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| 906 | <p><span·class="versionmodified·deprecated">Deprecated·since·version·2.0.0:·</span>Will·be·removed·in·MDAnalysis·3.0.0.·Please·use | 906 | <p><span·class="versionmodified·deprecated">Deprecated·since·version·2.0.0:·</span>Will·be·removed·in·MDAnalysis·3.0.0.·Please·use |
| 907 | <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> | 907 | <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> |
| 908 | </div> | 908 | </div> |
| 909 | </dd></dl> | 909 | </dd></dl> |
| 910 | <dl·class="py·attribute"> | 910 | <dl·class="py·attribute"> |
| 911 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS"> | 911 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS"> |
| 912 | <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">('O',</span>·<span·class="pre">' | 912 | <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">('OC1',</span>·<span·class="pre">'SG',</span>·<span·class="pre">'OH2',</span>·<span·class="pre">'OW',</span>·<span·class="pre">'OG',</span>·<span·class="pre">'OD1',</span>·<span·class="pre">'SD',</span>·<span·class="pre">'O',</span>·<span·class="pre">'OC2',</[·...·truncated·by·diffoscope;·len:·535,·SHA:·d0f66522fe15634052063de8ef86f33c96db8a8a9c68a7a7547fe0a0a2f7ae49·...·]'),</span>·<span·class="pre">'other':</span>·<span·class="pre">()}</span></em><a·class="headerlink"·href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_ACCEPTORS"·title="Link·to·this·definition">¶</a></dt> |
| 913 | <dd><p>default·atom·names·that·are·treated·as·hydrogen·<em>acceptors</em> | 913 | <dd><p>default·atom·names·that·are·treated·as·hydrogen·<em>acceptors</em> |
| 914 | (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>); | 914 | (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>); |
| 915 | use·the·keyword·<cite>acceptors</cite>·to·add·a·list·of·additional·acceptor·names.</p> | 915 | use·the·keyword·<cite>acceptors</cite>·to·add·a·list·of·additional·acceptor·names.</p> |
| 916 | </dd></dl> | 916 | </dd></dl> |
| 917 | <dl·class="py·attribute"> | 917 | <dl·class="py·attribute"> |
| 918 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS"> | 918 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS"> |
| 919 | <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">('NZ',</span>·<span·class="pre">' | 919 | <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">('NZ',</span>·<span·class="pre">'SG',</span>·<span·class="pre">'NE2',</span>·<span·class="pre">'NH1',</span>·<span·class="pre">'OH2',</span>·<span·class="pre">'OH',</span>·<span·class="pre">'OW',</span>·<span·class="pre">'NH2',</span>·<span·class="pre">'ND1',</span>·<span·class="pre">'N',[·...·truncated·by·diffoscope;·len:·257,·SHA:·5d2583585a7b20fcbd4702e479cd48145d6835db11666e4c4b48d0c49b2ee07d·...·]',</span>·<span·class="pre">'N',</span>·<span·class="pre">'NT',</span>·<span·class="pre">'OH'),</span>·<span·class="pre">'other':</span>·<span·class="pre">()}</span></em><a·class="headerlink"·href="#MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.DEFAULT_DONORS"·title="Link·to·this·definition">¶</a></dt> |
| 920 | <dd><p>default·heavy·atom·names·whose·hydrogens·are·treated·as·<em>donors</em> | 920 | <dd><p>default·heavy·atom·names·whose·hydrogens·are·treated·as·<em>donors</em> |
| 921 | (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>); | 921 | (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>); |
| 922 | use·the·keyword·<cite>donors</cite>·to·add·a·list·of·additional·donor·names.</p> | 922 | use·the·keyword·<cite>donors</cite>·to·add·a·list·of·additional·donor·names.</p> |
| 923 | </dd></dl> | 923 | </dd></dl> |
| 924 | <dl·class="py·method"> | 924 | <dl·class="py·method"> |
| 925 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_time"> | 925 | <dt·class="sig·sig-object·py"·id="MDAnalysis.analysis.hydrogenbonds.wbridge_analysis.WaterBridgeAnalysis.count_by_time"> |
| Offset 554, 24 lines modified | Offset 554, 24 lines modified | ||
| 554 | ············List·of·hydrogen·bonds·between·the·selection·1·or·selection·2·and | 554 | ············List·of·hydrogen·bonds·between·the·selection·1·or·selection·2·and |
| 555 | ············the·bridging·waters,·for·each·frame. | 555 | ············the·bridging·waters,·for·each·frame. |
| 556 | ············Added·in·version·2.0.0. | 556 | ············Added·in·version·2.0.0. |
| 557 | ········timeseries¶ | 557 | ········timeseries¶ |
| 558 | ············Alias·to·the·results.timeseries·attribute. | 558 | ············Alias·to·the·results.timeseries·attribute. |
| 559 | ············Deprecated·since·version·2.0.0:·Will·be·removed·in·MDAnalysis | 559 | ············Deprecated·since·version·2.0.0:·Will·be·removed·in·MDAnalysis |
| 560 | ············3.0.0.·Please·use·results.timeseries·instead. | 560 | ············3.0.0.·Please·use·results.timeseries·instead. |
| 561 | ········DEFAULT_ACCEPTORS·=·{'CHARMM27':·('O',·' | 561 | ········DEFAULT_ACCEPTORS·=·{'CHARMM27':·('OC1',·'SG',·'OH2',·'OW',·'OG', |
| 562 | ········'OE1',·'ND1',·'OD2',·'OD1',·'OH',·'OW',·'OG1',·'SD',·'OC1',·'OC2', | ||
| 563 | ········' | 562 | ········'OD1',·'SD',·'O',·'OC2',·'OE1',·'NE2',·'OD2',·'OH',·'ND1',·'OG1', |
| 563 | ········'OE2'),·'GLYCAM06':·('SM',·'OY',·'OH',·'OW',·'OS',·'N',·'NT',·'O2', | ||
| 564 | ········'O | 564 | ········'O'),·'other':·()}¶ |
| 565 | ············default·atom·names·that·are·treated·as·hydrogen·acceptors·(see | 565 | ············default·atom·names·that·are·treated·as·hydrogen·acceptors·(see |
| 566 | ············Default_heavy_atom_names_for_CHARMM27_force_field.);·use·the | 566 | ············Default_heavy_atom_names_for_CHARMM27_force_field.);·use·the |
| 567 | ············keywordacceptorsto·add·a·list·of·additional·acceptor·names. | 567 | ············keywordacceptorsto·add·a·list·of·additional·acceptor·names. |
| 568 | ········DEFAULT_DONORS·=·{'CHARMM27':·('NZ',·' | 568 | ········DEFAULT_DONORS·=·{'CHARMM27':·('NZ',·'SG',·'NE2',·'NH1',·'OH2',·'OH', |
| 569 | ········'O | 569 | ········'OW',·'NH2',·'ND1',·'N',·'NE1',·'OG',·'ND2',·'OG1',·'NE'),·'GLYCAM06': |
| 570 | ········(' | 570 | ········('N3',·'OW',·'N',·'NT',·'OH'),·'other':·()}¶ |
| 571 | ············default·heavy·atom·names·whose·hydrogens·are·treated·as·donors·(see | 571 | ············default·heavy·atom·names·whose·hydrogens·are·treated·as·donors·(see |
| 572 | ············Default_heavy_atom_names_for_CHARMM27_force_field.);·use·the | 572 | ············Default_heavy_atom_names_for_CHARMM27_force_field.);·use·the |
| 573 | ············keyworddonorsto·add·a·list·of·additional·donor·names. | 573 | ············keyworddonorsto·add·a·list·of·additional·donor·names. |
| 574 | ········count_by_time(analysis_func=None,·**kwargs)[source]¶ | 574 | ········count_by_time(analysis_func=None,·**kwargs)[source]¶ |
| 575 | ············Counts·the·number·of·water·bridges·per·timestep. | 575 | ············Counts·the·number·of·water·bridges·per·timestep. |
| 576 | ············The·counting·behaviour·can·be·adjusted·by·supplying·analysis_func. | 576 | ············The·counting·behaviour·can·be·adjusted·by·supplying·analysis_func. |
| 577 | ············See·Use_count_by_time·for·details. | 577 | ············See·Use_count_by_time·for·details. |