def __buildCif(self, rD, containerName="vrpt"):
""" Construct a mmCIF data category objects for the input
extracted data.
Args:
rD (dict): extracted data organized by category.
containerName (str) : data block name
Returns:
containers (list): data container list
"""
#
curContainer = DataContainer(containerName)
for elName in rD:
catName = elName
if (not rD[elName]) or (not self.__attribD[catName]) or (
catName in ["programs"]):
continue
hasOrdinal = "ordinal" in self.__attribD[catName]
rowList = rD[elName]
# Find the unique attribute content across the rowlist and the ordinal value
atS = set()
for ii, rowD in enumerate(rowList, 1):
if hasOrdinal:
rowD["ordinal"] = ii
if "icode" in rowD:
rowD["icode"] = str(rowD["icode"]).strip()
if "altcode" in rowD:
rowD["altcode"] = str(rowD["altcode"]).strip()
atS.update(rowD.keys())
attributeNameList = list(atS)
#
# Set a reasonable order for these attributes
#
sD = {ky: self.__atOrdD[ky] for ky in attributeNameList}
srtAtL = [
tup[0]
for tup in sorted(sD.items(), key=operator.itemgetter(1))
]
logger.debug("Category %s sorted attributes %r", catName, srtAtL)
aCat = DataCategory(catName, srtAtL, rowList)
curContainer.append(aCat)
#
# Adjust schema names -
#
atD = self.__dictionaryMap["attributes"]
for catName in curContainer.getObjNameList():
catObj = curContainer.getObj(catName)
atNameList = catObj.getAttributeList()
mapD = {}
mapCatName = self.__dictionaryMap["categories"][
catName] if catName in self.__dictionaryMap[
"categories"] else catName
for atName in atNameList:
mapD[atName] = atD[(catName, atName)]["at"] if (
catName, atName) in atD else atName
catObj.renameAttributes(mapD)
catObj.setName(mapCatName)
#
# Map provenance items from programs.properties -
#
catObj = curContainer.getObj("program")
if catObj and catObj.hasAttribute("properties"):
for iRow in range(catObj.getRowCount()):
pV = catObj.getValue("properties", iRow)
pVL = [v.strip() for v in pV.split(",")]
nL = [
self.__atMap[ky] if ky in self.__atMap else ky
for ky in pVL
]
catObj.setValue(",".join(nL), "properties", iRow)
# logger.info("Row %r properties %r" % (iRow, pV))
#
return [curContainer]
class mmCIFUtil:
"""Using pdbx mmCIF utility to parse mmCIF file"""
def __init__(self, verbose=False, log=sys.stderr, filePath=None): # pylint: disable=unused-argument
# self.__verbose = verbose
self.__lfh = log
self.__filePath = filePath
self.__dataList = []
self.__dataMap = {}
self.__container = None
self.__blockID = None
self.__read()
#
def __read(self):
if not self.__filePath:
return
#
try:
ifh = open(self.__filePath, "r")
pRd = PdbxReader(ifh)
pRd.read(self.__dataList)
ifh.close()
if self.__dataList:
self.__container = self.__dataList[0]
self.__blockID = self.__container.getName()
idx = 0
for container in self.__dataList:
self.__dataMap[container.getName()] = idx
idx += 1
#
#
except Exception as e:
self.__lfh.write("Read %s failed %s.\n" %
(self.__filePath, str(e)))
#
def GetBlockID(self):
"""Return first block ID"""
return self.__blockID
def GetValueAndItemByBlock(self, blockName, catName):
"""Get category values and item names"""
dList = []
iList = []
if blockName not in self.__dataMap:
return dList, iList
#
catObj = self.__dataList[self.__dataMap[blockName]].getObj(catName)
if not catObj:
return dList, iList
#
iList = catObj.getAttributeList()
rowList = catObj.getRowList()
for row in rowList:
tD = {}
for idxIt, itName in enumerate(iList):
if row[idxIt] != "?" and row[idxIt] != ".":
tD[itName] = row[idxIt]
#
if tD:
dList.append(tD)
#
#
return dList, iList
def GetValueAndItem(self, catName):
dList, iList = self.GetValueAndItemByBlock(self.__blockID, catName)
return dList, iList
def GetValue(self, catName):
"""Get category values based on category name 'catName'. The results are stored
in a list of dictionaries with item name as key
"""
dList, _iList = self.GetValueAndItemByBlock(self.__blockID, catName)
return dList
def GetSingleValue(self, catName, itemName):
"""Get the first value of item name 'itemName' from 'itemName' item in 'catName' category."""
text = ""
dlist = self.GetValue(catName)
if dlist:
if itemName in dlist[0]:
text = dlist[0][itemName]
return text
#
def UpdateSingleRowValue(self, catName, itemName, row, value):
"""Update value in single row"""
catObj = self.__container.getObj(catName)
if catObj is None:
return
#
catObj.setValue(value, itemName, row)
def UpdateMultipleRowsValue(self, catName, itemName, value):
"""Update value in multiple rows"""
catObj = self.__container.getObj(catName)
if catObj is None:
return
#
rowNo = catObj.getRowCount()
for row in range(0, rowNo):
catObj.setValue(value, itemName, row)
#
def AddBlock(self, blockID):
"""Add Data Block"""
self.__container = DataContainer(blockID)
self.__blockID = blockID
self.__dataMap[blockID] = len(self.__dataList)
self.__dataList.append(self.__container)
def AddCategory(self, categoryID, items):
"""Add Category"""
category = DataCategory(categoryID)
for item in items:
category.appendAttribute(item)
#
self.__container.append(category)
def RemoveCategory(self, categoryID):
return self.__container.remove(categoryID)
def InsertData(self, categoryID, dataList):
""""""
catObj = self.__container.getObj(categoryID)
if catObj is None:
return
#
for data in dataList:
catObj.append(data)
#
def WriteCif(self, outputFilePath=None):
"""Write out cif file"""
if not outputFilePath:
return
#
ofh = open(outputFilePath, "w")
pdbxW = PdbxWriter(ofh)
pdbxW.write(self.__dataList)
ofh.close()
def GetCategories(self):
return self.__container.getObjNameList()
def GetAttributes(self, category):
return self.__container.getObj(category).getAttributeList()
def category_as_dict(self, category, block=None):
if block is None:
block = self.__blockID
values, attributes = self.GetValueAndItemByBlock(block, category)
data = [[x[y] if y in x else None for y in attributes] for x in values]
return {category: {"Items": attributes, "Values": data}}
def block_as_dict(self, block=None):
if block is None:
block = self.__blockID
data = {}
for category in self.GetCategories():
data.update(self.category_as_dict(category, block=block))
return data
