Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
SBL.Colored_MISA Namespace Reference

Variables

 MISA
 
 color_engine
 
 verbose
 
 all_MISA
 
 odir
 
 SSE_parser
 
 BSA_parser
 
 Delta_ASA_parser
 
 B_factor_parser
 
 all_cMISA
 
 prefix
 
 subodir
 
 bool_legend
 
 all_coloring_displays
 

Constructions

def __init__ (self, MISA, color_engine)
 Default constructor. More...
 
def __init__ (self, verbose, all_MISA, idir, vdir, odir, pdb_id2path, normalize_b_factor)
 Initialize with the MISA and the several ColorEngine Parser. More...
 
def record_BSA (self, BSA_MISA)
 Record the BSA of each chain in the odir directory. More...
 
def run (self)
 Create the colored MISA and apply the coloring to each of them. More...
 
def __init__ (self, verbose, prefix, all_cMISA, odir, bool_legend)
 Default constructor. More...
 
def create_html (self, output_directory, title, html_list)
 Create a html file in the odir directory from a title and a list of html Istrings. More...
 
def translated_sequence (self, cMISA, chain_name, begin_resid, end_resid)
 Translate the portion of the I string between indexes beginresid and endresid into an html string. More...
 
def header_html (self, cMISA)
 Create the header of the html containing the legend and the color encoding. More...
 
def create_single_coloring_output_files (self, cMISA)
 Adjust the spacing for the different chain names and call the different functions necessary to create the output files. More...
 
def create_block_sequences (self, cMISA, dic_between_space, begin_resid, end_resid, display_names=True)
 Display a block of Istring alignment from a beginning index up to an end index. More...
 
def generate_html_pdf (self, cMISA, dic_between_space, len_align)
 Create both html and pdf files. More...
 
def create_all_coloring_output_files (self)
 Create one big file per MISA_id containing all the different colorings for this MISA_id. More...
 

Internal Methods

def roundupperten (x)
 Round up an index to the nearest upper ten index. More...
 
def get_ten_resid (self, cMISA, resid)
 Return the residue index rounded to the nearest upper ten index. More...
 
def gather_equal_chain_by_cMISA (self, cMISA)
 Identify the chains with identical display and associate to each group thus constituted a representant chain They are recorded in cMISA.equal_chains as follows : {representant_chain_name : [names, from, all, identical, chains]}. More...
 
def get_index_str (self, cMISA, res_index)
 Return the index in string mode. More...
 
def get_number_of_resids_between (self, cMISA, begin_resid, end_resid)
 Return the number of resids included between a pair of indexes. More...
 

Class Documentation

◆ SBL::Colored_MISA::cMISA_constructor

class SBL::Colored_MISA::cMISA_constructor

Construct all the colored MISA (cMISA).

Construct from each MISA one colored MISA (cMISA) per ColorEngine (SSE, BSA, Delta ASA, B factor). Construct all the colored MISA (cMISA).

◆ SBL::Colored_MISA::cMISA_recorder

class SBL::Colored_MISA::cMISA_recorder

Record all the colored MISA.

Create the different output files and associated figures to record the MISA. Record all the colored MISA.

◆ SBL::Colored_MISA::Colored_MISA

class SBL::Colored_MISA::Colored_MISA

Store a MISA and its associated ColorEngine.

Only a container. Store a MISA and its associated ColorEngine.

◆ SBL::Colored_MISA::SBL

class SBL::Colored_MISA::SBL

Function Documentation

◆ __init__() [1/3]

def SBL.Colored_MISA.__init__ (   self,
  MISA,
  color_engine 
)

Default constructor.

◆ __init__() [2/3]

def SBL.Colored_MISA.__init__ (   self,
  verbose,
  all_MISA,
  idir,
  vdir,
  odir,
  pdb_id2path,
  normalize_b_factor 
)

Initialize with the MISA and the several ColorEngine Parser.

◆ __init__() [3/3]

def SBL.Colored_MISA.__init__ (   self,
  verbose,
  prefix,
  all_cMISA,
  odir,
  bool_legend 
)

Default constructor.

◆ create_all_coloring_output_files()

def SBL.Colored_MISA.create_all_coloring_output_files (   self)

Create one big file per MISA_id containing all the different colorings for this MISA_id.

◆ create_block_sequences()

def SBL.Colored_MISA.create_block_sequences (   self,
  cMISA,
  dic_between_space,
  begin_resid,
  end_resid,
  display_names = True 
)

Display a block of Istring alignment from a beginning index up to an end index.

◆ create_html()

def SBL.Colored_MISA.create_html (   self,
  output_directory,
  title,
  html_list 
)

Create a html file in the odir directory from a title and a list of html Istrings.

◆ create_single_coloring_output_files()

def SBL.Colored_MISA.create_single_coloring_output_files (   self,
  cMISA 
)

Adjust the spacing for the different chain names and call the different functions necessary to create the output files.

◆ gather_equal_chain_by_cMISA()

def SBL.Colored_MISA.gather_equal_chain_by_cMISA (   self,
  cMISA 
)

Identify the chains with identical display and associate to each group thus constituted a representant chain They are recorded in cMISA.equal_chains as follows : {representant_chain_name : [names, from, all, identical, chains]}.

◆ generate_html_pdf()

def SBL.Colored_MISA.generate_html_pdf (   self,
  cMISA,
  dic_between_space,
  len_align 
)

Create both html and pdf files.

◆ get_index_str()

def SBL.Colored_MISA.get_index_str (   self,
  cMISA,
  res_index 
)

Return the index in string mode.

◆ get_number_of_resids_between()

def SBL.Colored_MISA.get_number_of_resids_between (   self,
  cMISA,
  begin_resid,
  end_resid 
)

Return the number of resids included between a pair of indexes.

◆ get_ten_resid()

def SBL.Colored_MISA.get_ten_resid (   self,
  cMISA,
  resid 
)

Return the residue index rounded to the nearest upper ten index.

◆ header_html()

def SBL.Colored_MISA.header_html (   self,
  cMISA 
)

Create the header of the html containing the legend and the color encoding.

◆ record_BSA()

def SBL.Colored_MISA.record_BSA (   self,
  BSA_MISA 
)

Record the BSA of each chain in the odir directory.

◆ roundupperten()

def SBL.Colored_MISA.roundupperten (   x)
static

Round up an index to the nearest upper ten index.

◆ run()

def run (   self)

Create the colored MISA and apply the coloring to each of them.

Gather the chains with the same representation to lighten the display and create all the output files.

◆ translated_sequence()

def SBL.Colored_MISA.translated_sequence (   self,
  cMISA,
  chain_name,
  begin_resid,
  end_resid 
)

Translate the portion of the I string between indexes beginresid and endresid into an html string.

Variable Documentation

◆ all_cMISA

all_cMISA

◆ all_coloring_displays

all_coloring_displays

◆ all_MISA

all_MISA

◆ B_factor_parser

B_factor_parser

◆ bool_legend

bool_legend

◆ BSA_parser

BSA_parser

◆ color_engine

color_engine

◆ Delta_ASA_parser

Delta_ASA_parser

◆ MISA

MISA

◆ odir

odir

◆ prefix

prefix

◆ SSE_parser

SSE_parser

◆ subodir

subodir

◆ verbose

verbose