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<title>fpocket: fparams.c File Reference</title>
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<h1>fparams.c File Reference</h1><code>#include "<a class="el" href="fparams_8h-source.html">../headers/fparams.h</a>"</code><br>
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<p>
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<a href="fparams_8c-source.html">Go to the source code of this file.</a><table border="0" cellpadding="0" cellspacing="0">
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<tr><td></td></tr>
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<tr><td colspan="2"><br><h2>Functions</h2></td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="structs__fparams.html">s_fparams</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#7f23db4971a109deb1ab5e841ace1607">init_def_fparams</a> (void)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top"><a class="el" href="structs__fparams.html">s_fparams</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#c1806d3567baea11616fc5fdfca417d7">get_fpocket_args</a> (int nargs, char **args)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#8471dca4fb8f09806aed3be18a79c6b2">parse_clust_max_dist</a> (char *str, <a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#da442addde23a799e50cecae103974bf">parse_sclust_max_dist</a> (char *str, <a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#39b0715eb1fb67b993d494570f866135">parse_sclust_min_nneigh</a> (char *str, <a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#40cf684e6c79bc0d5494cf63ee40b8d3">parse_min_apol_neigh</a> (char *str, <a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#0356665c59c8eda7fb483f47dbbe8d3b">parse_asph_min_size</a> (char *str, <a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#8ba1cfff825efc1d30099d85f1f85b01">parse_asph_max_size</a> (char *str, <a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#ffc4eabc99149ff419340f11297312c6">parse_mc_niter</a> (char *str, <a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#bb8b6f641fc59aea7b6915fd3c197fba">parse_basic_vol_div</a> (char *str, <a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#cca6c1f10d064997753458d61e052f7d">parse_refine_dist</a> (char *str, <a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#a08e358edc9c6941f595da45c4741fe0">parse_refine_minaap</a> (char *str, <a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#c09155f5ca513066b30c9d1485d810a8">parse_min_pock_nb_asph</a> (char *str, <a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#bdc82d2e467d8dd8765d605d1ae26dc6">is_fpocket_opt</a> (const char opt)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#112335ac520ae98bdcf93e0c75c3c5db">free_fparams</a> (<a class="el" href="structs__fparams.html">s_fparams</a> *p)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#ab8c5397c1eaa6388ae24aa9ae605481">print_pocket_usage</a> (FILE *f)</td></tr>
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<tr><td class="memItemLeft" nowrap align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="fparams_8c.html#00d0d0ea58e0b3fd1f6a785427e6b5f1">print_fparams</a> (<a class="el" href="structs__fparams.html">s_fparams</a> *p, FILE *f)</td></tr>
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</table>
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<hr><h2>Function Documentation</h2>
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<a class="anchor" name="112335ac520ae98bdcf93e0c75c3c5db"></a><!-- doxytag: member="fparams.c::free_fparams" ref="112335ac520ae98bdcf93e0c75c3c5db" args="(s_fparams *p)" -->
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<div class="memitem">
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<div class="memproto">
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<table class="memname">
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<tr>
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<td class="memname">void free_fparams </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
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<td class="paramname"> <em>p</em> </td>
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<td> ) </td>
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<td></td>
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<div class="memdoc">
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<p>
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## FUNCTION: free_fparams<p>
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## SPECIFICATION: Free parameters<p>
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## PARAMETRES: @ s_params *p: Pointer to the structure to free<p>
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## RETURN: void
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<p>Definition at line <a class="el" href="fparams_8c-source.html#l00562">562</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
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<p>References <a class="el" href="memhandler_8c-source.html#l00255">my_free()</a>, <a class="el" href="fparams_8h-source.html#l00138">s_fparams::npdb</a>, and <a class="el" href="fparams_8h-source.html#l00137">s_fparams::pdb_lst</a>.</p>
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<p>Referenced by <a class="el" href="check_8c-source.html#l00105">check_fpocket()</a>, <a class="el" href="dparams_8c-source.html#l00440">free_dparams()</a>, <a class="el" href="mdparams_8c-source.html#l00397">free_mdparams()</a>, <a class="el" href="tparams_8c-source.html#l00397">free_tparams()</a>, <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>, and <a class="el" href="fpmain_8c-source.html#l00071">main()</a>.</p>
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<div class="fragment"><pre class="fragment"><a name="l00563"></a>00563 {
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<a name="l00564"></a>00564 <span class="keywordtype">int</span> i ;
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<a name="l00565"></a>00565 <span class="keywordflow">if</span>(p) {
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<a name="l00566"></a>00566 <span class="keywordflow">if</span>(p-><a class="code" href="structs__fparams.html#5427055e24cc2dea5c41a9fd6bba8cac">npdb</a> > 0 && p-><a class="code" href="structs__fparams.html#b620ac1ea6b8ad4c4ed0b95a8664a560">pdb_lst</a> != NULL) {
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<a name="l00567"></a>00567 <span class="keywordflow">for</span> (i = 0 ; i < p-><a class="code" href="structs__fparams.html#5427055e24cc2dea5c41a9fd6bba8cac">npdb</a> ; i++) {
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<a name="l00568"></a>00568 <span class="keywordflow">if</span>(p-><a class="code" href="structs__fparams.html#b620ac1ea6b8ad4c4ed0b95a8664a560">pdb_lst</a>[i] != NULL) <a class="code" href="memhandler_8c.html#a49400242a007d208c641f79856ea4c6">my_free</a>(p-><a class="code" href="structs__fparams.html#b620ac1ea6b8ad4c4ed0b95a8664a560">pdb_lst</a>[i]) ;
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<a name="l00569"></a>00569 }
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<a name="l00570"></a>00570 <a class="code" href="memhandler_8c.html#a49400242a007d208c641f79856ea4c6">my_free</a>(p-><a class="code" href="structs__fparams.html#b620ac1ea6b8ad4c4ed0b95a8664a560">pdb_lst</a>) ;
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<a name="l00571"></a>00571 }
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<a name="l00572"></a>00572 <a class="code" href="memhandler_8c.html#a49400242a007d208c641f79856ea4c6">my_free</a>(p) ;
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<a name="l00573"></a>00573 }
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<a name="l00574"></a>00574 }
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</pre></div>
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<p>
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</div>
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</div><p>
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<a class="anchor" name="c1806d3567baea11616fc5fdfca417d7"></a><!-- doxytag: member="fparams.c::get_fpocket_args" ref="c1806d3567baea11616fc5fdfca417d7" args="(int nargs, char **args)" -->
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<tr>
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<td class="memname"><a class="el" href="structs__fparams.html">s_fparams</a>* get_fpocket_args </td>
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<td>(</td>
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<td class="paramtype">int </td>
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<td class="paramname"> <em>nargs</em>, </td>
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</tr>
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<tr>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype">char ** </td>
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<td class="paramname"> <em>args</em></td><td> </td>
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</tr>
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<tr>
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<td></td>
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<td>)</td>
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<td></td><td></td><td></td>
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</table>
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</div>
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<div class="memdoc">
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<p>
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## FUNCTION: get_fpocket_args<p>
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## SPECIFICATION: This function analyse the user's command line and parse it to store parameters for the pocket finder programm.<p>
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## PARAMETRES: @ int nargs : Number of arguments @ char **args : Arguments of main program<p>
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## RETURN: s_params*: Pointer to parameters
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<p>Definition at line <a class="el" href="fparams_8c-source.html#l00088">88</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
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<p>References <a class="el" href="fparams_8h-source.html#l00141">s_fparams::db_run</a>, <a class="el" href="fparams_8c-source.html#l00562">free_fparams()</a>, <a class="el" href="fparams_8c-source.html#l00048">init_def_fparams()</a>, <a class="el" href="utils_8h-source.html#l00057">M_MAX_PDB_NAME_LEN</a>, <a class="el" href="fparams_8h-source.html#l00089">M_PAR_BASIC_VOL_DIVISION</a>, <a class="el" href="fparams_8h-source.html#l00085">M_PAR_CLUST_MAX_DIST</a>, <a class="el" href="fparams_8h-source.html#l00093">M_PAR_DB_RUN</a>, <a class="el" href="fparams_8h-source.html#l00082">M_PAR_MAX_ASHAPE_SIZE</a>, <a class="el" href="fparams_8h-source.html#l00088">M_PAR_MC_ITER</a>, <a class="el" href="fparams_8h-source.html#l00084">M_PAR_MIN_APOL_NEIGH</a>, <a class="el" href="fparams_8h-source.html#l00083">M_PAR_MIN_ASHAPE_SIZE</a>, <a class="el" href="fparams_8h-source.html#l00090">M_PAR_MIN_POCK_NB_ASPH</a>, <a class="el" href="fparams_8h-source.html#l00080">M_PAR_PDB_FILE</a>, <a class="el" href="fparams_8h-source.html#l00081">M_PAR_PDB_LIST</a>, <a class="el" href="fparams_8h-source.html#l00091">M_PAR_REFINE_DIST</a>, <a class="el" href="fparams_8h-source.html#l00092">M_PAR_REFINE_MIN_NAPOL_AS</a>, <a class="el" href="fparams_8h-source.html#l00086">M_PAR_SL_MAX_DIST</a>, <a class="el" href="fparams_8h-source.html#l00087">M_PAR_SL_MIN_NUM_NEIGH</a>, <a class="el" href="memhandler_8c-source.html#l00121">my_malloc()</a>, <a class="el" href="fparams_8h-source.html#l00138">s_fparams::npdb</a>, <a class="el" href="fparams_8c-source.html#l00358">parse_asph_max_size()</a>, <a class="el" href="fparams_8c-source.html#l00330">parse_asph_min_size()</a>, <a class="el" href="fparams_8c-source.html#l00415">parse_basic_vol_div()</a>, <a class="el" href="fparams_8c-source.html#l00214">parse_clust_max_dist()</a>, <a class="el" href="fparams_8c-source.html#l00387">parse_mc_niter()</a>, <a class="el" href="fparams_8c-source.html#l00300">parse_min_apol_neigh()</a>, <a class="el" href="fparams_8c-source.html#l00499">parse_min_pock_nb_asph()</a>, <a class="el" href="fparams_8c-source.html#l00443">parse_refine_dist()</a>, <a class="el" href="fparams_8c-source.html#l00471">parse_refine_minaap()</a>, <a class="el" href="fparams_8c-source.html#l00243">parse_sclust_max_dist()</a>, <a class="el" href="fparams_8c-source.html#l00271">parse_sclust_min_nneigh()</a>, <a class="el" href="fparams_8h-source.html#l00137">s_fparams::pdb_lst</a>, <a class="el" href="fparams_8h-source.html#l00136">s_fparams::pdb_path</a>, and <a class="el" href="fparams_8c-source.html#l00590">print_pocket_usage()</a>.</p>
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<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="dparams_8c-source.html#l00113">get_dpocket_args()</a>, <a class="el" href="mdparams_8c-source.html#l00123">get_mdpocket_args()</a>, <a class="el" href="tparams_8c-source.html#l00108">get_tpocket_args()</a>, and <a class="el" href="fpmain_8c-source.html#l00071">main()</a>.</p>
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<div class="fragment"><pre class="fragment"><a name="l00089"></a>00089 {
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<a name="l00090"></a>00090 <span class="keywordtype">int</span> i,
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<a name="l00091"></a>00091 npdb = 0,
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<a name="l00092"></a>00092 status = 0 ;
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<a name="l00093"></a>00093
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<a name="l00094"></a>00094 <a class="code" href="structs__fparams.html">s_fparams</a> *par = <a class="code" href="fparams_8c.html#7f23db4971a109deb1ab5e841ace1607">init_def_fparams</a>() ;
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<a name="l00095"></a>00095 <span class="keywordtype">char</span> *pdb_lst = NULL ;
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<a name="l00096"></a>00096
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<a name="l00097"></a>00097 <span class="comment">//read arguments by flags</span>
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<a name="l00098"></a>00098 <span class="keywordflow">for</span> (i = 1; i < nargs; i++) {
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<a name="l00099"></a>00099 <span class="keywordflow">if</span> (strlen(args[i]) == 2 && args[i][0] == <span class="charliteral">'-'</span> && i <= (nargs-1)) {
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<a name="l00100"></a>00100
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<a name="l00101"></a>00101 <span class="keywordflow">switch</span> (args[i][1]) {
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<a name="l00102"></a>00102 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#9fe722d12f7ed6c181c1022aace70e21">M_PAR_MAX_ASHAPE_SIZE</a> :
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<a name="l00103"></a>00103 status += <a class="code" href="fparams_8c.html#8ba1cfff825efc1d30099d85f1f85b01">parse_asph_max_size</a>(args[++i], par) ; break ;
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<a name="l00104"></a>00104 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#c2dcc50d93bac7e0fe16850062556626">M_PAR_MIN_ASHAPE_SIZE</a> :
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<a name="l00105"></a>00105 status += <a class="code" href="fparams_8c.html#0356665c59c8eda7fb483f47dbbe8d3b">parse_asph_min_size</a>(args[++i], par) ; break ;
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<a name="l00106"></a>00106 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#6868a969cd3e83643a099bb3a93498fb">M_PAR_MIN_APOL_NEIGH</a> :
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<a name="l00107"></a>00107 status += <a class="code" href="fparams_8c.html#40cf684e6c79bc0d5494cf63ee40b8d3">parse_min_apol_neigh</a>(args[++i], par) ; break ;
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<a name="l00108"></a>00108 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#ace76e1ea0d5b9bd44c7833fc257f9d5">M_PAR_CLUST_MAX_DIST</a> :
|
|
<a name="l00109"></a>00109 status += <a class="code" href="fparams_8c.html#8471dca4fb8f09806aed3be18a79c6b2">parse_clust_max_dist</a>(args[++i], par) ; break ;
|
|
<a name="l00110"></a>00110 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#e5eccb0710c00b2c304cc688b8041f54">M_PAR_SL_MAX_DIST</a> :
