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<h1 class="epydoc">Source Code for <a href="Bio.PDB-module.html">Package Bio.PDB</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable Bio.PDB.AbstractPropertyMap.__doc__=Bio.PDB.AbstractPropertyMap-module.html#__doc__,Variable Bio.PDB.Atom.__doc__=Bio.PDB.Atom-module.html#__doc__,Variable Bio.PDB.Chain.__doc__=Bio.PDB.Chain-module.html#__doc__,Variable Bio.PDB.Entity.__doc__=Bio.PDB.Entity-module.html#__doc__,Variable Bio.PDB.HSExposure.__doc__=Bio.PDB.HSExposure-module.html#__doc__,Variable Bio.PDB.MMCIF2Dict.__doc__=Bio.PDB.MMCIF2Dict-module.html#__doc__,Variable Bio.PDB.MMCIFParser.__doc__=Bio.PDB.MMCIFParser-module.html#__doc__,Variable Bio.PDB.Model.__doc__=Bio.PDB.Model-module.html#__doc__,Variable Bio.PDB.NACCESS.__doc__=Bio.PDB.NACCESS-module.html#__doc__,Variable Bio.PDB.NeighborSearch.__doc__=Bio.PDB.NeighborSearch-module.html#__doc__,Variable Bio.PDB.PDBExceptions.__doc__=Bio.PDB.PDBExceptions-module.html#__doc__,Variable Bio.PDB.Polypeptide.__doc__=Bio.PDB.Polypeptide-module.html#__doc__,Variable Bio.PDB.Residue.__doc__=Bio.PDB.Residue-module.html#__doc__,Variable Bio.PDB.Selection.__doc__=Bio.PDB.Selection-module.html#__doc__,Variable Bio.PDB.Structure.__doc__=Bio.PDB.Structure-module.html#__doc__,Variable Bio.PDB.StructureBuilder.__doc__=Bio.PDB.StructureBuilder-module.html#__doc__,Variable Bio.PDB.__doc__=Bio.PDB-module.html#__doc__"><a title="Bio.PDB.AbstractPropertyMap.__doc__
Bio.PDB.Atom.__doc__
Bio.PDB.Chain.__doc__
Bio.PDB.Entity.__doc__
Bio.PDB.HSExposure.__doc__
Bio.PDB.MMCIF2Dict.__doc__
Bio.PDB.MMCIFParser.__doc__
Bio.PDB.Model.__doc__
Bio.PDB.NACCESS.__doc__
Bio.PDB.NeighborSearch.__doc__
Bio.PDB.PDBExceptions.__doc__
Bio.PDB.Polypeptide.__doc__
Bio.PDB.Residue.__doc__
Bio.PDB.Selection.__doc__
Bio.PDB.Structure.__doc__
Bio.PDB.StructureBuilder.__doc__
Bio.PDB.__doc__" class="py-name" href="#" onclick="return doclink('link-0', '__doc__', 'link-0');">__doc__</a></tt><tt class="py-op">=</tt><tt class="py-docstring">"""</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">Classes that deal with macromolecular crystal structures. (eg.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">PDB and mmCIF parsers, a Structure class, a module to keep </tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">a local copy of the PDB up-to-date, selective IO of PDB files,</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring">etc.). Author: Thomas Hamelryck. Additional code by Kristian </tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring">Rother.</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-comment"># Get a Structure object from a PDB file</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Class Bio.PDB.PDBParser'.PDBParser=Bio.PDB.PDBParser%27.PDBParser-class.html"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-1', 'PDBParser', 'link-1');">PDBParser</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="Bio.PDB.PDBParser'.PDBParser" class="py-name" href="#" onclick="return doclink('link-2', 'PDBParser', 'link-1');">PDBParser</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-comment"># Get a Structure object from an mmCIF file</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">from</tt> <tt id="link-3" class="py-name" targets="Module Bio.PDB.MMCIFParser=Bio.PDB.MMCIFParser-module.html,Class Bio.PDB.MMCIFParser.MMCIFParser=Bio.PDB.MMCIFParser.MMCIFParser-class.html"><a title="Bio.PDB.MMCIFParser
