ModelData
(model_name, structure_name, model_fname, structure_fname, log_fname, tmscore, rmsd, nr_residues_common)[source]¶Bases: object
Class to store model data
Attributes: |
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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)
Methods
binary_avail (binary) |
Check if TM binary is available |
compare_structures (models, structures[, …]) |
Compare a list of model structures to a second list of reference structures |
comparison (models, structures) |
Compare a list of model structures to a second list of reference structures |
compare_structures
(models, structures, all_vs_all=False)[source]¶Compare a list of model structures to a second list of reference structures
Parameters: |
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Returns: |
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TMapps
(executable, method, wdir=None, **kwargs)[source]¶Bases: object
Superclass of TMscore and TMalign
Attributes: |
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Methods
binary_avail (binary) |
Check if TM binary is available |
comparison (models, structures) |
Compare a list of model structures to a second list of reference structures |
binary_avail
(binary)[source]¶Check if TM binary is available
Returns: |
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Raises: |
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comparison
(models, structures)[source]¶Compare a list of model structures to a second list of reference structures
Parameters: |
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Returns: |
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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)
Methods
binary_avail (binary) |
Check if TM binary is available |
compare_structures (models, structures[, …]) |
Compare a list of model structures to a second list of reference structures |
comparison (models, structures) |
Compare a list of model structures to a second list of reference structures |
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: |
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Returns: |
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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.