Skip to content

problem with parseObjMol in pymol2glmol.py #13

@garyo

Description

@garyo

Hi; in pymol2glmol.py (https://raw.githubusercontent.com/Pymol-Scripts/Pymol-script-repo/master/pymol2glmol.py), there is this code:

def parseObjMol(obj):
    name = obj[0]
    ids = []
    sphere = []
    trace = []
    ribbon = []
    stick = []
    surface = []
    line = []
    cross = []
    smallSphere = []
    helix = []
    sheet = []
    colors = {}
    for atom in obj[5][7]:
        rep = atom[20] + [0] * 12
        serial = atom[22]
        ss = atom[10]
        bonded = (atom[25] == 1)
        if (rep[5] == 1):
            ribbon.append(serial)
        if (rep[1] == 1):
            sphere.append(serial)
        if (rep[2] == 1):
            surface.append(serial)
        if (rep[7] == 1):
            line.append(serial)
        if (rep[6] == 1):
            trace.append(serial)
        if (rep[4] == 1 and not bonded):
            smallSphere.append(serial)
        if (rep[11] == 1 and not bonded):
            cross.append(serial)
        if (rep[0] == 1 and bonded):
            stick.append(serial)
        if (ss == 'S'):
            sheet.append(serial)
        if (ss == 'H'):
            helix.append(serial)
        ...

There seem to be two problems with this code. The first is that at least with python3 and recent pymol, the line rep = atom[20] + [0] * 12 causes an exception, because atom[20] is an int ("visRep"), and python can't do int + list. I worked around that by doing rep = [atom[20]] + [0] * 12. But now I'm confused because the last part of the code checks for various elements of rep, but rep is never set to anything but all zeros (except the first element). So again it seems to be something wrong with the initialization of rep.
Any hints?

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions