load_fcz

load Foldcomp fcz binary into PyMOL

Foldcomp https://github.com/steineggerlab/foldcomp

PyMOL https://github.com/schrodinger/pymol-open-source

Usage

Before using this, install foldcomp via pip bundled with your PyMOL. And then,

run load_fcz.py
load_fcz yourfcz.fcz

Advanced usage

If defining this function in the importing.py of (core of) PyMOL, it allows loading fcz files when launching PyMOL. Example importing.py is available from this repo, but be very careful to replace your original importing.py by this because there may be version differences. Please take backups of your original importing.py before you edit it.

How to modify your importing py

0. Install foldcomp

Install foldcomp by pip bundled with PyMOL.

1. Add function (snippet below) to importing.py

import foldcomp
def load_fcz(filename, object=None, state=0, *, _self=cmd):
  with open(filename, "rb") as fcz:
  fcz_binary = fcz.read()
  (name, pdb) = foldcomp.decompress(fcz_binary)
  if (object == None):
    object = name
  cmd.read_pdbstr(pdb, object)

2. Add load_fcz to the loader list

At the bottom of importing.py, you will find the loader list. Add there your load_fcz. Example is below.

loadfunctions = {
        'mae': incentive_format_not_available_func,
        'pdbml': 'pymol.lazyio:load_pdbml',
        'cml': 'pymol.lazyio:load_cml',
        'mtz': load_mtz,
        'py': lambda filename, _self: _self.do("_ run %s" % filename),
        'pml': lambda filename, _self: _self.do("_ @%s" % filename),
        'pwg': _processPWG,
        'aln': 'pymol.seqalign:load_aln_multi',
        'fasta': _processFASTA,
        'png': 'pymol.viewing:load_png',
        'idx': load_idx,
        'pse': load_pse,
        'psw': load_pse,
        'ply': load_ply,
        'r3d': load_r3d,
        'cc1': load_cc1,
        'pdb': read_pdbstr,
        'stl': 'pymol.lazyio:read_stlstr',
        'dae': 'pymol.lazyio:read_collada',
        'fcz': load_fcz,

        # Incentive
        'vis': incentive_format_not_available_func,
        'moe': incentive_format_not_available_func,
        'phypo': incentive_format_not_available_func,
    }

3. Check if it works

From the commandline, launch pymol specifying some fcz files

pymol test.fcz test2.fcz

License

Follows PyMOL's and foldcomp license.

I'm not aware how to contribute to PyMOL software. Your advice will help.

yakomaxa / load_fcz_PyMOL