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<h1>s_fparams Struct Reference</h1><!-- doxytag: class="s_fparams" --><code>#include &lt;<a class="el" href="fparams_8h-source.html">fparams.h</a>&gt;</code>
<p>
<table border="0" cellpadding="0" cellspacing="0">
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<tr><td colspan="2"><br><h2>Data Fields</h2></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">char&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#4e1b3892d1e42947408cdcaed497bf97">pdb_path</a> [M_MAX_PDB_NAME_LEN]</td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">char **&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#b620ac1ea6b8ad4c4ed0b95a8664a560">pdb_lst</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#5427055e24cc2dea5c41a9fd6bba8cac">npdb</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#771a10e1c94346d353eb6cb87b4abb18">flag_do_asa_and_volume_calculations</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#b0875eddf8815f766657713b3f4ba0b0">min_apol_neigh</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#b23279857aaf7861b452cd2bf463f624">sl_clust_min_nneigh</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#8caeadbae2db7d24763497290e6b9220">nb_mcv_iter</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#289a1193bf0ffa2f737cd9dc914b63e0">basic_volume_div</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#2ccafe788e970f4e00bdae591d834865">min_pock_nb_asph</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">int&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#b8d794447932a12435a628f3462df7ad">db_run</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#cd506e600d2b5077f7925847be38c854">clust_max_dist</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#50d6211ea1f5d9b90c10f866c82e54b8">refine_min_apolar_asphere_prop</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#71691bbfb98d90e12ca8cb3c79e2688c">sl_clust_max_dist</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#8ba147c559344c3f0406c1e7a86b98d1">refine_clust_dist</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#545b7bea97958089689608fff6b8910d">asph_min_size</a></td></tr>
<tr><td class="memItemLeft" nowrap align="right" valign="top">float&nbsp;</td><td class="memItemRight" valign="bottom"><a class="el" href="structs__fparams.html#7439af209766e39dad7e39f4c6e19711">asph_max_size</a></td></tr>
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<hr><a name="_details"></a><h2>Detailed Description</h2>
Structure containing all necessary parameters that can be changed by the user. This structure is commun to both programs (validation and pocket finding), even if the pocked finding programm doesn't need some parameters.
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00134">134</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<hr><h2>Field Documentation</h2>
<a class="anchor" name="4e1b3892d1e42947408cdcaed497bf97"></a><!-- doxytag: member="s_fparams::pdb_path" ref="4e1b3892d1e42947408cdcaed497bf97" args="[M_MAX_PDB_NAME_LEN]" -->
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<td class="memname">char <a class="el" href="structs__fparams.html#4e1b3892d1e42947408cdcaed497bf97">s_fparams::pdb_path</a>[M_MAX_PDB_NAME_LEN] </td>
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<p>
The pdb file
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00136">136</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="check_8c-source.html#l00173">check_fparams()</a>, <a class="el" href="check_8c-source.html#l00105">check_fpocket()</a>, <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fpmain_8c-source.html#l00071">main()</a>, <a class="el" href="fparams_8c-source.html#l00611">print_fparams()</a>, and <a class="el" href="tpocket_8c-source.html#l00082">test_fpocket()</a>.</p>
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<a class="anchor" name="b620ac1ea6b8ad4c4ed0b95a8664a560"></a><!-- doxytag: member="s_fparams::pdb_lst" ref="b620ac1ea6b8ad4c4ed0b95a8664a560" args="" -->
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<td class="memname">char** <a class="el" href="structs__fparams.html#b620ac1ea6b8ad4c4ed0b95a8664a560">s_fparams::pdb_lst</a> </td>
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<p>
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00137">137</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00562">free_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, and <a class="el" href="fpmain_8c-source.html#l00071">main()</a>.</p>
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<a class="anchor" name="5427055e24cc2dea5c41a9fd6bba8cac"></a><!-- doxytag: member="s_fparams::npdb" ref="5427055e24cc2dea5c41a9fd6bba8cac" args="" -->
