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.
Tests the CrosslinkerMover, using it to place and minimize 1,3,5-tris(bromomethyl)benzene in a peptide.
Author: Vikram K. Mulligan, Ph.D., Baker laboratory, University of Washington (vmullig@uw.edu).
Brief Diff:
Files /home/benchmark/working_dir/main:62147/threefoldlinkermover_tbmb/log and /home/benchmark/working_dir/main:62148/threefoldlinkermover_tbmb/log differ
Full Diff:
diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62147/threefoldlinkermover_tbmb/log /home/benchmark/working_dir/main:62148/threefoldlinkermover_tbmb/log
37c37
< core.import_pose.import_pose: File 'inputs/TBStest1.pdb' automatically determined to be of type PDB
---
> core.import_pose.import_pose: File 'inputs/TBStest1.pdb' automatically determined to be of type PDB from contents.