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<hr><h1>molshape.h</h1><div class="fragment"><pre>00001 <font class="comment">//</font>
00002 <font class="comment">// molshape.h</font>
00003 <font class="comment">//</font>
00004 <font class="comment">// Copyright (C) 1996 Limit Point Systems, Inc.</font>
00005 <font class="comment">//</font>
00006 <font class="comment">// Author: Curtis Janssen &lt;cljanss@limitpt.com&gt;</font>
00007 <font class="comment">// Maintainer: LPS</font>
00008 <font class="comment">//</font>
00009 <font class="comment">// This file is part of the SC Toolkit.</font>
00010 <font class="comment">//</font>
00011 <font class="comment">// The SC Toolkit is free software; you can redistribute it and/or modify</font>
00012 <font class="comment">// it under the terms of the GNU Library General Public License as published by</font>
00013 <font class="comment">// the Free Software Foundation; either version 2, or (at your option)</font>
00014 <font class="comment">// any later version.</font>
00015 <font class="comment">//</font>
00016 <font class="comment">// The SC Toolkit is distributed in the hope that it will be useful,</font>
00017 <font class="comment">// but WITHOUT ANY WARRANTY; without even the implied warranty of</font>
00018 <font class="comment">// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</font>
00019 <font class="comment">// GNU Library General Public License for more details.</font>
00020 <font class="comment">//</font>
00021 <font class="comment">// You should have received a copy of the GNU Library General Public License</font>
00022 <font class="comment">// along with the SC Toolkit; see the file COPYING.LIB.  If not, write to</font>
00023 <font class="comment">// the Free Software Foundation, 675 Mass Ave, Cambridge, MA 02139, USA.</font>
00024 <font class="comment">//</font>
00025 <font class="comment">// The U.S. Government is granted a limited license as per AL 91-7.</font>
00026 <font class="comment">//</font>
00027 
00028 <font class="preprocessor">#ifndef _chemistry_molecule_molshape_h</font>
00029 <font class="preprocessor"></font><font class="preprocessor">#define _chemistry_molecule_molshape_h</font>
00030 <font class="preprocessor"></font>
00031 <font class="preprocessor">#ifdef __GNUC__</font>
00032 <font class="preprocessor"></font><font class="preprocessor">#pragma interface</font>
00033 <font class="preprocessor"></font><font class="preprocessor">#endif</font>
00034 <font class="preprocessor"></font>
00035 <font class="preprocessor">#include &lt;util/misc/formio.h&gt;</font>
00036 
00037 <font class="preprocessor">#include &lt;math/isosurf/shape.h&gt;</font>
00038 <font class="preprocessor">#include &lt;chemistry/molecule/atominfo.h&gt;</font>
00039 <font class="preprocessor">#include &lt;chemistry/molecule/molecule.h&gt;</font>
00040 
00041 <font class="keyword">namespace </font>sc {
00042 
<a name="l00047"></a><a class="code" href="class_sc__VDWShape.html">00047</a> <font class="keyword">class </font>VDWShape: <font class="keyword">public</font> UnionShape {
00048  <font class="keyword">private</font>:
00049     Ref&lt;AtomInfo&gt; atominfo_;
00050  <font class="keyword">public</font>:
00051     VDWShape(<font class="keyword">const</font> Ref&lt;Molecule&gt;&amp;);
00052     VDWShape(<font class="keyword">const</font> Ref&lt;KeyVal&gt;&amp;);
00053     ~VDWShape();
00054     <font class="keywordtype">void</font> initialize(<font class="keyword">const</font> Ref&lt;Molecule&gt;&amp;);
00055 };  
00056 
<a name="l00061"></a><a class="code" href="class_sc__DiscreteConnollyShape.html">00061</a> <font class="keyword">class </font>DiscreteConnollyShape: <font class="keyword">public</font> UnionShape {
00062   <font class="keyword">private</font>:
00063     <font class="keywordtype">double</font> radius_scale_factor_;
00064     Ref&lt;AtomInfo&gt; atominfo_;
00065  <font class="keyword">public</font>:
00066     DiscreteConnollyShape(<font class="keyword">const</font> Ref&lt;KeyVal&gt;&amp;);
00067     ~DiscreteConnollyShape();
00068     <font class="keywordtype">void</font> initialize(<font class="keyword">const</font> Ref&lt;Molecule&gt;&amp;,<font class="keywordtype">double</font> probe_radius);
00069 };
00070 
00071 <font class="preprocessor">#ifndef COUNT_CONNOLLY</font>
