Branch:
lyskov/rosetta-ci:main
「revision: №1」
Test:
colab.none.root.ColabDesign
SubTest:
ColabDesign/af/examples/partial_hallucination_rewire
SubTest files:
「file-system-view」
Daemon:
devel
State:
ColabDesign/af/examples/partial_hallucination_rewire
Input Notebook: ColabDesign/af/examples/partial_hallucination_rewire.ipynb
Output Notebook: /root/working_dir/ColabDesign_af_examples_partial_hallucination_rewire.ipynb
Executing: 0% 0/7 [00:00<?, ?cell/s]Executing notebook with kernel: python3
Executing: 14% 1/7 [00:00<00:05, 1.12cell/s]
Executing: 43% 3/7 [00:01<00:02, 1.70cell/s]
Executing: 57% 4/7 [00:02<00:01, 1.90cell/s]
Executing: 71% 5/7 [00:02<00:01, 1.74cell/s]
Traceback (most recent call last):
File "/usr/local/bin/papermill", line 8, in <module>
sys.exit(papermill())
File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 235, in papermill
execute_notebook(
File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 131, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 251, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [3]":
AssertionErrorTraceback (most recent call last)
<ipython-input-3-4bc5e61a63f6> in <cell line: 7>()
5 # balance weights [dgram_cce = restraint weight], [con = hallucination weight]
6 model.set_weights(dgram_cce=1, con=0)
----> 7 model.design_3stage(300,100,10)
~/working_dir/colabdesign/af/design.py in design_3stage(self, soft_iters, temp_iters, hard_iters, ramp_recycles, **kwargs)
374 if soft_iters > 0:
375 if verbose: print("Stage 1: running (logits → soft)")
--> 376 self.design_logits(soft_iters, e_soft=1,
377 ramp_recycles=ramp_recycles, **kwargs)
378 self._tmp["seq_logits"] = self.aux["seq"]["logits"]
~/working_dir/colabdesign/af/design.py in design_logits(self, iters, **kwargs)
352 def design_logits(self, iters=100, **kwargs):
353 ''' optimize logits '''
--> 354 self.design(iters, **kwargs)
355
356 def design_soft(self, iters=100, temp=1, **kwargs):
~/working_dir/colabdesign/af/design.py in design(self, iters, soft, e_soft, temp, e_temp, hard, e_hard, step, e_step, dropout, opt, weights, num_recycles, ramp_recycles, num_models, sample_models, models, backprop, callback, save_best, verbose)
346 lr_scale = step * ((1 - self.opt["soft"]) + (self.opt["soft"] * self.opt["temp"]))
347
--> 348 self.step(lr_scale=lr_scale, num_recycles=num_recycles,
349 num_models=num_models, sample_models=sample_models, models=models,
350 backprop=backprop, callback=callback, save_best=save_best, verbose=verbose)
~/working_dir/colabdesign/af/design.py in step(self, lr_scale, num_recycles, num_models, sample_models, models, backprop, callback, save_best, verbose)
212
213 # run
--> 214 self.run(num_recycles=num_recycles, num_models=num_models, sample_models=sample_models,
215 models=models, backprop=backprop, callback=callback)
216
~/working_dir/colabdesign/af/design.py in run(self, num_recycles, num_models, sample_models, models, backprop, callback, model_nums, return_aux)
88 if model_nums is None:
89 model_nums = self._get_model_nums(num_models, sample_models, models)
---> 90 assert len(model_nums) > 0, "ERROR: no model params defined"
91
92 # loop through model params
AssertionError: ERROR: no model params defined
[NbConvertApp] Converting notebook /root/working_dir/ColabDesign_af_examples_partial_hallucination_rewire.ipynb to html
[NbConvertApp] Writing 294107 bytes to /root/working_dir/ColabDesign_af_examples_partial_hallucination_rewire.html
[NbConvertApp] Converting notebook /root/working_dir/ColabDesign_af_examples_partial_hallucination_rewire.ipynb to asciidoc
/usr/local/lib/python3.10/dist-packages/nbconvert/utils/pandoc.py:51: RuntimeWarning: You are using an unsupported version of pandoc (2.9.2.1).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
check_pandoc_version()
[NbConvertApp] Writing 6000 bytes to /root/working_dir/ColabDesign_af_examples_partial_hallucination_rewire.asciidoc
----------------------------------------------------------------
An Exception was encountered at `In [3]'.
