-
Notifications
You must be signed in to change notification settings - Fork 32
BOAConstructor_Examples
Thomas Kemmer edited this page Feb 24, 2015
·
2 revisions
Note to Editors: Note, this page belongs to the ballaxy server, do not remove!
The following input examples deliberately contain only single bonds, so that the effect of bond order assignment can be easily seen. Each molecule can be either copied and pasted into the URL/Text - Box in BALLaxy's "Get Data => Upload File" - tool, or downloaded from here and then uploaded in "Get Data => Upload File". It is then entered into your Galaxy history (seen on the right hand side). If you are logged in, this history will be preserved, otherwise, it will be only kept for the current session.
After you uploaded the file, you can then use it as input for the BOA Constructor workflow, as described in BOAConstructor_Tutorial.
- Input with incorrect bond orders: Image(wiki:ballaxy/BOAConstructor_Examples:benzene_input.png)
- Correct solution: Image(wiki:ballaxy/BOAConstructor_Examples:benzene.png)
The corresponding input file:
@<TRIPOS>MOLECULE
benzene
12 12 1 0 0
SMALL
NO_CHARGES
@<TRIPOS>ATOM
1 C1 1.207 2.091 0.000 C.ar 1 BENZENE 0.000
2 C2 2.414 1.394 0.000 C.ar 1 BENZENE 0.000
3 C3 2.414 0.000 0.000 C.ar 1 BENZENE 0.000
4 C4 1.207 -0.697 0.000 C.ar 1 BENZENE 0.000
5 C5 0.000 0.000 0.000 C.ar 1 BENZENE 0.000
6 C6 0.000 1.394 0.000 C.ar 1 BENZENE 0.000
7 H1 1.207 3.175 0.000 H 1 BENZENE 0.000
8 H2 3.353 1.936 0.000 H 1 BENZENE 0.000
9 H3 3.353 -0.542 0.000 H 1 BENZENE 0.000
10 H4 1.207 -1.781 0.000 H 1 BENZENE 0.000
11 H5 -0.939 -0.542 0.000 H 1 BENZENE 0.000
12 H6 -0.939 1.936 0.000 H 1 BENZENE 0.000
@<TRIPOS>BOND
1 1 2 1
2 1 6 1
3 2 3 1
4 3 4 1
5 4 5 1
6 5 6 1
7 1 7 1
8 2 8 1
9 3 9 1
10 4 10 1
11 5 11 1
12 6 12 1
@<TRIPOS>SUBSTRUCTURE
1 BENZENE 1 PERM 0 **** **** 0 ROOT
This molecule has 7 equally possible solutions.
- Input with incorrect bond orders: Image(wiki:ballaxy/BOAConstructor_Examples:nontrivial_input_1.png)
- Correct solution: 1 (4 and 6 are symmetry equivalent wrt to the ring system) Image(wiki:ballaxy/BOAConstructor_Examples:nontrivial_1.png)
- Correct solution: 2 (equivalent to 5) Image(wiki:ballaxy/BOAConstructor_Examples:BOA_nontrivial_1_sol_2.png)
- Correct solution: 3 (equivalent to 7 Image(wiki:ballaxy/BOAConstructor_Examples:BOA_nontrivial_1_sol_3.png)
The corresponding input file:
@<TRIPOS>MOLECULE
****
21 22 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 H 23.2335 -8.8791 0 H 1 **** 0
2 N 21.4501 -7.9466 0 N.pl3 1 **** 0
3 C 21.4509 -6.1349 0 C.2 1 **** 0
4 N 23.0201 -5.2294 0 N.3 1 **** 0
5 N 19.8825 -5.2283 0 N.2 1 **** 0
6 C 18.3129 -6.1334 0 C.2 1 **** 0
7 N 16.744 -5.2274 0 N.3 1 **** 1
8 C 18.3126 -7.9459 0 C.ar 1 **** 0
9 C 16.7435 -8.8518 0 C.ar 1 **** 0
10 C 16.7435 -10.6636 0 C.ar 1 **** 0
11 H 15.1747 -11.5699 0 H 1 **** 0
12 C 18.3126 -11.5694 0 C.ar 1 **** 0
13 C 19.8816 -10.6636 0 C.ar 1 **** 0
14 C 19.8816 -8.8518 0 C.ar 1 **** 0
15 H 23.0205 -3.4176 0 H 1 **** 0
16 H 24.589 -6.1355 0 H 1 **** 0
17 H 15.1749 -6.1331 0 H 1 **** 0
18 H 16.7441 -3.4156 0 H 1 **** 0
19 H 15.1742 -7.9464 0 H 1 **** 0
20 H 18.313 -13.3812 0 H 1 **** 0
21 H 21.4507 -11.569 0 H 1 **** 0
@<TRIPOS>BOND
1 1 2 1
2 2 14 1
3 2 3 1
4 3 5 1
5 3 4 1
6 4 16 1
7 4 15 1
8 5 6 1
9 6 8 1
10 6 7 1
11 7 18 1
12 7 17 1
13 8 14 1
14 8 9 1
15 9 19 1
16 9 10 1
17 10 12 1
18 10 11 1
19 12 20 1
20 12 13 1
21 13 21 1
22 13 14 1
- Input with incorrect bond orders: Image(wiki:ballaxy/BOAConstructor_Examples:nontrivial_input_2.png)
- Correct solution: Image(wiki:ballaxy/BOAConstructor_Examples:nontrivial_2.png)
- sub-optimal solution 1: Image(wiki:ballaxy/BOAConstructor_Examples:BOA_nontrivial_2_sol_2.png)
- sub-optimal solution 2: Image(wiki:ballaxy/BOAConstructor_Examples:BOA_nontrivial_2_sol_3.png)
- sub-optimal solution 3: Image(wiki:ballaxy/BOAConstructor_Examples:BOA_nontrivial_2_sol_4.png)
The corresponding input file:
@<TRIPOS>MOLECULE
****
11 11 0
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 S 12.1715 -7.0195 0 S.3 1 **** 0
2 N 13.2359 -8.4844 0 N.2 1 **** 0
3 C 12.1715 -9.9493 0 C.2 1 **** 0
4 C 10.4494 -9.3898 0 C.2 1 **** 0
5 N 10.4494 -7.5791 0 N.2 1 **** 0
6 N 12.7311 -11.6714 0 N.3 1 **** 0
7 N 8.9845 -10.4541 0 N.2 1 **** 0
8 N 7.3304 -9.7176 0 N.2 1 **** 1
9 N 5.6762 -8.9811 0 N.1 1 **** -1
10 H 14.5022 -12.0479 0 H 1 **** 0
11 H 11.5195 -13.0171 0 H 1 **** 0
@<TRIPOS>BOND
1 1 5 1
2 1 2 1
3 2 3 1
4 3 6 1
5 3 4 1
6 4 7 1
7 4 5 1
8 6 11 1
9 6 10 1
10 7 8 1
11 8 9 1