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IMP Reference Guide
2.5.0
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 21 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 upperbound: maximum distance to be marked More... | |
| def IMP.pmi.io.xltable.XLTable.load_crosslinks | ( | self, | |
| CrossLinkDataBase | |||
| ) |
read crosslinks from a CSV file.
provide a CrossLinkDataBaseKeywordsConverter to explain the columns
Definition at line 252 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) |
ote This function returns an error if the sequence for each chain has NOT been read
Definition at line 122 of file xltable.py.
| def IMP.pmi.io.xltable.XLTable.load_rmf_coordinates | ( | self, | |
| rmf_name, | |||
| rmf_frame_index, | |||
| chain_names | |||
| ) |
read coordinates from a rmf file.
It needs IMP to run. rmf has been created using IMP.pmi conventions. It gets the highest resolution atomatically. Also appends to distance maps
| rmf_name | file for reading coords |
| rmf_frame_index | frame index from the rmf |
Definition at line 162 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 104 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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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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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:
Definition at line 309 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 259 of file xltable.py.
| def IMP.pmi.io.xltable.XLTable.setup_contact_map | ( | self | ) |
loop through each distance map and get frequency of contacts upperbound: maximum distance to be marked
Definition at line 274 of file xltable.py.