Bio.PDB.MMCIFParser.MMCIFParser" class="py-name" href="#" onclick="return doclink('link-3', 'MMCIFParser', 'link-3');">MMCIFParser</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name"><a title="Bio.PDB.MMCIFParser
Bio.PDB.MMCIFParser.MMCIFParser" class="py-name" href="#" onclick="return doclink('link-4', 'MMCIFParser', 'link-3');">MMCIFParser</a></tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-comment"># Not compiled I guess </tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-comment"># Download from the PDB</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name" targets="Class Bio.PDB.PDBList'.PDBList=Bio.PDB.PDBList%27.PDBList-class.html"><a title="Bio.PDB.PDBList'.PDBList" class="py-name" href="#" onclick="return doclink('link-5', 'PDBList', 'link-5');">PDBList</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name"><a title="Bio.PDB.PDBList'.PDBList" class="py-name" href="#" onclick="return doclink('link-6', 'PDBList', 'link-5');">PDBList</a></tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-comment"># Parse PDB header directly</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name" targets="Function Bio.PDB.parse_pdb_header'.parse_pdb_header()=Bio.PDB.parse_pdb_header%27-module.html#parse_pdb_header"><a title="Bio.PDB.parse_pdb_header'.parse_pdb_header" class="py-name" href="#" onclick="return doclink('link-7', 'parse_pdb_header', 'link-7');">parse_pdb_header</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name"><a title="Bio.PDB.parse_pdb_header'.parse_pdb_header" class="py-name" href="#" onclick="return doclink('link-8', 'parse_pdb_header', 'link-7');">parse_pdb_header</a></tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-comment"># Find connected polypeptides in a Structure</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-9" class="py-name" targets="Module Bio.PDB.Polypeptide=Bio.PDB.Polypeptide-module.html,Class Bio.PDB.Polypeptide.Polypeptide=Bio.PDB.Polypeptide.Polypeptide-class.html"><a title="Bio.PDB.Polypeptide
Bio.PDB.Polypeptide.Polypeptide" class="py-name" href="#" onclick="return doclink('link-9', 'Polypeptide', 'link-9');">Polypeptide</a></tt> <tt class="py-keyword">import</tt> <tt id="link-10" class="py-name" targets="Class Bio.PDB.Polypeptide.PPBuilder=Bio.PDB.Polypeptide.PPBuilder-class.html"><a title="Bio.PDB.Polypeptide.PPBuilder" class="py-name" href="#" onclick="return doclink('link-10', 'PPBuilder', 'link-10');">PPBuilder</a></tt><tt class="py-op">,</tt> <tt id="link-11" class="py-name" targets="Class Bio.PDB.Polypeptide.CaPPBuilder=Bio.PDB.Polypeptide.CaPPBuilder-class.html"><a title="Bio.PDB.Polypeptide.CaPPBuilder" class="py-name" href="#" onclick="return doclink('link-11', 'CaPPBuilder', 'link-11');">CaPPBuilder</a></tt><tt class="py-op">,</tt> <tt id="link-12" class="py-name" targets="Function Bio.PDB.Polypeptide.is_aa()=Bio.PDB.Polypeptide-module.html#is_aa"><a title="Bio.PDB.Polypeptide.is_aa" class="py-name" href="#" onclick="return doclink('link-12', 'is_aa', 'link-12');">is_aa</a></tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name" targets="Variable Bio.PDB.DSSP'.standard_aa_names=Bio.PDB.DSSP%27-module.html#standard_aa_names,Variable Bio.PDB.FragmentMapper'.standard_aa_names=Bio.PDB.FragmentMapper%27-module.html#standard_aa_names,Variable Bio.PDB.HSExposure.standard_aa_names=Bio.PDB.HSExposure-module.html#standard_aa_names,Variable Bio.PDB.PSEA.standard_aa_names=Bio.PDB.PSEA-module.html#standard_aa_names,Variable Bio.PDB.Polypeptide.standard_aa_names=Bio.PDB.Polypeptide-module.html#standard_aa_names,Variable Bio.PDB.ResidueDepth'.standard_aa_names=Bio.PDB.ResidueDepth%27-module.html#standard_aa_names,Variable Bio.PDB.StructureAlignment'.standard_aa_names=Bio.PDB.StructureAlignment%27-module.html#standard_aa_names"><a title="Bio.PDB.DSSP'.standard_aa_names
Bio.PDB.FragmentMapper'.standard_aa_names
Bio.PDB.HSExposure.standard_aa_names
Bio.PDB.PSEA.standard_aa_names
Bio.PDB.Polypeptide.standard_aa_names
Bio.PDB.ResidueDepth'.standard_aa_names
Bio.PDB.StructureAlignment'.standard_aa_names" class="py-name" href="#" onclick="return doclink('link-13', 'standard_aa_names', 'link-13');">standard_aa_names</a></tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-comment"># This is also useful :-)</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-14" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-14', 'Bio', 'link-14');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Package Bio.SCOP=Bio.SCOP-module.html,Module Bio.WWW.SCOP=Bio.WWW.SCOP-module.html"><a title="Bio.SCOP
Bio.WWW.SCOP" class="py-name" href="#" onclick="return doclink('link-15', 'SCOP', 'link-15');">SCOP</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Module Bio.SCOP.Raf=Bio.SCOP.Raf-module.html"><a title="Bio.SCOP.Raf" class="py-name" href="#" onclick="return doclink('link-16', 'Raf', 'link-16');">Raf</a></tt> <tt class="py-keyword">import</tt> <tt id="link-17" class="py-name" targets="Variable Bio.PDB.DSSP'.to_one_letter_code=Bio.PDB.DSSP%27-module.html#to_one_letter_code,Variable Bio.PDB.FragmentMapper'.to_one_letter_code=Bio.PDB.FragmentMapper%27-module.html#to_one_letter_code,Variable Bio.PDB.HSExposure.to_one_letter_code=Bio.PDB.HSExposure-module.html#to_one_letter_code,Variable Bio.PDB.PSEA.to_one_letter_code=Bio.PDB.PSEA-module.html#to_one_letter_code,Variable Bio.PDB.ResidueDepth'.to_one_letter_code=Bio.PDB.ResidueDepth%27-module.html#to_one_letter_code,Variable Bio.PDB.StructureAlignment'.to_one_letter_code=Bio.PDB.StructureAlignment%27-module.html#to_one_letter_code,Variable Bio.SCOP.Raf.to_one_letter_code=Bio.SCOP.Raf-module.html#to_one_letter_code"><a title="Bio.PDB.DSSP'.to_one_letter_code
Bio.PDB.FragmentMapper'.to_one_letter_code
Bio.PDB.HSExposure.to_one_letter_code
Bio.PDB.PSEA.to_one_letter_code
Bio.PDB.ResidueDepth'.to_one_letter_code
Bio.PDB.StructureAlignment'.to_one_letter_code
Bio.SCOP.Raf.to_one_letter_code" class="py-name" href="#" onclick="return doclink('link-17', 'to_one_letter_code', 'link-17');">to_one_letter_code</a></tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt class="py-comment"># IO of PDB files (including flexible selective output)</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-18" class="py-name" targets="Class Bio.PDB.PDBIO'.PDBIO=Bio.PDB.PDBIO%27.PDBIO-class.html"><a title="Bio.PDB.PDBIO'.PDBIO" class="py-name" href="#" onclick="return doclink('link-18', 'PDBIO', 'link-18');">PDBIO</a></tt> <tt class="py-keyword">import</tt> <tt id="link-19" class="py-name"><a title="Bio.PDB.PDBIO'.PDBIO" class="py-name" href="#" onclick="return doclink('link-19', 'PDBIO', 'link-18');">PDBIO</a></tt><tt class="py-op">,</tt> <tt id="link-20" class="py-name" targets="Class Bio.PDB.PDBIO'.Select=Bio.PDB.PDBIO%27.Select-class.html"><a title="Bio.PDB.PDBIO'.Select" class="py-name" href="#" onclick="return doclink('link-20', 'Select', 'link-20');">Select</a></tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-comment"># Some methods to eg. get a list of Residues</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># from a list of Atoms.</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt id="link-21" class="py-name" targets="Package Bio.GA.Selection=Bio.GA.Selection-module.html,Module Bio.PDB.Selection=Bio.PDB.Selection-module.html"><a title="Bio.GA.Selection