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<td class="memname">int <a class="el" href="structs__fparams.html#5427055e24cc2dea5c41a9fd6bba8cac">s_fparams::npdb</a> </td>
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<p>
number of pdb files
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00138">138</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00562">free_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, and <a class="el" href="fpmain_8c-source.html#l00071">main()</a>.</p>
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<a class="anchor" name="771a10e1c94346d353eb6cb87b4abb18"></a><!-- doxytag: member="s_fparams::flag_do_asa_and_volume_calculations" ref="771a10e1c94346d353eb6cb87b4abb18" args="" -->
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<td class="memname">int <a class="el" href="structs__fparams.html#771a10e1c94346d353eb6cb87b4abb18">s_fparams::flag_do_asa_and_volume_calculations</a> </td>
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<p>
if 1, asa and volume calculations are performed(slower), if 0, not
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00139">139</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="dpocket_8c-source.html#l00336">get_explicit_desc()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="mdpocket_8c-source.html#l00217">mdpocket_characterize()</a>, <a class="el" href="mdpocket_8c-source.html#l00089">mdpocket_detect()</a>, and <a class="el" href="pocket_8c-source.html#l00582">set_pockets_descriptors()</a>.</p>
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<a class="anchor" name="b0875eddf8815f766657713b3f4ba0b0"></a><!-- doxytag: member="s_fparams::min_apol_neigh" ref="b0875eddf8815f766657713b3f4ba0b0" args="" -->
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<td class="memname">int <a class="el" href="structs__fparams.html#b0875eddf8815f766657713b3f4ba0b0">s_fparams::min_apol_neigh</a> </td>
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<p>
Min number of apolar neighbours for an a-sphere to be an apolar a-sphere
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00141">141</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="check_8c-source.html#l00173">check_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00300">parse_min_apol_neigh()</a>, <a class="el" href="fparams_8c-source.html#l00611">print_fparams()</a>, <a class="el" href="tparams_8c-source.html#l00458">print_params()</a>, and <a class="el" href="fpocket_8c-source.html#l00082">search_pocket()</a>.</p>
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<a class="anchor" name="b23279857aaf7861b452cd2bf463f624"></a><!-- doxytag: member="s_fparams::sl_clust_min_nneigh" ref="b23279857aaf7861b452cd2bf463f624" args="" -->
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<td class="memname">int <a class="el" href="structs__fparams.html#b23279857aaf7861b452cd2bf463f624">s_fparams::sl_clust_min_nneigh</a> </td>
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<p>
Min number of neighbours for single linkage clustering
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00141">141</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="check_8c-source.html#l00173">check_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00271">parse_sclust_min_nneigh()</a>, <a class="el" href="cluster_8c-source.html#l00290">pck_ml_clust()</a>, <a class="el" href="cluster_8c-source.html#l00376">pck_ml_clust_test()</a>, <a class="el" href="fparams_8c-source.html#l00611">print_fparams()</a>, <a class="el" href="tparams_8c-source.html#l00458">print_params()</a>, and <a class="el" href="mdpout_8c-source.html#l00095">write_md_grid()</a>.</p>
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<a class="anchor" name="8caeadbae2db7d24763497290e6b9220"></a><!-- doxytag: member="s_fparams::nb_mcv_iter" ref="8caeadbae2db7d24763497290e6b9220" args="" -->
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<td class="memname">int <a class="el" href="structs__fparams.html#8caeadbae2db7d24763497290e6b9220">s_fparams::nb_mcv_iter</a> </td>
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<p>
Number of iteration for the Monte Carlo volume calculation
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00141">141</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="dpocket_8c-source.html#l00184">desc_pocket()</a>, <a class="el" href="dpocket_8c-source.html#l00336">get_explicit_desc()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="mdpocket_8c-source.html#l00217">mdpocket_characterize()</a>, <a class="el" href="fparams_8c-source.html#l00387">parse_mc_niter()</a>, <a class="el" href="fparams_8c-source.html#l00611">print_fparams()</a>, <a class="el" href="tparams_8c-source.html#l00458">print_params()</a>, <a class="el" href="tpocket_8c-source.html#l00881">set_overlap_volumes()</a>, <a class="el" href="pocket_8c-source.html#l00582">set_pockets_descriptors()</a>, and <a class="el" href="tpocket_8c-source.html#l00440">test_set()</a>.</p>
