst | 1 Adding hydrogens and assigning parameters 31 Reconstruct missing atoms (hydrogens) 41 …R file and visualize in a molecular graphics program to examine how the hydrogens were added and h…
|
/dports/science/cdk/cdk-cdk-2.3/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/ |
H A D | InChITautomerGenerator.java | 365 String hydrogens = ""; in parseMobileHydrogens() local 368 hydrogens = inchi.substring(inchi.indexOf("/h") + 2); in parseMobileHydrogens() 369 if (hydrogens.indexOf('/') != -1) { in parseMobileHydrogens() 370 hydrogens = hydrogens.substring(0, hydrogens.indexOf('/')); in parseMobileHydrogens() 372 String mobileHydrogens = hydrogens.substring(hydrogens.indexOf('(')); in parseMobileHydrogens()
|
/dports/science/cdk/cdk-cdk-2.3/storage/smiles/src/test/java/org/openscience/cdk/smiles/ |
H A D | BeamToCDKTest.java | 97 IAtom a = g2c.toCDKAtom(AtomBuilder.aliphatic(Element.Carbon).hydrogens(4).build(), 4); in methaneAtom() 104 IAtom a = g2c.toCDKAtom(AtomBuilder.aliphatic(Element.Oxygen).hydrogens(2).build(), 2); in waterAtom() 111 … IAtom a = g2c.toCDKAtom(AtomBuilder.aliphatic(Element.Oxygen).hydrogens(1).anion().build(), 1); in oxidanide() 119 … IAtom a = g2c.toCDKAtom(AtomBuilder.aliphatic(Element.Nitrogen).hydrogens(4).cation().build(), 4); in azaniumAtom() 127 IAtom a = g2c.toCDKAtom(AtomBuilder.aliphatic(Element.Carbon).hydrogens(4).build(), 4); in unspecifiedMass() 133 …IAtom a = g2c.toCDKAtom(AtomBuilder.aliphatic(Element.Carbon).hydrogens(4).isotope(12).build(), 4); in carbon_12() 139 …IAtom a = g2c.toCDKAtom(AtomBuilder.aliphatic(Element.Carbon).hydrogens(4).isotope(13).build(), 4); in carbon_13() 145 …IAtom a = g2c.toCDKAtom(AtomBuilder.aliphatic(Element.Carbon).hydrogens(4).isotope(14).build(), 4); in carbon_14()
|
/dports/science/plumed/plumed2-2.7.2/user-doc/tutorials/old_tutorials/trieste-1/.solutions/ |
H A D | plumed-ex1.dat | 16 # Select water hydrogens only: 25 # Compute coordination of RNA with water hydrogens
|
/dports/science/apbs/apbs-pdb2pqr-apbs-1.5-102-g500c1473/pdb2pqr/propka30/Source/ |
H A D | output.py | 55 def writePDB(protein, file=None, filename=None, hydrogens=False, options=None): argument 77 if hydrogens == False and atom.element == "H": 89 def writePQR(protein, label=None, hydrogens=False, options=None): argument 127 elif hydrogens == False and atom.element == "H":
|
/dports/science/p5-Chemistry-File-SLN/Chemistry-File-SLN-0.11/lib/Chemistry/File/ |
H A D | SLN.pm | 226 hydrogens => $node->{hcount}, 461 my $h_count = $neighbor->hydrogens; 463 $neighbor->hydrogens($h_count); 498 my $h_count = $atom->hydrogens;
|
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-SLN-0.11/lib/Chemistry/File/ |
H A D | SLN.pm | 226 hydrogens => $node->{hcount}, 461 my $h_count = $neighbor->hydrogens; 463 $neighbor->hydrogens($h_count); 498 my $h_count = $atom->hydrogens;
|
/dports/science/p5-Chemistry-File-SMILES/Chemistry-File-SMILES-0.47/ |
H A D | SMILES.pm | 370 defined $hcount && $atom->hydrogens($hcount); 440 unless (defined $atom->hydrogens) { 442 $atom->hydrogens($h_count); 627 my $h_count = $atom->hydrogens;
|
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-File-SMILES-0.44/ |
H A D | SMILES.pm | 369 defined $hcount && $atom->hydrogens($hcount); 434 unless (defined $atom->hydrogens) { 436 $atom->hydrogens($h_count); 621 my $h_count = $atom->hydrogens;
|
/dports/science/xtb/xtb-6.4.1/src/io/reader/ |
H A D | ctfile.f90 | 130 sdf(iatom)%hydrogens = list12(4) 169 if (any(mol%sdf%hydrogens > 1)) then
|