When reading a PDB generated by Packmol, an empty REMARK field is generated before the atom fields and this causes the parsing error.
Example:
HEADER
TITLE Built with Packmol
REMARK Packmol generated pdb file
REMARK Home-Page: http://m3g.iqm.unicamp.br/packmol
REMARK
HETATM 1 C1 LIG A 1 -0.463 -1.344 0.002 0.00 1.00 C
HETATM 2 C2 LIG A 1 -1.369 -0.309 0.001 0.00 1.00 C
HETATM 3 C3 LIG A 1 -0.895 1.105 -0.002 0.00 1.00 C
...
The error:
Unhandled exception: Cursor out of current line (Chem::ParseException)
from /path/lib/chem/src/chem/pull_parser.cr:396:7 in 'error'
from /path/lib/chem/src/chem/pull_parser.cr:99:34 in 'at'
from /path/lib/chem/src/chem/formats/pdb.cr:145:16 in 'decode_header'
from /path/lib/chem/src/chem/formats/pdb.cr:39:7 in 'next_entry'
from /path/lib/chem/src/chem/format_reader.cr:181:7 in 'read_entry'
from /path/lib/chem/src/chem/register_format.cr:270:1 in 'from_pdb'
from /path/src/utilities/testing.cr:116:5 in '__crystal_main'
from /opt/crystal-1.13.1-1/share/crystal/src/crystal/main.cr:118:5 in 'main_user_code'
from /opt/crystal-1.13.1-1/share/crystal/src/crystal/main.cr:104:7 in 'main'
from /opt/crystal-1.13.1-1/share/crystal/src/crystal/main.cr:130:3 in 'main'
from /lib/x86_64-linux-gnu/libc.so.6 in '__libc_start_main'
from /path/bin/testing in '_start'
from ???
When reading a PDB generated by Packmol, an empty REMARK field is generated before the atom fields and this causes the parsing error. Example:
The error: