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- __builtin__.dict(__builtin__.object)
-
- score
- scorelist
- __builtin__.list(__builtin__.object)
-
- headerclass
- scorelist_iter
class headerclass(__builtin__.list) |
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- Method resolution order:
- headerclass
- __builtin__.list
- __builtin__.object
Methods defined here:
- __init__(self, line='')
- __str__(self)
- abut(self, other)
Data and other attributes defined here:
- __dict__ = <dictproxy object>
- dictionary for instance variables (if defined)
- __weakref__ = <attribute '__weakref__' of 'headerclass' objects>
- list of weak references to the object (if defined)
Methods inherited from __builtin__.list:
- __add__(...)
- x.__add__(y) <==> x+y
- __contains__(...)
- x.__contains__(y) <==> y in x
- __delitem__(...)
- x.__delitem__(y) <==> del x[y]
- __delslice__(...)
- x.__delslice__(i, j) <==> del x[i:j]
Use of negative indices is not supported.
- __eq__(...)
- x.__eq__(y) <==> x==y
- __ge__(...)
- x.__ge__(y) <==> x>=y
- __getattribute__(...)
- x.__getattribute__('name') <==> x.name
- __getitem__(...)
- x.__getitem__(y) <==> x[y]
- __getslice__(...)
- x.__getslice__(i, j) <==> x[i:j]
Use of negative indices is not supported.
- __gt__(...)
- x.__gt__(y) <==> x>y
- __hash__(...)
- x.__hash__() <==> hash(x)
- __iadd__(...)
- x.__iadd__(y) <==> x+=y
- __imul__(...)
- x.__imul__(y) <==> x*=y
- __iter__(...)
- x.__iter__() <==> iter(x)
- __le__(...)
- x.__le__(y) <==> x<=y
- __len__(...)
- x.__len__() <==> len(x)
- __lt__(...)
- x.__lt__(y) <==> x<y
- __mul__(...)
- x.__mul__(n) <==> x*n
- __ne__(...)
- x.__ne__(y) <==> x!=y
- __repr__(...)
- x.__repr__() <==> repr(x)
- __rmul__(...)
- x.__rmul__(n) <==> n*x
- __setitem__(...)
- x.__setitem__(i, y) <==> x[i]=y
- __setslice__(...)
- x.__setslice__(i, j, y) <==> x[i:j]=y
Use of negative indices is not supported.
- append(...)
- L.append(object) -- append object to end
- count(...)
- L.count(value) -> integer -- return number of occurrences of value
- extend(...)
- L.extend(iterable) -- extend list by appending elements from the iterable
- index(...)
- L.index(value, [start, [stop]]) -> integer -- return first index of value
- insert(...)
- L.insert(index, object) -- insert object before index
- pop(...)
- L.pop([index]) -> item -- remove and return item at index (default last)
- remove(...)
- L.remove(value) -- remove first occurrence of value
- reverse(...)
- L.reverse() -- reverse *IN PLACE*
- sort(...)
- L.sort(cmpfunc=None) -- stable sort *IN PLACE*; cmpfunc(x, y) -> -1, 0, 1
Data and other attributes inherited from __builtin__.list:
- __new__ = <built-in method __new__ of type object>
- T.__new__(S, ...) -> a new object with type S, a subtype of T
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class score(__builtin__.dict) |
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- Method resolution order:
- score
- __builtin__.dict
- __builtin__.object
Methods defined here:
- __init__(self, header=None, data=[])
- __str__(self, printunknown=True)
- abut(self, other)
- hasUnknown(self)
- key(self)
Data and other attributes defined here:
- __dict__ = <dictproxy object>
- dictionary for instance variables (if defined)
- __weakref__ = <attribute '__weakref__' of 'score' objects>
- list of weak references to the object (if defined)
Methods inherited from __builtin__.dict:
- __cmp__(...)
- x.__cmp__(y) <==> cmp(x,y)
- __contains__(...)
- x.__contains__(y) <==> y in x
- __delitem__(...)
- x.__delitem__(y) <==> del x[y]
- __eq__(...)
- x.__eq__(y) <==> x==y
- __ge__(...)
- x.__ge__(y) <==> x>=y
- __getattribute__(...)
- x.__getattribute__('name') <==> x.name
- __getitem__(...)
- x.__getitem__(y) <==> x[y]
- __gt__(...)
- x.__gt__(y) <==> x>y
- __hash__(...)
- x.__hash__() <==> hash(x)
- __iter__(...)
- x.__iter__() <==> iter(x)
- __le__(...)
- x.__le__(y) <==> x<=y
- __len__(...)
- x.__len__() <==> len(x)
- __lt__(...)
- x.__lt__(y) <==> x<y
- __ne__(...)
- x.__ne__(y) <==> x!=y
- __repr__(...)
- x.__repr__() <==> repr(x)
- __setitem__(...)
- x.__setitem__(i, y) <==> x[i]=y
- clear(...)
- D.clear() -> None. Remove all items from D.
- copy(...)
- D.copy() -> a shallow copy of D
- get(...)
- D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.
- has_key(...)
- D.has_key(k) -> True if D has a key k, else False
- items(...)
- D.items() -> list of D's (key, value) pairs, as 2-tuples
- iteritems(...)
- D.iteritems() -> an iterator over the (key, value) items of D
- iterkeys(...)
- D.iterkeys() -> an iterator over the keys of D
- itervalues(...)
- D.itervalues() -> an iterator over the values of D
- keys(...)
- D.keys() -> list of D's keys
- pop(...)
- D.pop(k[,d]) -> v, remove specified key and return the corresponding value
If key is not found, d is returned if given, otherwise KeyError is raised
- popitem(...)
