User 0f28873a29
23-02-2008 15:41:28
Hi:
I have some quetion related with the chemaxon, perhaps this is a developer quetion.
- First of all I'll want to import a gz file (mol2) to my own database. I'll want to take from each molecule the
@<TRIPOS>MOLECULE
DSD01234
the field of name of molecule to insert in the database.
- I'll want to take the offset of the molecule in the file to insert.
Are these things posible.
Thanks for all.
Yasset.
ChemAxon a3d59b832c
25-02-2008 14:58:10
Hi,
I moved this question to the database forum. Can you give an example file that you would like to put in the database?
Thanks,
Szabolcs
User 0f28873a29
26-02-2008 01:02:52
This is an example of gz file. A need to know how can I read this kind of file with the marvin..
thanks for all....
ChemAxon a3d59b832c
26-02-2008 11:33:00
Currently the mol2 format is not supported in JChem databases. You need to convert them into mrv or sdf first, for example by
molconvert:
Code: |
molconvert sdf compounds.mol2.gz -o converted.sdf |
Then you will be able to import the sdf file into the database. In the longer term, JChem will support all file formats that Marvin (and so molconvert) understands.
Unfortunately, it is not yet directly supported to import the embedded molecule name into a separate database field, but it will also be added later, and can be solved by a little programming. See: http://www.chemaxon.com/forum/ftopic3559.html
Best regards,
Szabolcs
User 0f28873a29
27-02-2008 15:43:18
thank for your answer:
Now I 'm using your api to insert the molecules in our in house database. The only problem is to generate smiles format from mol2 file. For example in the case of this molecule:
@<TRIPOS>MOLECULE
ZINC00391820
34 35 0 0 0
SMALL
USER_CHARGES
N-[(4-hydroxyphenyl)methyleneamino]-2-(2-methylimidazol-1-yl)-acetamide
@<TRIPOS>ATOM
1 C1 2.5016 0.6732 -2.5295 C.3 1 <0> -0.1150
2 C2 2.9517 0.4640 -1.1066 C.cat 1 <0> 0.3298
3 C3 4.0489 -0.2472 0.6101 C.2 1 <0> 0.0090
4 C4 3.1067 0.5965 1.0727 C.2 1 <0> 0.0303
5 N1 2.4066 1.0434 -0.0153 N.pl3 1 <0> -0.4027
6 C5 1.2803 1.9801 0.0005 C.3 1 <0> 0.0811
7 C6 -0.0144 1.2089 0.0087 C.2 1 <0> 0.5138
8 O1 0.0021 -0.0041 0.0020 O.2 1 <0> -0.4867
9 N2 -1.1906 1.8669 0.0178 N.am 1 <0> -0.5742
10 N3 -2.3943 1.1500 0.0197 N.2 1 <0> -0.2467
11 C7 -3.5269 1.7835 0.0285 C.2 1 <0> 0.1491
12 C8 -4.7935 1.0291 0.0304 C.ar 1 <0> -0.0878
13 C9 -4.7770 -0.3681 0.0169 C.ar 1 <0> -0.0550
14 C10 -5.9634 -1.0691 0.0242 C.ar 1 <0> -0.1537
15 C11 -7.1744 -0.3889 0.0336 C.ar 1 <0> 0.1382
16 C12 -7.1957 0.9999 0.0417 C.ar 1 <0> -0.1511
17 C13 -6.0142 1.7092 0.0399 C.ar 1 <0> -0.0626
18 O2 -8.3415 -1.0840 0.0345 O.3 1 <0> -0.4976
19 H1 3.0473 1.5109 -2.9637 H 1 <0> 0.1240
20 H2 2.6988 -0.2285 -3.1092 H 1 <0> 0.1207
21 H3 1.4332 0.8885 -2.5446 H 1 <0> 0.1099
22 H4 4.7739 -0.7787 1.2087 H 1 <0> 0.2259
23 H5 2.9349 0.8668 2.1042 H 1 <0> 0.2231
24 H6 1.3211 2.6123 -0.8866 H 1 <0> 0.1516
25 H7 1.3381 2.6027 0.8933 H 1 <0> 0.1586
26 H8 -1.2038 2.8368 0.0232 H 1 <0> 0.3913
27 H9 -3.5416 2.8634 0.0344 H 1 <0> 0.1287
28 H10 -3.8359 -0.8977 0.0047 H 1 <0> 0.1377
29 H11 -5.9516 -2.1490 0.0179 H 1 <0> 0.1363
30 H12 -8.1396 1.5246 0.0490 H 1 <0> 0.1391
31 H13 -6.0317 2.7890 0.0454 H 1 <0> 0.1365
32 H14 -8.6831 -1.2802 -0.8486 H 1 <0> 0.3994
33 N4 3.9326 -0.3058 -0.7240 N.pl3 1 <0> -0.4817
34 H15 4.5234 -0.8686 -1.3472 H 1 <0> 0.4804
@<TRIPOS>BOND
1 1 2 1
2 1 19 1
3 1 20 1
4 1 21 1
5 2 5 1
6 2 33 2
7 3 4 2
8 3 22 1
9 3 33 1
10 4 5 1
11 4 23 1
12 5 6 1
13 6 7 1
14 6 24 1
15 6 25 1
16 7 8 2
17 7 9 am
18 9 10 1
19 9 26 1
20 10 11 2
21 11 12 1
22 11 27 1
23 12 17 ar
24 12 13 ar
25 13 14 ar
26 13 28 1
27 14 15 ar
28 14 29 1
29 15 16 ar
30 15 18 1
31 16 17 ar
32 16 30 1
33 17 31 1
34 18 32 1
35 33 34 1
With my scrip:
while ((mol = importerMol2.read()) != null){
this.molCount++;
System.out.println(mol.toFormat("smiles:u,a-H"));
}
I generate an smile like this: CC1=NC=CN1C[C+](=O)[N-]\N=C\c1ccc(O)cc1
This positive charge in the carbon atom is correct?
Is this a valid smiles?
Thank in advance
ChemAxon a3d59b832c
28-02-2008 08:29:41
Hi,
Could you upload the mol2 source as an attachment? The forum engine removed all white space and it cannot be imported into Marvin to have a better look.
Thanks,
Szabolcs
User 0f28873a29
28-02-2008 12:50:17
This is the mol2 file....
ChemAxon a3d59b832c
29-02-2008 14:18:27