== AfDesign - rewire (partial hallucination)
+*In[1]:*+
[source, ipython3]
----
#@title setup
import os
if not os.path.isdir("params"):
# get code
os.system("pip -q install git+https://github.com/sokrypton/ColabDesign.git@v1.1.1")
# for debugging
os.system("ln -s /usr/local/lib/python3.*/dist-packages/colabdesign colabdesign")
# download params
os.system("mkdir params")
os.system("apt-get install aria2 -qq")
os.system("aria2c -q -x 16 https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar")
os.system("tar -xf alphafold_params_2022-12-06.tar -C params")
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
import os
from colabdesign import mk_afdesign_model, clear_mem
from IPython.display import HTML
from google.colab import files
import numpy as np
def get_pdb(pdb_code=""):
if pdb_code is None or pdb_code == "":
upload_dict = files.upload()
pdb_string = upload_dict[list(upload_dict.keys())[0]]
with open("tmp.pdb","wb") as out: out.write(pdb_string)
return "tmp.pdb"
elif os.path.isfile(pdb_code):
return pdb_code
elif len(pdb_code) == 4:
os.system(f"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb")
return f"{pdb_code}.pdb"
else:
os.system(f"wget -qnc https://alphafold.ebi.ac.uk/files/AF-{pdb_code}-F1-model_v3.pdb")
return f"AF-{pdb_code}-F1-model_v3.pdb"
----
+*In[2]:*+
[source, ipython3]
----
# setup the model
clear_mem()
model = mk_afdesign_model(protocol="partial",
use_templates=False) # set True to constrain positions using template input
# define positions we want to constrain (input PDB numbering)
old_pos = "4-9,13-26,30-33,37-50,54-59,63-76,80-84,112-125"
model.prep_inputs(get_pdb("2MR5"), chain="A",
pos=old_pos, # define positions to contrain
length=100, # define if the desired length is different from input PDB
fix_seq=False) # set True to constrain the sequence
# set positions (if different from PDB)
# reorder the segments,
model.rewire(order = [1,2,3,0,7,4,5,6], # set order of segments
loops = [3,3,3,4,3,3,4], # change loop length inbetween segments
offset=0) # essentially loop length at the N term
print(model.opt["pos"])
----
+*Out[2]:*+
----
WARNING: 'model_1_ptm' not found
WARNING: 'model_2_ptm' not found
WARNING: 'model_3_ptm' not found
WARNING: 'model_4_ptm' not found
WARNING: 'model_5_ptm' not found
[17 18 19 20 21 22 26 27 28 29 30 31 32 33 34 35 36 37 38 39 43 44 45 46
0 1 2 3 4 5 6 7 8 9 10 11 12 13 94 95 96 97 98 99 51 52 53 54
55 56 57 58 59 60 61 62 63 64 68 69 70 71 72 76 77 78 79 80 81 82 83 84
85 86 87 88 89]
----
[#papermill-error-cell]#Execution using papermill encountered an
exception here and stopped:#
+*In[3]:*+
[source, ipython3]
----
# restart optimization
model.restart()
# model.set_seq(mode="wildtype") # initialize with wildtype sequence
# balance weights [dgram_cce = restraint weight], [con = hallucination weight]
model.set_weights(dgram_cce=1, con=0)
model.design_3stage(300,100,10)
----
+*Out[3]:*+
----
Stage 1: running (logits → soft)
AssertionErrorTraceback (most recent call last)
<ipython-input-3-4bc5e61a63f6> in <cell line: 7>()
5 # balance weights [dgram_cce = restraint weight], [con = hallucination weight]
6 model.set_weights(dgram_cce=1, con=0)
----> 7 model.design_3stage(300,100,10)
~/working_dir/colabdesign/af/design.py in design_3stage(self, soft_iters, temp_iters, hard_iters, ramp_recycles, **kwargs)
374 if soft_iters > 0:
375 if verbose: print("Stage 1: running (logits → soft)")
--> 376 self.design_logits(soft_iters, e_soft=1,
377 ramp_recycles=ramp_recycles, **kwargs)
378 self._tmp["seq_logits"] = self.aux["seq"]["logits"]
~/working_dir/colabdesign/af/design.py in design_logits(self, iters, **kwargs)
352 def design_logits(self, iters=100, **kwargs):
353 ''' optimize logits '''
--> 354 self.design(iters, **kwargs)
355
356 def design_soft(self, iters=100, temp=1, **kwargs):
~/working_dir/colabdesign/af/design.py in design(self, iters, soft, e_soft, temp, e_temp, hard, e_hard, step, e_step, dropout, opt, weights, num_recycles, ramp_recycles, num_models, sample_models, models, backprop, callback, save_best, verbose)
346 lr_scale = step * ((1 - self.opt["soft"]) + (self.opt["soft"] * self.opt["temp"]))
347
--> 348 self.step(lr_scale=lr_scale, num_recycles=num_recycles,
349 num_models=num_models, sample_models=sample_models, models=models,
350 backprop=backprop, callback=callback, save_best=save_best, verbose=verbose)
~/working_dir/colabdesign/af/design.py in step(self, lr_scale, num_recycles, num_models, sample_models, models, backprop, callback, save_best, verbose)
212
213 # run
--> 214 self.run(num_recycles=num_recycles, num_models=num_models, sample_models=sample_models,
215 models=models, backprop=backprop, callback=callback)
216
~/working_dir/colabdesign/af/design.py in run(self, num_recycles, num_models, sample_models, models, backprop, callback, model_nums, return_aux)
88 if model_nums is None:
89 model_nums = self._get_model_nums(num_models, sample_models, models)
---> 90 assert len(model_nums) > 0, "ERROR: no model params defined"
91
92 # loop through model params
AssertionError: ERROR: no model params defined
----
+*In[ ]:*+
[source, ipython3]
----
model.save_pdb(f"{model.protocol}.pdb")
model.plot_pdb()
----
+*In[ ]:*+
[source, ipython3]
----
HTML(model.animate())
----