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3 ·cae36096407500661fc9d285be5ff1f3·1964784·python·optional·python3-mdanalysis_2.7.0-5_amd64.deb3 ·cae36096407500661fc9d285be5ff1f3·1964784·python·optional·python3-mdanalysis_2.7.0-5_amd64.deb
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./usr/share/doc/python-mdanalysis-doc/html/documentation_pages/analysis/wbridge_analysis.html
    
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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·use906 <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">('OD1',</span>·<span·class="pre">'SG',</span>·<span·class="pre">'O',</span>·<span·class="pre">'OG',</span>·<span·class="pre">'OE1',</span>·<span·class="pre">'OC2',</span>·<span·class="pre">'ND1',</span>·<span·class="pre">'NE2',</span>·<span·class="pre">'SD',</span>·<span·class="pre">'OC1',[·...·truncated·by·diffoscope;·len:·504,·SHA:·4ad4b6d3d2bebbd34b1313641aee977f9bfd45428dfc6dfd091c6535ed65dc34·...·]'),</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>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">('OD1',</span>·<span·class="pre">'OC1',</span>·<span·class="pre">'OW',</span>·<span·class="pre">'OG',</span>·<span·class="pre">'SG',</span>·<span·class="pre">'NE2',</span>·<span·class="pre">'OC2',</span>·<span·class="pre">'O',</span>·<span·class="pre">'OH2',</span>·<span·class="pre">'OD2',[·...·truncated·by·diffoscope;·len:·504,·SHA:·3e566cc93a2d4f1509c1870cdd88f50aa50adb3829ada4e4d0efe98cf9d951ff·...·]'),</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">('SG',</span>·<span·class="pre">'NE1',</span>·<span·class="pre">'N',</span>·<span·class="pre">'OG',</span>·<span·class="pre">'OG1',</span>·<span·class="pre">'OH2',</span>·<span·class="pre">'NH2',</span>·<span·class="pre">'NZ',</span>·<span·class="pre">'NH1',[·...·truncated·by·diffoscope;·len:·380,·SHA:·038ebf6bb226717be473534a625ec02d24a7af9910ed3b0be66d87acaf6bc0e8·...·]'),</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>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">('N',</span>·<span·class="pre">'NH1',</span>·<span·class="pre">'NZ',</span>·<span·class="pre">'NE',</span>·<span·class="pre">'OW',</span>·<span·class="pre">'ND1',</span>·<span·class="pre">'NE1',</span>·<span·class="pre">'OG',</span>·<span·class="pre">'ND2',<[·...·truncated·by·diffoscope;·len:·380,·SHA:·1a83be845ccd8b67ca4c219ccb717277ece6921b4c423c008b6be1b938000806·...·]'),</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">
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554 ············List·of·hydrogen·bonds·between·the·selection·1·or·selection·2·and554 ············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_\x8557 ········timeseries_\x8
558 ············Alias·to·the·_\x8r_\x8e_\x8s_\x8u_\x8l_\x8t_\x8s_\x8._\x8t_\x8i_\x8m_\x8e_\x8s_\x8e_\x8r_\x8i_\x8e_\x8s·attribute.558 ············Alias·to·the·_\x8r_\x8e_\x8s_\x8u_\x8l_\x8t_\x8s_\x8._\x8t_\x8i_\x8m_\x8e_\x8s_\x8e_\x8r_\x8i_\x8e_\x8s·attribute.
559 ············Deprecated·since·version·2.0.0:·Will·be·removed·in·MDAnalysis559 ············Deprecated·since·version·2.0.0:·Will·be·removed·in·MDAnalysis
560 ············3.0.0.·Please·use·_\x8r_\x8e_\x8s_\x8u_\x8l_\x8t_\x8s_\x8._\x8t_\x8i_\x8m_\x8e_\x8s_\x8e_\x8r_\x8i_\x8e_\x8s·instead.560 ············3.0.0.·Please·use·_\x8r_\x8e_\x8s_\x8u_\x8l_\x8t_\x8s_\x8._\x8t_\x8i_\x8m_\x8e_\x8s_\x8e_\x8r_\x8i_\x8e_\x8s·instead.
