def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'polymerSequenceExtractorTest')
self.sc = SparkContext(conf=conf)
pdbIds = ["1STP", "4HHB"]
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName('piscesTest')
self.sc = SparkContext(conf=conf)
# "4R4X.A" and "5X42.B" should pass filter
pdbIds = ["5X42","4R4X","2ONX","1JLP"]
self.pdb = downloadMmtfFiles(pdbIds,self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName('containsDProteinChainTest')
self.sc = SparkContext(conf=conf)
pdbIds = ['2ONX','1JLP','5X6H','5L2G','2MK1','2V5W','5XDP','5GOD']
self.pdb = downloadMmtfFiles(pdbIds,self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'secondaryStructureSegmentExtractorTest')
self.sc = SparkContext(conf=conf)
pdbIds = ["1STP"]
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'advancedQueryTest')
self.sc = SparkContext(conf=conf)
pdbIds = ["5JDE", "5CU4", "5L6W", "5UFU", "5IHB"]
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def test2(self):
pdbIds = ["5NV3"]
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
pdb_2 = self.pdb.flatMap(structureToBioassembly()) \
.flatMap(structureToProteinDimers(8,20,False, True))
self.assertTrue(pdb_2.count() == 12)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'containsDProteinChainTest')
pdbIds = [
"2ONX", "5VLN", "5VAI", "5JXV", "5K7N", "3PDM", "5MNX", "5I1R",
"5MON", "5LCB", "3J07"
]
self.sc = SparkContext(conf=conf)
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName('testrFreeFilter')
self.sc = SparkContext(conf=conf)
# 1AIE: all alpha protein 20 alpha out of 31 = 0.645 helical
# 1E0N: all beta protein, NMR structure with 10 models, 13 beta out of 27 = 0.481 sheet
# 1EM7: alpha + beta, 14 alpha + 23 beta out of 56 = 0.25 helical and 0.411 sheet
# 2C7M: 2 chains, alpha + beta (DSSP in MMTF doesn't match DSSP on RCSB PDB website)
pdbIds = ["1AIE", "1E0N", "1EM7", "2C7M"]
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'testContainsAlternativeLocations')
self.sc = SparkContext(conf=conf)
# 4QXX: has alternative location ids
# 2ONX: has no alternative location ids
pdbIds = ['4QXX', '2ONX']
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
self.pdb = self.pdb.map(lambda x: (x[0], x[1].set_alt_loc_list()))
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'containsDProteinChainTest')
self.sc = SparkContext(conf=conf)
# 5KE8: contains Zinc finger motif
# 1JLP: does not contain Zinc finger motif
# 5VAI: contains Walker P loop
pdbIds = ['5KE8', '1JLP', '5VAI']
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName('testrFreeFilter')
self.sc = SparkContext(conf=conf)
# 2ONX: 0.202 rfree x-ray resolution
# 2OLX: 0.235 rfree x-ray resolution
# 3REC: n/a NMR structure
# 1LU3: n/a EM structure
pdbIds = ['2ONX', '2OLX', '3REC', '1LU3']
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName('testrFreeFilter')
self.sc = SparkContext(conf=conf)
# 4MYA: deposited on 2013-09-27
# 1O6Y: deposited on 2002-10-21
# 3VCO: deposited on 2012-01-04
# 5N0Y: deposited on 2017-02-03
pdbIds = ['1O6Y', '4MYA', '3VCO', '5N0Y']
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName('testrFreeFilter')
pdbIds = ['1O6Y', '4MYA', '3VCO', '5N0Y']
# 1O6Y: released on 2003-01-30
# 4MYA: released on 2014-01-01
# 3VCO: released on 2013-03-06
# 5N0Y: released on 2017-05-24
self.sc = SparkContext(conf=conf)
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'testContainsAlternativeLocations')
self.sc = SparkContext(conf=conf)
# 2ONX: only L-protein chain
# 1JLP: single L-protein chains with non-polymer capping group (NH2)
# 5X6H: L-protein and non-std. DNA chain
# 5L2G: DNA chain
# 2MK1: D-saccharide
pdbIds = ['2ONX', '1JLP', '5X6H', '5L2G', '2MK1']
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def test4(self):
pdbIds = ["1BZ5"]
# C5-B4
# C6-B3
# D7-A2
# D8-A1
# E10-E9
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
pdb_4 = self.pdb.flatMap(structureToBioassembly()) \
.flatMap(structureToProteinDimers(9,20,False, True))
self.assertTrue(pdb_3.count() == 5)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'containsDProteinChainTest')
self.sc = SparkContext(conf=conf)