Bio.PDB.Selection" class="py-name" href="#" onclick="return doclink('link-21', 'Selection', 'link-21');">Selection</a></tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt class="py-comment"># Superimpose atom sets</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-22" class="py-name" targets="Class Bio.PDB.Superimposer'.Superimposer=Bio.PDB.Superimposer%27.Superimposer-class.html"><a title="Bio.PDB.Superimposer'.Superimposer" class="py-name" href="#" onclick="return doclink('link-22', 'Superimposer', 'link-22');">Superimposer</a></tt> <tt class="py-keyword">import</tt> <tt id="link-23" class="py-name"><a title="Bio.PDB.Superimposer'.Superimposer" class="py-name" href="#" onclick="return doclink('link-23', 'Superimposer', 'link-22');">Superimposer</a></tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-comment"># 3D vector class</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-24" class="py-name" targets="Class Bio.PDB.Vector'.Vector=Bio.PDB.Vector%27.Vector-class.html"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-24', 'Vector', 'link-24');">Vector</a></tt> <tt class="py-keyword">import</tt> <tt id="link-25" class="py-name"><a title="Bio.PDB.Vector'.Vector" class="py-name" href="#" onclick="return doclink('link-25', 'Vector', 'link-24');">Vector</a></tt><tt class="py-op">,</tt> <tt id="link-26" class="py-name" targets="Function Bio.PDB.Vector'.calc_angle()=Bio.PDB.Vector%27-module.html#calc_angle"><a title="Bio.PDB.Vector'.calc_angle" class="py-name" href="#" onclick="return doclink('link-26', 'calc_angle', 'link-26');">calc_angle</a></tt><tt class="py-op">,</tt> <tt id="link-27" class="py-name" targets="Function Bio.PDB.Vector'.calc_dihedral()=Bio.PDB.Vector%27-module.html#calc_dihedral"><a title="Bio.PDB.Vector'.calc_dihedral" class="py-name" href="#" onclick="return doclink('link-27', 'calc_dihedral', 'link-27');">calc_dihedral</a></tt><tt class="py-op">,</tt> <tt id="link-28" class="py-name" targets="Function Bio.PDB.Vector'.refmat()=Bio.PDB.Vector%27-module.html#refmat"><a title="Bio.PDB.Vector'.refmat" class="py-name" href="#" onclick="return doclink('link-28', 'refmat', 'link-28');">refmat</a></tt><tt class="py-op">,</tt> <tt id="link-29" class="py-name" targets="Function Bio.PDB.Vector'.rotmat()=Bio.PDB.Vector%27-module.html#rotmat"><a title="Bio.PDB.Vector'.rotmat" class="py-name" href="#" onclick="return doclink('link-29', 'rotmat', 'link-29');">rotmat</a></tt><tt class="py-op">,</tt> <tt class="py-name">rotaxis</tt><tt class="py-op">,</tt>\ </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt id="link-30" class="py-name" targets="Function Bio.PDB.Vector'.vector_to_axis()=Bio.PDB.Vector%27-module.html#vector_to_axis"><a title="Bio.PDB.Vector'.vector_to_axis" class="py-name" href="#" onclick="return doclink('link-30', 'vector_to_axis', 'link-30');">vector_to_axis</a></tt><tt class="py-op">,</tt> <tt id="link-31" class="py-name" targets="Function Bio.PDB.Vector'.m2rotaxis()=Bio.PDB.Vector%27-module.html#m2rotaxis"><a