ModelData
(model_name, structure_name, model_fname, structure_fname, log_fname, tmscore, rmsd, nr_residues_common)[source]¶Bases: object
Class to store model data
gdtha
¶gdtts
¶log_fname
¶maxsub
¶model_fname
¶model_name
¶nr_residues_common
¶rmsd
¶seq_id
¶structure_fname
¶structure_name
¶tmscore
¶TMalign
(executable, wdir=None, **kwargs)[source]¶Bases: ample.util.tm_util.TMapps
Wrapper to handle TMalign scoring for one or more structures
Examples
>>> models = ["<MODEL_1>", "<MODEL_2>", "<MODEL_3>"]
>>> references = ["<REFERENCE_1>", "<REFERENCE>", "<REFERENCE>"]
>>> tm = TMalign("<PATH_TO_EXE>")
>>> entries = tm.compare_structures(models, references)
TMapps
(executable, method, wdir='.', **kwargs)[source]¶Bases: object
Superclass of TMscore and TMalign
binary_avail
(binary)[source]¶Check if TM binary is available
Returns: | |
---|---|
Return type: | bool |
Raises: | ValueError – The binary is not TMalign or TMscore |
TMscore
(executable, wdir=None, **kwargs)[source]¶Bases: ample.util.tm_util.TMapps
Wrapper to handle TMscoring for one or more structures
Examples
>>> models = ["<MODEL_1>", "<MODEL_2>", "<MODEL_3>"]
>>> references = ["<REFERENCE_1>", "<REFERENCE>", "<REFERENCE>"]
>>> tm = TMscore("<PATH_TO_EXE>")
>>> entries = tm.compare_structures(models, references)
compare_structures
(models, structures, fastas=None, all_vs_all=False)[source]¶Compare a list of model structures to a second list of reference structures
Parameters: | |
---|---|
Returns: | entries – List of TMscore data entries on a per-model basis |
Return type: |
Notes
If a FASTA sequence is provided, a much more accurate comparison can be carried out. However, to by-pass this there is also an option to run the comparison without it. This might work just fine for larger models.