Better debugging on CIF file read in. (#356)
Issue #355 indicates that errors in mmCIF parsing are not well handled. This commit attempts to fix that in two ways.
The first is to add a 'from extension' fallback if the from-contents parser doesn't like it. We assume that if you're naming it xyz.pdb, you want it parsed as a PDB.
The second is to print the diagnostics report for mmCIF files to the tracer -- this is what's being used to autodetect mmCIF format, so better transparency of what the failure issue is would be warranted.
Integration test for the simple_cycpep_predict pilot app. This tests cyclic peptide prediction with angle minimization.
Author: Vikram K. Mulligan, Ph.D., Baker laboratory, University of Washington (vmullig@uw.edu).
Brief Diff:
Files /home/benchmark/working_dir/main:62147/simple_cycpep_predict_angle/log2 and /home/benchmark/working_dir/main:62148/simple_cycpep_predict_angle/log2 differ
Full Diff:
diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62147/simple_cycpep_predict_angle/log2 /home/benchmark/working_dir/main:62148/simple_cycpep_predict_angle/log2
72c72
< core.import_pose.import_pose: File 'inputs/native.pdb' automatically determined to be of type PDB
---
> core.import_pose.import_pose: File 'inputs/native.pdb' automatically determined to be of type PDB from contents.