Hi Nicolas,
> -> first, is there a silent mode, to avoid the printing of the descriptors
> loading ?
All debug, info, error messages can be switched off in the
joelib/src/log4j.properties
file.
So switch all DEBUG and INFO to ERROR and nothing will be printed.
> -> second, what is the meaning of the order of the values when for example
> you ask for "Atom_in_donor" descriptor and you have as output the following
> line: 5<0,0,1,0,0> ?
> Is this mean that the atom label 2 is donor ?
No, atom starts with 1,2,3, ..., N
So atom 3 is a Donor.
You can also use the general
joelib.molecule.types.AtomProperties
interface
> -> third, I have asked for Gasteiger-Marsili calculation: a first one is
> done without adding Hydrogens, and the second one with adding H in my
> molecules. But, at the end the results are different. What does it means ? I
> thought that this calculation take always the Hydrogens influence ?
Oh, this is a critical question and has no general answer.
From the computer science standpoint of view you these are two cases
and some descriptors are sensitive to hydrogens, others are not.
Why are some descriptors hydrogen independent ?
1. Some use only heavy weight atoms to calculate the descriptors.
2. Some simply remove the hydrogens, before they are calculated.
Of course, this is a serious problem, when having the case that one
whants all sigma partial charges and on the other side you are
interested in one special descriptor using only heavy weight atoms BUT
here with the sigma partial charge atom property.
So this is and indexing conflict and of course can not be the same.
So, if calculating and accessing atom properties you can/should check
the hydrogen atom state of the molecule, which is not big deal.
I've at least checked these things for the standard descriptor
calculation class.
The easiest solution is to remove hydrogens, because they are still
implicitely available via the JOELib expert system, but on the other
hand the user might be interested in protonated molecules assigned by
another program, e.g. Corina which is also really good to assign hydrogens.
> -> and fourth, how could you explain that, for the same molecule:
> "Atom_in_donor" is 5<0,0,1,0,0>
> "Atom_in_acceptor" is 5<0,0,0,1,0>
> "Atom_in_donor_or_acceptor" is 5<0,0,0,0,0> ?
It's only one kind of possible and really huge discrete assignment/label
space.
So, if you have a look at the used SMARTS pattern in and all literature
references given there:
joelib.desc.types.AtomInDonAcc
joelib.desc.types.AtomInDonor
joelib.desc.types.AtomInAcceptor
see also
joelib.desc.types.HBA1
joelib.desc.types.HBA2
joelib.desc.types.HBD1
joelib.desc.types.HBD2
you can see that they use all different descriptions. And additionally
then remind that SMARTS matching is based on the chemical expert systems
used, so even if you use the same SMARTS, you will with a high
probability get a nice number of mismatches.
E.g. i got once a time a complained from a NCI which compared the NCI
and JOELib results. YES, that's a problem and i complain every time and
in all publications, that we need here an 'chemical expert' system
standard which we can test against.
http://www-ra.informatik.uni-tuebingen.de/software/joelib/tutorial/atomtyper.html
If you do not like them, create your own descriptor. If you want it more
dynamic use SMARTS from a text file, but then i recommend to inroduce
also an ID as done for the JOELib expert systems. This guarantees you
that you will notice if another user changes on single SMARTS entry,
which can definitely occur, because we are talking about expert systems.
Which are a really evolving type of label assignment (or more general
model/hypothesis).
See here interfaces:
joelib.data.SoftCodedKernel
joelib.data.HardCodedKernel
Kind regards, Joerg
--
Dipl. Chem. Joerg K. Wegner
Center of Bioinformatics Tuebingen (ZBIT)
Department of Computer Architecture
Univ. Tuebingen, Sand 1, D-72076 Tuebingen, Germany
Phone: (+49/0) 7071 29 78970
Fax: (+49/0) 7071 29 5091
E-Mail: mailto:we...@in...
WWW: http://www-ra.informatik.uni-tuebingen.de
--
Never mistake motion for action.
(E. Hemingway)
Never mistake action for meaningful action.
(Hugo Kubinyi,2004)
|
