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bioinf_tools.html
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html><head><title>Python: module bioinf_tools</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head><body bgcolor="#f0f0f8">
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="heading">
<tr bgcolor="#7799ee">
<td valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"> <br><big><big><strong>bioinf_tools</strong></big></big></font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:c%3A%5Cusers%5Cwynal%5Conedrive%5Cpulpit%5Cgotowy_projekt_licencjacki%5Cprojekt%5Cbioinf_tools.py">c:\users\wynal\onedrive\pulpit\gotowy_projekt_licencjacki\projekt\bioinf_tools.py</a></font></td></tr></table>
<p></p>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#aa55cc">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
<tr><td bgcolor="#aa55cc"><tt> </tt></td><td> </td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="xml.dom.minidom.html">xml.dom.minidom</a><br>
</td><td width="25%" valign=top><a href="platform.html">platform</a><br>
</td><td width="25%" valign=top><a href="urllib3.html">urllib3</a><br>
</td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ee77aa">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
<tr><td bgcolor="#ee77aa"><tt> </tt></td><td> </td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="builtins.html#object">builtins.object</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="bioinf_tools.html#Atom">Atom</a>
</font></dt><dt><font face="helvetica, arial"><a href="bioinf_tools.html#Chain">Chain</a>
</font></dt><dt><font face="helvetica, arial"><a href="bioinf_tools.html#Colors">Colors</a>
</font></dt><dt><font face="helvetica, arial"><a href="bioinf_tools.html#Ligand">Ligand</a>
</font></dt><dt><font face="helvetica, arial"><a href="bioinf_tools.html#Pfam_domain">Pfam_domain</a>
</font></dt><dt><font face="helvetica, arial"><a href="bioinf_tools.html#Residue">Residue</a>
</font></dt><dt><font face="helvetica, arial"><a href="bioinf_tools.html#Structure">Structure</a>
</font></dt><dt><font face="helvetica, arial"><a href="bioinf_tools.html#Termination_symbol">Termination_symbol</a>
</font></dt><dt><font face="helvetica, arial"><a href="bioinf_tools.html#Unp_record">Unp_record</a>
</font></dt></dl>
</dd>
</dl>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Atom">class <strong>Atom</strong></a>(<a href="builtins.html#object">builtins.object</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Atom">Atom</a>(atom_name, element_symbol, x_coordinate, y_coordinate, z_coordinate)<br>
<br>
Klasa służąca do przechowywania informacji o pojedynczych atomach pobranych ze struktury białka (nazwa, symbol, położenie w R^3 [A]).<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Atom-__init__"><strong>__init__</strong></a>(self, atom_name, element_symbol, x_coordinate, y_coordinate, z_coordinate)</dt><dd><tt>Initialize self. See help(type(self)) for accurate signature.</tt></dd></dl>
<hr>
Data descriptors defined here:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</tt></dd>
</dl>
</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Chain">class <strong>Chain</strong></a>(<a href="builtins.html#object">builtins.object</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Chain">Chain</a>(chain_name)<br>
<br>
Klasa zawierająca grupę wczytanych reszt aminokwasowych (klasa: <a href="#Residue">Residue</a>), stanowiąca reprezentację łańcucha białkowego.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Chain-__init__"><strong>__init__</strong></a>(self, chain_name)</dt><dd><tt>Initialize self. See help(type(self)) for accurate signature.</tt></dd></dl>
<dl><dt><a name="Chain-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Return repr(self).</tt></dd></dl>
<dl><dt><a name="Chain-push_residue"><strong>push_residue</strong></a>(self, next_residue: bioinf_tools.Residue)</dt></dl>
<hr>
Data descriptors defined here:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</tt></dd>
</dl>
</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Colors">class <strong>Colors</strong></a>(<a href="builtins.html#object">builtins.object</a>)</font></td></tr>
<tr><td bgcolor="#ffc8d8"><tt> </tt></td><td> </td>
<td width="100%">Data descriptors defined here:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</tt></dd>
</dl>
<hr>
Data and other attributes defined here:<br>
<dl><dt><strong>BLUE</strong> = ''</dl>
<dl><dt><strong>END</strong> = ''</dl>
<dl><dt><strong>GREEN</strong> = ''</dl>
<dl><dt><strong>RED</strong> = ''</dl>
<dl><dt><strong>YELLOW</strong> = ''</dl>
</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Ligand">class <strong>Ligand</strong></a>(<a href="builtins.html#object">builtins.object</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Ligand">Ligand</a>(residue_name, residue_sequence_number)<br>
<br>
Klasa zawierająca grupę wczytanych atomów (klasa: <a href="#Atom">Atom</a>), stanowiąca reprezentację cząsteczki liganda.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Ligand-__init__"><strong>__init__</strong></a>(self, residue_name, residue_sequence_number)</dt><dd><tt>Initialize self. See help(type(self)) for accurate signature.</tt></dd></dl>
<dl><dt><a name="Ligand-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Return repr(self).</tt></dd></dl>
<dl><dt><a name="Ligand-push_atom"><strong>push_atom</strong></a>(self, next_atom: bioinf_tools.Atom)</dt></dl>
<hr>
Data descriptors defined here:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</tt></dd>
</dl>
</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Pfam_domain">class <strong>Pfam_domain</strong></a>(<a href="builtins.html#object">builtins.object</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Pfam_domain">Pfam_domain</a>(chain_name, pfam_accession, pfam_id, start, end)<br>
<br>
Klasa służąca do przechowywania informacji o domenach białkowych (Pfam).<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Pfam_domain-__init__"><strong>__init__</strong></a>(self, chain_name, pfam_accession, pfam_id, start, end)</dt><dd><tt>Initialize self. See help(type(self)) for accurate signature.</tt></dd></dl>
<dl><dt><a name="Pfam_domain-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Return repr(self).</tt></dd></dl>
<hr>
Data descriptors defined here:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</tt></dd>
</dl>
</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Residue">class <strong>Residue</strong></a>(<a href="builtins.html#object">builtins.object</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Residue">Residue</a>(residue_name, residue_sequence_number)<br>
<br>
Klasa zawierająca grupę wczytanych atomów (klasa: <a href="#Atom">Atom</a>), stanowiąca reprezentację reszty aminokwasowej.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Residue-__init__"><strong>__init__</strong></a>(self, residue_name, residue_sequence_number)</dt><dd><tt>Initialize self. See help(type(self)) for accurate signature.</tt></dd></dl>
<dl><dt><a name="Residue-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Return repr(self).</tt></dd></dl>
<dl><dt><a name="Residue-push_atom"><strong>push_atom</strong></a>(self, next_atom: bioinf_tools.Atom)</dt></dl>
<hr>
Data descriptors defined here:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</tt></dd>
</dl>
</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Structure">class <strong>Structure</strong></a>(<a href="builtins.html#object">builtins.object</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Structure">Structure</a>(structure_PDB_ID)<br>
<br>
Klasa zawierająca grupę wczytanych łańcuchów aminokwasowych (klasa: <a href="#Chain">Chain</a>), stanowiąca reprezentację całego białka.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Structure-__init__"><strong>__init__</strong></a>(self, structure_PDB_ID)</dt><dd><tt>Initialize self. See help(type(self)) for accurate signature.</tt></dd></dl>
<dl><dt><a name="Structure-collect_data_from_Pfam"><strong>collect_data_from_Pfam</strong></a>(self, backup_folder)</dt><dd><tt>Funkcja pobierająca informacje o architekturach domenowych z bazy danych Pfam (pod warunkiem, że danych tych w postaci plików *.xml nie ma w lokalnym repozytorium).</tt></dd></dl>
<dl><dt><a name="Structure-get_ligands_binding_domains"><strong>get_ligands_binding_domains</strong></a>(self) -> list</dt><dd><tt>Funkcja zwracająca domeny białkowe wiążące wskazane ligandy (nie uwzględniono wielokrotnych miejsc wiązania dla tego samego liganda w obrębie tej samej domeny).</tt></dd></dl>
<dl><dt><a name="Structure-get_ligands_binding_domains_detailed"><strong>get_ligands_binding_domains_detailed</strong></a>(self) -> list</dt><dd><tt>Funkcja zwracająca domeny białkowe wiążące wskazane ligandy (uwzględniono wielokrotne miejsca wiązania dla tego samego liganda w obrębie tej samej domeny).</tt></dd></dl>
<dl><dt><a name="Structure-get_ligands_environment"><strong>get_ligands_environment</strong></a>(self) -> list</dt><dd><tt>Funkcja zwracająca listę znalezionych miejsc kontaktu ligand - białko.</tt></dd></dl>
<hr>
Data descriptors defined here:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</tt></dd>
</dl>
</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Termination_symbol">class <strong>Termination_symbol</strong></a>(<a href="builtins.html#object">builtins.object</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Termination_symbol">Termination_symbol</a>(residue_name, residue_sequence_number)<br>
<br>
Znacznik końca łańcucha aminokwasowego.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Termination_symbol-__init__"><strong>__init__</strong></a>(self, residue_name, residue_sequence_number)</dt><dd><tt>Initialize self. See help(type(self)) for accurate signature.</tt></dd></dl>
<hr>
Data descriptors defined here:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</tt></dd>
</dl>
</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom> <br>
<font color="#000000" face="helvetica, arial"><a name="Unp_record">class <strong>Unp_record</strong></a>(<a href="builtins.html#object">builtins.object</a>)</font></td></tr>
<tr bgcolor="#ffc8d8"><td rowspan=2><tt> </tt></td>
<td colspan=2><tt><a href="#Unp_record">Unp_record</a>(chain_name, unp_accession, unp_id)<br>
<br>
Klasa służąca do przechowywania odniesień do bazy danych UniProt znalezionych w plikach PDB.<br> </tt></td></tr>
<tr><td> </td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Unp_record-__init__"><strong>__init__</strong></a>(self, chain_name, unp_accession, unp_id)</dt><dd><tt>Initialize self. See help(type(self)) for accurate signature.</tt></dd></dl>
<dl><dt><a name="Unp_record-__repr__"><strong>__repr__</strong></a>(self)</dt><dd><tt>Return repr(self).</tt></dd></dl>
<hr>
Data descriptors defined here:<br>
<dl><dt><strong>__dict__</strong></dt>
<dd><tt>dictionary for instance variables (if defined)</tt></dd>
</dl>
<dl><dt><strong>__weakref__</strong></dt>
<dd><tt>list of weak references to the object (if defined)</tt></dd>
</dl>
</td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#eeaa77">
<td colspan=3 valign=bottom> <br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Functions</strong></big></font></td></tr>
<tr><td bgcolor="#eeaa77"><tt> </tt></td><td> </td>
<td width="100%"><dl><dt><a name="-parse_PDB_file"><strong>parse_PDB_file</strong></a>(pdb_file_path, ligands: list = []) -> bioinf_tools.Structure</dt><dd><tt>Funkcja parsująca pliki PDB. Zwraca wczytaną cząsteczkę w postaci obiektu klasy <a href="#Structure">Structure</a>.</tt></dd></dl>
</td></tr></table>
</body></html>