Your file othermol.sdf was a proper sdf file but the molecules all had a
title "$$$$". The use of the delimiter string as a title is not good
practice and confused OpenBabel. I'll see if I can correct this, but if
you change the titles to Mol1, Mol2, etc. and name PatternMol, the
command below gives:
>PatternMol
>Mol1 Tanimoto from PatternMol = 0.5
>Mol2 Tanimoto from PatternMol = 0.575
>Mol3 Tanimoto from PatternMol = 0.95
>Mol4 Tanimoto from PatternMol = 0.825
>Mol5 Tanimoto from PatternMol = 0.673913
which is I think what you want. The revised othermols.sdf is attached.
Chris
On 25/01/2011 02:47, chakravar...@ncbs.res.in wrote:
Dear Chris Morley,
I tried your technique of holding ctrl to input more than one file. It helps,
but,
I did not get desired output.
Here is my input and output.
========================================================
Input:
[ OpenBabel12221015072D
23 22 0 0 0 0 0 0 0 0999 V2000
7.7424 -9.2926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
.................................................................
.................................................................
2.6281 -18.1511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
...................
...................
22 23 1 0 0 0 0
M END
$$$$
$$$$ ] n times
OpenBabel12221015072D
25 24 0 0 0 0 0 0 0 0999 V2000
7.7424 -9.2926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
.................................................................
.................................................................
6.7196 -7.5210 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
...................
...................
24 25 1 0 0 0 0
M END
$$$$
=====================================================
Output:
Tanimoto from first mol = 0.869565
Possible superstructure of first mol
=====================================================
The command I am using is (in linux) -> babel patternmol.sdf othermols.sdf
-ofpt
Both in Windows GUI and linux I receive same error message. It reads...
=================================================
*** Open Babel Warning in ReadMolecule
WARNING: Problems reading a MDL file
Cannot read atom and bond count
Expected standard 6 character atom and bond count
==================================================
Both in linux and windows, output contains tanimoto coefficient only for first
molecule in othermols.sdf.
Is the problem arising because of othermols.sdf format ? Molecule separators "M
END" "$$$$" ? ( Enclosed patternmol.sdf and othermols.sdf files )
It must be a trivial problem, but I could not figure it out all by myself.
Any help is greatly appreciated
Thankyou
Chakravarthy
From: Chris Morley<c.morley@ga...> - 2011-01-24 10:34
When there are only a small number of molecules, fpt format will give
you what you want; you are nearly there.
In the GUI, select sdf for the input format and ftp for the output.
Open the sdf file with the pattern molecule, then open the sdf file with
all the other molecules you want to compare to it, holding CTRL as you
leave the open dialog (which allows more than one input file).
Click Convert, and you will get a list of the Tanimoto coefficients
between the first molecule and each of the rest, using the default FP2
fingerprint.
On the command line (Windows or Linux):
obabel patternmol.sdf othermols.sdf -ofpt
Chris
Mol1
OpenBabel12221014542D
21 20 0 0 0 0 0 0 0 0999 V2000
6.1643 -9.2613 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1872 -8.6708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1643 -10.4424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1415 -11.0330 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1415 -12.2141 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1186 -12.8046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1186 -13.9857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0958 -14.5763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0958 -15.7574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0729 -16.3480 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1872 -7.4897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.2101 -6.8991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.2101 -5.7180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.2329 -5.1275 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.2329 -7.4897 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.2558 -6.8991 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
9.2329 -3.9464 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
8.2101 -3.3558 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
7.1872 -5.1275 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
7.1872 -3.9464 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
6.1643 -5.7180 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
2 11 1 0 0 0 0
4 5 1 0 0 0 0
4 3 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
11 12 1 0 0 0 0
12 13 1 0 0 0 0
12 15 1 0 0 0 0
13 14 1 0 0 0 0
13 19 1 0 0 0 0
14 17 1 0 0 0 0
15 16 1 0 0 0 0
17 18 1 0 0 0 0
19 20 1 0 0 0 0
19 21 1 0 0 0 0
M END
$$$$
Mol2
OpenBabel12221014572D
23 22 0 0 0 0 0 0 0 0999 V2000
7.9748 -8.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9977 -7.4695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.9748 -9.2411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9520 -9.8317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9520 -11.0128 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9291 -11.6033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9291 -12.7844 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9063 -13.3750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9063 -14.5561 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8834 -15.1467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9977 -6.2884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.0206 -5.6978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.0206 -4.5167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.0434 -3.9262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.0434 -6.2884 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
12.0663 -5.6978 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
