What this tool does
Shape-it is a tool that aligns a reference molecule against a set of database molecules using the shape of the molecules as the align criterion. It is based on the use of gaussian volumes as descriptor for molecular shape as it was introduced by Grant and Pickup.
The program expects one reference molecule with its three-dimensional coordinates and one database files containing one or more molecules in three dimensions. The results are either the alignment of all database molecules and their respective scores or the N best scoring molecules of the complete database.
Input
Example:
- database 27 28 0 0 0 0 0 0 0999 V2000 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 15 1 0 0 0 0 3 8 1 0 0 0 0 3 26 1 0 0 0 0 4 9 1 0 0 0 0 4 27 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 ..... - reference 30 31 0 0 0 0 0 0 0999 V2000 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 15 1 0 0 0 0 3 16 1 0 0 0 0 3 30 1 0 0 0 0 4 16 2 0 0 0 0 5 7 1 0 0 0 0 5 9 1 0 0 0 0 5 22 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 ...... - cutoff : 0.0
Output
Example:
27 28 0 0 0 0 0 0 0 0999 V2000 -4.8550 1.3401 0.2120 Cl 0 0 0 0 0 0 0 0 0 0 0 0 4.8529 -1.3406 0.2121 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -0.1809 -2.1668 -0.3789 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1788 2.1664 -0.3787 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0011 -0.0002 1.4744 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2222 -0.2738 0.6597 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2377 0.2772 0.6480 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2586 -1.3462 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2565 1.3457 -0.2314 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3343 0.5568 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3322 -0.5574 0.7972 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4069 -1.5879 -0.9855 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4048 1.5875 -0.9852 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4827 0.3152 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4807 -0.3156 0.0435 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5190 -0.7571 -0.8481 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5170 0.7568 -0.8478 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1548 0.8649 2.1342 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1601 -0.8435 2.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3089 1.3938 1.4913 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3053 -1.3909 1.4943 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4415 -2.4213 -1.6818 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4469 2.4191 -1.6835 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4070 -0.9574 -1.4422 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4050 0.9570 -1.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2961 -2.2262 0.4641 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3872 2.8487 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0 1 14 1 0 0 0 0 2 15 1 0 0 0 0 3 8 1 0 0 0 0 3 26 1 0 0 0 0 4 9 1 0 0 0 0 4 27 1 0 0 0 0 5 6 1 0 0 0 0 5 7 1 0 0 0 0 5 18 1 0 0 0 0 5 19 1 0 0 0 0 6 8 2 0 0 0 0 ......
Cite
Silicos-it - shape-it