title="Bio.PDB.Vector'.m2rotaxis" class="py-name" href="#" onclick="return doclink('link-31', 'm2rotaxis', 'link-31');">m2rotaxis</a></tt><tt class="py-op">,</tt> <tt id="link-32" class="py-name" targets="Function Bio.PDB.Vector'.rotaxis2m()=Bio.PDB.Vector%27-module.html#rotaxis2m"><a title="Bio.PDB.Vector'.rotaxis2m" class="py-name" href="#" onclick="return doclink('link-32', 'rotaxis2m', 'link-32');">rotaxis2m</a></tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"><tt class="py-comment"># Alignment module</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-33" class="py-name" targets="Class Bio.PDB.StructureAlignment'.StructureAlignment=Bio.PDB.StructureAlignment%27.StructureAlignment-class.html"><a title="Bio.PDB.StructureAlignment'.StructureAlignment" class="py-name" href="#" onclick="return doclink('link-33', 'StructureAlignment', 'link-33');">StructureAlignment</a></tt> <tt class="py-keyword">import</tt> <tt id="link-34" class="py-name"><a title="Bio.PDB.StructureAlignment'.StructureAlignment" class="py-name" href="#" onclick="return doclink('link-34', 'StructureAlignment', 'link-33');">StructureAlignment</a></tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt class="py-comment"># DSSP handle </tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># (secondary structure and solvent accessible area calculation)</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-35" class="py-name" targets="Class Bio.PDB.DSSP'.DSSP=Bio.PDB.DSSP%27.DSSP-class.html"><a title="Bio.PDB.DSSP'.DSSP" class="py-name" href="#" onclick="return doclink('link-35', 'DSSP', 'link-35');">DSSP</a></tt> <tt class="py-keyword">import</tt> <tt id="link-36" class="py-name"><a title="Bio.PDB.DSSP'.DSSP" class="py-name" href="#" onclick="return doclink('link-36', 'DSSP', 'link-35');">DSSP</a></tt><tt class="py-op">,</tt> <tt id="link-37" class="py-name" targets="Function Bio.PDB.DSSP'.make_dssp_dict()=Bio.PDB.DSSP%27-module.html#make_dssp_dict"><a title="Bio.PDB.DSSP'.make_dssp_dict" class="py-name" href="#" onclick="return doclink('link-37', 'make_dssp_dict', 'link-37');">make_dssp_dict</a></tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"><tt class="py-comment"># Residue depth: </tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># distance of residue atoms from solvent accessible surface</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-38" class="py-name" targets="Class Bio.PDB.ResidueDepth'.ResidueDepth=Bio.PDB.ResidueDepth%27.ResidueDepth-class.html"><a title="Bio.PDB.ResidueDepth'.ResidueDepth" class="py-name" href="#" onclick="return doclink('link-38', 'ResidueDepth', 'link-38');">ResidueDepth</a></tt> <tt class="py-keyword">import</tt> <tt id="link-39" class="py-name"><a title="Bio.PDB.ResidueDepth'.ResidueDepth" class="py-name" href="#" onclick="return doclink('link-39', 'ResidueDepth', 'link-38');">ResidueDepth</a></tt><tt class="py-op">,</tt> <tt id="link-40" class="py-name" targets="Function Bio.PDB.ResidueDepth'.get_surface()=Bio.PDB.ResidueDepth%27-module.html#get_surface"><a title="Bio.PDB.ResidueDepth'.get_surface" class="py-name" href="#" onclick="return doclink('link-40', 'get_surface', 'link-40');">get_surface</a></tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"><tt class="py-comment"># Calculation of Half Sphere Solvent Exposure</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-41" class="py-name" targets="Module Bio.PDB.HSExposure=Bio.PDB.HSExposure-module.html"><a title="Bio.PDB.HSExposure" class="py-name" href="#" onclick="return doclink('link-41', 'HSExposure', 'link-41');">HSExposure</a></tt> <tt class="py-keyword">import</tt> <tt id="link-42" class="py-name" targets="Class Bio.PDB.HSExposure.HSExposureCA=Bio.PDB.HSExposure.HSExposureCA-class.html"><a title="Bio.PDB.HSExposure.HSExposureCA" class="py-name" href="#" onclick="return doclink('link-42', 'HSExposureCA', 'link-42');">HSExposureCA</a></tt><tt class="py-op">,</tt> <tt id="link-43" class="py-name" targets="Class Bio.PDB.HSExposure.HSExposureCB=Bio.PDB.HSExposure.HSExposureCB-class.html"><a title="Bio.PDB.HSExposure.HSExposureCB" class="py-name" href="#" onclick="return doclink('link-43', 'HSExposureCB', 'link-43');">HSExposureCB</a></tt><tt class="py-op">,</tt> <tt id="link-44" class="py-name" targets="Class Bio.PDB.HSExposure.ExposureCN=Bio.PDB.HSExposure.ExposureCN-class.html"><a title="Bio.PDB.HSExposure.ExposureCN" class="py-name" href="#" onclick="return doclink('link-44', 'ExposureCN', 'link-44');">ExposureCN</a></tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"><tt class="py-comment"># Kolodny et al.'s backbone libraries</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-45" class="py-name" targets="Class Bio.PDB.FragmentMapper'.FragmentMapper=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html"><a title="Bio.PDB.FragmentMapper'.FragmentMapper" class="py-name" href="#" onclick="return doclink('link-45', 'FragmentMapper', 'link-45');">FragmentMapper</a></tt> <tt class="py-keyword">import</tt> <tt id="link-46" class="py-name"><a title="Bio.PDB.FragmentMapper'.FragmentMapper" class="py-name" href="#" onclick="return doclink('link-46', 'FragmentMapper', 'link-45');">FragmentMapper</a></tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"><tt class="py-comment"># Write out chain(start-end) to PDB file</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-47" class="py-name" targets="Module Bio.PDB.Dice=Bio.PDB.Dice-module.html"><a title="Bio.PDB.Dice" class="py-name" href="#" onclick="return doclink('link-47', 'Dice', 'link-47');">Dice</a></tt> <tt class="py-keyword">import</tt> <tt id="link-48" class="py-name" targets="Function Bio.PDB.Dice.extract()=Bio.PDB.Dice-module.html#extract"><a title="Bio.PDB.Dice.extract" class="py-name" href="#" onclick="return doclink('link-48', 'extract', 'link-48');">extract</a></tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"><tt class="py-comment"># Fast atom neighbor search</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Depends on KDTree C++ module</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-49" class="py-name" targets="Module Bio.PDB.NeighborSearch=Bio.PDB.NeighborSearch-module.html,Class Bio.PDB.NeighborSearch.NeighborSearch=Bio.PDB.NeighborSearch.NeighborSearch-class.html"><a title="Bio.PDB.NeighborSearch
Bio.PDB.NeighborSearch.NeighborSearch" class="py-name" href="#" onclick="return doclink('link-49', 'NeighborSearch', 'link-49');">NeighborSearch</a></tt> <tt class="py-keyword">import</tt> <tt id="link-50" class="py-name"><a title="Bio.PDB.NeighborSearch
Bio.PDB.NeighborSearch.NeighborSearch" class="py-name" href="#" onclick="return doclink('link-50', 'NeighborSearch', 'link-49');">NeighborSearch</a></tt> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"><tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> </tt><script type="text/javascript">
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