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IMP Reference Guide  develop.ba5ef9f91e,2024/02/26
The Integrative Modeling Platform
IMP.pmi1.io.xltable.XLTable Class Reference

class to read, analyze, and plot xlink data on contact maps Canonical way to read the data: 1) load sequences and name them 2) load coordinates for those sequences from PDB file 3) add crosslinks 4) create contact map 5) plot More...

Detailed Description

class to read, analyze, and plot xlink data on contact maps Canonical way to read the data: 1) load sequences and name them 2) load coordinates for those sequences from PDB file 3) add crosslinks 4) create contact map 5) plot

Deprecated:
As of IMP release 2.8.

See the IMP Deprecation Policy for more information about deprecation in IMP. Use PMI2, IMP.pmi1.macros.AnalysisReplicaExchange, instead

Note
This class is only available in Python.

Definition at line 28 of file xltable.py.

Public Member Functions

def load_crosslinks
 read crosslinks from a CSV file. More...
 
def load_pdb_coordinates
 read coordinates from a pdb file. More...
 
def load_rmf_coordinates
 read coordinates from a rmf file. More...
 
def load_sequence_from_fasta_file
 read sequence. More...
 
def plot_table
 plot the xlink table with optional contact map. More...
 
def set_residue_pairs_to_display
 select the atom names of residue pairs to plot on the contact map list of residues types must be single letter code e.g. More...
 
def setup_contact_map
 loop through each distance map and get frequency of contacts More...
 

Member Function Documentation

def IMP.pmi1.io.xltable.XLTable.load_crosslinks (   self,
  CrossLinkDataBase,
  distance_field = None 
)

read crosslinks from a CSV file.

provide a CrossLinkDataBaseKeywordsConverter to explain the columns is the optional keyword for the distance to be read form the file. This can skip the rmf reading to calculate the distance of cross-links if already provided in the csv file.

Definition at line 289 of file xltable.py.

def IMP.pmi1.io.xltable.XLTable.load_pdb_coordinates (   self,
  pdbfile,
  chain_to_name_map 
)

read coordinates from a pdb file.

also appends to distance maps

Parameters
pdbfilefile for reading coords
chain_to_name_mapcorrespond chain ID with protein name (will ONLY read these chains) Key: PDB chain ID. Value: Protein name (set in sequence reading)

ote This function returns an error if the sequence for each chain has NOT been read

Definition at line 161 of file xltable.py.

def IMP.pmi1.io.xltable.XLTable.load_rmf_coordinates (   self,
  rmf_name,
  rmf_frame_index,
  chain_names,
  nomap = False 
)

read coordinates from a rmf file.

It needs IMP to run. rmf has been created using IMP.pmi1 conventions. It gets the highest resolution automatically. Also appends to distance maps

Parameters
rmf_namefile for reading coords
rmf_frame_indexframe index from the rmf
nomapDefault False, if True it will not calculate the contact map

Definition at line 199 of file xltable.py.

def IMP.pmi1.io.xltable.XLTable.load_sequence_from_fasta_file (   self,
  fasta_file,
  id_in_fasta_file,
  protein_name 
)

read sequence.

structures are displayed in the same order as sequences are read. fasta_file: file to read id_in_fasta_file: id of desired sequence protein_name: identifier for this sequence (use same name when handling coordinates) can provide the fasta name (for retrieval) and the protein name (for storage)

Definition at line 145 of file xltable.py.

def IMP.pmi1.io.xltable.XLTable.plot_table (   self,
  prot_listx = None,
  prot_listy = None,
  no_dist_info = False,
  confidence_info = False,
  filter = None,
  display_residue_pairs = False,
  contactmap = False,
  filename = None,
  confidence_classes = None,
  alphablend = 0.1,
  scale_symbol_size = 1.0,
  gap_between_components = 0,
  dictionary_of_gaps = {},
  colormap = cm.binary,
  crosslink_threshold = None,
  colornorm = None,
  cbar_labels = None,
  labels = False,
  show_mpld3 = False,
  color_crosslinks_by_distance = True 
)

plot the xlink table with optional contact map.

prot_listx: list of protein names on the x-axis prot_listy: list of protein names on the y-axis no_dist_info: plot only the cross-links as grey spots confidence_info: filter: list of tuples to filter on. each one contains: keyword in the database to be filtered on relationship ">","==","<" a value example ("ID_Score",">",40) display_residue_pairs: display all pairs defined in self.residue_pair_list contactmap: display the contact map filename: save to file (adds .pdf extension) confidence_classes: alphablend: scale_symbol_size: rescale the symbol for the crosslink gap_between_components: the numbeber of residues to leave blannk between each component dictionary_of_gaps: add extra space after the given protein. dictionary_of_gaps={prot_name:extra_gap}

Definition at line 580 of file xltable.py.

def IMP.pmi1.io.xltable.XLTable.set_residue_pairs_to_display (   self,
  residue_type_pair 
)

select the atom names of residue pairs to plot on the contact map list of residues types must be single letter code e.g.

residue_type_pair=("K","K")

Definition at line 322 of file xltable.py.

def IMP.pmi1.io.xltable.XLTable.setup_contact_map (   self)

loop through each distance map and get frequency of contacts

Definition at line 337 of file xltable.py.


The documentation for this class was generated from the following file: