parmed.formats.pdbx.PdbxContainers module

A collection of container classes supporting the PDBx/mmCIF storage model.

A base container class is defined which supports common features of data and definition containers. PDBx data files are organized in sections called data blocks which are mapped to data containers. PDBx dictionaries contain definition sections and data sections which are mapped to definition and data containes respectively.

Data in both PDBx data files and dictionaries are organized in data categories. In the PDBx syntax individual items or data identified by labels of the form ‘_categoryName.attributeName’. The terms category and attribute in PDBx jargon are analogous table and column in relational data model, or class and attribute in an object oriented data model.

The DataCategory class provides base storage container for instance data and definition meta data.

class parmed.formats.pdbx.PdbxContainers.CifName

Bases: object

Class of utilities for CIF-style data names -

Methods

attributePart
categoryPart

static attributePart(name)

static categoryPart(name)

class parmed.formats.pdbx.PdbxContainers.ContainerBase(name)

Bases: object

Container base class for data and definition objects.

Methods

append(obj)	Add the input object to the current object catalog.
remove(curName)	Revmove object by name.
rename(curName, newName)	Change the name of an object in place -
replace(obj)	Replace an existing object with the input object

exists
getName
getObj
getObjNameList
getType
printIt
setName
setType

append(obj)

Add the input object to the current object catalog. An existing object of the same name will be overwritten.

exists(name)

getName()

getObj(name)

getObjNameList()

getType()

printIt(fh=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>, type='brief')

remove(curName)

Revmove object by name. Return True on success or False otherwise.

rename(curName, newName)

Change the name of an object in place -

replace(obj)

Replace an existing object with the input object

setName(name)

setType(type)

class parmed.formats.pdbx.PdbxContainers.DataCategory(name, attributeNameList=None, rowList=None)

Bases: parmed.formats.pdbx.PdbxContainers.DataCategoryBase

Methods for creating, accessing, and formatting PDBx cif data categories.

Methods

getFullRow(index)	Return a full row based on the length of the the attribute list.
renameAttribute(curAttributeName, …)	Change the name of an attribute in place -

append
appendAttribute
appendAttributeExtendRows
dumpIt
get
getAttributeCount
getAttributeIndex
getAttributeLengthMaximumList
getAttributeList
getAttributeListWithOrder
getAttributeValueMaxLengthList
getCurrentAttribute
getFormatTypeList
getFormatTypeListX
getIndex
getItemNameList
getName
getRow
getRowCount
getRowIndex
getRowList
getValue
getValueFormatted
getValueFormattedByIndex
hasAttribute
invokeAttributeMethod
invokeCategoryMethod
printIt
removeRow
replaceSubstring
replaceValue
setAttributeNameList
setName
setRowList
setValue

append(row)

appendAttribute(attributeName)

appendAttributeExtendRows(attributeName)

dumpIt(fh=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)

getAttributeCount()

getAttributeIndex(attributeName)

getAttributeLengthMaximumList()

getAttributeList()

getAttributeListWithOrder()

getAttributeValueMaxLengthList(steps=1)

getCurrentAttribute()

getFormatTypeList(steps=1)

getFormatTypeListX()

getFullRow(index)

Return a full row based on the length of the the attribute list.

getIndex(attributeName)

getItemNameList()

getName()

getRow(index)

getRowCount()

getRowIndex()

getRowList()

getValue(attributeName=None, rowIndex=None)

getValueFormatted(attributeName=None, rowIndex=None)

getValueFormattedByIndex(attributeIndex, rowIndex)

hasAttribute(attributeName)

invokeAttributeMethod(attributeName, type, method, db)

invokeCategoryMethod(type, method, db)

printIt(fh=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)

removeRow(index)

renameAttribute(curAttributeName, newAttributeName)

Change the name of an attribute in place -

replaceSubstring(oldValue, newValue, attributeName)

replaceValue(oldValue, newValue, attributeName)

setValue(value, attributeName=None, rowIndex=None)

class parmed.formats.pdbx.PdbxContainers.DataCategoryBase(name, attributeNameList=None, rowList=None)

Bases: object

Base object definition for a data category -

Methods

get
setAttributeNameList
setName
setRowList

get()

setAttributeNameList(attributeNameList)

setName(name)

setRowList(rowList)

class parmed.formats.pdbx.PdbxContainers.DataContainer(name)

Bases: parmed.formats.pdbx.PdbxContainers.ContainerBase

Container class for DataCategory objects.

Methods

append(obj)	Add the input object to the current object catalog.
remove(curName)	Revmove object by name.
rename(curName, newName)	Change the name of an object in place -
replace(obj)	Replace an existing object with the input object

exists
getGlobal
getName
getObj
getObjNameList
getType
invokeDataBlockMethod
printIt
setGlobal
setName
setType

getGlobal()

invokeDataBlockMethod(type, method, db)

setGlobal()

class parmed.formats.pdbx.PdbxContainers.DefinitionContainer(name)

Bases: parmed.formats.pdbx.PdbxContainers.ContainerBase

Methods

append(obj)	Add the input object to the current object catalog.
remove(curName)	Revmove object by name.
rename(curName, newName)	Change the name of an object in place -
replace(obj)	Replace an existing object with the input object

exists
getName
getObj
getObjNameList
getType
isAttribute
isCategory
printIt
setName
setType

isAttribute()

isCategory()

printIt(fh=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>, type='brief')