00072 <font class="preprocessor"></font><font class="preprocessor"># define COUNT_CONNOLLY 1</font>
00073 <font class="preprocessor"></font><font class="preprocessor">#endif</font>
00074 <font class="preprocessor"></font>
00075 <font class="comment">// This is a utility class needed by ConnollyShape2</font>
00076 <font class="keyword">class </font>CS2Sphere
00077 {
00078     SCVector3 _v;
00079     <font class="keywordtype">double</font> _radius;
00080 
00081   <font class="keyword">public</font>:
00082 <font class="preprocessor">#if COUNT_CONNOLLY</font>
00083 <font class="preprocessor"></font>    <font class="keyword">static</font> <font class="keywordtype">int</font> n_no_spheres_;
00084     <font class="keyword">static</font> <font class="keywordtype">int</font> n_probe_enclosed_by_a_sphere_;
00085     <font class="keyword">static</font> <font class="keywordtype">int</font> n_probe_center_not_enclosed_;
00086     <font class="keyword">static</font> <font class="keywordtype">int</font> n_surface_of_s0_not_covered_;
00087     <font class="keyword">static</font> <font class="keywordtype">int</font> n_plane_totally_covered_;
00088     <font class="keyword">static</font> <font class="keywordtype">int</font> n_internal_edge_not_covered_;
00089     <font class="keyword">static</font> <font class="keywordtype">int</font> n_totally_covered_;
00090 <font class="preprocessor">#endif</font>
00091 <font class="preprocessor"></font>
00092     CS2Sphere(<font class="keyword">const</font> SCVector3&amp; v, <font class="keywordtype">double</font> rad):
00093     _v(v),_radius(rad){}
00094     CS2Sphere(<font class="keywordtype">double</font> x, <font class="keywordtype">double</font> y, <font class="keywordtype">double</font> z, <font class="keywordtype">double</font> rad):
00095     _v(x,y,z),_radius(rad){}
00096     CS2Sphere(<font class="keywordtype">void</font>)<font class="keyword"> </font>{};
00097     <font class="keywordtype">void</font> initialize(SCVector3&amp; v, <font class="keywordtype">double</font> rad)<font class="keyword"> </font>{
00098         _v = v; _radius = rad; }
00099 
00100     CS2Sphere&amp; operator=(<font class="keyword">const</font> CS2Sphere&amp;s)<font class="keyword"> </font>{
00101         _v = s._v; _radius = s._radius; <font class="keywordflow">return</font> *<font class="keyword">this</font>; }
00102     
00103     <font class="comment">// Return the distance between the centers of the two</font>
00104     <font class="comment">// spheres</font>
00105     <font class="keywordtype">double</font> distance(CS2Sphere &amp;asphere)<font class="keyword"></font>
00106 <font class="keyword">    </font>{ <font class="keywordflow">return</font> sqrt((_v[0]-asphere._v[0])*(_v[0]-asphere._v[0])+
00107                   (_v[1]-asphere._v[1])*(_v[1]-asphere._v[1])+
00108                   (_v[2]-asphere._v[2])*(_v[2]-asphere._v[2]));}  
00109 
00110     <font class="comment">// Return the radius of the circle intersecting the two spheres</font>
00111     <font class="comment">// Note that this assumes the spheres do overlap!</font>
00112     <font class="keywordtype">double</font> common_radius(CS2Sphere &amp;asphere);
00113 
00114     <font class="comment">// Return the center</font>
00115     <font class="keyword">const</font> SCVector3&amp; center(<font class="keywordtype">void</font>)<font class="keyword"> const </font>{ <font class="keywordflow">return</font> _v; }
00116     <font class="keywordtype">double</font> x()<font class="keyword"> const </font>{ <font class="keywordflow">return</font> _v[0]; }
00117     <font class="keywordtype">double</font> y()<font class="keyword"> const </font>{ <font class="keywordflow">return</font> _v[1]; }
00118     <font class="keywordtype">double</font> z()<font class="keyword"> const </font>{ <font class="keywordflow">return</font> _v[2]; }
00119 
00120     <font class="comment">// Return the vector3d connecting the two centers</font>
00121     SCVector3 center_vec(<font class="keyword">const</font> CS2Sphere &amp;asphere)<font class="keyword"> </font>{ <font class="keywordflow">return</font> _v - asphere._v; }
00122 
00123     <font class="keywordtype">double</font> radius(<font class="keywordtype">void</font>)<font class="keyword"> const </font>{<font class="keywordflow">return</font> _radius;}
00124 
00125     <font class="keywordtype">void</font> recenter(<font class="keyword">const</font> SCVector3 &amp;v)<font class="keyword"> </font>{ _v -= v; }
00126     <font class="keywordtype">void</font> print(std::ostream&amp; os=ExEnv::out0()) <font class="keyword">const</font>
00127     {
00128       os &lt;&lt; indent
00129          &lt;&lt; scprintf(<font class="stringliteral">"Rad=%lf, Center=(%lf,%lf,%lf), From origin=%lf\n"</font>,
00130                      _radius, _v[0], _v[1], _v[2], _v.norm());
00131     }
00132 
00133     <font class="comment">// Function to determine if there is any portion of this that </font>
00134     <font class="comment">// is not inside one or more of the spheres in s[].  Returns</font>
00135     <font class="comment">// 1 if the intersection is empty, otherwise 0 is returned.</font>
00136     <font class="comment">// Warning: the spheres in s are modified.</font>
00137     <font class="keywordtype">int</font> intersect(CS2Sphere *s,
00138                   <font class="keywordtype">int</font> n_spheres) <font class="keyword">const</font>;
00139 
00140     <font class="keyword">static</font> <font class="keywordtype">void</font> print_counts(std::ostream&amp; = ExEnv::out0());
00141 };
00142 
00143 <font class="preprocessor">#define CONNOLLYSHAPE_N_WITH_NSPHERE_DIM 10</font>
00144 <font class="preprocessor"></font>
<a name="l00148"></a><a class="code" href="class_sc__ConnollyShape.html">00148</a> <font class="keyword">class </font>ConnollyShape: <font class="keyword">public</font> Shape {
00149   <font class="keyword">private</font>:
00150     CS2Sphere* sphere;
00151     <font class="keywordtype">double</font> probe_r;
00152     <font class="keywordtype">double</font> radius_scale_factor_;
00153     <font class="keywordtype">int</font> n_spheres;
00154     Ref&lt;AtomInfo&gt; atominfo_;
00155 
00156     Arrayint ***box_;
00157     <font class="keywordtype">double</font> l_;
00158     <font class="keywordtype">int</font> xmax_;
00159     <font class="keywordtype">int</font> ymax_;
00160     <font class="keywordtype">int</font> zmax_;
00161     SCVector3 lower_;
00162 
00163     <font class="keywordtype">int</font> get_box(<font class="keyword">const</font> SCVector3 &amp;v, <font class="keywordtype">int</font> &amp;x, <font class="keywordtype">int</font> &amp;y, <font class="keywordtype">int</font> &amp;z) <font class="keyword">const</font>;
00164 
00165 <font class="preprocessor">#if COUNT_CONNOLLY</font>
00166 <font class="preprocessor"></font>    <font class="keyword">static</font> <font class="keywordtype">int</font> n_total_;
00167     <font class="keyword">static</font> <font class="keywordtype">int</font> n_inside_vdw_;
00168     <font class="keyword">static</font> <font class="keywordtype">int</font> n_with_nsphere_[CONNOLLYSHAPE_N_WITH_NSPHERE_DIM];
00169 <font class="preprocessor">#endif</font>
00170 <font class="preprocessor"></font>
00171   <font class="keyword">public</font>:
00172     ConnollyShape(<font class="keyword">const</font> Ref&lt;KeyVal&gt;&amp;);
00173     ~ConnollyShape();
00174     <font class="keywordtype">void</font> initialize(<font class="keyword">const</font> Ref&lt;Molecule&gt;&amp;,<font class="keywordtype">double</font> probe_radius);
00175     <font class="keywordtype">void</font> clear();
00176     <font class="keywordtype">double</font> distance_to_surface(<font class="keyword">const</font> SCVector3&amp;r,
00177                                SCVector3*grad=0) <font class="keyword">const</font>;
00178     <font class="keywordtype">void</font> boundingbox(<font class="keywordtype">double</font> valuemin,
00179                      <font class="keywordtype">double</font> valuemax,
00180                      SCVector3&amp; p1, SCVector3&amp; p2);
00181 
00182     <font class="keyword">static</font> <font class="keywordtype">void</font> print_counts(std::ostream&amp; = ExEnv::out0());
00183 };
00184 
00185 }
00186 
00187 <font class="preprocessor">#endif</font>
00188 <font class="preprocessor"></font>
00189 <font class="comment">// Local Variables:</font>
00190 <font class="comment">// mode: c++</font>
00191 <font class="comment">// c-file-style: "CLJ"</font>
00192 <font class="comment">// End:</font>
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