"obrotate" - Rotate Dihedral Angles with SMARTS
What Is "obrotate" command? How to use it to batch-rotate dihedral angles matching SMARTS patterns?
"obrotate" command is a command line tool provided in the Open Babel package that allows you to batch-rotate dihedral angles matching SMARTS patterns.
Here is the user manual of the "obrotamer" command.
NAME obrotate -- batch-rotate dihedral angles matching SMARTS patterns SYNOPSIS obrotate 'SMARTS-pattern' filename atom1 atom2 atom3 atom4 angle DESCRIPTION The obrotate program rotates the torsional (dihedral) angle of a specified bond in molecules to that defined by the user. In other words, it does the same as a user setting an angle in a molecular modeling package, but much faster and in batch mode (i.e. across multiple molecules in a file). The four atom IDs required are indexes into the SMARTS pattern, which starts at atom 0 (zero). The angle supplied is in degrees. The two atoms used to set the dihedral angle <atom1> and <atom4> do not need to be connected to the atoms of the bond <atom2> and <atom3> in any way. The order of the atoms matters -- the portion of the molecule attached to <atom1> and <atom2> remain fixed, but the portion bonded to <atom3> and & <atom4> moves. EXAMPLES Let's say that you want to define the conformation of a large number of molecules with a pyridyl scaffold and substituted with an aliphatic chain at the 3-position, for example for docking or 3D-QSAR purposes. To set the value of the first dihedral angle to 90 degrees: obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90 Here 6 and 7 define the bond to rotate in the SMARTS pattern, i.e., c1-C and atoms 5 and 8 define the particular dihedral angle to rotate. Since the atoms to define the dihedral do not need to be directly connected, the nitrogen in the pyridine can be used: obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90 Keep the pyridyl ring fixed and moves the aliphatic chain: obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90 Keep the aliphatic chain fixed and move the pyridyl ring: obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90
1. Create a molecule with a pyridyl ring and an aliphatic chain.
fyicenter$ obabel -:c1ccncc1CCC -O pyridine.sdf --gen3D -d 1 molecule converted
2. Move the aliphatic chain with the "obrotate" command:
fyicenter$ obrotate 'c1ccncc1CCC' pyridine.sdf 5 6 7 8 90 > pyridine-rotate-chain.sdf
3. Move the pyridyl ring with the "obrotate" command:
fyicenter$ obrotate 'c1ccncc1CCC' pyridine.sdf 8 7 6 5 90 > pyridine-rotate-ring.sdf
To see differences of the rotated structures, you can open them in the PubChem 3D Viewer.
2020-10-26, 713🔥, 0💬
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