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/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/analysis/
H A Dtest_hydrogenbondautocorrel.py58 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 DAtom.t40 # 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 DAtom.t40 # 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 DAtomSuppression.java69 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 DCanon.java98 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 DREADME22 // 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 DStandardAtomGenerator.java374 …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 DFeatDirUtilsRD.py138 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 DAtomContainerManipulator.java538 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 Dobenergy.cpp60 bool hydrogens = false; in main() local
73 hydrogens = true; in main()
124 if (hydrogens) in main()
H A Dobminimize.cpp47 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 Dhbond_analysis.py788 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 Dfunctional_groups.py213 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 Dions.par74 # 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 Dions.par74 # 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 Dadding-hydrogens.rst1 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 DInChITautomerGenerator.java365 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 DBeamToCDKTest.java97 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 Dplumed-ex1.dat16 # 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 Doutput.py55 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 DSLN.pm226 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 DSLN.pm226 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 DSMILES.pm370 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 DSMILES.pm369 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 Dctfile.f90130 sdf(iatom)%hydrogens = list12(4)
169 if (any(mol%sdf%hydrogens > 1)) then

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