|
|
<a name="l00111"></a>00111 status += <a class="code" href="fparams_8c.html#da442addde23a799e50cecae103974bf">parse_sclust_max_dist</a>(args[++i], par) ; break ;
|
|
<a name="l00112"></a>00112 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#bc2dc478b856e70af235992072620d91">M_PAR_SL_MIN_NUM_NEIGH</a> :
|
|
<a name="l00113"></a>00113 status += <a class="code" href="fparams_8c.html#39b0715eb1fb67b993d494570f866135">parse_sclust_min_nneigh</a>(args[++i], par) ; break ;
|
|
<a name="l00114"></a>00114 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#bdef86070652cf4d0fa5493ccf73d4fa">M_PAR_MC_ITER</a> :
|
|
<a name="l00115"></a>00115 status += <a class="code" href="fparams_8c.html#ffc4eabc99149ff419340f11297312c6">parse_mc_niter</a>(args[++i], par) ; break ;
|
|
<a name="l00116"></a>00116 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#74ad0900c04fd7855cb4914deabe0ba3">M_PAR_BASIC_VOL_DIVISION</a> :
|
|
<a name="l00117"></a>00117 status += <a class="code" href="fparams_8c.html#bb8b6f641fc59aea7b6915fd3c197fba">parse_basic_vol_div</a>(args[++i], par) ; break ;
|
|
<a name="l00118"></a>00118 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#2558ed6c1ac5aefc7366c607caefde34">M_PAR_MIN_POCK_NB_ASPH</a> :
|
|
<a name="l00119"></a>00119 status += <a class="code" href="fparams_8c.html#c09155f5ca513066b30c9d1485d810a8">parse_min_pock_nb_asph</a>(args[++i], par) ; break ;
|
|
<a name="l00120"></a>00120 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#9bbf5319350592125ab3504cea9c10e4">M_PAR_REFINE_DIST</a> :
|
|
<a name="l00121"></a>00121 status += <a class="code" href="fparams_8c.html#cca6c1f10d064997753458d61e052f7d">parse_refine_dist</a>(args[++i], par) ; break ;
|
|
<a name="l00122"></a>00122 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#a53522d41aaa000c99a53f29ea5c60cf">M_PAR_REFINE_MIN_NAPOL_AS</a>:
|
|
<a name="l00123"></a>00123 status += <a class="code" href="fparams_8c.html#a08e358edc9c6941f595da45c4741fe0">parse_refine_minaap</a>(args[++i], par) ;
|
|
<a name="l00124"></a>00124 break ;
|
|
<a name="l00125"></a>00125 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#598416cef61191786dcc416d92da84dd">M_PAR_DB_RUN</a> :
|
|
<a name="l00126"></a>00126 par-><a class="code" href="structs__fparams.html#b8d794447932a12435a628f3462df7ad">db_run</a>=1;
|
|
<a name="l00127"></a>00127 <span class="keywordflow">break</span>;
|
|
<a name="l00128"></a>00128
|
|
<a name="l00129"></a>00129 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#c9f20b54cb35b4bcc3b7a1b49b6e5ebe">M_PAR_PDB_LIST</a> :
|
|
<a name="l00130"></a>00130 pdb_lst = args[++i] ;
|
|
<a name="l00131"></a>00131 break ;
|
|
<a name="l00132"></a>00132
|
|
<a name="l00133"></a>00133 <span class="keywordflow">case</span> <a class="code" href="fparams_8h.html#7773b427778268b6569aae255f04c68c">M_PAR_PDB_FILE</a> :
|
|
<a name="l00134"></a>00134 <span class="keywordflow">if</span>(npdb >= 1) fprintf(stderr,
|
|
<a name="l00135"></a>00135 <span class="stringliteral">"! Only first input pdb will be used.\n"</span>) ;
|
|
<a name="l00136"></a>00136 <span class="keywordflow">else</span> {
|
|
<a name="l00137"></a>00137 strcpy(par-><a class="code" href="structs__fparams.html#4e1b3892d1e42947408cdcaed497bf97">pdb_path</a>, args[++i]) ; npdb++ ;
|
|
<a name="l00138"></a>00138 }
|
|
<a name="l00139"></a>00139 break ;
|
|
<a name="l00140"></a>00140 <span class="keywordflow">default</span>: break ;
|
|
<a name="l00141"></a>00141 }
|
|
<a name="l00142"></a>00142 }
|
|
<a name="l00143"></a>00143 }
|
|
<a name="l00144"></a>00144
|
|
<a name="l00145"></a>00145 <span class="keywordflow">if</span>(status > 0) {
|
|
<a name="l00146"></a>00146 <a class="code" href="fparams_8c.html#112335ac520ae98bdcf93e0c75c3c5db">free_fparams</a>(par) ;
|
|
<a name="l00147"></a>00147 <a class="code" href="fparams_8c.html#ab8c5397c1eaa6388ae24aa9ae605481">print_pocket_usage</a>(stdout);
|
|
<a name="l00148"></a>00148 <span class="keywordflow">return</span> NULL ;
|
|
<a name="l00149"></a>00149 }
|
|
<a name="l00150"></a>00150
|
|
<a name="l00151"></a>00151 par-><a class="code" href="structs__fparams.html#5427055e24cc2dea5c41a9fd6bba8cac">npdb</a> = npdb ;
|
|
<a name="l00152"></a>00152
|
|
<a name="l00153"></a>00153 <span class="comment">/* Handle a file containing a list of PDB */</span>
|
|
<a name="l00154"></a>00154 <span class="keywordflow">if</span>(pdb_lst != NULL) {
|
|
<a name="l00155"></a>00155 FILE *f = fopen(pdb_lst, <span class="stringliteral">"r"</span>) ;
|
|
<a name="l00156"></a>00156 <span class="keywordflow">if</span>(f != NULL) {
|
|
<a name="l00157"></a>00157 <span class="comment">/* Count the number of lines */</span>
|
|
<a name="l00158"></a>00158 <span class="keywordtype">int</span> n = 0 ;
|
|
<a name="l00159"></a>00159 <span class="keywordtype">char</span> cline [<a class="code" href="utils_8h.html#ea69486910da420cbfe816d80ecc8b0c">M_MAX_PDB_NAME_LEN</a> + 1] ;
|
|
<a name="l00160"></a>00160
|
|
<a name="l00161"></a>00161 <span class="keywordflow">while</span>(fgets(cline, <a class="code" href="utils_8h.html#ea69486910da420cbfe816d80ecc8b0c">M_MAX_PDB_NAME_LEN</a>, f) != NULL) {
|
|
<a name="l00162"></a>00162 <span class="keywordflow">if</span>(strcmp(<span class="stringliteral">"\n"</span>, cline) != 0) {
|
|
<a name="l00163"></a>00163 n ++ ;
|
|
<a name="l00164"></a>00164 }
|
|
<a name="l00165"></a>00165 }
|
|
<a name="l00166"></a>00166 fclose(f) ;
|
|
<a name="l00167"></a>00167 <span class="keywordflow">if</span>(n == 0) {
|
|
<a name="l00168"></a>00168 <span class="keywordflow">return</span> par ;
|
|
<a name="l00169"></a>00169 }
|
|
<a name="l00170"></a>00170
|
|
<a name="l00171"></a>00171 <span class="comment">/* Allocate memory and store each line */</span>
|
|
<a name="l00172"></a>00172 par-><a class="code" href="structs__fparams.html#b620ac1ea6b8ad4c4ed0b95a8664a560">pdb_lst</a> = (<span class="keywordtype">char</span> **)<a class="code" href="memhandler_8c.html#52d7260a38c396cb2dd1dd7abcfd61cb">my_malloc</a>(n*<span class="keyword">sizeof</span>(<span class="keywordtype">char</span>*)) ;
|
|
<a name="l00173"></a>00173
|
|
<a name="l00174"></a>00174 f = fopen (pdb_lst, <span class="stringliteral">"r"</span>) ;
|
|
<a name="l00175"></a>00175 <span class="keywordtype">int</span> i = 0, l = 0 ;
|
|
<a name="l00176"></a>00176 <span class="keywordtype">char</span> *line;
|
|
<a name="l00177"></a>00177 <span class="keywordflow">while</span>(fgets(cline, <a class="code" href="utils_8h.html#ea69486910da420cbfe816d80ecc8b0c">M_MAX_PDB_NAME_LEN</a>, f) != NULL) {
|
|
<a name="l00178"></a>00178 <span class="keywordflow">if</span>(strcmp(<span class="stringliteral">"\n"</span>, cline) != 0) {
|
|
<a name="l00179"></a>00179 l = strlen(cline) ;
|
|
<a name="l00180"></a>00180 <span class="keywordflow">if</span>(cline[l-1] == <span class="charliteral">'\n'</span>) {
|
|
<a name="l00181"></a>00181 l-- ;
|
|
<a name="l00182"></a>00182 cline[l] = <span class="charliteral">'\0'</span> ;
|
|
<a name="l00183"></a>00183 }
|
|
<a name="l00184"></a>00184 line = (<span class="keywordtype">char</span> *) <a class="code" href="memhandler_8c.html#52d7260a38c396cb2dd1dd7abcfd61cb">my_malloc</a>((l+1)*<span class="keyword">sizeof</span>(char)) ;
|
|
<a name="l00185"></a>00185 memcpy (line, cline, l+1);
|
|
<a name="l00186"></a>00186
|
|
<a name="l00187"></a>00187 par-><a class="code" href="structs__fparams.html#b620ac1ea6b8ad4c4ed0b95a8664a560">pdb_lst</a>[i] = line ;
|
|
<a name="l00188"></a>00188 i ++ ;
|
|
<a name="l00189"></a>00189 }
|
|
<a name="l00190"></a>00190 }
|
|
<a name="l00191"></a>00191
|
|
<a name="l00192"></a>00192 par-><a class="code" href="structs__fparams.html#5427055e24cc2dea5c41a9fd6bba8cac">npdb</a> = n ;
|
|
<a name="l00193"></a>00193 }
|
|
<a name="l00194"></a>00194 }
|
|
<a name="l00195"></a>00195
|
|
<a name="l00196"></a>00196 <span class="keywordflow">return</span> par;
|
|
<a name="l00197"></a>00197 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="7f23db4971a109deb1ab5e841ace1607"></a><!-- doxytag: member="fparams.c::init_def_fparams" ref="7f23db4971a109deb1ab5e841ace1607" args="(void)" -->
|
|
<div class="memitem">
|
|
<div class="memproto">
|
|
<table class="memname">
|
|
<tr>
|
|
<td class="memname"><a class="el" href="structs__fparams.html">s_fparams</a>* init_def_fparams </td>
