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- __builtin__.list(__builtin__.object)
-
- molecule
- mol2reader
class molecule(__builtin__.list) |
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- Method resolution order:
- molecule
- __builtin__.list
- __builtin__.object
Methods defined here:
- __str__(self)
- atoms(self)
- Returns a list of lines containing the atom records of them mol2.
- babel(self, format='smi', options='')
- Converts this mol2 data into another format with an external call to babel2.
Returns babel2 output and raises a ValueError if babel exits with an error code (mol2 not in correct format or babel2 couldn't be found.
- bonds(self)
- Returns a list of lines containing the bond records of the mol2.
- coord(self)
- Returns list of tuples corresponding to coordinates of the atoms.
- fingerprint(self, bits=1024, path_lengths=6)
- fingerprint_atom(self, atom_number, bits=6, path_lengths=3)
- graph(self)
- Returns a graph represntation of the mol2 file.
Output=(verts, edges)
verts=dictionary keyed to atom number containing atom type (truncated)
edges=dicitonary keyed to atom number containing list of bond tuples (dest atom, bond type)
- name(self, new_name=None)
- Returns or sets the molecule's name.
- score(self, getFingerprint=False, bits=512, header=None)
- Returns a dictionary containing the scores in the mol2 file in DOCK format.
Data and other attributes defined here:
- __dict__ = <dictproxy object>
- dictionary for instance variables (if defined)
- __weakref__ = <attribute '__weakref__' of 'molecule' 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
- __init__(...)
- x.__init__(...) initializes x; see x.__class__.__doc__ for signature
- __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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