ihm.startmodel Python module¶
Classes to handle starting models.
The denominator used while calculating the sequence identity. One of these constants can be passed to
Arithmetic mean sequence length
Number of aligned residue pairs (not including the gaps)
Number of aligned positions (including gaps)
Another method not covered here
Length of the shorter sequence
SequenceIdentity(value, denominator=<SequenceIdentityDenominator.SHORTER_LENGTH: 1>)¶
Describe the identity between template and target sequences. See
- value – Percentage sequence identity.
- denominator – Way in which sequence identity was calculated -
Template(dataset, asym_id, seq_id_range, template_seq_id_range, sequence_identity, alignment_file=None)¶
A PDB file used as a comparative modeling template for part of a starting model.
- dataset (
Dataset) – Pointer to where this template is stored.
- asym_id (str) – The asymmetric unit (chain) to use from the template dataset (not necessarily the same as the starting model’s asym_id or the ID of the asym_unit in the final IHM model).
- seq_id_range (tuple) – The sequence range in the dataset that
is modeled by this template. Note that this numbering may differ
from the IHM numbering. See offset in
- template_seq_id_range (tuple) – The sequence range of the template that is used in comparative modeling.
- sequence_identity (
SequenceIdentityor float) – Sequence identity between template and the target sequence.
- alignment_file (
Location) – Reference to the external file containing the template-target alignment.
- dataset (
StartingModel(asym_unit, dataset, asym_id, templates=None, offset=0, metadata=None, software=None, script_file=None, description=None)¶
A starting guess for modeling of an asymmetric unit
- asym_unit (
AsymUnitRange) – The asymmetric unit (or part of one) this starting model represents.
- dataset (
Dataset) – Pointer to where this model is stored.
- asym_id (str) – The asymmetric unit (chain) to use from the starting model’s dataset (not necessarily the same as the ID of the asym_unit in the final model).
- templates (list) – A list of
Templateobjects, if this is a comparative model.
- offset (int) – Offset between the residue numbering in the dataset and the IHM model (the offset is added to the starting model numbering to give the IHM model numbering).
- metadata (list) – List of PDB metadata, such as HELIX records.
- software (
Software) – The software used to generate the starting model.
- script_file (
Location) – Reference to the external file containing the script used to generate the starting model (usually a
- description (str) – Additional text describing the starting model.
Atomobjects that represent this starting model. This allows the starting model coordinates to be embedded in the mmCIF file, which is useful if the starting model is not available elsewhere (or it has been modified).
The default implementation returns an internal list of atoms; it is usually necessary to subclass and override this method. See
ihm.model.Model.get_spheres()for more details.
Note that the returned atoms should be those used in modeling, not those stored in the file. In particular, the numbering scheme should be that used in the IHM model (add offset to the dataset numbering). If any residues were changed (for example it is common to mutate MSE in the dataset to MET in the modeling) the final mutated name should be used (MET in this case) and
get_seq_dif()overridden to note the change.
- asym_unit (
Represent a HELIX record from a PDB file.
SeqDif(db_seq_id, seq_id, db_comp_id, details=None)¶
- db_seq_id (int) – The residue index in the dataset.
- seq_id (int) – The residue index in the starting model. This should normally be db_seq_id + offset.
- db_comp_id (str) – The name of the residue in the dataset.
- details (str) – Descriptive text for the sequence difference.