# 2ONX: only L-protein chain
# 1JLP: single L-protein chains with non-polymer capping group (NH2)
# 5X6H: L-protein and L-DNA chain
# 5L2G: L-DNA chain
# 2MK1: As of V5 of PDBx/mmCIF, saccharides seem to be represented as monomers,
# instead of polysaccharides, so none of these tests returns true anymore.
pdbIds = ['2ONX', '1JLP', '5X6H', '5L2G', '2MK1']
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'advancedQueryTest')
self.sc = SparkContext(conf=conf)
# 1PEN wildtype query 100 matches: 1PEN:1
# 1OCZ two entities wildtype query 100 matches: 1OCZ:1, 1OCZ:2
# 2ONX structure result for author query
# 5L6W two chains: chain L is EC 2.7.11.1, chain chain C is not EC 2.7.11.1
# 5KHU many chains, chain Q is EC 2.7.11.1
# 1F3M entity 1: chains A,B, entity 2: chains B,C, all chains are EC 2.7.11.1
pdbIds = ["1PEN", "1OCZ", "2ONX", "5L6W", "5KHU", "1F3M"]
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName('testrFreeFilter')
self.sc = SparkContext(conf=conf)
# 2ONX: only L-protein chain
# 1JLP: single L-protein chains with non-polymer capping group (NH2)
# 5X6H: L-protein and non-std. DNA chain
# 5L2G: DNA chain
# 2MK1: D-saccharide
# 5UZT: RNA chain (with std. nucleotides)
# 1AA6: contains SEC, selenocysteine (21st amino acid)
# 1NTH: contains PYL, pyrrolysine (22nd amino acid)
pdbIds = ['2ONX','1JLP','5X6H','5L2G','2MK1','5UZT','1AA6','1NTH']
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'containsDProteinChainTest')
self.sc = SparkContext(conf=conf)
# 2ONX: only L-protein chain
# 1JLP: single L-protein chains with non-polymer capping group (NH2)
# 5X6H: L-protein and DNA chain
# 5L2G: DNA chain
# 2MK1: D-saccharide
# 5UX0: 2 L-protein, 2 RNA, 2 DNA chains
# 2NCQ: 2 RNA chains
pdbIds = ['2ONX', '1JLP', '5X6H', '5L2G', '2MK1', '5UX0', '2NCQ']
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'testContainsAlternativeLocations')
self.sc = SparkContext(conf=conf)
# 1STP: 1 L-protein chain:
# 4HHB: 4 polymer chains
# 1JLP: 1 L-protein chains with non-polymer capping group (NH2)
# 5X6H: 1 L-protein and 1 DNA chain
# 5L2G: 2 DNA chain
# 2MK1: 0 polymer chains
# --------------------
# tot: 10 chains
pdbIds = ["1STP", "4HHB", "1JLP", "5X6H", "5L2G", "2MK1"]
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName(
'testContainsAlternativeLocations')
self.sc = SparkContext(conf=conf)
# 2ONX: only L-protein chain
# 1JLP: single L-protein chains with non-polymer capping group (NH2)
# 5X6H: L-protein and DNA chain (with std. nucleotides)
# 5L2G: DNA chain (with non-std. nucleotide)
# 2MK1: D-saccharide
# 5UZT: RNA chain (with std. nucleotides)
# 1AA6: contains SEC, selenocysteine (21st amino acid)
# 1NTH: contains PYL, pyrrolysine (22nd amino acid)
pdbIds = [
"2ONX", "1JLP", "5X6H", "5L2G", "2MK1", "5UZT", "1AA6", "1NTH"
]
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
def test3(self):
pdbIds = ["4GIS"]
# A3-A2
# A4-A1
# B5-A1
# B6-A2
# B6-B5
# B7-A3
# B7-A4
# B8-A4
# B8-B7
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
pdb_3 = self.pdb.flatMap(structureToBioassembly()) \
.flatMap(structureToProteinDimers(8,20,False, True))
self.assertTrue(pdb_3.count() == 9)
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName('blastClustersTest')
self.sc = SparkContext(conf=conf)
pdbIds = ["1O06","2ONX"]
self.pdb = downloadMmtfFiles(pdbIds,self.sc)
def main(argv):
#Configure Spark
conf = SparkConf().setAppName(APP_NAME)
conf = conf.setMaster("local[*]")
conf = conf.set("spark.executor.memory", "64g")
conf = conf.set("spark.driver.cores","32")
sc = SparkContext(conf=conf)
#Get command line input
try :
opts,args = getopt.getopt(argv,"p:",["--path="])
except getopt.GetoptError:
print("traverse.py -p <path_to_mmtf>")
sys.exit()
for opt,arg in opts:
if opt in ["-p","--path"]:
path = arg
#Mmtf sequence file reader
pdbIds = ['1AQ1','5GOD']
pdb = downloadMmtfFiles(pdbIds,sc)
def getChainToEntityIndex(structure):
entityChainIndex = [0] * structure.num_chains
for i in range(0, len(structure.entity_list)):
for j in structure.entity_list[i]["chainIndexList"]:
entityChainIndex[j] = i
return entityChainIndex
def listOfBytesToString(listOfBytes):
newList = []
for i in range(0, len(listOfBytes)):
newList.append(listOfBytes[i].decode("utf-8"))
return newList
def listToString(temp):
return("[" + ", ".join(map(str, temp)) + "]")
def printMmtfInfo(structure):
print("*** MMMTF INFO ***")
print("MmtfProducer : " + structure.mmtf_producer)
print("MmtfVersion : " + structure.mmtf_version)
print();
def printMetadata(structure):
print("*** METADATA ***")
print("StructureId : " + structure.structure_id)
print("Title : " + structure.title)
print("Deposition date : " + structure.deposition_date)
print("Release date : " + structure.release_date)
print("Experimental method(s): " + listToString(listOfBytesToString(structure.experimental_methods)))
print("Resolution : " + str(structure.resolution))
print("Rfree : " + str("%0.2f" % structure.r_free))
print("Rwork : " + str("%0.2f" % structure.r_work))
print()
def printCrystallographicData(structure):
print("*** CRYSTALLOGRAPHIC DATA ***")
print("Space group : " + structure.space_group.decode('utf-8'))
print("Unit cell dimensions : " + listToString(["%0.2f" % i for i in structure.unit_cell]))
print()
def printBioAssemblyData(structure):
print("*** BIOASSEMBLY DATA ***")
print("Number bioassemblies: " + str(len(structure.bio_assembly)))
for i in range(0, len(structure.bio_assembly)):
print("bioassembly: " + structure.bio_assembly[i][b"name"].decode('utf-8'))
transformations = structure.bio_assembly[i][b"transformList"]
print(" Number transformations: " + str(len(transformations)))
for j in range(0, len(transformations)):
print(" transformation: " + str(j))
print(" chains: " + str(transformations[j][b"chainIndexList"]))
print(" rotTransMatrix: " + str(transformations[j][b"matrix"]))
def traverse(structure):
print("*** STRUCTURE DATA ***")
print("Number of models: " + str(structure.num_models))
print("Number of chains: " + str(structure.num_chains))
print("Number of groups: " + str(structure.num_groups))
print("Number of atoms : " + str(structure.num_atoms))
chainIndex = 0
groupIndex = 0
atomIndex = 0
for i in range(0, structure.num_models):
for j in range(0, structure.chains_per_model[i]):
for k in range(0, structure.groups_per_chain[chainIndex]):
groupType = structure.group_type_list[groupIndex]
for m in range(0, (len(structure.group_list[groupType]["atomNameList"]))):
atomIndex = atomIndex + 1
groupIndex = groupIndex + 1
chainIndex = chainIndex + 1
print("chainIndex: " + str(chainIndex))
print("groupIndex: " + str(groupIndex))
print("atomIndex : " + str(atomIndex))
print()
def printChainInfo(structure):
print("*** CHAIN DATA ***")
print("Number of chains: " + str(structure.num_chains))
chainIndex = 0
for i in range(0, structure.num_models):
print("model: " + str(i+1))
for j in range(0, structure.chains_per_model[i]):
chainName = structure.chain_name_list[chainIndex]
chainId = structure.chain_id_list[chainIndex]
groups = structure.groups_per_chain[chainIndex]
print("chainName: " + chainName + ", chainId: " + chainId + ", groups: " + str(groups))
chainIndex = chainIndex + 1
print()
def printChainGroupInfo(structure):
print("*** CHAIN AND GROUP DATA ***")
chainIndex = 0
groupIndex = 0
for i in range(0, structure.num_models):
print("model: " + str(i+1))
for j in range(0, structure.chains_per_model[i]):
chainName = structure.chain_name_list[chainIndex]
chainId = structure.chain_id_list[chainIndex]
groups = structure.groups_per_chain[chainIndex]
print("chainName: " + chainName + ", chainId: " + chainId + ", groups: " + str(groups))
for k in range(0, structure.groups_per_chain[chainIndex]):
groupId = structure.group_id_list[groupIndex]
insertionCode = structure.ins_code_list[groupIndex]
secStruct = structure.sec_struct_list[groupIndex]
seqIndex = structure.sequence_index_list[groupIndex]
groupType = structure.group_type_list[groupIndex]
groupName = structure.group_list[groupType]["groupName"]
chemCompType = structure.group_list[groupType]["chemCompType"]
oneLetterCode = structure.group_list[groupType]["singleLetterCode"]
numAtoms = len(structure.group_list[groupType]["atomNameList"])
numBonds = len(structure.group_list[groupType]["bondOrderList"])
print(" groupName : " + groupName)
print(" oneLetterCode : " + oneLetterCode)
print(" seq. index : " + str(seqIndex))
print(" numAtoms : " + str(numAtoms))
print(" numBonds : " + str(numBonds))
print(" chemCompType : " + chemCompType)
print(" groupId : " + str(groupId))
print(" insertionCode : " + insertionCode)
print(" DSSP secStruct.: " + dsspSecondaryStructure.getDsspCode(secStruct).getOneLetterCode())
print()
groupIndex = groupIndex + 1
chainIndex = chainIndex + 1
print()
def printChainEntityGroupAtomInfo(structure):
print("*** CHAIN ENTITY GROUP ATOM DATA ***")
chainToEntityIndex = getChainToEntityIndex(structure)
chainIndex = 0
groupIndex = 0
atomIndex = 0
for i in range(0, structure.num_models):
print("model: " + str(i+1))
for j in range(0, structure.chains_per_model[i]):
chainName = structure.chain_name_list[chainIndex]
chainId = structure.chain_id_list[chainIndex]
groups = structure.groups_per_chain[chainIndex]
print("chainName: " + chainName + ", chainId: " + chainId + ", groups: " + str(groups))
entityType = structure.entity_list[chainToEntityIndex[chainIndex]]["type"]
entityDescription = structure.entity_list[chainToEntityIndex[chainIndex]]["description"]
entitySequence = structure.entity_list[chainToEntityIndex[chainIndex]]["sequence"]
print("entity type : " + entityType);
print("entity description : " + entityDescription);
print("entity sequence : " + entitySequence);
for k in range(0, structure.groups_per_chain[chainIndex]):
groupId = structure.group_id_list[groupIndex]
insertionCode = structure.ins_code_list[groupIndex]
secStruct = structure.sec_struct_list[groupIndex]
seqIndex = structure.sequence_index_list[groupIndex]
groupType = structure.group_type_list[groupIndex]
groupName = structure.group_list[groupType]["groupName"]
chemCompType = structure.group_list[groupType]["chemCompType"]
oneLetterCode = structure.group_list[groupType]["singleLetterCode"]
numAtoms = len(structure.group_list[groupType]["atomNameList"])
numBonds = len(structure.group_list[groupType]["bondOrderList"])
print(" groupName : " + groupName)
print(" oneLetterCode : " + oneLetterCode)
print(" seq. index : " + str(seqIndex))
print(" numAtoms : " + str(numAtoms))
print(" numBonds : " + str(numBonds))
print(" chemCompType : " + chemCompType)
print(" groupId : " + str(groupId))
print(" insertionCode : " + insertionCode)
print(" DSSP secStruct.: " + dsspSecondaryStructure.getDsspCode(secStruct).getOneLetterCode())
print(" Atoms : ")
for m in range(0, (len(structure.group_list[groupType]["atomNameList"]))):
atomId = structure.atom_id_list[atomIndex]
altLocId = structure.alt_loc_list[atomIndex]
x = structure.x_coord_list[atomIndex]
y = structure.y_coord_list[atomIndex]
z = structure.z_coord_list[atomIndex]
occupancy = structure.occupancy_list[atomIndex]
bFactor = structure.b_factor_list[atomIndex]
atomName = structure.group_list[groupType]["atomNameList"][m]
element = structure.group_list[groupType]["elementList"][m]
print(" " + str(atomId) + "\t" + atomName + "\t" + altLocId +
"\t" + str(x) + "\t" + str(y) + "\t" + str(z) +
"\t" + str(occupancy) + "\t" + str(bFactor) + "\t" + element)
atomIndex = atomIndex + 1
groupIndex = groupIndex + 1
chainIndex = chainIndex + 1
print()
def TraverseStructureHierarchy(structure):
structure = structure.set_alt_loc_list()
print(structure.entity_list)
printMmtfInfo(structure)
printMetadata(structure)
printCrystallographicData(structure)
traverse(structure)
printChainInfo(structure)
printChainGroupInfo(structure)
printChainEntityGroupAtomInfo(structure)
printBioAssemblyData(structure)
pdb.foreach(lambda t: TraverseStructureHierarchy(t[1]))
def setUp(self):
conf = SparkConf().setMaster("local[*]").setAppName('wildTypeTest')
self.sc = SparkContext(conf=conf)
pdbIds = ["1PEN", "1OCZ", "2ONX"]
self.pdb = downloadMmtfFiles(pdbIds, self.sc)
