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Correctly read/write CONECT in PDB files - Thanks Simon Sun
Simon found issues when reading and writing CONECT statements in PDB io and provided code to fix it. yay Reading: OpenStructure did not read CONECT statements at all. By default, it still doesnt. Many PDB files out there don't provide these statements and we really don't want to rely on them. We rather want to assign connectivity based on the chemical component dictionary from the PDB. However, a valid use case are novel compounds that are not in the component dictionary. Reading connect statements can now be enabled in the pdb reader through the IOProfile. This may give issues in processing after reading. OpenStructure implements processors that are responsible for connectivity. Now that we build some of the connectivity already at the reading stage, this might cause trouble. To remedy most of the nightmares that can come out of that, the processors can now optionally skip connectivities between Hetatoms. Writing: That was a plain bug when writing CONECT statements for bond orders > 1.
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- modules/conop/doc/connectivity.rst 16 additions, 2 deletionsmodules/conop/doc/connectivity.rst
- modules/conop/pymod/export_heuristic.cc 2 additions, 1 deletionmodules/conop/pymod/export_heuristic.cc
- modules/conop/pymod/export_processor.cc 2 additions, 0 deletionsmodules/conop/pymod/export_processor.cc
- modules/conop/pymod/export_rule_based.cc 2 additions, 1 deletionmodules/conop/pymod/export_rule_based.cc
- modules/conop/src/heuristic.hh 3 additions, 2 deletionsmodules/conop/src/heuristic.hh
- modules/conop/src/processor.cc 6 additions, 0 deletionsmodules/conop/src/processor.cc
- modules/conop/src/processor.hh 16 additions, 8 deletionsmodules/conop/src/processor.hh
- modules/conop/src/rule_based.hh 2 additions, 2 deletionsmodules/conop/src/rule_based.hh
- modules/conop/tests/test_heuristic_conop.cc 44 additions, 0 deletionsmodules/conop/tests/test_heuristic_conop.cc
- modules/conop/tests/test_rule_based_conop.cc 49 additions, 2 deletionsmodules/conop/tests/test_rule_based_conop.cc
- modules/io/doc/profile.rst 11 additions, 1 deletionmodules/io/doc/profile.rst
- modules/io/pymod/__init__.py 15 additions, 1 deletionmodules/io/pymod/__init__.py
- modules/io/pymod/export_pdb_io.cc 3 additions, 1 deletionmodules/io/pymod/export_pdb_io.cc
- modules/io/src/mol/io_profile.hh 6 additions, 4 deletionsmodules/io/src/mol/io_profile.hh
- modules/io/src/mol/pdb_reader.cc 69 additions, 5 deletionsmodules/io/src/mol/pdb_reader.cc
- modules/io/src/mol/pdb_reader.hh 3 additions, 1 deletionmodules/io/src/mol/pdb_reader.hh
- modules/io/src/mol/pdb_writer.cc 10 additions, 8 deletionsmodules/io/src/mol/pdb_writer.cc
- modules/io/tests/test_io_pdb.cc 8 additions, 6 deletionsmodules/io/tests/test_io_pdb.cc
- modules/io/tests/test_io_pdb.py 30 additions, 1 deletionmodules/io/tests/test_io_pdb.py
- modules/io/tests/testfiles/pdb/conect.pdb 14 additions, 14 deletionsmodules/io/tests/testfiles/pdb/conect.pdb
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