|
|
<td>(</td>
|
|
<td class="paramtype">void </td>
|
|
<td class="paramname"> </td>
|
|
<td> ) </td>
|
|
<td></td>
|
|
</tr>
|
|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: init_def_fparams<p>
|
|
## SPECIFICATION: Initialisation of default parameters<p>
|
|
## PARAMETRES: void<p>
|
|
## RETURN: s_fparams*: Pointer to allocated paramers.
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00048">48</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="fparams_8h-source.html#l00150">s_fparams::asph_max_size</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::asph_min_size</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::basic_volume_div</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::clust_max_dist</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::db_run</a>, <a class="el" href="fparams_8h-source.html#l00139">s_fparams::flag_do_asa_and_volume_calculations</a>, <a class="el" href="fparams_8h-source.html#l00076">M__MIN_APOL_NEIGH_DEFAULT</a>, <a class="el" href="fparams_8h-source.html#l00072">M_BASIC_VOL_DIVISION</a>, <a class="el" href="fparams_8h-source.html#l00060">M_CLUST_MAX_DIST</a>, <a class="el" href="fparams_8h-source.html#l00078">M_DB_RUN</a>, <a class="el" href="fparams_8h-source.html#l00058">M_MAX_ASHAPE_SIZE_DEFAULT</a>, <a class="el" href="fparams_8h-source.html#l00070">M_MC_ITER</a>, <a class="el" href="fparams_8h-source.html#l00056">M_MIN_ASHAPE_SIZE_DEFAULT</a>, <a class="el" href="fparams_8h-source.html#l00074">M_MIN_POCK_NB_ASPH</a>, <a class="el" href="fparams_8h-source.html#l00062">M_REFINE_DIST</a>, <a class="el" href="fparams_8h-source.html#l00064">M_REFINE_MIN_PROP_APOL_AS</a>, <a class="el" href="fparams_8h-source.html#l00066">M_SLCLUST_MAX_DIST</a>, <a class="el" href="fparams_8h-source.html#l00068">M_SLCLUST_MIN_NUM_NEIGH</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::min_apol_neigh</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::min_pock_nb_asph</a>, <a class="el" href="memhandler_8c-source.html#l00121">my_malloc()</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::nb_mcv_iter</a>, <a class="el" href="fparams_8h-source.html#l00138">s_fparams::npdb</a>, <a class="el" href="fparams_8h-source.html#l00137">s_fparams::pdb_lst</a>, <a class="el" href="fparams_8h-source.html#l00136">s_fparams::pdb_path</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::refine_clust_dist</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::refine_min_apolar_asphere_prop</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::sl_clust_max_dist</a>, and <a class="el" href="fparams_8h-source.html#l00141">s_fparams::sl_clust_min_nneigh</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00049"></a>00049 {
|
|
<a name="l00050"></a>00050 <a class="code" href="structs__fparams.html">s_fparams</a> *par = (<a class="code" href="structs__fparams.html">s_fparams</a> *) <a class="code" href="memhandler_8c.html#52d7260a38c396cb2dd1dd7abcfd61cb">my_malloc</a>(<span class="keyword">sizeof</span>(<a class="code" href="structs__fparams.html">s_fparams</a>)) ;
|
|
<a name="l00051"></a>00051
|
|
<a name="l00052"></a>00052 par-><a class="code" href="structs__fparams.html#b0875eddf8815f766657713b3f4ba0b0">min_apol_neigh</a> = <a class="code" href="fparams_8h.html#243ad6dc96e3f975fb8a224426810bb6">M__MIN_APOL_NEIGH_DEFAULT</a> ;
|
|
<a name="l00053"></a>00053 par-><a class="code" href="structs__fparams.html#545b7bea97958089689608fff6b8910d">asph_min_size</a> = <a class="code" href="fparams_8h.html#f83d8c1f0a4a16b144b63e88d6b211bf">M_MIN_ASHAPE_SIZE_DEFAULT</a> ;
|
|
<a name="l00054"></a>00054 par-><a class="code" href="structs__fparams.html#7439af209766e39dad7e39f4c6e19711">asph_max_size</a> = <a class="code" href="fparams_8h.html#50c6e2d2eb22a7c7b529c67fc04b56c9">M_MAX_ASHAPE_SIZE_DEFAULT</a> ;
|
|
<a name="l00055"></a>00055 par-><a class="code" href="structs__fparams.html#71691bbfb98d90e12ca8cb3c79e2688c">sl_clust_max_dist</a> = <a class="code" href="fparams_8h.html#e5f7357fe7ddb5b03bc18b45159f64c4">M_SLCLUST_MAX_DIST</a> ;
|
|
<a name="l00056"></a>00056 par-><a class="code" href="structs__fparams.html#b23279857aaf7861b452cd2bf463f624">sl_clust_min_nneigh</a> = <a class="code" href="fparams_8h.html#721fc2c4a9b89fa4a0c0de0f31967d9a">M_SLCLUST_MIN_NUM_NEIGH</a> ;
|
|
<a name="l00057"></a>00057 par-><a class="code" href="structs__fparams.html#4e1b3892d1e42947408cdcaed497bf97">pdb_path</a>[0] = 0 ;
|
|
<a name="l00058"></a>00058 par-><a class="code" href="structs__fparams.html#289a1193bf0ffa2f737cd9dc914b63e0">basic_volume_div</a> = <a class="code" href="fparams_8h.html#4caa4e2b63f97eae1c52a1e7cf51dc5b">M_BASIC_VOL_DIVISION</a> ;
|
|
<a name="l00059"></a>00059 par-><a class="code" href="structs__fparams.html#8caeadbae2db7d24763497290e6b9220">nb_mcv_iter</a> = <a class="code" href="fparams_8h.html#17764121ba6792298aba0da59482cc60">M_MC_ITER</a> ;
|
|
<a name="l00060"></a>00060 par-><a class="code" href="structs__fparams.html#2ccafe788e970f4e00bdae591d834865">min_pock_nb_asph</a> = <a class="code" href="fparams_8h.html#d6f4bc5db7427ee0e333f483e1632022">M_MIN_POCK_NB_ASPH</a> ;
|
|
<a name="l00061"></a>00061 par-><a class="code" href="structs__fparams.html#8ba147c559344c3f0406c1e7a86b98d1">refine_clust_dist</a> = <a class="code" href="fparams_8h.html#37a7ca05610fcb4aff8759267e83e4af">M_REFINE_DIST</a> ;
|
|
<a name="l00062"></a>00062 par-><a class="code" href="structs__fparams.html#50d6211ea1f5d9b90c10f866c82e54b8">refine_min_apolar_asphere_prop</a> = <a class="code" href="fparams_8h.html#cadff4aad15c6ece2eb248488b4221eb">M_REFINE_MIN_PROP_APOL_AS</a> ;
|
|
<a name="l00063"></a>00063 par-><a class="code" href="structs__fparams.html#cd506e600d2b5077f7925847be38c854">clust_max_dist</a> = <a class="code" href="fparams_8h.html#0f6138f1929550d8ff600529496b83b4">M_CLUST_MAX_DIST</a> ;
|
|
<a name="l00064"></a>00064 par-><a class="code" href="structs__fparams.html#5427055e24cc2dea5c41a9fd6bba8cac">npdb</a> = 0 ;
|
|
<a name="l00065"></a>00065 par-><a class="code" href="structs__fparams.html#b620ac1ea6b8ad4c4ed0b95a8664a560">pdb_lst</a> = NULL ;
|
|
<a name="l00066"></a>00066 par-><a class="code" href="structs__fparams.html#771a10e1c94346d353eb6cb87b4abb18">flag_do_asa_and_volume_calculations</a>=1;
|
|
<a name="l00067"></a>00067 par-><a class="code" href="structs__fparams.html#b8d794447932a12435a628f3462df7ad">db_run</a>=<a class="code" href="fparams_8h.html#43a40d4fa640254998f4e0cf2a3fd7a6">M_DB_RUN</a>;
|
|
<a name="l00068"></a>00068
|
|
<a name="l00069"></a>00069 <span class="keywordflow">return</span> par ;
|
|
<a name="l00070"></a>00070 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="bdc82d2e467d8dd8765d605d1ae26dc6"></a><!-- doxytag: member="fparams.c::is_fpocket_opt" ref="bdc82d2e467d8dd8765d605d1ae26dc6" args="(const char opt)" -->
|
|
<div class="memitem">
|
|
<div class="memproto">
|
|
<table class="memname">
|
|
<tr>
|
|
<td class="memname">int is_fpocket_opt </td>
|
|
<td>(</td>
|
|
<td class="paramtype">const char </td>
|
|
<td class="paramname"> <em>opt</em> </td>
|
|
<td> ) </td>
|
|
<td></td>
|
|
</tr>
|
|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: is_fpocket_opt<p>
|
|
## SPECIFICATION: Say either or not a single letter code is a fpocket option (excluding input file/list option.)<p>
|
|
## PARAMETRES: @ const char opt: The one letter code option.<p>
|
|
## RETURN: integer: 1 if it's a valid option parmeter, 0 if not.
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00529">529</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="fparams_8h-source.html#l00089">M_PAR_BASIC_VOL_DIVISION</a>, <a class="el" href="fparams_8h-source.html#l00085">M_PAR_CLUST_MAX_DIST</a>, <a class="el" href="fparams_8h-source.html#l00082">M_PAR_MAX_ASHAPE_SIZE</a>, <a class="el" href="fparams_8h-source.html#l00088">M_PAR_MC_ITER</a>, <a class="el" href="fparams_8h-source.html#l00084">M_PAR_MIN_APOL_NEIGH</a>, <a class="el" href="fparams_8h-source.html#l00083">M_PAR_MIN_ASHAPE_SIZE</a>, <a class="el" href="fparams_8h-source.html#l00090">M_PAR_MIN_POCK_NB_ASPH</a>, <a class="el" href="fparams_8h-source.html#l00091">M_PAR_REFINE_DIST</a>, <a class="el" href="fparams_8h-source.html#l00092">M_PAR_REFINE_MIN_NAPOL_AS</a>, <a class="el" href="fparams_8h-source.html#l00086">M_PAR_SL_MAX_DIST</a>, and <a class="el" href="fparams_8h-source.html#l00087">M_PAR_SL_MIN_NUM_NEIGH</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="dparams_8c-source.html#l00113">get_dpocket_args()</a>, <a class="el" href="mdparams_8c-source.html#l00123">get_mdpocket_args()</a>, and <a class="el" href="tparams_8c-source.html#l00108">get_tpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00530"></a>00530 {
|
|
<a name="l00531"></a>00531 <span class="keywordflow">if</span>( opt == <a class="code" href="fparams_8h.html#9fe722d12f7ed6c181c1022aace70e21">M_PAR_MAX_ASHAPE_SIZE</a> ||
|
|
<a name="l00532"></a>00532 opt == <a class="code" href="fparams_8h.html#c2dcc50d93bac7e0fe16850062556626">M_PAR_MIN_ASHAPE_SIZE</a> ||
|
|
<a name="l00533"></a>00533 opt == <a class="code" href="fparams_8h.html#6868a969cd3e83643a099bb3a93498fb">M_PAR_MIN_APOL_NEIGH</a> ||
|
|
<a name="l00534"></a>00534 opt == <a class="code" href="fparams_8h.html#ace76e1ea0d5b9bd44c7833fc257f9d5">M_PAR_CLUST_MAX_DIST</a> ||
|
|
<a name="l00535"></a>00535 opt == <a class="code" href="fparams_8h.html#e5eccb0710c00b2c304cc688b8041f54">M_PAR_SL_MAX_DIST</a> ||
|
|
<a name="l00536"></a>00536 opt == <a class="code" href="fparams_8h.html#bc2dc478b856e70af235992072620d91">M_PAR_SL_MIN_NUM_NEIGH</a> ||
|
|