561 ········DEFAULT_ACCEPTORS·=\x8=·{\x8{'\x8'C\x8CH\x8HA\x8AR\x8RM\x8MM\x8M2\x827\x87'\x8':\x8:·(\x8('\x8'O\x8OD\x8D1\x81'\x8',\x8,·'\x8'S.SG.G'.',.,·'.'O.O'.',.,·'.'O.OG.G'.',.,·'.'O.OE.E1.1'.',.,·'.'O.OC.C2.2'\x8',\x8,561 ········DEFAULT_ACCEPTORS·=\x8=·{\x8{'\x8'C\x8CH\x8HA\x8AR\x8RM\x8MM\x8M2\x827\x87'\x8':\x8:·(\x8('\x8'O\x8OD\x8D1\x81'\x8',\x8,·'\x8'O.OC.C1.1'.',.,·'.'O.OW.W'.',.,·'.'O.OG.G'.',.,·'.'S.SG.G'\x8',\x8,
562 ········'\x8'N\x8ND\x8D1\x81'\x8',\x8,·'\x8'N\x8NE\x8E2\x82'\x8',\x8,·'\x8'S\x8SD\x8D'\x8',\x8,·'\x8'O\x8OC\x8C1\x81'\x8',\x8,·'\x8'O\x8OG\x8G1\x81'\x8',\x8,·'\x8'O\x8OH\x8H2\x82'\x8',\x8,·'\x8'O\x8OD\x8D2\x82'\x8',\x8,·'\x8'O\x8OE\x8E2\x82'\x8',\x8,·'\x8'O\x8OH\x8H'\x8',\x8,·'\x8'O\x8OW\x8W'\x8')\x8),\x8, 
563 ········'\x8'G.GL.LY.YC.CA.AM.M0.06.6'.':.:·(.('.'N.N'.',.,·'.'S.SM.M'.',.,·'.'O.O'.',.,·'.'O.OY.Y'.',.,·'.'O.OS.S'.',.,·'.'N.NT.T'.',.,·'.'O.OH.H'.',.,·'.'O.OW.W'.',.,·'.'O.O2.2'.').),\x8,562 ········'\x8'N.NE.E2.2'.',.,·'.'O.OC.C2.2'.',.,·'.'O.O'.',.,·'.'O.OH.H2.2'.',.,·'.'O.OD.D2.2'.',.,·'.'N.ND.D1.1'.',.,·'.'O.OE.E2.2'.',.,·'.'S.SD.D'.',.,·'.'O.OE.E1.1'.',.,·'.'O.OG.G1.1'.',\x8,
 563 ········'\x8'O\x8OH\x8H'\x8')\x8),\x8,·'\x8'G\x8GL\x8LY\x8YC\x8CA\x8AM\x8M0\x806\x86'\x8':\x8:·(\x8('\x8'N\x8N'\x8',\x8,·'\x8'O\x8OS\x8S'\x8',\x8,·'\x8'O\x8OY\x8Y'\x8',\x8,·'\x8'N\x8NT\x8T'\x8',\x8,·'\x8'O\x8OW\x8W'\x8',\x8,·'\x8'S\x8SM\x8M'\x8',\x8,·'\x8'O\x8O'\x8',\x8,·'\x8'O\x8O2\x82'\x8',\x8,
564 ········'\x8'o\x8ot\x8th\x8he\x8er\x8r'\x8':\x8:·(\x8()\x8)}\x8}_\x8564 ········'\x8'O.OH.H'.').),.,·'.'o\x8ot\x8th\x8he\x8er\x8r'\x8':\x8:·(\x8()\x8)}\x8}_\x8
565 ············default·atom·names·that·are·treated·as·hydrogen·a\x8ac\x8cc\x8ce\x8ep\x8pt\x8to\x8or\x8rs\x8s·(see565 ············default·atom·names·that·are·treated·as·hydrogen·a\x8ac\x8cc\x8ce\x8ep\x8pt\x8to\x8or\x8rs\x8s·(see
