Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
BioPDB_vs_XML_Etree Class Reference

Internal Methods

def convert_PDB_header_to_XML_ElementTree (header)
 Convert the header of a PDB file to an XML ETree. More...
 
def convert_PDB_atom_to_XML_ElementTree (atom)
 Convert a PDB atom to an XML ETree. More...
 
def convert_PDB_residue_to_XML_ElementTree (residue)
 Convert a PDB residue to an XML ETree. More...
 
def convert_PDB_chain_to_XML_ElementTree (chain)
 Convert a PDB chain to an XML ETree. More...
 
def convert_PDB_model_to_XML_ElementTree (model)
 Convert a PDB model to an XML ETree. More...
 
def convert_PDB_structure_to_XML_ElementTree (structure)
 Convert a PDB structure to an XML ETree. More...
 
def convert_PDB_to_XML_Etree (filename)
 Convert a PDB file to an XML ETree. More...
 

Load PDB files

def load_PDB_file (filename)
 Function that load a PDB file from filename and convert the output dictionary to a XML tree of this database. More...
 
def load_PDB_files (filelist)
 Function that load all PDB files in the filelist and convert the output dictionaries to XML trees of this database. More...
 
def load_PDB_files_from_directory (input_dir, regex="")
 Function that load all PDB files in the input directory matching the regexp. More...
 

Detailed Description

Manipulations between the PDB format from BioPython and XML Etrees. The class allows loading directly a text PDB file into an ETree, without using the PDBML format.

Member Function Documentation

◆ convert_PDB_atom_to_XML_ElementTree()

def convert_PDB_atom_to_XML_ElementTree (   atom)
static

Convert a PDB atom to an XML ETree.

Should not be called directly !

◆ convert_PDB_chain_to_XML_ElementTree()

def convert_PDB_chain_to_XML_ElementTree (   chain)
static

Convert a PDB chain to an XML ETree.

Should not be called directly !

◆ convert_PDB_header_to_XML_ElementTree()

def convert_PDB_header_to_XML_ElementTree (   header)
static

Convert the header of a PDB file to an XML ETree.

Should not be called directly !

◆ convert_PDB_model_to_XML_ElementTree()

def convert_PDB_model_to_XML_ElementTree (   model)
static

Convert a PDB model to an XML ETree.

Should not be called directly !

◆ convert_PDB_residue_to_XML_ElementTree()

def convert_PDB_residue_to_XML_ElementTree (   residue)
static

Convert a PDB residue to an XML ETree.

Should not be called directly !

◆ convert_PDB_structure_to_XML_ElementTree()

def convert_PDB_structure_to_XML_ElementTree (   structure)
static

Convert a PDB structure to an XML ETree.

Should not be called directly !

◆ convert_PDB_to_XML_Etree()

def convert_PDB_to_XML_Etree (   filename)
static

Convert a PDB file to an XML ETree.

Should not be called directly !

◆ load_PDB_file()

def load_PDB_file (   filename)
static

Function that load a PDB file from filename and convert the output dictionary to a XML tree of this database.

◆ load_PDB_files()

def load_PDB_files (   filelist)
static

Function that load all PDB files in the filelist and convert the output dictionaries to XML trees of this database.

◆ load_PDB_files_from_directory()

def load_PDB_files_from_directory (   input_dir,
  regex = "" 
)
static

Function that load all PDB files in the input directory matching the regexp.