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IMP Reference Guide
2.6.2
The Integrative Modeling Platform
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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...
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
Definition at line 26 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... | |
| def IMP.pmi.io.xltable.XLTable.load_crosslinks | ( | self, | |
| CrossLinkDataBase, | |||
distance_field = None |
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| ) |
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 298 of file xltable.py.
| def IMP.pmi.io.xltable.XLTable.load_pdb_coordinates | ( | self, | |
| pdbfile, | |||
| chain_to_name_map | |||
| ) |
read coordinates from a pdb file.
also appends to distance maps
| pdbfile | file for reading coords |
| chain_to_name_map | correspond 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 170 of file xltable.py.
| def IMP.pmi.io.xltable.XLTable.load_rmf_coordinates | ( | self, | |
| rmf_name, | |||
| rmf_frame_index, | |||
| chain_names, | |||
nomap = False |
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| ) |
read coordinates from a rmf file.
It needs IMP to run. rmf has been created using IMP.pmi conventions. It gets the highest resolution automatically. Also appends to distance maps
| rmf_name | file for reading coords |
| rmf_frame_index | frame index from the rmf |
| nomap | Default False, if True it will not calculate the contact map |
Definition at line 208 of file xltable.py.
| def IMP.pmi.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 154 of file xltable.py.
| def IMP.pmi.io.xltable.XLTable.plot_table | ( | self, | |
prot_listx = None, |
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prot_listy = None, |
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no_dist_info = False, |
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confidence_info = False, |
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filter = None, |
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display_residue_pairs = False, |
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contactmap = False, |
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filename = None, |
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confidence_classes = None, |
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alphablend = 0.1, |
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scale_symbol_size = 1.0, |
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gap_between_components = 0, |
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dictionary_of_gaps = {}, |
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colormap = cm.binary, |
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crosslink_threshold = None, |
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colornorm = None, |
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cbar_labels = None, |
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labels = False, |
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show_mpld3 = False, |
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color_crosslinks_by_distance = True |
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| ) |
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 633 of file xltable.py.
| def IMP.pmi.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 323 of file xltable.py.
| def IMP.pmi.io.xltable.XLTable.setup_contact_map | ( | self | ) |
loop through each distance map and get frequency of contacts
Definition at line 338 of file xltable.py.
