Schrodinger python api.

schrodinger.job.queue module¶. A class for running multiple concurrent jobs. This module provides the class JobDJ.. The name JobDJ refers to an old implementation of “Job-control for Distributed-Job drivers,” and the module name “queue” reflects the fact that added jobs are queued until ready to run.. Like the original JobDJ, its main purpose is to provide for …AIMpy: A Python code to solve Schr ̈odinger-like equations with The Asymptotic Iteration Method. Mesut Karakoc ̧∗. Department of Physics, Faculty of Science, …Integer indexes for the atoms to transform. If the list is not specified then all atoms in the structure are transformed. If the list is empty, none of the atoms are transformed. schrodinger.structutils.transform.get_centroid(st, atom_list=None) ¶. Returns the structure’s centroid as a 4-element numpy array:The Python Module Overview included with the Schrodinger distribution gives an expository introduction to the Schrodinger Python API. It is available at …

schrodinger.structutils.analyze module. ¶. Functions for analyzing Structure objects. AslLigandSearcher is a class that identifies putative ligands in a structure. Each putative found ligand is contained in a Ligand instance. There are also a number of functions for using SMARTS, ASL, and SMILES (e.g. evaluate_smarts_canvas or generate_smiles ).Automatically orient the membrane according to the protein in self.ct. Translate the protein so that the membrane will be located at the origin and rotate the protein so that membrane is along the z-axis. Assumes that center/orientation/thickness are set. At the end the protein will not have vector atoms.schrodinger.job.queue module¶. A class for running multiple concurrent jobs. This module provides the class JobDJ.. The name JobDJ refers to an old implementation of “Job-control for Distributed-Job drivers,” and the module name “queue” reflects the fact that added jobs are queued until ready to run.. Like the original JobDJ, its main purpose is to provide for …

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This module provides the APIs behind the Ligand Designer panel and workflow. It combines binding site Phase hypothesis generation with R-group enumeration and Glide grid generation and docking. The docking uses a Glide HTTP server for speed. class schrodinger.application.glide.ligand_designer.State ¶. Bases: enum.Enum.schrodinger.project.project module. ¶. Interface to the active Maestro Project. Projects may be accessed while within Maestro or without Maestro from a python script that imports this module. Usually when running from within Maestro the Project object would be returned via maestro.project_table_get ()schrodinger.application.pathfinder.reaction.is_reagent_file(filename) ¶. Check whether a given file is usable as a reagent file. A reagent file must be a structure file and the structures need to have a title. In the case of a csv file, we look for columns named ‘s_m_title’ or ‘NAME’. Parameters: schrodinger.application.glide.glide — Schrödinger Python API 2021-2 documentation. Source code for schrodinger.application.glide.glide. """Classes for creating Grid Generation and Ligand Docking DICE (Impact) inputfiles from user-friendly keyword/value pairs.The classes use the mm.mmim* wrappers to convert the keywords and values intothe ... May 11, 2022 · schrodinger.application.glide.glide module. ¶. Classes for creating Grid Generation and Ligand Docking DICE (Impact) input files from user-friendly keyword/value pairs. The classes use the mm.mmim* wrappers to convert the keywords and values into the actual DICE input files. Job parameters are …

Introduction. ¶. At the highest level, the Schrödinger Python API provides a base molecular structure class and allows for programmatic interaction with Maestro and Schrödinger computational products. It allows you to create scripts …

Introduction ¶. Introduction. ¶. At the highest level, the Schrödinger Python API provides a base molecular structure class and allows for programmatic interaction with Maestro and Schrödinger computational products. You can use it to automate workflows and extend our software’s core functionality.

Oct 20, 2022 · schrodinger.structure module ¶. schrodinger.structure module. ¶. A context manager to enable manual update mode to update the structure by calling update only once before exiting , and then restores the original manual update state. These represent varying bond types, which are independent from bond orders. Introduction. ¶. At the highest level, the Schrödinger Python API provides a base molecular structure class and allows for programmatic interaction with Maestro and Schrödinger computational products. It allows you to create scripts that automate and extend our core functionality. Core Concepts ¶. Structures ¶. The Structure class is the fundamental class in our modules, and will probably be used in all of the code you write. Structure objects … schrodinger.application.msv.seqio. valid_uniprot_id (uniprot_id: str) → bool [source] ¶ UniProt ID must be 6 characters or 10 characters starting with a letter. Returns. Whether the ID appears to be a valid UniProt ID. schrodinger.application.msv.seqio. valid_swiss_prot_name (swiss_prot_name: str) → bool [source] ¶ schrodinger.job.launcher module. ¶. A class for launching individual executables under job control. Launcher is a Python wrapper for using the external ‘jlaunch’ script. It simplifies the creation of the “startup script” for a script running under job control. NOTE: Launcher is designed for use within startup scripts only.schrodinger.protein.captermini.cap_termini (st) [source] ¶ Cap the termini on the specified st Function interface for CapTermini class. schrodinger.protein.captermini.add_terminal_oxygens (st, frag_min_atoms = 150) [source] ¶ Add OXT oxygen to the C-terminal of each poly-peptide chain. A hydrogen will first be … schrodinger.structutils.analyze module. ¶. Functions for analyzing Structure objects. AslLigandSearcher is a class that identifies putative ligands in a structure. Each putative found ligand is contained in a Ligand instance. There are also a number of functions for using SMARTS, ASL, and SMILES (e.g. evaluate_smarts_canvas or generate_smiles ).

schrodinger.application.glide.glide module. ¶. Classes for creating Grid Generation and Ligand Docking DICE (Impact) input files from user-friendly keyword/value pairs. The classes use the mm.mmim* wrappers to convert the keywords and values into the actual DICE input files. Job parameters are specified by passing a dictionary of keyword/value ...May 11, 2022 · schrodinger.structutils.sort module. ¶. A module for sorting structure files by Structure-level property values. The module supports multi-key sorting, ‘block’ sorting, and file merging. ‘sort_criteria’ and ‘intra_block_sort_criteria’ are lists of tuples, where each tuple is an ct-level property dataname and …Jobcontrol ¶. Jobcontrol. ¶. Jobcontrol is a way to allow tasks to run asynchronously, and provides support for starting tasks on a different machine than their execution. For example, you may launch a task from a laptop (running Maestro) to a compute node, so that the task runs on several cores. Jobcontrol takes care of transferring input ...Parameters: struc – The structure to create the surface for; name (str) – The name of the surface.; asl (str or NoneType) – If given, the surface will only be created for atoms in the structure that match the provided ASL.Note that only one of asl and atoms may be given. If neither are given, then the surface will be created for all atoms in the structure.def __init__ (self, values, n_clusters = 8, ** kmeans_args): """ Cluster the specified list of values (e.g. coordinates) into the given number of clusters. NOTE: This clustering algorithm is an inherintly random process, so results from different runs may not be consistent.:type values: List or numpy array of values to cluster.Each item can be a float or a list of floats …Aug 8, 2020 · Returns True if at least one of the residue in the given structure has missing side-chain atoms (backbone atoms are ignored). schrodinger.application.prepwizard.fix_sulfur_charges(st) ¶. Post process by fixing the charge on zero-order-bonded Sulfurs Gives -1 or -2 charge to Sulfurs as …

Feb 13, 2023 · schrodinger.application.glide.glide module. ¶. Classes for creating Grid Generation and Ligand Docking DICE (Impact) input files from user-friendly keyword/value pairs. The classes use the mm.mmim* wrappers to convert the keywords and values into the actual DICE input files. Job parameters are … Introduction. ¶. At the highest level, the Schrödinger Python API provides a base molecular structure class and allows for programmatic interaction with Maestro and Schrödinger computational products. It allows you to create scripts that automate and extend our core functionality.

addCommandLineOptions (parser, distributed=False, use_group=False) ¶. Add top-level and App options to the OptionParser ‘parser’. With this method, the application-specific parser can include top-level and App options in its usage/help statement, though the actual parsing of those arguments is handled elsewhere. schrodinger.application.glide.glide module. ¶. Classes for creating Grid Generation and Ligand Docking DICE (Impact) input files from user-friendly keyword/value pairs. The classes use the mm.mmim* wrappers to convert the keywords and values into the actual DICE input files. Job parameters are specified by passing a dictionary of keyword/value ... Feb 13, 2023 · Within this document, we use the invocation setInputFile ("myscript.py") to register the current jobcontrol script as an input file, intending the script file to be saved and run as myscript.py . Other input files for the job can be added in the same way. Similarly, output files can be registered with the …How can I use my own Python libraries with the Schrödinger Python API ...Feb 5, 2020 · The Scripting with Python tutorial is part of the General documentation and can be accessed from within Maestro’s Help facility from the Manuals Index. Setting regenerate_markers to True (default) will force Maestro to update markers for distances, labels, etc. and to apply any changes to the Workspace structure.Aug 6, 2019 · This module provides the APIs behind the Ligand Designer panel and workflow. It combines binding site Phase hypothesis generation with R-group enumeration and Glide grid generation and docking. The docking uses a Glide HTTP server for speed. class schrodinger.application.glide.ligand_designer.State ¶. …schrodinger.structutils.transform module. ¶. Manipulate atom coordinates with matrix operations. Provides array methods to translate and rotate atoms in a structure.Structure. The coin of the realm is a four by four numpy array. The first 3x3 is a rotation matrix, the last 3x1 is translation matrix, and the 4th row is a spectator row.The stage takes one set of input structure files and generates one set of corresponding output files. NOTE: SMILES format files can only be filtered on the title. """. [docs] def filterFile(self, ligfile, outfile): """ Filter the file <ligfile> based on PROPERTY & VALUE_FILE and add the output file to self.output_files list """ st_num = 0 ...

Introduction. ¶. At the highest level, the Schrödinger Python API provides a base molecular structure class and allows for programmatic interaction with Maestro and Schrödinger computational products. It allows you to create scripts …

Jul 30, 2021 · Example 1: Setting up jobs. Example 2: Launching jobs and parsing the output. Example 3: Chaining jobs using the restart file. Example 4: Setting up a constrained geometry optimization. Example 5: Running Jaguar jobs in parallel batches. Enrichment. Calculate Enrichment from Virtual Screening. Product …

Feb 13, 2023 · schrodinger.utils.ligfilter module. ¶. Support module for Ligfilter applications, including parsing functions, filtering criteria, constants, and setting up of the default composite SMARTS patterns. The basic idea is to provide a set of criteria for filtering structures based on properties, function evaluation, or collections of …schrodinger.project.project module. ¶. Interface to the active Maestro Project. Projects may be accessed while within Maestro or without Maestro from a python script that imports this module. Usually when running from within Maestro the Project object would be returned via maestro.project_table_get ()schrodinger.protein.captermini.cap_termini (st) [source] ¶ Cap the termini on the specified st Function interface for CapTermini class. schrodinger.protein.captermini.add_terminal_oxygens (st, frag_min_atoms = 150) [source] ¶ Add OXT oxygen to the C-terminal of each poly-peptide chain. A hydrogen will first be …Atom objects are accessed from the list-like schrodinger.structure.Structure.atom attribute. Each atom is an instance of the _StructureAtom class. See the “Properties” section of the schrodinger.structure._StructureAtom documentation for a list of available attributes (implemented again as python properties). For example, the atomic number ...May 11, 2022 · The stage takes one set of input structure files and generates one set of corresponding output files. NOTE: SMILES format files can only be filtered on the title. """. [docs] def filterFile(self, ligfile, outfile): """ Filter the file <ligfile> based on PROPERTY & VALUE_FILE and add the output file to self.output_files list """ …Jul 30, 2021 · Example 1: Setting up jobs. Example 2: Launching jobs and parsing the output. Example 3: Chaining jobs using the restart file. Example 4: Setting up a constrained geometry optimization. Example 5: Running Jaguar jobs in parallel batches. Enrichment. Calculate Enrichment from Virtual Screening. Product …Chatbot API technology is quickly becoming a popular tool for businesses looking to automate customer service and communication. With the help of artificial intelligence (AI) and n...schrodinger.rdkit.substructure. apply_substructure_coordinates_from_mapping (mol: rdkit.Chem.rdchem.Mol, template_mol: rdkit.Chem.rdchem.Mol, atom_mapping: Iterable [Tuple [int, int]]) ¶ Applies coordinates from the provided template to the input mol utilizing an explicit atom mappingclass schrodinger.utils.pymol.PymolInstance(pymol_command=('pymol',)) ¶. Bases: object. Represents a remote PyMOL instance (controlled via a one-way pipe) Acts like a proxy to the cmd module, without return values on function calls (which would actually be very usefull). See also: PyMOL XMLRPC server (pymol -R)

This module defines classes for principal component analysis (PCA) and essential dynamics analysis (EDA) calculations. class schrodinger.trajectory.prody.pca.PCA(name='Unknown') ¶. Bases: schrodinger.trajectory.prody.nma.NMA. A class for Principal Component Analysis (PCA) of conformational ensembles. See examples in pca.Source code for schrodinger.application.glide.poseviewconvert. """ Functions for creating or converting pose viewer files. The module can convert a 'pose viewer' type file into a series of complexes, and convert complexes into ligand-only, receptor-only, or pose viewer files. The script pv_convert.py is the preferred command-line interface to ...Using the Schrödinger Python API ¶. This document can be accessed from the Schrödinger website at www.schrodinger.com/pythonapi. Contents ¶. …disableDyncalc ¶. Disable the execution of _dyncalc(). This is used to avoid redundant _precalc() calculations delegated in _dyncalc(). isDynamic ¶ class schrodinger.application.desmond.packages.analysis.PlanarAngle (* args, ** kwargs) ¶. Bases: schrodinger.application.desmond.packages.staf.GeomAnalyzerBase Calculate …Instagram:https://instagram. saw x showtimes near amc sunrise 8digital encyclopedia made by microsoft crossword cluestr8upgayporn.comshow stoppers of a sort crossword clue At the highest level, the Schrödinger Python API provides a base molecular structure class and allows for programmatic interaction with Maestro and … loma linda sdn 2024store manager salary foot locker In Python, “strip” is a method that eliminates specific characters from the beginning and the end of a string. By default, it removes any white space characters, such as spaces, ta... shark robot vacuum flashing red exclamation point At the highest level, the Schrödinger Python API provides a base molecular structure class and allows for programmatic interaction with Maestro and Schrödinger computational products. You can use it to automate workflows and extend our software’s core functionality.Nov 12, 2021 · The Python Module Overview included with the Schrodinger distribution gives an expository introduction to the Schrodinger Python API. ... NOTE: Deprecated in favor of get_mmshare_version() If the current Schrodinger python version is less than the minimum, an Exception will be raised. If the current …