11.0434 -2.7451 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.0206 -2.1545 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
8.9977 -3.9262 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.9977 -2.7451 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
7.9748 -4.5167 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
7.9748 -5.6978 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.9520 -6.2884 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
2 11 1 0 0 0 0
4 5 1 0 0 0 0
4 3 1 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
11 12 1 0 0 0 0
11 22 1 0 0 0 0
12 13 1 0 0 0 0
12 15 1 0 0 0 0
13 14 1 0 0 0 0
13 19 1 0 0 0 0
14 17 1 0 0 0 0
15 16 1 0 0 0 0
17 18 1 0 0 0 0
19 20 1 0 0 0 0
19 21 1 0 0 0 0
22 23 1 0 0 0 0
M END
$$$$
Mol3
OpenBabel12221015052D
23 22 0 0 0 0 0 0 0 0999 V2000
7.7424 -9.2926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -8.7021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7424 -10.4737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7196 -11.0643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7196 -12.2454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6967 -12.8359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6967 -14.0170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6739 -14.6076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6739 -15.7887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6510 -16.3793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -7.5210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.7882 -6.9304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.7882 -5.7493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8110 -5.1588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8110 -7.5210 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
11.8339 -6.9304 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
10.8110 -3.9777 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9.7882 -3.3871 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -5.1588 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -3.9777 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
7.7424 -5.7493 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
7.7424 -6.9304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.7196 -7.5210 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
2 11 1 0 0 0 0
4 5 1 0 0 0 0
4 3 2 0 0 0 0
5 6 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
11 12 1 0 0 0 0
11 22 1 0 0 0 0
12 13 1 0 0 0 0
12 15 1 0 0 0 0
13 14 1 0 0 0 0
13 19 1 0 0 0 0
14 17 1 0 0 0 0
15 16 1 0 0 0 0
17 18 1 0 0 0 0
19 20 1 0 0 0 0
19 21 1 0 0 0 0
22 23 1 0 0 0 0
M END
$$$$
Mol4
OpenBabel12221015062D
21 20 0 0 0 0 0 0 0 0999 V2000
7.7424 -9.2926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -8.7021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7424 -10.4737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7196 -11.0643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7196 -12.2454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6967 -12.8359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6967 -14.0170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6739 -14.6076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6739 -15.7887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6510 -16.3793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -7.5210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.7882 -6.9304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.7882 -5.7493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8110 -5.1588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8110 -7.5210 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
11.8339 -6.9304 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
10.8110 -3.9777 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9.7882 -3.3871 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -5.1588 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -3.9777 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
7.7424 -5.7493 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
2 11 1 0 0 0 0
4 5 1 0 0 0 0
4 3 2 0 0 0 0
6 7 1 0 0 0 0
6 5 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
11 12 1 0 0 0 0
12 13 1 0 0 0 0
12 15 1 0 0 0 0
13 14 1 0 0 0 0
13 19 1 0 0 0 0
14 17 1 0 0 0 0
15 16 1 0 0 0 0
17 18 1 0 0 0 0
19 20 1 0 0 0 0
19 21 1 0 0 0 0
M END
$$$$
Mol5
OpenBabel12221015062D
21 20 0 0 0 0 0 0 0 0999 V2000
7.7424 -9.2926 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -8.7021 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.7424 -10.4737 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7196 -11.0643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.7196 -12.2454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6967 -12.8359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6967 -14.0170 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6739 -14.6076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6739 -15.7887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6510 -16.3793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -7.5210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.7882 -6.9304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.7882 -5.7493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8110 -5.1588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8110 -7.5210 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
11.8339 -6.9304 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
10.8110 -3.9777 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
9.7882 -3.3871 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -5.1588 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
8.7653 -3.9777 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
7.7424 -5.7493 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
2 11 1 0 0 0 0
4 5 1 0 0 0 0
4 3 2 0 0 0 0
5 6 2 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
11 12 1 0 0 0 0
12 13 1 0 0 0 0
12 15 1 0 0 0 0
13 14 1 0 0 0 0
13 19 1 0 0 0 0
14 17 1 0 0 0 0
15 16 1 0 0 0 0
17 18 1 0 0 0 0
19 20 1 0 0 0 0
19 21 1 0 0 0 0
M END
$$$$
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