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sort before dssp #649

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sort before dssp #649

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7 changes: 6 additions & 1 deletion vermouth/dssp/dssp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@
from ..pdb import pdb
from ..system import System
from ..processors.processor import Processor
from ..processors import SortMoleculeAtoms
from ..selectors import is_protein, selector_has_position, filter_minimal, select_all
from .. import utils
from ..log_helpers import StyleAdapter, get_logger
Expand Down Expand Up @@ -176,10 +177,14 @@ def run_mdtraj(system):
The secondary structure sequences of all the molecules are combined
in a single list without delimitation.
"""
sys_copy = system.copy()
# precaution for large systems; mdtraj requires all residues to be
# grouped together otherwise dssp fails
SortMoleculeAtoms(target_attr='atomid').run_system(sys_copy)
tmpfile_handle, tmpfile_name = tempfile.mkstemp(suffix='.pdb', text=True,
dir='.', prefix='dssp_in_')
tmpfile_handle = os.fdopen(tmpfile_handle, mode='w')
tmpfile_handle.write(pdb.write_pdb_string(system, conect=False))
tmpfile_handle.write(pdb.write_pdb_string(sys_copy, conect=False))
tmpfile_handle.close()

try:
Expand Down
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