mmLib.PDB.PDBRecord

Package mmLib :: Module PDB :: Class PDBRecord

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Type PDBRecord

object --+    
         |    
      dict --+
             |
            PDBRecord

Known Subclasses:: ANISOU, ATOM, AUTHOR, CAVEAT, CISPEP, COMPND, CONECT, CRYSTn, DBREF, END, ENDMDL, EXPDTA, FORMUL, HEADER, HELIX, HET, HETNAM, HETSYN, HYDBND, JRNL, KEYWDS, LINK, MASTER, MODEL, MODRES, MTRIXn, OBSLTE, ORIGXn, REMARK, REVDAT, SCALEn, SEQADV, SEQRES, SHEET, SIGATM, SIGUIJ, SITE, SLTBRG, SOURCE, SPRSDE, SSBOND, TER, TITLE, TURN, TVECT

Base class for all PDB file records.

Method Summary
	`__str__(self)`
	`read(self, line)` Read the PDB record line and convert the fields to the appropriate dictionary values for this class.
	`reccat(self, rec_list, field)` Return the concatenation of field in all the records in rec_list.
	`reccat_dictlist(self, rec_list, field, master_key)`
	`reccat_list(self, rec_list, field, sep)` Call reccat, then split the result by the seperator.
	`reccat_multi(self, rec_list, primary_key, translations)` Create a list of dictionaries from a list of records.
	`reccat_tuplelist(self, rec_list, field, sep1, sep2)` Call reccat_list with sep1 as the list seperator, then split the items into tuples by sep2.
	`write(self)` Return a properly formed PDB record string from the instance dictionary values.
Inherited from dict
	`__init__(...)` x.__init__(...) initializes x; see x.__class__.__doc__ for signature
	`__cmp__(x, y)` x.__cmp__(y) <==> cmp(x,y)
	`__contains__(D, k)` D.__contains__(k) -> True if D has a key k, else False
	`__delitem__(x, y)` x.__delitem__(y) <==> del x[y]
	`__eq__(x, y)` x.__eq__(y) <==> x==y
	`__ge__(x, y)` x.__ge__(y) <==> x>=y
	`__getattribute__(...)` x.__getattribute__('name') <==> x.name
	`__getitem__(x, y)` x.__getitem__(y) <==> x[y]
	`__gt__(x, y)` x.__gt__(y) <==> x>y
	`__hash__(x)` x.__hash__() <==> hash(x)
	`__iter__(x)` x.__iter__() <==> iter(x)
	`__le__(x, y)` x.__le__(y) <==> x<=y
	`__len__(x)` x.__len__() <==> len(x)
	`__lt__(x, y)` x.__lt__(y) <==> x<y
	`__ne__(x, y)` x.__ne__(y) <==> x!=y
	`__new__(T, S, ...)` T.__new__(S, ...) -> a new object with type S, a subtype of T
	`__repr__(x)` x.__repr__() <==> repr(x)
	`__setitem__(x, i, y)` x.__setitem__(i, y) <==> x[i]=y
	`clear(D)` D.clear() -> None.
	`copy(D)` D.copy() -> a shallow copy of D
	`get(D, k, d)` D.get(k[,d]) -> D[k] if k in D, else d.
	`has_key(D, k)` D.has_key(k) -> True if D has a key k, else False
	`items(D)` D.items() -> list of D's (key, value) pairs, as 2-tuples
	`iteritems(D)` D.iteritems() -> an iterator over the (key, value) items of D
	`iterkeys(D)` D.iterkeys() -> an iterator over the keys of D
	`itervalues(D)` D.itervalues() -> an iterator over the values of D
	`keys(D)` D.keys() -> list of D's keys
	`pop(D, k, d)` If key is not found, d is returned if given, otherwise KeyError is raised
	`popitem(D)` 2-tuple; but raise KeyError if D is empty
	`setdefault(D, k, d)` D.setdefault(k[,d]) -> D.get(k,d), also set D[k]=d if k not in D
	`update(...)` D.update(E, **F) -> None.
	`values(D)` D.values() -> list of D's values
Inherited from object
	`__delattr__(...)` x.__delattr__('name') <==> del x.name
	`__reduce__(...)` helper for pickle
	`__reduce_ex__(...)` helper for pickle
	`__setattr__(...)` x.__setattr__('name', value) <==> x.name = value
Inherited from type
	`fromkeys(dict, S, v)` v defaults to None.

Method Details

read(self, line)

Read the PDB record line and convert the fields to the appropriate dictionary values for this class.

reccat(self, rec_list, field)

Return the concatenation of field in all the records in rec_list.

reccat_list(self, rec_list, field, sep)

Call reccat, then split the result by the seperator.

reccat_multi(self, rec_list, primary_key, translations)

Create a list of dictionaries from a list of records. This method has complex behavior to support translations of several PDB records into a Python format. The primary key is used to seperate the dictionaries within the list, and the translation argument is a list of strings or 2-tuples, If the translation is a string, the value from the PDB record field is copied to the return dictionary. If the field is a 2-tuple==t, then t[0] is the return dictionary key whose value is a list formed from the list of PDB fields in t[1].

reccat_tuplelist(self, rec_list, field, sep1, sep2)

Call reccat_list with sep1 as the list seperator, then split the items into tuples by sep2.

write(self)

Return a properly formed PDB record string from the instance dictionary values.

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