Frequently asked questions
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How to install Balloon?
The distribution contains two files, the executable and a force field parameters file, in a compressed archive. Uncompress the archive to some suitable directory and you're done. Optionally, you can set the environment variable BALLOON_FORCEFIELD to point to the force field parameter file (MMFF94.mff), which saves you the trouble of typing the file location on the command line.
Usage examples
Balloon lists available options when called with '-h' or '--help'. In order to perform energy minimization using the MMFF94-like force field, Balloon needs to know the location of the force field parameter file (named 'MMFF94.mff' in the distribution). The location of the file is given using the '--forcefield' ('-f' for short) switch or via the environment variable BALLOON_FORCEFIELD. If the parameter file is not found, Balloon uses distance geometry only. The conformer sampling genetic algorithm always requires the force field parameters.
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Generate an ensemble of conformations
balloon -f /path/to/MMFF94.mff --nconfs 20 --nGenerations 300 --rebuildGeometry in.sdf out.sdf
The option 'rebuildGeometry' causes conformations to be created from scratch. Otherwise, if the input structure has 3D coordinates, Balloon will use it as the initial conformation that the genetic algorithm alters to create new conformations. If valid 3D structures are used as input, the option 'rebuildGeometry' should be omitted. Note that although the initial ensemble size is 20 conformations, the final ensemble may contain more or less depending on the flexibility of the structure.
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Generate one random conformation from SMILES
This example uses only distance geometry and no energy minimization:
balloon --nconfs 1 --noGA "C[n]1cnc2N(C)C(=O)N(C)C(=O)c12" caffeine.sdf
Now the same as above, but with energy minimization (just provide the force field parameter file):
balloon -f /path/to/MMFF94.mff --nconfs 1 --noGA "C[n]1cnc2N(C)C(=O)N(C)C(=O)c12" caffeine_min.sdf
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Assign MMFF94-like partial atomic charges
The output is in MOL2 format, geometry untouched:
balloon -f /path/to/MMFF94.mff --onlycharge in.sdf out.mol2
(Note that the charge models other than MMFF94 are not intended to be used while performing geometry optimization, only when assigning partial charges - see options 'onlycharge' and 'chargemodel')