OVERLAP-TOOLKIT

Utility tool(s) for protein-ligand modeling

o-lap

Prune out overlapping atoms from mol2-formatted file

o-lap model.mol2

Usage

Usage: o-lap [options] model
Remove overlapping atoms from a model.

May use Markov Cluster Algorithm (MCL) tool for clustering.
Output is either a mol2 model, input for MCL, or atom types in MCL clusters.

Options:
  -h, --help             Displays help on commandline options.
  --help-all             Displays help including Qt specific options.
  -v, --version          Displays version information.
  --cutoffs <file/json>  JSON formatted cutoffs for atom types. Defaults are
                         are from file 'cutoffs.json'.
  -c, --cutoff <num>     Cutoff distance. Effective only when shorter than
                         default atomtype specific values (default: 1.1)
  --showcutoffs          Show JSON formatted cutoffs for atom types and exit.
  --similarjson <file>   JSON formatted atom types.
  --showsimilar          Show similar atom types and exit.
  -s, --similar          Cluster similar atom types. Types are similar, if in
                         same category. See '--showsimilar'
  --chargediff <num>     Charges must be within <num> to cluster (default:
                         0.2).
  --deletetypes <str>    Comma-separated list of atom types to discard
                         completely.
  --nib                  Convert atom types to (positive) N.3, (negative) O.3,
                         and (neutral) C.3/C.ar based on charge in NIB-like
                         manner.
  --nibthreshold <num>   Threshold of charge to bin atoms into N, C, O classes
                         (default: 0.2).
  --nibcharged           Keep all charges in model processed with nib option.
  --clustermin <int>     Minimum size of cluster to include (default: 1).
  --clusterminchr <int>  Minimum size of cluster for charged atoms. Atom is
                         charged, if abs(charge) exceeds nibthreshold. (default:
                         clustermin)
  --abcout               Create ABC-format input for MCL and exit.
  --mcl                  Create ABC-format input for MCL and run MCL.
  --mclI <num>           MCL main inflation value.
  --mclte <int>          MCL expansion thread number.
  --mapmcl <file>        Map mcl clusters to atoms. The <file> must be output
                         from MCL that corresponds to the model.
  --mcltype              Show types of clustered atoms.  Requires mapmcl.
  --prefix <str>         Prefix of the output molecule's name (default: model).

Arguments:
  model                  Mol2-file

Option --cutoffs requires a file or a value that is in JSON format. An example for latter:

o-lap --cutoffs '{"O.co2":2.2,"C.ar":1.1}' model.mol2

will use different cutoff for two atomtypes (and program's defaults for other types):

Type	Cutoff
O.co2	2.2
C.ar	1.1

The default atom typing and cutoffs are in INSTALL_PREFIX/share/SBL/o-lap/.

Dependencies

• Qt 5: application and UI framework
• MCL: Markov cluster algorithm (optional)

License

GPLv3 (or later). See LICENSE.

How to build

Build requires C++ compiler that supports C++17, Qt 5, and CMake (version 3.10 or later)

Build and install with CMake

cd overlap-toolkit
cmake -B build -DCMAKE_INSTALL_PREFIX=mypath
cmake --build build
cmake --install build

The CMAKE_INSTALL_PREFIX is ~/.local by default. Override that with -DCMAKE_INSTALL_PREFIX=mypath to direct installation into mypath.

If you did install to mypath, then mypath/bin must be on PATH. For option --mcl the Markov cluster algorithm program mcl must be on PATH.

How to cite Overlap Toolkit methods

1. For o-lap: Moyano-Gómez et al. 2024; J Cheminform 16, 97 (2024). doi: 10.1186/s13321-024-00857-6; https://doi.org/10.1186/s13321-024-00857-6