566 ············_\x8D_\x8e_\x8f_\x8a_\x8u_\x8l_\x8t_\x8·_\x8h_\x8e_\x8a_\x8v_\x8y_\x8·_\x8a_\x8t_\x8o_\x8m_\x8·_\x8n_\x8a_\x8m_\x8e_\x8s_\x8·_\x8f_\x8o_\x8r_\x8·_\x8C_\x8H_\x8A_\x8R_\x8M_\x8M_\x82_\x87_\x8·_\x8f_\x8o_\x8r_\x8c_\x8e_\x8·_\x8f_\x8i_\x8e_\x8l_\x8d_\x8.);·use·the566 ············_\x8D_\x8e_\x8f_\x8a_\x8u_\x8l_\x8t_\x8·_\x8h_\x8e_\x8a_\x8v_\x8y_\x8·_\x8a_\x8t_\x8o_\x8m_\x8·_\x8n_\x8a_\x8m_\x8e_\x8s_\x8·_\x8f_\x8o_\x8r_\x8·_\x8C_\x8H_\x8A_\x8R_\x8M_\x8M_\x82_\x87_\x8·_\x8f_\x8o_\x8r_\x8c_\x8e_\x8·_\x8f_\x8i_\x8e_\x8l_\x8d_\x8.);·use·the
567 ············keywordacceptorsto·add·a·list·of·additional·acceptor·names.567 ············keywordacceptorsto·add·a·list·of·additional·acceptor·names.
568 ········DEFAULT_DONORS·=\x8=·{\x8{'\x8'C\x8CH\x8HA\x8AR\x8RM\x8MM\x8M2\x827\x87'\x8':\x8:·(\x8('\x8'S\x8SG\x8G'\x8',\x8,·'\x8'N\x8NE\x8E1\x81'\x8',\x8,·'\x8'N\x8N'\x8',\x8,·'\x8'O\x8OG\x8G'\x8',\x8,·'\x8'O\x8OG\x8G1\x81'\x8',\x8,·'\x8'O\x8OH\x8H2\x82'\x8',\x8, 
569 ········'.'N.NH.H2.2'.',.,·'.'N.NZ.Z'.',.,·'.'N.NH.H1.1'.',.,·'.'N.ND.D2.2'.',.,·'.'O.OH.H'.',.,·'.'N.ND.D1.1'.',.,·'.'N.NE.E'.',.,·'.'O.OW.W'.',.,·'.'N.NE.E2.2'.').),.,·'.'G.GL.LY.YC.CA.AM.M0.06.6'.':.:568 ········DEFAULT_DONORS·=.=·{.{'.'C.CH.HA.AR.RM.MM.M2.27.7'.':.:·(.('.'N.N'.',.,·'.'N.NH.H1.1'.',.,·'.'N.NZ.Z'.',.,·'.'N.NE.E'.',.,·'.'O.OW.W'.',.,·'.'N.ND.D1.1'.',.,
 569 ········'\x8'N\x8NE\x8E1\x81'\x8',\x8,·'\x8'O\x8OG\x8G'\x8',\x8,·'\x8'N\x8ND\x8D2\x82'\x8',\x8,·'\x8'O\x8OG\x8G1\x81'\x8',\x8,·'\x8'S\x8SG\x8G'\x8',\x8,·'\x8'N\x8NE\x8E2\x82'\x8',\x8,·'\x8'N\x8NH\x8H2\x82'\x8',\x8,·'\x8'O\x8OH\x8H2\x82'\x8',\x8,·'\x8'O\x8OH\x8H'\x8')\x8),\x8,
