PdbxContainers
Container base class for data and definition objects.
Source code in mmcif/api/PdbxContainers.py
class ContainerBase(object):
"""Container base class for data and definition objects."""
def __init__(self, name):
# The enclosing scope of the data container (e.g. data_/save_)
self.__name = name
# List of category names within this container -
self.__objNameList = []
# dictionary of DataCategory objects keyed by category name.
self.__objCatalog = {}
# dictionary for properties of the container
self.__propCatalog = {}
self.__type = None
def __eq__(self, other):
if not isinstance(other, type(self)):
return NotImplemented
return (
self.__name == other.getName()
and self.__objNameList == other.getObjNameList()
and self.__objCatalog == other.getObjCatalog()
and self.__type == other.getType()
and self.__propCatalog == other.getPropCatalog()
)
def __hash__(self):
return hash((self.__name, tuple(self.__objNameList), self.__type, tuple(self.__objCatalog.items()), tuple(self.__propCatalog.items())))
def getObjCatalog(self):
return self.__objCatalog
def getPropCatalog(self):
return self.__propCatalog
def setProp(self, propName, value):
try:
self.__propCatalog[propName] = value
return True
except Exception:
return False
def getProp(self, propName):
try:
return self.__propCatalog[propName]
except Exception:
return None
def getType(self):
return self.__type
def setType(self, cType):
self.__type = cType
def getName(self):
return self.__name
def setName(self, name):
self.__name = name
def exists(self, name):
if name in self.__objCatalog:
return True
else:
return False
def getObj(self, name):
if name in self.__objCatalog:
return self.__objCatalog[name]
else:
return None
def getObjNameList(self):
return self.__objNameList
def append(self, obj):
"""Add the input object to the current object catalog. An existing object
of the same name will be overwritten.
"""
if obj.getName() is not None:
if obj.getName() not in self.__objCatalog:
# self.__objNameList is keeping track of object order here --
self.__objNameList.append(obj.getName())
self.__objCatalog[obj.getName()] = obj
def replace(self, obj):
"""Replace an existing object with the input object"""
if (obj.getName() is not None) and (obj.getName() in self.__objCatalog):
self.__objCatalog[obj.getName()] = obj
def printIt(self, fh=sys.stdout, pType="brief"):
fh.write("+ %s container: %30s contains %4d categories\n" % (self.getType(), self.getName(), len(self.__objNameList)))
for nm in self.__objNameList:
fh.write("--------------------------------------------\n")
fh.write("Data category: %s\n" % nm)
if pType == "brief":
self.__objCatalog[nm].printIt(fh)
else:
self.__objCatalog[nm].dumpIt(fh)
def rename(self, curName, newName):
"""Change the name of an object in place
Will fail if newName already exists or curName doesn't exist.
Args:
curName (str): current category name
newName (str): new category name
Returns:
(bool): True for success or False otherwise
"""
try:
# first check if requested new category already exists
if newName in self.__objNameList:
logger.error("Category already exists, %r", newName)
return False
# also check if current category exists
if curName not in self.__objNameList:
logger.error("Category doesn't exist, %r", curName)
return False
i = self.__objNameList.index(curName)
self.__objNameList[i] = newName
self.__objCatalog[newName] = self.__objCatalog[curName]
self.__objCatalog[newName].setName(newName)
del self.__objCatalog[curName]
return True
except Exception as e:
logger.exception("Failing with %s", str(e))
return False
def copy(self, curName, newName):
"""Copy the object to a new category name.
Will fail if newName already exists or curName doesn't exist.
Args:
curName (str): current category name
newName (str): new category name
Returns:
(bool): True for success or False otherwise
"""
try:
# first check if requested new category already exists
if newName in self.__objNameList:
logger.error("Category already exists, %r", newName)
return False
# also check if current category exists
if curName not in self.__objNameList:
logger.error("Category doesn't exist, %r", curName)
return False
# now do the copy
obj = copy.deepcopy(self.__objCatalog[curName])
obj.setName(newName)
self.append(obj)
return True
except Exception as e:
logger.exception("Failing with %s", str(e))
return False
def remove(self, curName):
"""Remove object by name. Return True on success or False otherwise."""
