obrotate - Online in the Cloud

PROGRAM:

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 modelling 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 patter, 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

Use obrotate online using onworks.net services