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<a class="anchor" name="289a1193bf0ffa2f737cd9dc914b63e0"></a><!-- doxytag: member="s_fparams::basic_volume_div" ref="289a1193bf0ffa2f737cd9dc914b63e0" args="" -->
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<td class="memname">int <a class="el" href="structs__fparams.html#289a1193bf0ffa2f737cd9dc914b63e0">s_fparams::basic_volume_div</a> </td>
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<p>
Box division factor for basic volume calculation
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00141">141</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00415">parse_basic_vol_div()</a>, <a class="el" href="fparams_8c-source.html#l00611">print_fparams()</a>, <a class="el" href="tparams_8c-source.html#l00458">print_params()</a>, and <a class="el" href="tpocket_8c-source.html#l00881">set_overlap_volumes()</a>.</p>
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<a class="anchor" name="2ccafe788e970f4e00bdae591d834865"></a><!-- doxytag: member="s_fparams::min_pock_nb_asph" ref="2ccafe788e970f4e00bdae591d834865" args="" -->
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<td class="memname">int <a class="el" href="structs__fparams.html#2ccafe788e970f4e00bdae591d834865">s_fparams::min_pock_nb_asph</a> </td>
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<p>
Minimump number of alpha spheres per pocket
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00141">141</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="check_8c-source.html#l00173">check_fparams()</a>, <a class="el" href="refine_8c-source.html#l00130">dropSmallNpolarPockets()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00499">parse_min_pock_nb_asph()</a>, and <a class="el" href="mdpout_8c-source.html#l00095">write_md_grid()</a>.</p>
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<a class="anchor" name="b8d794447932a12435a628f3462df7ad"></a><!-- doxytag: member="s_fparams::db_run" ref="b8d794447932a12435a628f3462df7ad" args="" -->
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<td class="memname">int <a class="el" href="structs__fparams.html#b8d794447932a12435a628f3462df7ad">s_fparams::db_run</a> </td>
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<p>
flag for running fpocket for db population
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00141">141</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fpmain_8c-source.html#l00071">main()</a>, and <a class="el" href="fpmain_8c-source.html#l00130">process_pdb()</a>.</p>
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<a class="anchor" name="cd506e600d2b5077f7925847be38c854"></a><!-- doxytag: member="s_fparams::clust_max_dist" ref="cd506e600d2b5077f7925847be38c854" args="" -->
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<td class="memname">float <a class="el" href="structs__fparams.html#cd506e600d2b5077f7925847be38c854">s_fparams::clust_max_dist</a> </td>
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<p>
First clustering distance criteria
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00150">150</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="check_8c-source.html#l00173">check_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00214">parse_clust_max_dist()</a>, <a class="el" href="fparams_8c-source.html#l00611">print_fparams()</a>, <a class="el" href="tparams_8c-source.html#l00458">print_params()</a>, <a class="el" href="pocket_8c-source.html#l00170">updateIds()</a>, and <a class="el" href="mdpout_8c-source.html#l00095">write_md_grid()</a>.</p>
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<a class="anchor" name="50d6211ea1f5d9b90c10f866c82e54b8"></a><!-- doxytag: member="s_fparams::refine_min_apolar_asphere_prop" ref="50d6211ea1f5d9b90c10f866c82e54b8" args="" -->
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<td class="memname">float <a class="el" href="structs__fparams.html#50d6211ea1f5d9b90c10f866c82e54b8">s_fparams::refine_min_apolar_asphere_prop</a> </td>
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<p>
Min proportion of apolar alpha spheres for each pocket
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00150">150</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="check_8c-source.html#l00173">check_fparams()</a>, <a class="el" href="refine_8c-source.html#l00130">dropSmallNpolarPockets()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00471">parse_refine_minaap()</a>, <a class="el" href="fparams_8c-source.html#l00611">print_fparams()</a>, and <a class="el" href="tparams_8c-source.html#l00458">print_params()</a>.</p>