<a name="l00537"></a>00537 opt == <a class="code" href="fparams_8h.html#bdef86070652cf4d0fa5493ccf73d4fa">M_PAR_MC_ITER</a> ||
|
|
<a name="l00538"></a>00538 opt == <a class="code" href="fparams_8h.html#74ad0900c04fd7855cb4914deabe0ba3">M_PAR_BASIC_VOL_DIVISION</a> ||
|
|
<a name="l00539"></a>00539 opt == <a class="code" href="fparams_8h.html#2558ed6c1ac5aefc7366c607caefde34">M_PAR_MIN_POCK_NB_ASPH</a> ||
|
|
<a name="l00540"></a>00540 opt == <a class="code" href="fparams_8h.html#9bbf5319350592125ab3504cea9c10e4">M_PAR_REFINE_DIST</a> ||
|
|
<a name="l00541"></a>00541 opt == <a class="code" href="fparams_8h.html#a53522d41aaa000c99a53f29ea5c60cf">M_PAR_REFINE_MIN_NAPOL_AS</a>) {
|
|
<a name="l00542"></a>00542 <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00543"></a>00543 }
|
|
<a name="l00544"></a>00544
|
|
<a name="l00545"></a>00545 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00546"></a>00546 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="8ba1cfff825efc1d30099d85f1f85b01"></a><!-- doxytag: member="fparams.c::parse_asph_max_size" ref="8ba1cfff825efc1d30099d85f1f85b01" args="(char *str, s_fparams *p)" -->
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<div class="memitem">
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<tr>
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|
<td class="memname">int parse_asph_max_size </td>
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|
<td>(</td>
|
|
<td class="paramtype">char * </td>
|
|
<td class="paramname"> <em>str</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
|
|
<td class="paramname"> <em>p</em></td><td> </td>
|
|
</tr>
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<tr>
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|
<td></td>
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<td>)</td>
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<td></td><td></td><td></td>
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</tr>
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</table>
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</div>
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<div class="memdoc">
|
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|
<p>
|
|
## FUNCTION: parse_asph_max_size<p>
|
|
## SPECIFICATION: Parsing function for the maximum radius of each alpha shpere<p>
|
|
## PARAMETERS: @ char *str : The string to parse @ <a class="el" href="structs__fparams.html">s_fparams</a> *p : The structure than will contain the parsed parameter<p>
|
|
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00358">358</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="fparams_8h-source.html#l00150">s_fparams::asph_max_size</a>, <a class="el" href="utils_8h-source.html#l00060">M_NO_SIGN</a>, and <a class="el" href="utils_8c-source.html#l00412">str_is_float()</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00359"></a>00359 {
|
|
<a name="l00360"></a>00360 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#b2155f59a3e9691956e8501985f5f362">str_is_float</a>(str, <a class="code" href="utils_8h.html#1d2d01db9e7d6bb5200d8cfd398217d6">M_NO_SIGN</a>)) {
|
|
<a name="l00361"></a>00361 p-><a class="code" href="structs__fparams.html#7439af209766e39dad7e39f4c6e19711">asph_max_size</a> = (float) atof(str) ;
|
|
<a name="l00362"></a>00362 }
|
|
<a name="l00363"></a>00363 <span class="keywordflow">else</span> {
|
|
<a name="l00364"></a>00364 fprintf(stdout, <span class="stringliteral">"! Invalid value (%s) given for the max radius of alpha shperes.\n"</span>, str) ;
|
|
<a name="l00365"></a>00365 <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00366"></a>00366 }
|
|
<a name="l00367"></a>00367
|
|
<a name="l00368"></a>00368 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00369"></a>00369 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="0356665c59c8eda7fb483f47dbbe8d3b"></a><!-- doxytag: member="fparams.c::parse_asph_min_size" ref="0356665c59c8eda7fb483f47dbbe8d3b" args="(char *str, s_fparams *p)" -->
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<td class="memname">int parse_asph_min_size </td>
|
|
<td>(</td>
|
|
<td class="paramtype">char * </td>
|
|
<td class="paramname"> <em>str</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
|
|
<td class="paramname"> <em>p</em></td><td> </td>
|
|
</tr>
|
|
<tr>
|
|
<td></td>
|
|
<td>)</td>
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<td></td><td></td><td></td>
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</table>
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|
</div>
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|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: parse_asph_min_size<p>
|
|
## SPECIFICATION: Parsing function for the minimum radius of each alpha shpere<p>
|
|
## PARAMETERS: @ char *str: The string to parse @ <a class="el" href="structs__fparams.html">s_fparams</a> *p: The structure than will contain the parsed parameter<p>
|
|
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00330">330</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="fparams_8h-source.html#l00150">s_fparams::asph_min_size</a>, <a class="el" href="utils_8h-source.html#l00060">M_NO_SIGN</a>, and <a class="el" href="utils_8c-source.html#l00412">str_is_float()</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00331"></a>00331 {
|
|
<a name="l00332"></a>00332 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#b2155f59a3e9691956e8501985f5f362">str_is_float</a>(str, <a class="code" href="utils_8h.html#1d2d01db9e7d6bb5200d8cfd398217d6">M_NO_SIGN</a>)) {
|
|
<a name="l00333"></a>00333 p-><a class="code" href="structs__fparams.html#545b7bea97958089689608fff6b8910d">asph_min_size</a> = (float) atof(str) ;
|
|
<a name="l00334"></a>00334 }
|
|
<a name="l00335"></a>00335 <span class="keywordflow">else</span> {
|
|
<a name="l00336"></a>00336 fprintf(stdout, <span class="stringliteral">"! Invalid value (%s) given for the min radius of alpha shperes.\n"</span>, str) ;
|
|
<a name="l00337"></a>00337 <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00338"></a>00338 }
|
|
<a name="l00339"></a>00339
|
|
<a name="l00340"></a>00340 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00341"></a>00341 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="bb8b6f641fc59aea7b6915fd3c197fba"></a><!-- doxytag: member="fparams.c::parse_basic_vol_div" ref="bb8b6f641fc59aea7b6915fd3c197fba" args="(char *str, s_fparams *p)" -->
|
|
<div class="memitem">
|
|
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|
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|
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|
<td class="memname">int parse_basic_vol_div </td>
|
|
<td>(</td>
|
|
<td class="paramtype">char * </td>
|
|
<td class="paramname"> <em>str</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
|
|
<td class="paramname"> <em>p</em></td><td> </td>
|
|
</tr>
|
|
<tr>
|
|
<td></td>
|
|
<td>)</td>
|
|
<td></td><td></td><td></td>
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|
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|
</table>
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|
</div>
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|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: parse_basic_vol_div<p>
|
|
## SPECIFICATION: Parsing function for the number of iteration for the basic volume calculation.<p>
|
|
## PARAMETERS: @ char *str : The string to parse @ <a class="el" href="structs__fparams.html">s_fparams</a> *p : The structure than will contain the parsed parameter<p>
|
|
## RETURN: int: 0 if the parameter is valid (here a valid integer), 1 if not
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00415">415</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="fparams_8h-source.html#l00141">s_fparams::basic_volume_div</a>, <a class="el" href="utils_8h-source.html#l00060">M_NO_SIGN</a>, and <a class="el" href="utils_8c-source.html#l00359">str_is_number()</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00416"></a>00416 {
|
|
<a name="l00417"></a>00417 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#bb731c23a19ad89ea0a69951672a1952">str_is_number</a>(str, <a class="code" href="utils_8h.html#1d2d01db9e7d6bb5200d8cfd398217d6">M_NO_SIGN</a>)) {
|
|
<a name="l00418"></a>00418 p-><a class="code" href="structs__fparams.html#289a1193bf0ffa2f737cd9dc914b63e0">basic_volume_div</a> = (int) atoi(str) ;
|
|
<a name="l00419"></a>00419 }
|
|
<a name="l00420"></a>00420 <span class="keywordflow">else</span> {
|
|
<a name="l00421"></a>00421 fprintf(stdout, <span class="stringliteral">"! Invalid value (%s) given for the precision of the basic volume calculation.\n"</span>, str) ;
|
|
<a name="l00422"></a>00422 <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00423"></a>00423 }
|
|
<a name="l00424"></a>00424
|
|
<a name="l00425"></a>00425 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00426"></a>00426 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="8471dca4fb8f09806aed3be18a79c6b2"></a><!-- doxytag: member="fparams.c::parse_clust_max_dist" ref="8471dca4fb8f09806aed3be18a79c6b2" args="(char *str, s_fparams *p)" -->
|
|
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|
|
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|
<tr>
|
|
<td class="memname">int parse_clust_max_dist </td>
|
|
<td>(</td>
|
|
<td class="paramtype">char * </td>
|
|
<td class="paramname"> <em>str</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
|
|
<td class="paramname"> <em>p</em></td><td> </td>
|
|
</tr>
|
|
<tr>
|
|
<td></td>
|
|
<td>)</td>
|
|
<td></td><td></td><td></td>
|
|
</tr>
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|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: parse_clust_max_dist<p>
