Analyze protein-ligand interactions (hydrogen bonds, salt bridges, pi-pi stacking, pi-cation) in a complex or Glide pose-viewer (*_pv.maegz) file. For a pose-viewer the first entry is the receptor and ligand_index (default 2) selects the pose; for a single complex give a ligand_asl. Returns a structured interaction report.

Stop a running job. Terminates the job's process group; the job directory and any partial outputs are left in place.

Compute 2D physicochemical molecular descriptors (MW, logP, TPSA, H-bond donors/acceptors, rotatable bonds, ring counts, etc.) with Canvas. Synchronous — returns the path to a CSV of descriptors, one row per molecule.

Generate a conformer ensemble for ligands with ConfGen. Input must contain explicit hydrogens (run ligprep first). Accepts .mae/.maegz/.mol2/.sdf. Long-running — returns a job_id; conformers are written to -out.maegz in the job directory.

Convert a structure file between formats (mae, maegz, sdf, pdb, mol2, smi, cif). Schrödinger infers the input format from its extension. Returns the output path.

Report the Schrödinger installation: root path, release/build, licensed products, configured job hosts, and GPU availability. Call this first to confirm the suite is found and to see which workflows are licensed. GPU-accelerated workflows (Desmond MD, FEP+) require an NVIDIA GPU and are unavailable on Apple Silicon.

Enumerate protonation/tautomeric states and estimate pKa for ligands with Epik. Accepts a structure file (.mae/.maegz/.sdf — non-Maestro inputs are auto-converted). Long-running — returns a job_id; states with pKa/penalty properties in <output_name>.

Download an experimental structure from the RCSB PDB by its 4-character ID (e.g. '1HSG'). Returns the path to the downloaded .pdb file. Use protein_prepwizard afterward to prepare it for docking.

Build a 2D structure report (PDF or HTML) of every structure in a file, each drawn in 2D and labeled with properties (e.g. docking scores from a pose-viewer). Great for sharing docking/screening results. properties is 'all' or a comma-separated list of property names. Returns the path to the report.

Build a Glide docking grid from a prepared receptor. Specify the binding-site center either explicitly via center [x,y,z] or by giving ligand_ref (a file containing a bound ligand whose centroid defines the site). Long-running — returns a job_id; the grid (<grid_name>) lands in the job dir and is the input to glide_dock.

Fetch a finished job's outputs: the list of produced files (poses, prepped structures, logs) and its final state. For docking jobs, follow up with summarize_docking on the produced pose-viewer (*_pv.maegz) file for a ranked table.

Check a submitted job. Returns state (submitted/running/completed/failed/ canceled), elapsed time, exit code, and a tail of the job log. Poll this after submitting any long-running workflow.

Dock prepared ligands into a Glide grid and score them. precision is 'SP' (standard, default) or 'XP' (extra-precision, slower). ligands_path should be a LigPrep-prepared file. Long-running — returns a job_id. When complete, run summarize_docking on the produced *_pv.maegz for a ranked GlideScore table.

Run a Jaguar quantum-mechanics calculation on a small molecule. calculation is 'optimization', 'energy', or 'frequency'. Accepts a structure file (.mae/.pdb/.sdf) — a Jaguar input is built automatically — or a prebuilt Jaguar .in file. Long-running; returns a job_id. Keep systems small (a few dozen atoms) on CPU-only hardware.

Render a 2D ligand-interaction diagram (PNG, shown inline) for a protein-ligand complex or Glide pose-viewer file: the ligand drawn in 2D with the atoms that make interactions highlighted by type (blue=H-bond, red=salt bridge, green=pi-pi, orange=pi-cation) and a legend mapping them to protein residues. Also writes the PNG.

Prepare ligands for docking: add hydrogens, generate ionization/tautomeric states (via Epik), enumerate stereoisomers, and produce optimized 3D structures. Accepts .smi/.csv/.sdf/.mae. Long-running — returns a job_id. Prepared ligands are written to <output_name> in the job directory (fetch the path with get_job_results).

List known async jobs, most recent first. Optionally filter by state (submitted/running/completed/failed/canceled).

Concatenate several structure files into one multi-structure file.

Rescore a receptor-ligand complex (or Glide pose-viewer file) with Prime MM-GBSA to estimate binding free energy (dG bind). Accepts a *_pv.maegz or a complex .mae. Long-running — returns a job_id; the output structures carry r_psp_MMGBSA_dG_Bind.

Prepare a protein structure for docking with the Protein Preparation Wizard: assign bond orders, add/optimize hydrogens, set het-group protonation states (Epik), optionally fill missing side chains/loops (Prime), and restrained-minimize. Accepts .pdb/.mae/.cif. Long-running — returns a job_id; prepared structure is <output_name>.

Predict ~50 ADMET properties (aqueous solubility, Caco-2/MDCK permeability, logP, logBB, CNS activity, HERG, etc.) for ligands with QikProp. Accepts most structure formats. Long-running — returns a job_id; results land as a .CSV plus structures annotated with QP* properties. Use structure_info on the output .mae to read them.

Render molecules as a 2D structure image (PNG) shown inline. Provide either a list of smiles or an input_path to a structure file (mae/sdf/pdb/...). For files you can pass legend_property (e.g. 'r_i_docking_score') to label each structure with that value. Also writes the PNG to disk.

Shape-based similarity screen: rank the 3D structures in screen_path by shape similarity to the query_path molecule. Both must be 3D structure files (prep ligands first). Long-running — returns a job_id; ranked hits with Shape_Sim scores are written to _align.maegz.

Detect and score potential ligand-binding sites on a protein with SiteMap. Accepts a prepared protein structure (.mae). Long-running — returns a job_id; site maps and SiteScore/Dscore are written to _out.maegz and per-site files.

Generate single-conformer 3D structures from a list of SMILES strings and write them to one file. Good for quick 3D embedding; for full ligand preparation (ionization, tautomers, stereoisomer enumeration) use the ligprep tool instead. Returns per-molecule results and the output path.

Split a multi-structure file into one file per structure. Returns the list of written files with their titles.

Inspect a structure file: number of structures, per-structure atom/bond counts, title, formal charge, molecular weight, chains/residues, and a sample of named properties (e.g. docking scores). Works on any format Schrödinger reads.

Parse a Glide pose-viewer file (*_pv.maegz) into a ranked table of GlideScores and key terms per ligand. Returns the best poses sorted by score (lower is better).