try:
if curName in self.__objCatalog:
del self.__objCatalog[curName]
i = self.__objNameList.index(curName)
del self.__objNameList[i]
return True
else:
return False
except Exception:
pass
return False
def merge(self, container):
"""Merge the contents of the input container with the contents of the current container."""
try:
objNameList = container.getObjNameList()
for objName in objNameList:
self.append(container.getObj(objName))
except Exception as e:
logger.exception("Failing with %s", str(e))
return False
return True
def filterObjectNameList(self, lastInOrder=None, selectOrder=None):
"""Return an ordered list of categories in the input container subject to
input -
lastInOrder: list: categories to be shifted to the end of the container.
selectOrder: list: ordered selection of container categories
returns:
filNameList: list: augmented category list or full list (default)
"""
filNameList = []
if lastInOrder:
objNameList = self.__objNameList
lastList = []
for nm in objNameList:
if nm in lastInOrder:
lastList.append(nm)
continue
filNameList.append(nm)
filNameList.extend(lastList)
elif selectOrder:
for nm in selectOrder:
if self.exists(nm):
filNameList.append(nm)
else:
filNameList = self.__objNameList
return filNameList
def toJSON(self):
return self.__objCatalog
append(self, obj)
Add the input object to the current object catalog. An existing object of the same name will be overwritten.
Source code in mmcif/api/PdbxContainers.py
def append(self, obj):
"""Add the input object to the current object catalog. An existing object
of the same name will be overwritten.
"""
if obj.getName() is not None:
if obj.getName() not in self.__objCatalog:
# self.__objNameList is keeping track of object order here --
self.__objNameList.append(obj.getName())
self.__objCatalog[obj.getName()] = obj
copy(self, curName, newName)
Copy the object to a new category name. Will fail if newName already exists or curName doesn't exist.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
curName |
str |
current category name |
required |
newName |
str |
new category name |
required |
Returns:
| Type | Description |
|---|---|
(bool) |
True for success or False otherwise |
Source code in mmcif/api/PdbxContainers.py
def copy(self, curName, newName):
"""Copy the object to a new category name.
Will fail if newName already exists or curName doesn't exist.
Args:
curName (str): current category name
newName (str): new category name
Returns:
(bool): True for success or False otherwise
"""
try:
# first check if requested new category already exists
if newName in self.__objNameList:
logger.error("Category already exists, %r", newName)
return False
# also check if current category exists
if curName not in self.__objNameList:
logger.error("Category doesn't exist, %r", curName)
return False
# now do the copy
obj = copy.deepcopy(self.__objCatalog[curName])
obj.setName(newName)
self.append(obj)
return True
except Exception as e:
logger.exception("Failing with %s", str(e))
return False
filterObjectNameList(self, lastInOrder=None, selectOrder=None)
Return an ordered list of categories in the input container subject to input -
lastInOrder: list: categories to be shifted to the end of the container. selectOrder: list: ordered selection of container categories
Returns:
| Type | Description |
|---|---|
filNameList |
list: augmented category list or full list (default) |
Source code in mmcif/api/PdbxContainers.py
def filterObjectNameList(self, lastInOrder=None, selectOrder=None):
"""Return an ordered list of categories in the input container subject to
input -
lastInOrder: list: categories to be shifted to the end of the container.
selectOrder: list: ordered selection of container categories
returns:
filNameList: list: augmented category list or full list (default)
"""
filNameList = []
if lastInOrder:
objNameList = self.__objNameList
lastList = []
for nm in objNameList:
if nm in lastInOrder:
lastList.append(nm)
continue
filNameList.append(nm)
filNameList.extend(lastList)
elif selectOrder:
for nm in selectOrder:
if self.exists(nm):
filNameList.append(nm)
else:
filNameList = self.__objNameList
return filNameList
merge(self, container)
Merge the contents of the input container with the contents of the current container.
Source code in mmcif/api/PdbxContainers.py
def merge(self, container):
"""Merge the contents of the input container with the contents of the current container."""
try:
objNameList = container.getObjNameList()
for objName in objNameList:
self.append(container.getObj(objName))
except Exception as e:
logger.exception("Failing with %s", str(e))
return False
return True
remove(self, curName)
Remove object by name. Return True on success or False otherwise.
