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Molecular
Design
Programs

Companion Programs

With the main executable, Moloc, comes a suite of associated programs to perform various background tasks.
Starting one of these program without parameters prints a usage line and a short description of parameters. Optionally, extended help texts ca be produced.
Most functionalities can also be addressed interactively from within Moloc, where often additional help is available.
NameShorthand Description of Functionality
Moloc -h produces just help output.
Gr2d draws 2-dimensional plots of several curves.
Mabch runs a MAB force-field minimization (or dynamics calculation) and is usually started from within Moloc.
Mcbch runs a C-alpha force field minimization or dynamics calculation.
Mbcd takes a pharmacophore file (.php), starts BIOCAD's HYPEDIT program to produce a hypothesis and issues a CATALYST database search.
Mol3d produces a .sd file containing 3-dimensional coordinates from a 2-dimensional .sd file
Msmab produces a file (.mab, .sd, or .tdt) of 3-dimensional structures from a list of smiles codes.
Mcnf performs a conformation analysis for the structures of a .sd file.
Msrfvl calculates surfaces volumes and additional descriptors for a set of structures given as .sd file.
Mtprgn,
Mtprsml,
Mtpr...
Several programs that produce a topological pharmacophore representations, perform similarity calculations, etc. They are used for database generation and mining, to perform diversity analyses for library design, and to produce topological pharmacophore descriptors for statistical model generation.
Mamber generates input files of small molecules for the program AMBER.
Mdck docks structures from a .sd file into a receptor cavity.
Movo builds structures out of the fragments of libraries into a receptor cavity.
Mngsd a manager for .sd-file handling
etc. various programs for smaller tasks (clustering, filtering, ...)