upgraded to new RCSB webservices

mmtfPyspark/webfilters/blastCluster.py

@@ -0,0 +1,69 @@
+#!/user/bin/env python
+'''blastCluster.py
+
+This filter passes through representative structures from the RCSB PDB
+MMseqs2 clusters. A sequence identity thresholds needs to be specified.
+The representative for each cluster is the first chain in a cluster.
+
+References
+----------
+BlastClust cluster field names:
+`Field names https://www.rcsb.org/docs/programmatic-access/file-download-services`_
+
+Examples
+--------
+Find representative PDB entries at 90% sequence identity:
+>>> sequenceIdentity = 90
+>>> pdb = pdb.filter(BlastCluster(90))
+
+'''
+__author__ = "Mars (Shih-Cheng) Huang"
+__maintainer__ = "Mars (Shih-Cheng) Huang"
+__email__ = "[email protected]"
+__version__ = "0.2.0"
+__status__ = "Done"
+
+import urllib.request
+
+
+class BlastCluster(object):
+	'''Filters blast clusters
+
+	Attributes
+	----------
+	sequenceIdentity : int
+	   sequence indentity for blast
+	'''
+	def __init__(self, sequenceIdentity):
+
+		clusters = self.get_blast_cluster(sequenceIdentity)
+
+		self.pdbIds = set()
+
+		for protein in clusters:
+			self.pdbIds.add(protein)
+			self.pdbIds.add(protein[:4])
+
+
+	def __call__(self, t):
+		return t[0] in self.pdbIds
+
+
+	def get_blast_cluster(self, sequenceIdentity):
+
+		if sequenceIdentity not in [30,40,50,70,90,95,100]:
+			raise Exception(f"Error: representative chains are not availible for \
+							sequence Identity {sequenceIdentity}.\n Must be in \
+							range [30,40,50,70,90,95,100]")
+			return
+
+		# coreUrl = "https://cdn.rcsb.org/sequence/clusters/"
+                coreUrl = "https://cdn.rcsb.org/resources/sequence/clusters/"
+		clusters = []
+		inputStream = urllib.request.urlopen(f"{coreUrl}bc-{sequenceIdentity}.out")
+
+		for line in inputStream:
+			line = str(line)[2:-3].replace("_",".").strip("\\n")
+			clusters += line.split(" ")
+
+		return clusters