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| 1005 | <p><span·class="versionmodified·deprecated">Deprecated·since·version·2.0.0:·</span>Will·be·removed·in·MDAnalysis·3.0.0.·Please·use | 1005 | <p><span·class="versionmodified·deprecated">Deprecated·since·version·2.0.0:·</span>Will·be·removed·in·MDAnalysis·3.0.0.·Please·use |
| 1006 | <a·class="reference·internal"·href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.results.timeseries"·title="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.results.timeseries"><code·class="xref·py·py-attr·docutils·literal·notranslate"><span·class="pre">results.timeseries</span></code></a>·instead.</p> | 1006 | <a·class="reference·internal"·href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.results.timeseries"·title="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.results.timeseries"><code·class="xref·py·py-attr·docutils·literal·notranslate"><span·class="pre">results.timeseries</span></code></a>·instead.</p> |
| 1007 | </div> | 1007 | </div> |
| 1008 | </dd></dl> | 1008 | </dd></dl> |
| 1009 | <dl·class="py·attribute"> | 1009 | <dl·class="py·attribute"> |
| 1010 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS"> | 1010 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS"> |
| 1011 | <span·class="sig-name·descname"><span·class="pre">DEFAULT_ACCEPTORS</span></span><em·class="property"><span·class="w">·</span><span·class="p"><span·class="pre">=</span></span><span·class="w">·</span><span·class="pre">{'CHARMM27':</span>·<span·class="pre">('OD | 1011 | <span·class="sig-name·descname"><span·class="pre">DEFAULT_ACCEPTORS</span></span><em·class="property"><span·class="w">·</span><span·class="p"><span·class="pre">=</span></span><span·class="w">·</span><span·class="pre">{'CHARMM27':</span>·<span·class="pre">('OD2',</span>·<span·class="pre">'OC2',</span>·<span·class="pre">'OH2',</span>·<span·class="pre">'OE2',</span>·<span·class="pre">'OC1',</span>·<span·class="pre">'OG1',</span>·<span·class="pre">'OW',</span>·<span·class="pre">'OH',</span>·<span·class="pre">'ND1'[·...·truncated·by·diffoscope;·len:·503,·SHA:·ed48ad0def2cfe3686fbcb1317e5733987eb20d00df23081dba443a29c831663·...·]',</span>·<span·class="pre">'O2'),</span>·<span·class="pre">'other':</span>·<span·class="pre">()}</span></em><a·class="headerlink"·href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS"·title="Permalink·to·this·definition"></a></dt> |
| 1012 | <dd><p>default·atom·names·that·are·treated·as·hydrogen·<em>acceptors</em> | 1012 | <dd><p>default·atom·names·that·are·treated·as·hydrogen·<em>acceptors</em> |
| 1013 | (see·<a·class="reference·internal"·href="#default-atom-names-for-water-bridge-analysis"><span·class="std·std-ref">Default·heavy·atom·names·for·CHARMM27·force·field.</span></a>); | 1013 | (see·<a·class="reference·internal"·href="#default-atom-names-for-water-bridge-analysis"><span·class="std·std-ref">Default·heavy·atom·names·for·CHARMM27·force·field.</span></a>); |
| 1014 | use·the·keyword·<cite>acceptors</cite>·to·add·a·list·of·additional·acceptor·names.</p> | 1014 | use·the·keyword·<cite>acceptors</cite>·to·add·a·list·of·additional·acceptor·names.</p> |
| 1015 | </dd></dl> | 1015 | </dd></dl> |
| 1016 | <dl·class="py·attribute"> | 1016 | <dl·class="py·attribute"> |
| 1017 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS"> | 1017 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS"> |
| 1018 | <span·class="sig-name·descname"><span·class="pre">DEFAULT_DONORS</span></span><em·class="property"><span·class="w">·</span><span·class="p"><span·class="pre">=</span></span><span·class="w">·</span><span·class="pre">{'CHARMM27':</span>·<span·class="pre">('ND | 1018 | <span·class="sig-name·descname"><span·class="pre">DEFAULT_DONORS</span></span><em·class="property"><span·class="w">·</span><span·class="p"><span·class="pre">=</span></span><span·class="w">·</span><span·class="pre">{'CHARMM27':</span>·<span·class="pre">('ND1',</span>·<span·class="pre">'NZ',</span>·<span·class="pre">'NE',</span>·<span·class="pre">'NE2',</span>·<span·class="pre">'N',</span>·<span·class="pre">'NH2',</span>·<span·class="pre">'OH2',</span>·<span·class="pre">'NE1',</span>·<span·class="pre">'NH1',<[·...·truncated·by·diffoscope;·len:·347,·SHA:·8307405121a55ee185d0ed39692844c9a2c654ed24bda3847c79c308793d8780·...·]',</span>·<span·class="pre">'N3'),</span>·<span·class="pre">'other':</span>·<span·class="pre">()}</span></em><a·class="headerlink"·href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS"·title="Permalink·to·this·definition"></a></dt> |
| 1019 | <dd><p>default·heavy·atom·names·whose·hydrogens·are·treated·as·<em>donors</em> | 1019 | <dd><p>default·heavy·atom·names·whose·hydrogens·are·treated·as·<em>donors</em> |
| 1020 | (see·<a·class="reference·internal"·href="#default-atom-names-for-water-bridge-analysis"><span·class="std·std-ref">Default·heavy·atom·names·for·CHARMM27·force·field.</span></a>); | 1020 | (see·<a·class="reference·internal"·href="#default-atom-names-for-water-bridge-analysis"><span·class="std·std-ref">Default·heavy·atom·names·for·CHARMM27·force·field.</span></a>); |
| 1021 | use·the·keyword·<cite>donors</cite>·to·add·a·list·of·additional·donor·names.</p> | 1021 | use·the·keyword·<cite>donors</cite>·to·add·a·list·of·additional·donor·names.</p> |
| 1022 | </dd></dl> | 1022 | </dd></dl> |
| 1023 | <dl·class="py·method"> | 1023 | <dl·class="py·method"> |
| 1024 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_time"> | 1024 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_time"> |
| Offset 634, 24 lines modified | Offset 634, 24 lines modified | ||
| 634 | ············List·of·hydrogen·bonds·between·the·selection·1·or·selection·2·and | 634 | ············List·of·hydrogen·bonds·between·the·selection·1·or·selection·2·and |
| 635 | ············the·bridging·waters,·for·each·frame. | 635 | ············the·bridging·waters,·for·each·frame. |
| 636 | ············New·in·version·2.0.0. | 636 | ············New·in·version·2.0.0. |
| 637 | ········timeseriesï | 637 | ········timeseriesï |
| 638 | ············Alias·to·the·results.timeseries·attribute. | 638 | ············Alias·to·the·results.timeseries·attribute. |
| 639 | ············Deprecated·since·version·2.0.0:·Will·be·removed·in·MDAnalysis | 639 | ············Deprecated·since·version·2.0.0:·Will·be·removed·in·MDAnalysis |
| 640 | ············3.0.0.·Please·use·results.timeseries·instead. | 640 | ············3.0.0.·Please·use·results.timeseries·instead. |
| 641 | ········DEFAULT_ACCEPTORS=·{'CHARMM27':·('OD1',·'SD',·'O',·'SG',·'ND1',·'OG1', | ||
| 642 | ········ | 641 | ········DEFAULT_ACCEPTORS=·{'CHARMM27':·('OD2',·'OC2',·'OH2',·'OE2',·'OC1', |
| 642 | ········'OG1',·'OW',·'OH',·'ND1',·'SD',·'OE1',·'O',·'NE2',·'SG',·'OD1',·'OG'), | ||
| 643 | ········'GLYCAM06':·(' | 643 | ········'GLYCAM06':·('SM',·'NT',·'O',·'OS',·'N',·'OY',·'OW',·'OH',·'O2'), |
| 644 | ········'other':·()}ï | 644 | ········'other':·()}ï |
| 645 | ············default·atom·names·that·are·treated·as·hydrogen·acceptors·(see | 645 | ············default·atom·names·that·are·treated·as·hydrogen·acceptors·(see |
| 646 | ············Default_heavy_atom_names_for_CHARMM27_force_field.);·use·the | 646 | ············Default_heavy_atom_names_for_CHARMM27_force_field.);·use·the |
| 647 | ············keywordacceptorsto·add·a·list·of·additional·acceptor·names. | 647 | ············keywordacceptorsto·add·a·list·of·additional·acceptor·names. |
| 648 | ········DEFAULT_DONORS=·{'CHARMM27':·('ND | 648 | ········DEFAULT_DONORS=·{'CHARMM27':·('ND1',·'NZ',·'NE',·'NE2',·'N',·'NH2', |
| 649 | ········'OH2',·' | 649 | ········'OH2',·'NE1',·'NH1',·'SG',·'OG1',·'OW',·'OH',·'ND2',·'OG'),·'GLYCAM06': |
| 650 | ········(' | 650 | ········('N',·'OW',·'NT',·'OH',·'N3'),·'other':·()}ï |
| 651 | ············default·heavy·atom·names·whose·hydrogens·are·treated·as·donors·(see | 651 | ············default·heavy·atom·names·whose·hydrogens·are·treated·as·donors·(see |
| 652 | ············Default_heavy_atom_names_for_CHARMM27_force_field.);·use·the | 652 | ············Default_heavy_atom_names_for_CHARMM27_force_field.);·use·the |
| 653 | ············keyworddonorsto·add·a·list·of·additional·donor·names. | 653 | ············keyworddonorsto·add·a·list·of·additional·donor·names. |
| 654 | ········count_by_time(analysis_func=None,·**kwargs)[source]ï | 654 | ········count_by_time(analysis_func=None,·**kwargs)[source]ï |
| 655 | ············Counts·the·number·of·water·bridges·per·timestep. | 655 | ············Counts·the·number·of·water·bridges·per·timestep. |
| 656 | ············The·counting·behaviour·can·be·adjusted·by·supplying·analysis_func. | 656 | ············The·counting·behaviour·can·be·adjusted·by·supplying·analysis_func. |
| 657 | ············See·Use_count_by_time·for·details. | 657 | ············See·Use_count_by_time·for·details. |