Source code in mmcif/api/PdbxContainers.py
def remove(self, curName):
"""Remove object by name. Return True on success or False otherwise."""
try:
if curName in self.__objCatalog:
del self.__objCatalog[curName]
i = self.__objNameList.index(curName)
del self.__objNameList[i]
return True
else:
return False
except Exception:
pass
return False
rename(self, curName, newName)
Change the name of an object in place Will fail if newName already exists or curName doesn't exist.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
curName |
str |
current category name |
required |
newName |
str |
new category name |
required |
Returns:
| Type | Description |
|---|---|
(bool) |
True for success or False otherwise |
Source code in mmcif/api/PdbxContainers.py
def rename(self, curName, newName):
"""Change the name of an object in place
Will fail if newName already exists or curName doesn't exist.
Args:
curName (str): current category name
newName (str): new category name
Returns:
(bool): True for success or False otherwise
"""
try:
# first check if requested new category already exists
if newName in self.__objNameList:
logger.error("Category already exists, %r", newName)
return False
# also check if current category exists
if curName not in self.__objNameList:
logger.error("Category doesn't exist, %r", curName)
return False
i = self.__objNameList.index(curName)
self.__objNameList[i] = newName
self.__objCatalog[newName] = self.__objCatalog[curName]
self.__objCatalog[newName].setName(newName)
del self.__objCatalog[curName]
return True
except Exception as e:
logger.exception("Failing with %s", str(e))
return False
replace(self, obj)
Replace an existing object with the input object
Source code in mmcif/api/PdbxContainers.py
def replace(self, obj):
"""Replace an existing object with the input object"""
if (obj.getName() is not None) and (obj.getName() in self.__objCatalog):
self.__objCatalog[obj.getName()] = obj
Source code in mmcif/api/PdbxContainers.py
class DefinitionContainer(ContainerBase):
def __init__(self, name):
super(DefinitionContainer, self).__init__(name)
self.setType("definition")
self.__globalFlag = False
def isCategory(self):
if self.exists("category"):
return True
return False
def isAttribute(self):
if self.exists("item"):
return True
return False
def getGlobal(self):
return self.__globalFlag
def printIt(self, fh=sys.stdout, pType="brief"):
fh.write("Definition container: %30s contains %4d categories\n" % (self.getName(), len(self.getObjNameList())))
if self.isCategory():
fh.write("Definition type: category\n")
elif self.isAttribute():
fh.write("Definition type: item\n")
else:
fh.write("Definition type: undefined\n")
for nm in self.getObjNameList():
fh.write("--------------------------------------------\n")
fh.write("Definition category: %s\n" % nm)
if pType == "brief":
self.getObj(nm).printIt(fh)
else:
self.getObj(nm).dumpId(fh)
Container class for DataCategory objects.
Source code in mmcif/api/PdbxContainers.py
class DataContainer(ContainerBase):
"""Container class for DataCategory objects."""
def __init__(self, name):
super(DataContainer, self).__init__(name)
self.setType("data")
self.__globalFlag = False
def invokeDataBlockMethod(self, mType, method, db):
_ = mType
_ = db
# self.__currentRow = 1
exec(method.getInline(), globals(), locals()) # pylint: disable=exec-used
def setGlobal(self):
self.__globalFlag = True
def getGlobal(self):
return self.__globalFlag
Source code in mmcif/api/PdbxContainers.py
class SaveFrameContainer(ContainerBase):
def __init__(self, name):
super(SaveFrameContainer, self).__init__(name)
self.setType("definition")
Class of utilities for CIF-style data names -
Source code in mmcif/api/PdbxContainers.py
class CifName(object):
"""Class of utilities for CIF-style data names -"""
def __init__(self):
pass
@staticmethod
def categoryPart(name):
tname = ""
try:
if name.startswith("_"):
tname = name[1:]
else:
tname = name
i = tname.find(".")
if i == -1:
return tname
else:
return tname[:i]
except Exception:
return tname
@staticmethod
def attributePart(name):
try:
i = name.find(".")
if i == -1:
return None
else:
return name[i + 1:]
except Exception:
return None
@staticmethod
def itemName(categoryName, attributeName):
try:
return "_" + str(categoryName) + "." + str(attributeName)
except Exception:
return None