Featurization Error

[matany58]

I noticed the error below while executing combind featurize features docking//_pv.maegz

assert os.path.exists(csv)
AssertionError

Does anyone know which CSV file is missing and in which directory/folder

[jpaggi]

I suspect this is arising in the mcss feature computation? If so, it is complaining that the mcss computation failed in an unexpected way. This part of the code requires use of Schrodinger "canvasMCS" utility. The code assumes that executable is at "$SCHRODINGER/utilities/canvasMCS" works. You might need to set the SCHRODINGER environmental variable to make this work.

[matany58]

How do I set the SCHRODINGER environment to make this work?
The error is initiated by
Computing mcss similarities.
ERROR: non-zero return code [1] from /hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/canvas-v4.7/bin/Linux-x86_64/canvasMCS

[matany58]

The executable is in schrodinger/install/2021-1/canvas-v4.7/bin/Linux-x86_64/canvasMCS
Please how do I make this work?

Thanks for your assistance

[jpaggi]

Ah I see. Sorry, I did not realize that some schrodinger installations have different directory structures.

You can solve this issue by updating line 72 of features/mcss.py from
cmd = "$SCHRODINGER/utilities/canvasMCS -imae {} -ocsv {} -stop 10 -atomtype C {}"
to
cmd = "schrodinger/install/2021-1/canvas-v4.7/bin/Linux-x86_64/canvasMCS -imae {} -ocsv {} -stop 10 -atomtype C {}"

You should use the absolute path to canvasMCS, instead of this relative path, so that the code can execute from any directory.

[matany58]

I change it but still having the same error the full error is
subprocess complete
Computing mcss similarities.
Traceback (most recent call last):
File "/hpcf/authorized_apps/rhel7_apps/combind/combind/combind", line 355, in
main()
File "/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/internal/lib/python3.8/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/internal/lib/python3.8/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/internal/lib/python3.8/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/internal/lib/python3.8/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/internal/lib/python3.8/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/hpcf/authorized_apps/rhel7_apps/combind/combind/combind", line 225, in featurize
features.compute_pair_features(poseviewers,
File "/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind/features/features.py", line 196, in compute_pair_features
self.compute_mcss(poses1, poses2, out)
File "/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind/features/features.py", line 256, in compute_mcss
rmsds = mcss(poses1, poses2, self.mcss_file)
File "/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind/features/mcss.py", line 32, in mcss
mcss = compute_mcss(st1, st2, mcss_types_file)
File "/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind/features/mcss.py", line 95, in compute_mcss
assert os.path.exists(csv)

[matany58]

Please any idea on how to resolve this issue?

[jpaggi]

Hello, could you add the following two print statements and share the output with me:

At line 83 of features/mcss.py:
print(cmd.format(os.path.basename(mae), os.path.basename(csv), os.path.abspath(mcss_types_file)))

At line 92 of features/mcss.py:
print(str(r.stderr))

Thank you!

[matany58]

Okay

[matany58]

Error generated is below;

Extracting glide scores.
Extracting names.
Computing RMSDs to native poses
Computing interaction fingerprints.
Computing interaction similarities.
Computing shape similarities.
$SCHRODINGER/shape_screen -shape poses1.maegz -screen poses2.maegz -pharm -norm 1 -distinct -inplace -NOJOBID
subprocess complete
Computing mcss similarities.
cmd:
/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/canvas-v4.7/bin/Linux-x86_64/canvasMCS -imae temp.maegz -ocsv temp.csv -stop 10 -atomtype C /home/manyanwu/features/mcss16.typ
Stdout:
None
Stderr:
b'cannot open /home/manyanwu/features/mcss16.typ to load rules\n\n'
Traceback (most recent call last):
File "/hpcf/authorized_apps/rhel7_apps/combind/combind/combind", line 355, in
main()
File "/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/internal/lib/python3.8/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/internal/lib/python3.8/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/internal/lib/python3.8/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/internal/lib/python3.8/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/hpcf/authorized_apps/rhel7_apps/schrodinger/install/2021-1/internal/lib/python3.8/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/hpcf/authorized_apps/rhel7_apps/combind/combind/combind", line 225, in featurize
features.compute_pair_features(poseviewers,
File "/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind/features/features.py", line 196, in compute_pair_features
self.compute_mcss(poses1, poses2, out)
File "/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind/features/features.py", line 256, in compute_mcss
rmsds = mcss(poses1, poses2, self.mcss_file)
File "/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind/features/mcss.py", line 32, in mcss
mcss = compute_mcss(st1, st2, mcss_types_file)
File "/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind/features/mcss.py", line 102, in compute_mcss
assert os.path.exists(csv)
AssertionError

[matany58]

It appears that it is looking for mcss16.typ in my home directory /home/manyanwu/features/mcss16.typ but the file is in the directory /research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind/features

[jpaggi]

Before running combind, you need to run source setup.sh from the root of the combind repo (/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind). This will set the path correctly.

[matany58]

got it working I run export COMBINDHOME=/research/rgs01/applications/hpcf/authorized_apps/rhel7_apps/combind/combind