schrodinger_utils

Various integrations to the Schrodinger ecosystem. With major interest on analysis tools for Molecular Dynamics simulations run with Desmond.

Please understand that this work is primarily meant to be used by co-workers and students of the LBBC lab @ University of Milan. Majority of the code was written during my Master/PhD and it was not originally meant to be shared, thus documentation must be improved.

Although -for the time being- this code is not optimized for general use, you can still find useful stuff here and most plugins/scripts should work. For anyone interested, please contact me at: [email protected] or open an issue.

IMPORTANT:

• Some plugins/scripts are still work in progress.
• Some plugins/scripts were written a long time ago, when I first started programming and I had limited knowledge of the Schrodinger API. Thus, despite best efforts, may not contain state-of-the-art code.
• trjpeek.sh and mkhosts.sh scripts contain hardcoded parameters that only make sense if you work with us.
• Some major tools, like mi.py for calculating Generalized correlations matrix, and flow.py to track the paths of certain molecules are also actively developed here and supporting other formats via MDAnalyis. These tools may soon find a new home.

Overview

• Maestro plugins
• Docs
• Shell scripts
• Input templates

Plugins for Maestro

• maestro_applycscheme.py: Map data to atom colors, requires python repl, exports map2color() function.
• maestro_dummy_at_center_of_mass.py: Add dummy atom at center of mass of current selection as a separate entry.
• maestro_interacting.py: Select interacting atoms between two groups or in current selection.
• maestro_moi.py: Draw principal moments of inertia of selected atoms.
• maestro_notes.py: Add and manage notes. Notes are added to project table entries as properties
• maestro_pbitches.py: Gain control over periodic box wrapping in the workspace. Make PBCs your ...
• maestro_renumber.py: Better residue renumbering GUI.
• maestro_resdist.py: Calculate per-residue distances between multiple versions of the same structure. Draws plots and consensus structure.
• maestro_resdist_v2.py: WIP, no GUI. As above, but structures need not be the same, read residue mapping from alignment.
• maestro_select_by_b_factor.py: Select residues with B factor above threshold within selection.
• maestro_transform.py: GUI to Rotate and Translate workspace structures. Transformations are applied relative to selected reference or to absolute coordinates.
• map_interactions_to_structure.py: Functions to parse trj_interactions.py output and map residue interactions to the workspace structure.
• parse_prime_interaction_energies.py: Functions to parse prime_calcenergy output and map interaction energies to workspace structure.

Docs

• schrodinger_tips.md: Some general tips and obscure features.

Scripts

• mi.py: Compute Mutal Information (Shannon Entropy / Generalized Correlations) matrix of selected atoms within Desmond Molecular Dynamics trajectory.
• trj_flow.py: Track trajectories of molecules that pass within a certain region during Molecular Dynamics.
• trj_act.py: Align, Center and Translate stuff in Desmond trajectories.
• trj_boxinfo.py: Report MD box info.
• trj_conv.py: Export Desmond trajectory and cms topology to pdb+xtc format.
• trj_ene.py: Report energies of and between selected atom groups as calculated by Desmond vrun.
• trj_fcluster.py: RMSD based clustering of Desmond trajectory.
• trj_gcluster.py: Implementation of gromos clustering method.
• trj_helix_axis.py: Report principal axis of α-helices.
• trj_interactions.py: Calculate interactions between selections in MD.
• trj_log.py: State and ETA of a running MD job.
• trj_query.py: Convert times and frame numbers.
• trj_measure.py: WIP. Various geometry analyses.
• trj_periodic_shortest_distance.py: Measure distances between selections across PBCs.
• trj_rmsd.py: Calculate RMSD and RMSF of selections.
• trj_sasa.py: Calculate SASA.
• trj_ssp.py: Calculate Secondary Structure information.
• kerseq2hills.py: Convert Desmond metadynamics kerseq file into plumed readable HILLS file.
• biasf.py: Convert between biasf and kT.
• enhsamp_patched.py: Patched version of enhsamp.py that returns a string compatible with msj/cfg files.
• trjpeek.sh: Get a copy of a running trajectory from its scratch directory
• mkhosts.sh: Bash utility to make user and version -specific schrodinger.hosts based on a template
• XL_dock.py: Toy tool to perform protein-protein docking of structures based on cross-link data.
• schrun: wrapper shell script to allow completions.
• _schrun: WIP zsh completion function. Its generation could be automated by parsing help messages.

Templates and obscure input files commands

• minimize.msj
• simulate.msj
• system-builder_template.csb
• system-setup.msj
• schrodinger.hosts.template