IO Profiles for entity importer¶
As of version 1.1, OpenStructure introduces IO profiles to fine-tune the
behaviour of the molecule importers. A profile aggregates flags and methods
that affect the import of molecular structures and influence both the behaviour
of conop and io.
Basic usage of IO profiles¶
You are most certainly reading this document because you were having trouble
loading PDB files. In that case, as a first step you will want to set the
profile parameter of LoadPDB(). The profile parameter can either be the
name of a profile or an instance of IOProfile. Both of the following
two examples are equivalent:
ent = io.LoadPDB('weird.pdb', profile=io.profiles['SLOPPY'])
ent = io.LoadPDB('weird.pdb', profile='SLOPPY')
Profiles is a dictionary-like object containing all the profiles known to
OpenStructure. You can add new ones by inserting them into the dictionary.
If you are loading a lot of structures, you may want to set the default profile
to avoid having to pass the profile every time you load a structure.
This is done by assigning a different profile to DEFAULT:
io.profiles['DEFAULT']='SLOPPY'
ent = io.LoadPDB('weird.pdb')
Again, you can either assign the name of the profile, or the profile itself. If none of the profiles available by default suits your needs, feel free to create one to your liking.
Available default profiles¶
The following profiles are available by default. For a detailed description of
what the different parameters mean, consult the documentation of
IOProfile.
STRICT
This profile is the default (also available as DEFAULT) and is known to work very well with PDB files coming from the official PDB website. It is equivalent to the following profile:
IOProfile(dialect='PDB', fault_tolerant=False, processor=conop.RuleBasedProcessor(conop.GetDefaultLib()))
SLOPPY:
This profile loads essentially everything
IOProfile(dialect='PDB', fault_tolerant=True, processor=conop.RuleBasedProcessor(conop.GetDefaultLib()))
CHARMM:
This format is the default when importing CHARMM trajectories and turns on the CHARMM specific compound dictionary.
IOProfile(dialect='CHARMM', fault_tolerant=True, processor=conop.RuleBasedProcessor(conop.GetDefaultLib()))
Note
The profiles are setup at the first import of the io module, i.e. something
like from ost import io or from ost.io import LoadPDB. The processor
parameter is set as stated above IF ost.conop.GetDefaultLib() returns
a valid compound library at that point in time. If not, the processor is set
to ost.conop.HeuristicProcessor(). Calling
ost.conop.SetDefaultLib() has thus no immediate effect on the default
profiles! Two exceptions: ost.io.LoadPDB() and
ost.io.LoadMMCIF() have a logic in place to override the processor of
the default profiles with ost.conop.GetDefaultLib(), using
HeuristicProcessor respectively. This logic does not apply to user
defined profiles.
The IOProfile Class¶
- class IOProfile(dialect='PDB', fault_tolerant=False, join_spread_atom_records=False, no_hetatms=False, calpha_only=False, read_conect=False, processor=None)¶
Aggregates flags that control the import of molecular structures.
- dialect¶
- Type:
str
The dialect to be used for PDB files. At the moment, this is either CHARMM or PDB. More will most likely come in the future. By setting the dialect to CHARMM, the loading is optimized for CHARMM PDB files. This turns on support for chain names with length up to 4 characters (column 72-76) and increase the size of the residue name to 4 residues.
- fault_tolerant¶
- Type:
bool
If true, the import will succeed, even if the PDB contains faulty records. The faulty records will be ignored and import continues as if the records are not present.
- join_spread_atom_records¶
- Type:
bool
If set to true, atom records belonging to the same residue are joined, even if they do not appear sequentially in the PDB file.
- no_hetatms¶
- Type:
bool
If set to true, HETATM records are ignored during import.
- calpha_only¶
- Type:
bool
When set to true, forces the importer to only load atoms named CA. This is most useful in combination with protein-only PDB files to speed up subsequent processing and importing.
- read_conect¶
- Type:
bool
Only relevant when reading files in PDB format. When set to true, reads CONECT statements and applies them in the PDB reader. This can result in hydrogen bonds, salt bridges etc. to be connected. Check the PDB format definition for more info. This may cause issues in subsequent processing, such as bonds being overriden, or extra, inconsistent bonds, as the processor suddenly has two separate sources of connectivity. For the use case where the input PDB file contains valid CONECT statements for all hetatms, you may want to disable processing of bonds between them in
ost.conop.Processor.connect_hetatm
- processor¶
-
Controls connectivity processing of loaded
ost.mol.EntityHandle. Even though its a keyword argument, processing will fail if not given.