|
|
## SPECIFICATION: Parsing function for the distance criteria first clustering algorithm.<p>
|
|
## PARAMETERS: @ char *str : The string to parse @ <a class="el" href="structs__fparams.html">s_fparams</a> *p : The structure than will contain the parsed parameter<p>
|
|
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00214">214</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="fparams_8h-source.html#l00150">s_fparams::clust_max_dist</a>, <a class="el" href="utils_8h-source.html#l00060">M_NO_SIGN</a>, and <a class="el" href="utils_8c-source.html#l00412">str_is_float()</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00215"></a>00215 {
|
|
<a name="l00216"></a>00216 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#b2155f59a3e9691956e8501985f5f362">str_is_float</a>(str, <a class="code" href="utils_8h.html#1d2d01db9e7d6bb5200d8cfd398217d6">M_NO_SIGN</a>)) {
|
|
<a name="l00217"></a>00217 p-><a class="code" href="structs__fparams.html#cd506e600d2b5077f7925847be38c854">clust_max_dist</a> = atof(str) ;
|
|
<a name="l00218"></a>00218 }
|
|
<a name="l00219"></a>00219 <span class="keywordflow">else</span> {
|
|
<a name="l00220"></a>00220 fprintf(stdout, <span class="stringliteral">"! Invalid value (%s) given for the single linkage max dist.\n"</span>, str) ;
|
|
<a name="l00221"></a>00221 <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00222"></a>00222 }
|
|
<a name="l00223"></a>00223
|
|
<a name="l00224"></a>00224 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00225"></a>00225 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="ffc4eabc99149ff419340f11297312c6"></a><!-- doxytag: member="fparams.c::parse_mc_niter" ref="ffc4eabc99149ff419340f11297312c6" args="(char *str, s_fparams *p)" -->
|
|
<div class="memitem">
|
|
<div class="memproto">
|
|
<table class="memname">
|
|
<tr>
|
|
<td class="memname">int parse_mc_niter </td>
|
|
<td>(</td>
|
|
<td class="paramtype">char * </td>
|
|
<td class="paramname"> <em>str</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
|
|
<td class="paramname"> <em>p</em></td><td> </td>
|
|
</tr>
|
|
<tr>
|
|
<td></td>
|
|
<td>)</td>
|
|
<td></td><td></td><td></td>
|
|
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|
|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: parse_mc_niter<p>
|
|
## SPECIFICATION: Parsing function for the number of iteration for the Monte Carlo volume calculation.<p>
|
|
## PARAMETERS: @ char *str : The string to parse @ <a class="el" href="structs__fparams.html">s_fparams</a> *p : The structure than will contain the parsed parameter<p>
|
|
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00387">387</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="utils_8h-source.html#l00060">M_NO_SIGN</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::nb_mcv_iter</a>, and <a class="el" href="utils_8c-source.html#l00412">str_is_float()</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00388"></a>00388 {
|
|
<a name="l00389"></a>00389 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#b2155f59a3e9691956e8501985f5f362">str_is_float</a>(str, <a class="code" href="utils_8h.html#1d2d01db9e7d6bb5200d8cfd398217d6">M_NO_SIGN</a>)) {
|
|
<a name="l00390"></a>00390 p-><a class="code" href="structs__fparams.html#8caeadbae2db7d24763497290e6b9220">nb_mcv_iter</a> = (int) atoi(str) ;
|
|
<a name="l00391"></a>00391 }
|
|
<a name="l00392"></a>00392 <span class="keywordflow">else</span> {
|
|
<a name="l00393"></a>00393 fprintf(stdout, <span class="stringliteral">"! Invalid value (%s) given for the number of monte-carlo iteration for the volume.\n"</span>, str) ;
|
|
<a name="l00394"></a>00394 <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00395"></a>00395 }
|
|
<a name="l00396"></a>00396
|
|
<a name="l00397"></a>00397 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00398"></a>00398 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="40cf684e6c79bc0d5494cf63ee40b8d3"></a><!-- doxytag: member="fparams.c::parse_min_apol_neigh" ref="40cf684e6c79bc0d5494cf63ee40b8d3" args="(char *str, s_fparams *p)" -->
|
|
<div class="memitem">
|
|
<div class="memproto">
|
|
<table class="memname">
|
|
<tr>
|
|
<td class="memname">int parse_min_apol_neigh </td>
|
|
<td>(</td>
|
|
<td class="paramtype">char * </td>
|
|
<td class="paramname"> <em>str</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
|
|
<td class="paramname"> <em>p</em></td><td> </td>
|
|
</tr>
|
|
<tr>
|
|
<td></td>
|
|
<td>)</td>
|
|
<td></td><td></td><td></td>
|
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</tr>
|
|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: parse_min_apol_neigh<p>
|
|
## SPECIFICATION: Parsing function for the minimum number of apolar contacted atom for an alpha sphere to be considered as apolar.<p>
|
|
## PARAMETERS: @ char *str : The string to parse @ <a class="el" href="structs__fparams.html">s_fparams</a> *p : The structure than will contain the parsed parameter<p>
|
|
## RETURN: int: 0 if the parameter is valid (here a valid int), 1 if not
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00300">300</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="utils_8h-source.html#l00060">M_NO_SIGN</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::min_apol_neigh</a>, and <a class="el" href="utils_8c-source.html#l00359">str_is_number()</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00301"></a>00301 {
|
|
<a name="l00302"></a>00302 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#bb731c23a19ad89ea0a69951672a1952">str_is_number</a>(str, <a class="code" href="utils_8h.html#1d2d01db9e7d6bb5200d8cfd398217d6">M_NO_SIGN</a>)) {
|
|
<a name="l00303"></a>00303 p-><a class="code" href="structs__fparams.html#b0875eddf8815f766657713b3f4ba0b0">min_apol_neigh</a> = (int) atoi(str) ;
|
|
<a name="l00304"></a>00304 <span class="keywordflow">if</span>(p-><a class="code" href="structs__fparams.html#b0875eddf8815f766657713b3f4ba0b0">min_apol_neigh</a> < 0) p-><a class="code" href="structs__fparams.html#b0875eddf8815f766657713b3f4ba0b0">min_apol_neigh</a> = 0 ;
|
|
<a name="l00305"></a>00305 <span class="keywordflow">if</span>(p-><a class="code" href="structs__fparams.html#b0875eddf8815f766657713b3f4ba0b0">min_apol_neigh</a> > 4) p-><a class="code" href="structs__fparams.html#b0875eddf8815f766657713b3f4ba0b0">min_apol_neigh</a> = 4 ;
|
|
<a name="l00306"></a>00306 }
|
|
<a name="l00307"></a>00307 <span class="keywordflow">else</span> {
|
|
<a name="l00308"></a>00308 fprintf(stdout, <span class="stringliteral">"! Invalid value (%s) given for the min radius of alpha shperes.\n"</span>, str) ;
|
|
<a name="l00309"></a>00309 <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00310"></a>00310 }
|
|
<a name="l00311"></a>00311
|
|
<a name="l00312"></a>00312 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00313"></a>00313 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="c09155f5ca513066b30c9d1485d810a8"></a><!-- doxytag: member="fparams.c::parse_min_pock_nb_asph" ref="c09155f5ca513066b30c9d1485d810a8" args="(char *str, s_fparams *p)" -->
|
|
<div class="memitem">
|
|
<div class="memproto">
|
|
<table class="memname">
|
|
<tr>
|
|
<td class="memname">int parse_min_pock_nb_asph </td>
|
|
<td>(</td>
|
|
<td class="paramtype">char * </td>
|
|
<td class="paramname"> <em>str</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
|
|
<td class="paramname"> <em>p</em></td><td> </td>
|
|
</tr>
|
|
<tr>
|
|
<td></td>
|
|
<td>)</td>
|
|
<td></td><td></td><td></td>
|
|
</tr>
|
|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: parse_min_pock_nb_asph<p>
|
|
## SPECIFICATION: Parsing function for the minimum number of alpha sphere per pocket.<p>
|
|
## PARAMETERS: @ char *str : The string to parse @ <a class="el" href="structs__fparams.html">s_fparams</a> *p : The structure than will contain the parsed parameter<p>
|
|
## RETURN: int: 0 if the parameter is valid (here a valid integer), 1 if not
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00499">499</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="utils_8h-source.html#l00060">M_NO_SIGN</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::min_pock_nb_asph</a>, and <a class="el" href="utils_8c-source.html#l00359">str_is_number()</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00500"></a>00500 {
|
|
<a name="l00501"></a>00501 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#bb731c23a19ad89ea0a69951672a1952">str_is_number</a>(str, <a class="code" href="utils_8h.html#1d2d01db9e7d6bb5200d8cfd398217d6">M_NO_SIGN</a>)) {
|
|
<a name="l00502"></a>00502 p-><a class="code" href="structs__fparams.html#2ccafe788e970f4e00bdae591d834865">min_pock_nb_asph</a> = (int) atoi(str) ;
|
|
<a name="l00503"></a>00503 }
|
|
<a name="l00504"></a>00504 <span class="keywordflow">else</span> {
|
|
<a name="l00505"></a>00505 fprintf(stdout, <span class="stringliteral">"! Invalid value (%s) given for the refine distance.\n"</span>, str) ;
|
|
<a name="l00506"></a>00506 <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00507"></a>00507 }
|
|
<a name="l00508"></a>00508
|
|
<a name="l00509"></a>00509 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00510"></a>00510 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="cca6c1f10d064997753458d61e052f7d"></a><!-- doxytag: member="fparams.c::parse_refine_dist" ref="cca6c1f10d064997753458d61e052f7d" args="(char *str, s_fparams *p)" -->
|
|
<div class="memitem">
|
|
<div class="memproto">
|
|
<table class="memname">
|
|
<tr>
|
|
<td class="memname">int parse_refine_dist </td>
|
|
<td>(</td>
|
|
<td class="paramtype">char * </td>
|
|
<td class="paramname"> <em>str</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
|
|
<td class="paramname"> <em>p</em></td><td> </td>
|
|
</tr>
|
|
<tr>
|
|
<td></td>
|
|
<td>)</td>
|
|
<td></td><td></td><td></td>
|
|
</tr>
|
|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: parse_refine_dist<p>
|
|
## SPECIFICATION: Parsing function for the distance in the refine algorithm<p>
|
|
## PARAMETERS: @ char *str : The string to parse @ <a class="el" href="structs__fparams.html">s_fparams</a> *p : The structure than will contain the parsed parameter<p>
|
|
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00443">443</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="utils_8h-source.html#l00060">M_NO_SIGN</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::refine_clust_dist</a>, and <a class="el" href="utils_8c-source.html#l00412">str_is_float()</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00444"></a>00444 {
|
|
<a name="l00445"></a>00445 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#b2155f59a3e9691956e8501985f5f362">str_is_float</a>(str, <a class="code" href="utils_8h.html#1d2d01db9e7d6bb5200d8cfd398217d6">M_NO_SIGN</a>)) {
|
|
<a name="l00446"></a>00446 p-><a class="code" href="structs__fparams.html#8ba147c559344c3f0406c1e7a86b98d1">refine_clust_dist</a> = (float) atof(str) ;
|
|
<a name="l00447"></a>00447 }
|
|
<a name="l00448"></a>00448 <span class="keywordflow">else</span> {
|
|
<a name="l00449"></a>00449 fprintf(stdout, <span class="stringliteral">"! Invalid value (%s) given for the refine distance.\n"</span>, str) ;
|
|
<a name="l00450"></a>00450 <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00451"></a>00451 }
|
|
<a name="l00452"></a>00452
|
|
<a name="l00453"></a>00453 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00454"></a>00454 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="a08e358edc9c6941f595da45c4741fe0"></a><!-- doxytag: member="fparams.c::parse_refine_minaap" ref="a08e358edc9c6941f595da45c4741fe0" args="(char *str, s_fparams *p)" -->
|
|
<div class="memitem">
|
|
<div class="memproto">
|
|
<table class="memname">
|
|
<tr>
|
|
<td class="memname">int parse_refine_minaap </td>
|
|
<td>(</td>
|
|
<td class="paramtype">char * </td>
|
|
<td class="paramname"> <em>str</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
|
|
<td class="paramname"> <em>p</em></td><td> </td>
|
|
</tr>
|
|
<tr>
|
|
<td></td>
|
|
<td>)</td>
|
|
<td></td><td></td><td></td>
|
|
</tr>
|
|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: parse_refine_min_apol<p>
|
|
## SPECIFICATION: Parsing function for the minimum number of apolar sphere per pocket.<p>
|
|
## PARAMETERS: @ char *str : The string to parse @ <a class="el" href="structs__fparams.html">s_fparams</a> *p : The structure than will contain the parsed parameter<p>
|
|
## RETURN: int: 0 if the parameter is valid (here a valid integer), 1 if not
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00471">471</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="utils_8h-source.html#l00060">M_NO_SIGN</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::refine_min_apolar_asphere_prop</a>, and <a class="el" href="utils_8c-source.html#l00412">str_is_float()</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00472"></a>00472 {
|
|
<a name="l00473"></a>00473 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#b2155f59a3e9691956e8501985f5f362">str_is_float</a>(str, <a class="code" href="utils_8h.html#1d2d01db9e7d6bb5200d8cfd398217d6">M_NO_SIGN</a>)) {
|
|
<a name="l00474"></a>00474 p-><a class="code" href="structs__fparams.html#50d6211ea1f5d9b90c10f866c82e54b8">refine_min_apolar_asphere_prop</a> = (float) atof(str) ;
|
|
<a name="l00475"></a>00475 }
|
|
<a name="l00476"></a>00476 <span class="keywordflow">else</span> {
|
|
<a name="l00477"></a>00477 fprintf(stdout, <span class="stringliteral">"! Invalid value (%s) given for the refine distance.\n"</span>, str) ;
|
|
<a name="l00478"></a>00478 <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00479"></a>00479 }
|
|
<a name="l00480"></a>00480
|
|
<a name="l00481"></a>00481 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00482"></a>00482 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="da442addde23a799e50cecae103974bf"></a><!-- doxytag: member="fparams.c::parse_sclust_max_dist" ref="da442addde23a799e50cecae103974bf" args="(char *str, s_fparams *p)" -->
|
|
<div class="memitem">
|
|
<div class="memproto">
|
|
<table class="memname">
|
|
<tr>
|
|
<td class="memname">int parse_sclust_max_dist </td>
|
|
<td>(</td>
|
|
<td class="paramtype">char * </td>
|
|
<td class="paramname"> <em>str</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
|
|
<td class="paramname"> <em>p</em></td><td> </td>
|
|
</tr>
|
|
<tr>
|
|
<td></td>
|
|
<td>)</td>
|
|
<td></td><td></td><td></td>
|
|
</tr>
|
|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: parse_sclust_max_dist<p>
|
|
## SPECIFICATION: Parsing function for the distance criteria in the single linkage clustering.<p>
|
|
## PARAMETERS: @ char *str : The string to parse @ <a class="el" href="structs__fparams.html">s_fparams</a> *p : The structure than will contain the parsed parameter<p>
|
|
## RETURN: int: 0 if the parameter is valid (here a valid float), 1 if not
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00243">243</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="utils_8h-source.html#l00060">M_NO_SIGN</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::sl_clust_max_dist</a>, and <a class="el" href="utils_8c-source.html#l00412">str_is_float()</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00244"></a>00244 {
|
|
<a name="l00245"></a>00245 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#b2155f59a3e9691956e8501985f5f362">str_is_float</a>(str, <a class="code" href="utils_8h.html#1d2d01db9e7d6bb5200d8cfd398217d6">M_NO_SIGN</a>)) {
|
|
<a name="l00246"></a>00246 p-><a class="code" href="structs__fparams.html#71691bbfb98d90e12ca8cb3c79e2688c">sl_clust_max_dist</a> = atof(str) ;
|
|
<a name="l00247"></a>00247 }
|
|
<a name="l00248"></a>00248 <span class="keywordflow">else</span> {
|
|
<a name="l00249"></a>00249 fprintf(stdout, <span class="stringliteral">"! Invalid value (%s) given for the single linkage max dist.\n"</span>, str) ;
|
|
<a name="l00250"></a>00250 <span class="keywordflow">return</span> 1 ;
|
|
<a name="l00251"></a>00251 }
|
|
<a name="l00252"></a>00252
|
|
<a name="l00253"></a>00253 <span class="keywordflow">return</span> 0 ;
|
|
<a name="l00254"></a>00254 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="39b0715eb1fb67b993d494570f866135"></a><!-- doxytag: member="fparams.c::parse_sclust_min_nneigh" ref="39b0715eb1fb67b993d494570f866135" args="(char *str, s_fparams *p)" -->
|
|
<div class="memitem">
|
|
<div class="memproto">
|
|
<table class="memname">
|
|
<tr>
|
|
<td class="memname">int parse_sclust_min_nneigh </td>
|
|
<td>(</td>
|
|
<td class="paramtype">char * </td>
|
|
<td class="paramname"> <em>str</em>, </td>
|
|
</tr>
|
|
<tr>
|
|
<td class="paramkey"></td>
|
|
<td></td>
|
|
<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
|
|
<td class="paramname"> <em>p</em></td><td> </td>
|
|
</tr>
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<tr>
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<td></td>
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<td>)</td>
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<td></td><td></td><td></td>
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</div>
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<div class="memdoc">
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<p>
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## FUNCTION: parse_sclust_min_nneigh<p>
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## SPECIFICATION: Parsing function for the number of neighbours in the single linkage clustering.<p>
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## PARAMETERS: @ char *str : The string to parse @ <a class="el" href="structs__fparams.html">s_fparams</a> *p : The structure than will contain the parsed parameter<p>
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## RETURN: int: 0 if the parameter is valid (here a valid int), 1 if not
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<p>Definition at line <a class="el" href="fparams_8c-source.html#l00271">271</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
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<p>References <a class="el" href="utils_8h-source.html#l00060">M_NO_SIGN</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::sl_clust_min_nneigh</a>, and <a class="el" href="utils_8c-source.html#l00359">str_is_number()</a>.</p>
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<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>.</p>
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<div class="fragment"><pre class="fragment"><a name="l00272"></a>00272 {
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<a name="l00273"></a>00273 <span class="keywordflow">if</span>(<a class="code" href="utils_8c.html#bb731c23a19ad89ea0a69951672a1952">str_is_number</a>(str, <a class="code" href="utils_8h.html#1d2d01db9e7d6bb5200d8cfd398217d6">M_NO_SIGN</a>)) {
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<a name="l00274"></a>00274 p-><a class="code" href="structs__fparams.html#b23279857aaf7861b452cd2bf463f624">sl_clust_min_nneigh</a> = atoi(str) ;
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<a name="l00275"></a>00275 }