- D.popitem() -> (k, v), remove and return some (key, value) pair as a
2-tuple; but raise KeyError if D is empty
- setdefault(...)
- D.setdefault(k[,d]) -> D.get(k,d), also set D[k]=d if k not in D
- update(...)
- D.update(E) -> None. Update D from E: for k in E.keys(): D[k] = E[k]
- values(...)
- D.values() -> list of D's values
Data and other attributes inherited from __builtin__.dict:
- __new__ = <built-in method __new__ of type object>
- T.__new__(S, ...) -> a new object with type S, a subtype of T
- fromkeys = <built-in method fromkeys of type object>
- dict.fromkeys(S[,v]) -> New dict with keys from S and values equal to v.
v defaults to None.
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class scorelist(__builtin__.dict) |
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- Method resolution order:
- scorelist
- __builtin__.dict
- __builtin__.object
Methods defined here:
- __init__(self)
- __iter__(self)
- __len__(self)
- abut(self, other, keepunknowns=False)
- Equivalent to an SQL join, this function abuts two scorelists
using columns specified by scorelist.header.key
- add_column(self, name, col, description='')
- append(self, score)
- append_list(self, other)
- Appends an interable of scores to this scorelist.
Does not add columns to the header. This must be done diretly through the header class.
- delete_column(self, name)
- ensure_column(self, key)
- get_column(self, name)
- Gets a column of data. Use this rather than scorelist['columnname'].
- get_score(self, n)
- Get's a score from the list by it's index.
- idx_of(self, searchfor='KNOWN')
- Return a list of tuples (index, match_object),
containing comments that match the 'searchfor' regular expression.
Match objects returnd can be use to extract row specific information from each index.
E.g. searchfor="pKi (?P<pki>.*)$" would allow you query the match objects using the group method for
'pki', parsing comments like '// pKi 5.83'.
- len(self)
- makedict(self, key='NAME')
- Utility function that adds a attribute 'dict' containing a mapping of names to indexes.
- mark_list(self, comment='')
- Simple function to annotate top of scorelist with comments applying to the whole list.
All comment lines begin with '//' which is automatically prepended by this function.
All list modifying functions should produce annotation. Comments stored in self.comment.
- mark_score(self, key, value, comment)
- Simple function to annotate specific element of scorelist with a comment pinned to it.
Regular expressions are permitted.
All comment lines begin with '//'
comments stored in self.comments.
- print2file(self, file, printunknown=True)
- Use this to print a scorelist to a file.
We don't implement __str__ because this object can be quite large and it make sense to print directly to file.
- read(self, file)
- readmol2(self, molseq, getFingerprint=False, bits=512)
- set_column(self, name, col)
- sort(self, key='NAME')
- Sort based on a key.
Automatically tries to convert data to float unless an exception is raised.
- transform_column(self, name, transform_function, description=None)
- Applies transform_function to every element of a particular column.
Data and other attributes defined here:
- __dict__ = <dictproxy object>
- dictionary for instance variables (if defined)
- __weakref__ = <attribute '__weakref__' of 'scorelist' objects>
- list of weak references to the object (if defined)
Methods inherited from __builtin__.dict:
- __cmp__(...)
- x.__cmp__(y) <==> cmp(x,y)
- __contains__(...)
- x.__contains__(y) <==> y in x
- __delitem__(...)
- x.__delitem__(y) <==> del x[y]
- __eq__(...)
- x.__eq__(y) <==> x==y
- __ge__(...)
- x.__ge__(y) <==> x>=y
- __getattribute__(...)
- x.__getattribute__('name') <==> x.name
- __getitem__(...)
- x.__getitem__(y) <==> x[y]
- __gt__(...)
- x.__gt__(y) <==> x>y
- __hash__(...)
- x.__hash__() <==> hash(x)
- __le__(...)
- x.__le__(y) <==> x<=y
- __lt__(...)
- x.__lt__(y) <==> x<y
- __ne__(...)
- x.__ne__(y) <==> x!=y
- __repr__(...)
- x.__repr__() <==> repr(x)
- __setitem__(...)
- x.__setitem__(i, y) <==> x[i]=y
- clear(...)
- D.clear() -> None. Remove all items from D.
- copy(...)
- D.copy() -> a shallow copy of D
- get(...)
- D.get(k[,d]) -> D[k] if k in D, else d. d defaults to None.
- has_key(...)
- D.has_key(k) -> True if D has a key k, else False
- items(...)
- D.items() -> list of D's (key, value) pairs, as 2-tuples
- iteritems(...)
- D.iteritems() -> an iterator over the (key, value) items of D
- iterkeys(...)
- D.iterkeys() -> an iterator over the keys of D
- itervalues(...)
- D.itervalues() -> an iterator over the values of D
- keys(...)
- D.keys() -> list of D's keys
- pop(...)
- D.pop(k[,d]) -> v, remove specified key and return the corresponding value
If key is not found, d is returned if given, otherwise KeyError is raised
- popitem(...)
- D.popitem() -> (k, v), remove and return some (key, value) pair as a
2-tuple; but raise KeyError if D is empty
- setdefault(...)
- D.setdefault(k[,d]) -> D.get(k,d), also set D[k]=d if k not in D
- update(...)
- D.update(E) -> None. Update D from E: for k in E.keys(): D[k] = E[k]
- values(...)
- D.values() -> list of D's values
Data and other attributes inherited from __builtin__.dict:
- __new__ = <built-in method __new__ of type object>
- T.__new__(S, ...) -> a new object with type S, a subtype of T
- fromkeys = <built-in method fromkeys of type object>
- dict.fromkeys(S[,v]) -> New dict with keys from S and values equal to v.
v defaults to None.
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