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config_template.yml
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config_template.yml
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# Configuration file for PyMol session representations.
# colors are defined with names, see: https://pymolwiki.org/index.php/Color_Values
chains:
chainA: # mandatory
name: <NAME TO DISPLAY FOR CHAIN A> # mandatory
color: <COLOR NAME> # mandatory
regions: # optional
region_1: # optional, if set the name of the region is the key for the region and the following fields are mandatory
start: <START POSITION>
end: <END POSITION>
color: <COLOR NAME> # mandatory
POI: # optional Position Of Interest
alterations: # optional
# reset positions in the chain depending if deletion or insertions events happens compared to the reference
# genome where the mutations are listed:
# for deletions, a positive number of the count of deleted residues. i.e del24-27, 24: 4
# for insertions, a negative number of the count of inserted residues. i.e 215insAPE: 215: -3
<EVENT1 POSITION>: <ALTERATION1 VALUE>
<EVENT2 POSITION>: <ALTERATION2 VALUE>
...
positions: # mutation positions index on the reference genome
- <POSITION MUTATION 1>
- <POSITION MUTATION 2>
- ...
contact color: <COLOR NAME> # mandatory
chainB: # mandatory
name: <NAME TO DISPLAY FOR CHAIN B> # mandatory
color: <COLOR NAME> # mandatory
regions: # optional
region_1: # optional, if set the name of the region is the key for the region and the following fields are mandatory
start: <START POSITION>
end: <END POSITION>
color: <COLOR NAME>
POI: # optional
alterations: # optional
<EVENT1 POSITION>: <ALTERATION1 VALUE>
<EVENT2 POSITION>: <ALTERATION2 VALUE>
...
positions: # mandatory
- <POSITION MUTATION 1>
- <POSITION MUTATION 2>
- ...
contact color: <COLOR NAME> # mandatory
chainC: # optional
...
# configuration of the polar_pairs function, see references/polarPairs.py
contacts:
# contact distance of atoms between chains in Angstroms
cutoff: <FLOAT DISTANCE> # optional, default is 4.0
angle: <FLOAT DEGREE> # optional, default is 63.0
# configuration of the heatmap generated with Altair
heatmap:
# dimensions in pixels
width: <INT PIXELS>
height: <INT PIXELS>
# format: html or json
format: <HTML OR JSON>