570 ········(.('.'N.N3.3'.',.,·'.'N.N'.',.,·'.'N.NT.T'.',.,·'.'O.OH.H'.',.,·'.'O.OW.W'\x8')\x8),\x8,·'\x8'o\x8ot\x8th\x8he\x8er\x8r'\x8':\x8:·(\x8()\x8)}\x8}_\x8570 ········'.'G.GL.LY.YC.CA.AM.M0.06.6'.':.:·(.('.'N.N'.',.,·'.'O.OW.W'.',.,·'.'N.NT.T'.',.,·'.'N.N3.3'.',.,·'.'O.OH.H'\x8')\x8),\x8,·'\x8'o\x8ot\x8th\x8he\x8er\x8r'\x8':\x8:·(\x8()\x8)}\x8}_\x8
571 ············default·heavy·atom·names·whose·hydrogens·are·treated·as·d\x8do\x8on\x8no\x8or\x8rs\x8s·(see571 ············default·heavy·atom·names·whose·hydrogens·are·treated·as·d\x8do\x8on\x8no\x8or\x8rs\x8s·(see
572 ············_\x8D_\x8e_\x8f_\x8a_\x8u_\x8l_\x8t_\x8·_\x8h_\x8e_\x8a_\x8v_\x8y_\x8·_\x8a_\x8t_\x8o_\x8m_\x8·_\x8n_\x8a_\x8m_\x8e_\x8s_\x8·_\x8f_\x8o_\x8r_\x8·_\x8C_\x8H_\x8A_\x8R_\x8M_\x8M_\x82_\x87_\x8·_\x8f_\x8o_\x8r_\x8c_\x8e_\x8·_\x8f_\x8i_\x8e_\x8l_\x8d_\x8.);·use·the572 ············_\x8D_\x8e_\x8f_\x8a_\x8u_\x8l_\x8t_\x8·_\x8h_\x8e_\x8a_\x8v_\x8y_\x8·_\x8a_\x8t_\x8o_\x8m_\x8·_\x8n_\x8a_\x8m_\x8e_\x8s_\x8·_\x8f_\x8o_\x8r_\x8·_\x8C_\x8H_\x8A_\x8R_\x8M_\x8M_\x82_\x87_\x8·_\x8f_\x8o_\x8r_\x8c_\x8e_\x8·_\x8f_\x8i_\x8e_\x8l_\x8d_\x8.);·use·the
573 ············keyworddonorsto·add·a·list·of·additional·donor·names.573 ············keyworddonorsto·add·a·list·of·additional·donor·names.
574 ········count_by_time(a\x8an\x8na\x8al\x8ly\x8ys\x8si\x8is\x8s_\x8_f\x8fu\x8un\x8nc\x8c=\x8=N\x8No\x8on\x8ne\x8e,·*\x8**\x8*k\x8kw\x8wa\x8ar\x8rg\x8gs\x8s)_\x8[_\x8s_\x8o_\x8u_\x8r_\x8c_\x8e_\x8]_\x8574 ········count_by_time(a\x8an\x8na\x8al\x8ly\x8ys\x8si\x8is\x8s_\x8_f\x8fu\x8un\x8nc\x8c=\x8=N\x8No\x8on\x8ne\x8e,·*\x8**\x8*k\x8kw\x8wa\x8ar\x8rg\x8gs\x8s)_\x8[_\x8s_\x8o_\x8u_\x8r_\x8c_\x8e_\x8]_\x8
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·_\x8U_\x8s_\x8e_\x8·_\x8c_\x8o_\x8u_\x8n_\x8t_\x8__\x8b_\x8y_\x8__\x8t_\x8i_\x8m_\x8e·for·details.577 ············See·_\x8U_\x8s_\x8e_\x8·_\x8c_\x8o_\x8u_\x8n_\x8t_\x8__\x8b_\x8y_\x8__\x8t_\x8i_\x8m_\x8e·for·details.
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