Dear all,
A couple days ago I created a branch to work on adding some
sanitization changes to the RDKit
(http://rdkit.svn.sourceforge.net/viewvc/rdkit/branches/SanitizationChanges_11Feb2012/).
I've added two things, the ability to specify which sanitization
operations should be carried out and the ability to get a return value
from the SanitizeMol function instead of having it raise an exception.
Here's what it looks like:
In [5]: Chem.SanitizeMol?
Type: function
Base Class: <type 'builtin_function_or_method'>
String Form:<Boost.Python.function object at 0x1ec6740>
Namespace: Interactive
Docstring:
SanitizeMol( (Mol)mol [,
(int)sanitizeOps=rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL [,
(bool)catchErrors=False]]) -> SanitizeFlags :
Kekulize, check valencies, set aromaticity, conjugation and hybridization
- The molecule is modified in place.
- If sanitization fails, an exception will be thrown unless
catchErrors is set
ARGUMENTS:
- mol: the molecule to be modified
- sanitizeOps: (optional) sanitization operations to be carried out
these should be constructed by or'ing together the
operations in rdkit.Chem.SanitizeFlags
- catchErrors: (optional) if provided, instead of raising an exception
when sanitization fails (the default behavior), the
operations that failed (as defined in
rdkit.Chem.SanitizeFlags)
is returned. Zero is returned on success.
C++ signature :
RDKit::MolOps::SanitizeFlags SanitizeMol(RDKit::ROMol {lvalue}
[,unsigned int=rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_ALL
[,bool=False]])
An example of using it:
#---------------------------
In [6]: m = Chem.MolFromSmiles('c1cccc1',sanitize=False)
In [7]: Chem.SanitizeMol(m)
[06:17:24] Can't kekulize mol
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
/scratch/RDKit_sanit/<ipython-input-7-dd6845fa341c> in <module>()
----> 1 Chem.SanitizeMol(m)
ValueError: Sanitization error: Can't kekulize mol
#---------------------------
That's the same as the current behavior.
Now let's see what the problem was:
#---------------------------
In [8]: m = Chem.MolFromSmiles('c1cccc1',sanitize=False)
In [9]: Chem.SanitizeMol(m,catchErrors=True)
[06:17:41] Can't kekulize mol
Out[9]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_KEKULIZE
#---------------------------
Ok, so it failed in sanitization, so let's try sanitizing the molecule
without doing the kekulization step:
#---------------------------
In [10]: m = Chem.MolFromSmiles('c1cccc1',sanitize=False)
In [11]:
Chem.SanitizeMol(m,sanitizeOps=Chem.SanitizeFlags.SANITIZE_ALL^Chem.SanitizeFlags.SANITIZE_KEKULIZE)
Out[11]: rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE
#---------------------------
Note that there is a change even in the default behavior in that
Chem.SanitizeMol now always returns a value. Previously it always
returned None, but now you get a value back.
Any comments or suggestions about the API?
-greg
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