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<a name="l00276"></a>00276 <span class="keywordflow">else</span> {
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<a name="l00277"></a>00277 fprintf(stdout, <span class="stringliteral">"! Invalid value (%s) given for the single linkage max dist.\n"</span>, str) ;
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<a name="l00278"></a>00278 <span class="keywordflow">return</span> 1 ;
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<a name="l00279"></a>00279 }
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<a name="l00280"></a>00280
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<a name="l00281"></a>00281 <span class="keywordflow">return</span> 0 ;
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<a name="l00282"></a>00282 }
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</pre></div>
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<p>
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</div>
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</div><p>
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<a class="anchor" name="00d0d0ea58e0b3fd1f6a785427e6b5f1"></a><!-- doxytag: member="fparams.c::print_fparams" ref="00d0d0ea58e0b3fd1f6a785427e6b5f1" args="(s_fparams *p, FILE *f)" -->
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<div class="memitem">
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<div class="memproto">
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<table class="memname">
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<tr>
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<td class="memname">void print_fparams </td>
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<td>(</td>
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<td class="paramtype"><a class="el" href="structs__fparams.html">s_fparams</a> * </td>
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<td class="paramname"> <em>p</em>, </td>
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</tr>
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<tr>
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<td class="paramkey"></td>
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<td></td>
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<td class="paramtype">FILE * </td>
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<td class="paramname"> <em>f</em></td><td> </td>
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</tr>
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<tr>
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<td></td>
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<td>)</td>
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<td></td><td></td><td></td>
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</div>
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<div class="memdoc">
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<p>
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## FUNCTION: print_fparams<p>
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|
## SPECIFICATION: Print function<p>
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|
## PARAMETRES: @ <a class="el" href="structs__fparams.html">s_fparams</a> *p : Parameters to print @ FILE *f : Buffer to write in<p>
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|
## RETURN:
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00611">611</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
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<p>References <a class="el" href="fparams_8h-source.html#l00150">s_fparams::asph_max_size</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::asph_min_size</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::basic_volume_div</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::clust_max_dist</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::min_apol_neigh</a>, <a class="el" href="fparams_8h-source.html#l00141">s_fparams::nb_mcv_iter</a>, <a class="el" href="fparams_8h-source.html#l00136">s_fparams::pdb_path</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::refine_clust_dist</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::refine_min_apolar_asphere_prop</a>, <a class="el" href="fparams_8h-source.html#l00150">s_fparams::sl_clust_max_dist</a>, and <a class="el" href="fparams_8h-source.html#l00141">s_fparams::sl_clust_min_nneigh</a>.</p>
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<div class="fragment"><pre class="fragment"><a name="l00612"></a>00612 {
|
|
<a name="l00613"></a>00613 <span class="keywordflow">if</span>(p) {
|
|
<a name="l00614"></a>00614 fprintf(f, <span class="stringliteral">"==============\nParameters of fpocket: \n"</span>);
|
|
<a name="l00615"></a>00615 fprintf(f, <span class="stringliteral">"> Minimum alpha sphere radius: %f\n"</span>, p-><a class="code" href="structs__fparams.html#545b7bea97958089689608fff6b8910d">asph_min_size</a>);
|
|
<a name="l00616"></a>00616 fprintf(f, <span class="stringliteral">"> Maximum alpha sphere radius: %f\n"</span>, p-><a class="code" href="structs__fparams.html#7439af209766e39dad7e39f4c6e19711">asph_max_size</a>);
|
|
<a name="l00617"></a>00617 fprintf(f, <span class="stringliteral">"> Minimum number of apolar neighbor: %d\n"</span>, p-><a class="code" href="structs__fparams.html#b0875eddf8815f766657713b3f4ba0b0">min_apol_neigh</a>);
|
|
<a name="l00618"></a>00618 fprintf(f, <span class="stringliteral">"> Maximum distance for first clustering algorithm: %f \n"</span>, p-><a class="code" href="structs__fparams.html#cd506e600d2b5077f7925847be38c854">clust_max_dist</a>) ;
|
|
<a name="l00619"></a>00619 fprintf(f, <span class="stringliteral">"> Single linkage clustering distance: %f\n"</span>, p-><a class="code" href="structs__fparams.html#71691bbfb98d90e12ca8cb3c79e2688c">sl_clust_max_dist</a>);
|
|
<a name="l00620"></a>00620 fprintf(f, <span class="stringliteral">"> Single linkage clustering neighbor: %d\n"</span>, p-><a class="code" href="structs__fparams.html#b23279857aaf7861b452cd2bf463f624">sl_clust_min_nneigh</a>);
|
|
<a name="l00621"></a>00621 fprintf(f, <span class="stringliteral">"> Refine clustering distance: %f\n"</span>, p-><a class="code" href="structs__fparams.html#8ba147c559344c3f0406c1e7a86b98d1">refine_clust_dist</a>);
|
|
<a name="l00622"></a>00622 fprintf(f, <span class="stringliteral">"> Min number of apolar sphere in refine to keep a pocket: %f\n"</span>, p-><a class="code" href="structs__fparams.html#50d6211ea1f5d9b90c10f866c82e54b8">refine_min_apolar_asphere_prop</a>) ;
|
|
<a name="l00623"></a>00623 fprintf(f, <span class="stringliteral">"> Monte carlo iterations: %d\n"</span>, p-><a class="code" href="structs__fparams.html#8caeadbae2db7d24763497290e6b9220">nb_mcv_iter</a>);
|
|
<a name="l00624"></a>00624 fprintf(f, <span class="stringliteral">"> Basic method for volume calculation: %d\n"</span>, p-><a class="code" href="structs__fparams.html#289a1193bf0ffa2f737cd9dc914b63e0">basic_volume_div</a>);
|
|
<a name="l00625"></a>00625 fprintf(f, <span class="stringliteral">"> PDB file: %s\n"</span>, p-><a class="code" href="structs__fparams.html#4e1b3892d1e42947408cdcaed497bf97">pdb_path</a>);
|
|
<a name="l00626"></a>00626 fprintf(f, <span class="stringliteral">"==============\n"</span>);
|
|
<a name="l00627"></a>00627 }
|
|
<a name="l00628"></a>00628 <span class="keywordflow">else</span> fprintf(f, <span class="stringliteral">"> No parameters detected\n"</span>);
|
|
<a name="l00629"></a>00629 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
|
</div><p>
|
|
<a class="anchor" name="ab8c5397c1eaa6388ae24aa9ae605481"></a><!-- doxytag: member="fparams.c::print_pocket_usage" ref="ab8c5397c1eaa6388ae24aa9ae605481" args="(FILE *f)" -->
|
|
<div class="memitem">
|
|
<div class="memproto">
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|
<table class="memname">
|
|
<tr>
|
|
<td class="memname">void print_pocket_usage </td>
|
|
<td>(</td>
|
|
<td class="paramtype">FILE * </td>
|
|
<td class="paramname"> <em>f</em> </td>
|
|
<td> ) </td>
|
|
<td></td>
|
|
</tr>
|
|
</table>
|
|
</div>
|
|
<div class="memdoc">
|
|
|
|
<p>
|
|
## FUNCTION: print_pocket_usage<p>
|
|
## SPECIFICATION: Displaying usage of the programm in the given buffer<p>
|
|
## PARAMETRES: @ FILE *f: buffer to print in<p>
|
|
## RETURN: void
|
|
<p>Definition at line <a class="el" href="fparams_8c-source.html#l00590">590</a> of file <a class="el" href="fparams_8c-source.html">fparams.c</a>.</p>
|
|
|
|
<p>References <a class="el" href="fparams_8h-source.html#l00095">M_FP_USAGE</a>.</p>
|
|
|
|
<p>Referenced by <a class="el" href="fparams_8c-source.html#l00088">get_fpocket_args()</a>, and <a class="el" href="fpmain_8c-source.html#l00071">main()</a>.</p>
|
|
<div class="fragment"><pre class="fragment"><a name="l00591"></a>00591 {
|
|
<a name="l00592"></a>00592 f = (f == NULL) ? stdout:f ;
|
|
<a name="l00593"></a>00593
|
|
<a name="l00594"></a>00594 fprintf(f, <a class="code" href="fparams_8h.html#6148535acc1f81ca26cbaaf678c1cfc5">M_FP_USAGE</a>) ;
|
|
<a name="l00595"></a>00595 }
|
|
</pre></div>
|
|
<p>
|
|
|
|
</div>
|
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</div><p>
|
|
</div>
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|
<hr size="1"><address style="text-align: right;"><small>Generated on Mon Jun 7 16:44:23 2010 for fpocket by
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|
<a href="http://www.doxygen.org/index.html">
|
|
<img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.5.6 </small></address>
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</body>
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