User 677b9c22ff
16-11-2006 04:37:59
Hi,
I like the little drop down window, which opens in the chemical terms filter and has currently only:
Bioavailability
Ghose filter
Lead likeness
Lipinski rule of 5
Muegge filter
Veber filter
I am thinking about a really nifty feature which
provides all terms from cxcalc, evaluator and all other possible ChemAxon and user resources.
http://www.chemaxon.com/jchem/doc/user/ChemicalTerms.html
It could even contain fingerprint features, like these which contain over 1000 fingerprints calculated from smarts/smiles:
ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.txt
The whole feature implemented as XML like in the TOOLS-Template-Manager would give a helpful resource to all users and could contain all the helpful material ChemAxon assembled over the years and which is sometimes hidden in the DOCs. These terms or features carefully
sorted in XML-subdirectories and divided in
default and
user would be really nice. Because over the years ChemAxon added many additional properties which can be calculated and which are sometimes lost in space. Each user could add their own needed terms.
This feature list would also be helpful provided in/during
1) the "query window"
2) the "add columns window"
3) the "add 1000 columns with these selected features" window
I must admit the combined drop down menu with the originally 5 combined terms inspired this idea and the GUI and such handy tools can make the whole Instant-JChem a really
powerful but easy to use tool.
Tobias
ChemAxon fa971619eb
16-11-2006 08:40:37
Two changes that will be happening at some stage should provide most of what you want.
Firstly the the chemical terms editor will provide code completion capabilitites, so that when you type in Ctrl-space you get a popup list of available terms, or if you have already typed the first few characters then you get the list of possible completions (you get descriptions of the terms in the popup list as well). This will make typing your own terms easier.
Secondly, we will be making the list of favourites user-editable, so that you can aded your own definitions to it.
User 677b9c22ff
17-11-2006 06:30:09
Hi Tim,
thats great, code completion is good. I like a tree-style selection also, because otherwise you dont know what kind of stuff you can select, but lets see first....
Tobias
User 677b9c22ff
12-01-2007 04:39:53
Hi,
I am not sure but, I remember Tim wrote that I can only define
the terms I want to calculate during DB import by adding them one after one.
Now it would be easy to code soemething in JAVA (I guess ;-)
so that one can calculate/import all terms at once during import, without typing them. See the table at end.
There are some atom based terms, but at least all the obvoius descriptors
would be nice, this could also solve the problem that constantly new descriptors or atom properties are added by ChemAxon, hence such a XML template could be updated with the Automatic Update Center too (a feature I really like a lot).
I dont know if it would make sense to add other features which require
the input of an additional value like pKa('pKa', '1') or such descriptors
which require the input of an atom number like stericHindrance(1) which would require an automatic drill-down analysis, hence when the molecule
has 14 carbon atoms it will provide a complete and automatic coverage
for atom 1..14 - ok maybe thats to complicated for Instant-JChem.
Tobias
Such an XML termplate table could/should include (+future extensions):
1 atomcount
2 composition
3 dotdisconnectedformula
4 elemanal
5 exactmass
6 formula
7 icomposition
8 iformula
9 mass
10 atompol
11 averagepol
12 avgpol
13 axxpol
14 ayypol
15 azzpol
16 charge
17 ioncharge
18 molpol
19 oen
20 orbitalelectronegativity
21 pol
22 polarizability
23 tpol
24 tpolarizability
25 conformers
26 hasvalidconformer
27 leconformer
28 moldyn
29 aliphaticatom
30 aliphaticatomcount
31 aliphaticbondcount
32 aliphaticringcount
33 angle
34 aromaticatom
35 aromaticatomcount
36 aromaticbondcount
37 aromaticringcount
38 asymmetricatom
39 asymmetricatomcount
40 balabanindex
41 bondcount
42 bondtype
43 carboaromaticringcount
44 carboringcount
45 chainatom
46 chainatomcount
47 chainbond
48 chainbondcount
49 chiralcenter
50 chiralcentercount
51 connected
52 connectedgraph
53 cyclomaticnumber
54 dihedral
55 distance
56 distancedegree
57 dreidingenergy
58 eccentricity
59 fusedaliphaticringcount
60 fusedaromaticringcount
61 fusedringcount
62 hararyindex
63 heteroaromaticringcount
64 heteroringcount
65 hindrance
66 hyperwienerindex
67 largestatomringsize
68 largestringsize
69 msa
70 plattindex
71 psa
72 randicindex
73 ringatom
74 ringatomcount
75 ringbond
76 ringbondcount
77 ringcount
78 ringcountofatom
79 rotatablebond
80 rotatablebondcount
81 shortestpath
82 smallestatomringsize
83 smallestringsize
84 stericeffectindex
85 szegedindex
86 topanal
87 wienerindex
88 wienerpolarity
89 canonicalresonant
90 canonicaltautomer
91 doublebondstereoisomers
92 resonantcount
93 resonants
94 stereoisomers
95 tautomercount
96 tautomers
97 tetrahedralstereoisomers
98 logd
99 logp
100 majorms
101 msdistr
102 pi
103 pka
104 acc
105 acceptor
106 acceptorcount
107 accsitecount
108 don
109 donor
110 donorcount
111 donsitecount
112 energy
113 hbda
114 huckel
115 msacc
116 msdon
117 order
118 pichargedensity
119 pienergy
120 refractivity
121 totalchargedensity
ChemAxon fa971619eb
12-01-2007 08:24:45
You mean you want to have all of those chem terms calculated for your structure tables? Really!
If this is the case then:
1. The import will be very slow as all the chem terms are being calculated
2. Some DBs will have problems as there are limits to the number of columns that can be in a table (32 for Oracle if a remember correctly, though this may be version dependent).
One thing that might be worth considering is defining your table with all the chem terms columns first and then importing the structures into it. That way adding the chem terms columns will be very fast as the table contains no strucutures, and the import will be slow as the calculations are being done as you import each structure. But his way you do not have to wait for each chem terms column to complete before you add the next, so the process should be easier.
In IJC 2.0 we have queing of adding columns, so that you can add a new one whilst a chem terms calculation is running. The addition get queued and starts when the previous one finishes.
We also plan to allow multiple columns to be added and calculated at once, but this is not yet implemented and may take some time to be ready.
Tim