Tutorial:Other Tools
From Open Babel
There are a number of included tools that have been built using Open Babel, including obprop, obgrep, obchiral, obfit, and obrotate.
Contents |
obprop
obprop calculates a couple of simple molecular properties (e.g., molecular mass and ring count).
PROMPT> obprop ' mymols.sdf' > 'outputfile.txt'
PROMPT> cat outputfile.txt
name MOL_00000067 mol_weight 191.989 num_rings 1 $$$$ name MOL_00000083 mol_weight 191.989 num_rings 1 $$$$ name MOL_00000105 mol_weight 191.989 num_rings 1 $$$$ name MOL_00000296 mol_weight 207.077 num_rings 1 $$$$
obgrep
obgrep can be used for structure-based searching for molecules inside multi-molecule files (e.g., SMILES, SDF, etc.) or across multiple files.
-c Print the number of matches
-f Full match, print matching-molecules only when the number of heavy
atoms is also equal to the number of atoms in the SMARTS pattern
-i<format>
Specifies input and output format,
-n Only print the name of the molecules
-t # Print a molecule only if the pattern occurs # times inside the mol-
ecule
-v Invert the matching, print non-matching molecules
To print just the names of those molecules containing bromobenzne:
PROMPT> obgrep -n 'c1ccccc1Br' 'mymols.sdf'
MOL_00000067 MOL_00000083 MOL_00000105 MOL_00016985 MOL_00042466 MOL_00045017 MOL_00077464 MOL_00191850 MOL_00857068 MOL_01812494 MOL_02660600 MOL_02683063 MOL_02683851 MOL_02683853 MOL_02683854 MOL_03411551 MOL_03428533 MOL_03428552 MOL_03789141 MOL_04038961
To simply count the number of molecules that match:
PROMPT> obgrep -c -t 2 'c1ccccc1Br' 'mymols.sdf' 20
To only select those compounds where the pattern occurs twice use:
PROMPT> obgrep -n -t 2 'c1ccccc1Br' 'mymols.sdf' MOL_04038961
obchiral
obchiral prints molecular chirality information:
PROMPT> mymols.sdf
Molecule 1: mol_1 Atom 2 Is Chiral C3 Volume= 8.35262 Atom refs= 1 2 3 4 Clockwise? 0 Molecule 2: mol_2 Atom 2 Is Chiral C3 Volume= -8.43506 Atom refs= 1 2 3 4 Clockwise? 0 Atom 3 Is Chiral N3 Volume= 2.15701 Atom refs= 1 2 3 4 Clockwise? 0 Molecule 3: mol_3 Atom 2 Is Chiral C3 Volume= -8.37849 Atom refs= 1 2 3 4 Clockwise? 0 Atom 3 Is Chiral N3 Volume= 1.84595 Atom refs= 1 2 3 4 Clockwise? 0 Atom 19 Is Chiral C3 Volume= 10.331 Atom refs= 1 2 3 4 Clockwise? 0
This information can be piped into a file like this:
PROMPT> obchiral 'mymols.sdf' > outputfile'.txt
obfit
obfit will superimpose molecules based on a SMARTS pattern. The atoms used to fit the two molecules are defined by the SMARTS pattern given by the user. It is useful to align congeneric series of molecules on a common structural scaffold for 3D-QSAR studies. It can also be useful for displaying the results of conformational generation.
PROMPT> obfit ' c1ccccc1Br ' static.sdf mymols.sdf
obrotate
obrotate will batch-rotate dihedral angles matching SMARTS patterns. 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. 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:
PROMPT> 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:
PROMPT> obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90
Keep the pyridyl ring fixed and moves the aliphatic chain:
PROMPT> obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90
Keep the aliphatic chain fixed and move the pyridyl ring:
PROMPT> obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90
