ample.util.tm_util module¶

class 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¶

class 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)

compare_structures(models, structures, all_vs_all=False)[source]¶

Compare a list of model structures to a second list of reference structures

Parameters:	models (list) – List containing the paths to the model structure files structures (list) – List containing the paths to the reference structure files all_vs_all (bool) – Flag to compare all models against all structures
Returns:	entries
Return type:	list

class TMapps(executable, method, wdir='.', **kwargs)[source]¶

Bases: object

Superclass of TMscore and TMalign

entries¶

List containing the TMscore entries on a per-model basis

Type:	list

structure¶

Path to the reference structure

Type:	str

method¶

One of [TMscore|TMalign]

Type:	str

executable¶

Path to the TMscore executable

Type:	str

work_dir¶

Path to the working directory

Type:	str

static binary_avail(binary)[source]¶

Check if TM binary is available

binary : str: The binary name of TMscore or TMalign

Returns:
Return type:	bool
Raises:	`ValueError` – The binary is not TMalign or TMscore

comparison(models, structures)[source]¶

Compare a list of model structures to a second list of reference structures

Parameters:	models (list) – List containing the paths to the model structure files structures (list) – List containing the paths to the reference structure files
Returns:	entries – List of TMscore data entries on a per-model basis
Return type:	list

class 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:	models (list) – List containing the paths to the model structure files structures (list) – List containing the paths to the reference structure files fastas (list) – List containing the paths to the FASTA files all_vs_all (bool) – Flag to compare all models against all structures
Returns:	entries – List of TMscore data entries on a per-model basis
Return type:	list

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.

main()[source]¶