Export to "flareplot"

[cbouy]

See GPCRviz/flareplot

Add a to_flareplot option to Fingerprint.

Script used for RDKit UGM poster to visualize difference in interactions between active and inactive PDB structures:

import json

jdict = {
    "edges": [],
    "trees": [{
        "treeLabel": "TMs",
        "treeProperties": []
    }],
    "tracks": [{
        "trackLabel": "TMs",
        "trackProperties": []
    }],
    "defaults": {
        "width": 2,
        "edgeOpacity": .85
    }
}
TM_COLORS = {
    "TM1": "#ccebc5",
    "TM2": "#e8ce85", #"#ffffb3",
    "TM3": "#bebada",
    "TM4": "#fb8072",
    "TM5": "#80b1d3",
    "TM6": "#bc80bd",
    "TM7": "#b3de69",
    "H8": "#fccde5",
}
EDGE_COLORS = {
    1: "#66c2a5",
    -1: "#fc8d62",
    0: "#a9a9a9"
}

def get_name(res):
    resid = plf.ResidueId.from_string(res)
    aa = mda.lib.util.inverse_aa_codes[resid.name]
    return f"{aa}{resid.number}"

# add nodes
residues = sorted(set([
    plf.ResidueId.from_string(r)
    for i in data.index.values
    for r in i
]))

for resid in residues:
    res = str(resid)
    resid = plf.ResidueId.from_string(res)
    info = get_opsd_info(resid.number)
    domain = info["Label"]
    color = TM_COLORS.get(domain, False)
    if color is False:
        continue
    name = get_name(res)
    jdict["trees"][0]["treeProperties"].append({
        "path": f"{domain}.{name}", "key": f"{resid.number}"
    })
    jdict["tracks"][0]["trackProperties"].append({
        "nodeName": name, "color": color, "size": .5
    })

done = set()
for (lres, pres), value in data.iteritems():
    color = EDGE_COLORS[value]
    key = frozenset([lres, pres])
    if key in done:
        continue
    done.add(key)
    jdict["edges"].append(
        {"name1": get_name(lres), "name2": get_name(pres), "frames": [0], "color": color}
    )

with open("flareplot.json", "w") as fh:
    json.dump(jdict, fh, indent=2)