def cull_main(similarities, thresholdPercentage, representativeChains, adjType, representativesReverse={}):
"""Perform the PDB redundancy removal.
@param similarities: A record of the percentage sequence identity between the chains/entries up for culling.
@type similarities : dictionary or file name (string)
@param thresholdPercentage: The maximum permissible percentage sequence identity that any two chains/entries may possess.
@type thresholdPercentage : float
"""
# Create the sparsematrix of the protein similarity graph.
if adjType == 'chain':
adjacent, proteinNames = adjlistcreation.pdb_chain_main(similarities, thresholdPercentage, representativeChains)
elif adjType == 'entry':
adjacent, proteinNames = adjlistcreation.pdb_entry_main(similarities, thresholdPercentage, representativeChains, representativesReverse)
# Choose which proteins to remove from the similarity graph.
if proteinNames == []:
# This is True if there are no similarities greater than the given percentage sequence identity. If there are no
# chains that are too similar, then there is no need to cull any chains from the network.
proteinsToCull = []
else:
# Choose which chains to remove from the similarity graph.
proteinsToCull, proteinsToKeep = Leafcull.main(adjacent, proteinNames)
return proteinsToCull
def cull_main(
similarities,
thresholdPercentage,
representativeChains,
adjType,
representativesReverse={},
verboseOutput=False,
startTime=0,
):
"""Perform the PDB redundancy removal.
@param similarities: A record of the percentage sequence identity between the chains/entries up for culling.
@type similarities : file name (string)
@param thresholdPercentage: The maximum permissible percentage sequence identity that any two chains/entries may possess.
@type thresholdPercentage : float
@param representativeChains: The names of the chains/entries that will compose the protein similarity graph.
@type representativeChains: set
@param adjType: 'chain' or 'entry' indicating the type of culling to be performed.
@type adjType: string
@param representativesReverse: A mapping of representative chains to the chains that they represent.
@type representativesReverse: dictionary
@param verboseOutput: Whether status updates should be printed out to the user.
@type verboseOutput: boolean
@param startTime: The time when the culling began. Used to output elapsed time.
@type startTime: integer
return @type: list
return @use: The redundant proteins to be removed from teh dataset.
"""
# Create the sparsematrix of the protein similarity graph.
if verboseOutput:
print "Creating the adjacency matrix. Time elapsed: ", time.time() - startTime
if adjType == "chain":
adjacent, proteinNames = adjlistcreation.pdb_chain_main(similarities, thresholdPercentage, representativeChains)
elif adjType == "entry":
adjacent, proteinNames = adjlistcreation.pdb_entry_main(
similarities, thresholdPercentage, representativeChains, representativesReverse
)
# Choose which proteins to remove from the similarity graph.
if proteinNames == []:
if verboseOutput:
print "No similarities found. Culling not needed. Time elapsed: ", time.time() - startTime
# This is True if there are no similarities greater than the given percentage sequence identity. If there are no
# chains that are too similar, then there is no need to cull any chains from the network.
proteinsToCull = []
else:
if verboseOutput:
print "Performing the culling. Time elapsed: ", time.time() - startTime
# Choose which chains to remove from the similarity graph.
proteinsToCull, proteinsToKeep = Leafcull.main(adjacent, proteinNames)
if verboseOutput:
print "Culling finished. Time elapsed: ", time.time() - startTime
return proteinsToCull