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<a class="anchor" name="71691bbfb98d90e12ca8cb3c79e2688c"></a><!-- doxytag: member="s_fparams::sl_clust_max_dist" ref="71691bbfb98d90e12ca8cb3c79e2688c" args="" -->
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<td class="memname">float <a class="el" href="structs__fparams.html#71691bbfb98d90e12ca8cb3c79e2688c">s_fparams::sl_clust_max_dist</a> </td>
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<p>
Single linkage clusturing distance criteria
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00150">150</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="check_8c-source.html#l00173">check_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00243">parse_sclust_max_dist()</a>, <a class="el" href="cluster_8c-source.html#l00070">pck_final_clust()</a>, <a class="el" href="cluster_8c-source.html#l00290">pck_ml_clust()</a>, <a class="el" href="cluster_8c-source.html#l00376">pck_ml_clust_test()</a>, <a class="el" href="fparams_8c-source.html#l00611">print_fparams()</a>, <a class="el" href="tparams_8c-source.html#l00458">print_params()</a>, and <a class="el" href="mdpout_8c-source.html#l00095">write_md_grid()</a>.</p>
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<a class="anchor" name="8ba147c559344c3f0406c1e7a86b98d1"></a><!-- doxytag: member="s_fparams::refine_clust_dist" ref="8ba147c559344c3f0406c1e7a86b98d1" args="" -->
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<td class="memname">float <a class="el" href="structs__fparams.html#8ba147c559344c3f0406c1e7a86b98d1">s_fparams::refine_clust_dist</a> </td>
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<p>
Refine clustering distance criteria
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00150">150</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="check_8c-source.html#l00173">check_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00443">parse_refine_dist()</a>, <a class="el" href="fparams_8c-source.html#l00611">print_fparams()</a>, <a class="el" href="tparams_8c-source.html#l00458">print_params()</a>, and <a class="el" href="mdpout_8c-source.html#l00095">write_md_grid()</a>.</p>
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<a class="anchor" name="545b7bea97958089689608fff6b8910d"></a><!-- doxytag: member="s_fparams::asph_min_size" ref="545b7bea97958089689608fff6b8910d" args="" -->
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<td class="memname">float <a class="el" href="structs__fparams.html#545b7bea97958089689608fff6b8910d">s_fparams::asph_min_size</a> </td>
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<p>
Minimum size of alpha spheres to keep
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00150">150</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="check_8c-source.html#l00173">check_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00330">parse_asph_min_size()</a>, <a class="el" href="fparams_8c-source.html#l00611">print_fparams()</a>, <a class="el" href="tparams_8c-source.html#l00458">print_params()</a>, <a class="el" href="fpocket_8c-source.html#l00082">search_pocket()</a>, and <a class="el" href="mdpout_8c-source.html#l00095">write_md_grid()</a>.</p>
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<a class="anchor" name="7439af209766e39dad7e39f4c6e19711"></a><!-- doxytag: member="s_fparams::asph_max_size" ref="7439af209766e39dad7e39f4c6e19711" args="" -->
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<td class="memname">float <a class="el" href="structs__fparams.html#7439af209766e39dad7e39f4c6e19711">s_fparams::asph_max_size</a> </td>
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<p>
Maximum size of alpha spheres to keep
<p>Definition at line <a class="el" href="fparams_8h-source.html#l00150">150</a> of file <a class="el" href="fparams_8h-source.html">fparams.h</a>.</p>
<p>Referenced by <a class="el" href="check_8c-source.html#l00173">check_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00358">parse_asph_max_size()</a>, <a class="el" href="fparams_8c-source.html#l00611">print_fparams()</a>, <a class="el" href="tparams_8c-source.html#l00458">print_params()</a>, <a class="el" href="fpocket_8c-source.html#l00082">search_pocket()</a>, and <a class="el" href="mdpout_8c-source.html#l00095">write_md_grid()</a>.</p>
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<hr>The documentation for this struct was generated from the following file:<ul>
<li><a class="el" href="fparams_8h-source.html">fparams.h</a></ul>
</div>
<hr size="1"><address style="text-align: right;"><small>Generated on Mon Jun 7 16:44:23 2010 for fpocket by&nbsp;
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<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.5.6 </small></address>
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