Schrodinger python api
Schrödinger Python API 2019-3 documentation ... params (list(schrodinger.infra.structure.AtomQueryParams)) – Parameters for accepting a donor/acceptor pair. st (structure.Structure) – Structure containing the two atom sets. atoms1 – First set of atom indices to check within st. If not specified, all atoms will be used. General Python Information; Getting Started; Upgrading from Python 2 to Python 3; Accessing Your Own Modules; Setting Up Your Code Editor; Core Concepts. Structures; Interacting with Maestro. Basic Concepts; Running Scripts from Maestro; Adding Your Script to the Maestro Scripts Menu; The Maestro Module; Interacting with the Project Table
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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 …The Jaguar documentation explains in detail how to write a Jaguar input file and launch jobs from the command line. A simple input file for a water molecule might look like this: When a command like this is launched, Jaguar will run and generate output files with names derived from the input file by default, in this case, h2o.out and h2o.01.mae ...If you’re looking to integrate Google services into your website or application, you’ll need a Google API key. This key acts as a unique identifier that allows you to access and ut...Online certification courses. Level up your skillset with hands-on, online molecular modeling courses using industry-leading technology. Enrollment in a Schrödinger Online Course includes access to Schrödinger software and support. Courses are entirely asynchronous so you can participate at your preferred pace. View all courses.May 15, 2566 BE ... At the heart of quantum mechanics lies the Schrödinger equation, a fundamental equation that describes the behavior of quantum systems.The two most important concepts are the Project Table and the Workspace. A Maestro project is a collection of Structure objects and associated data, and the Project Table is the way in which this data is viewed and modified. The Project Table contains zero or more rows. Each row is referred to as an entry and consists of a Structure object (a ... Cookbook. ¶. This cookbook aims to give short, self-contained, runnable code samples to perform common tasks that would be assembled into a larger script. This document is a work in progress. Our Python API is extremely extensive and we’ll continue to add to the recipes here each release. All the code is run as part of our test suite, so ... full path of the configuration file to manage the process under supervisord in the remote host. schrodinger.test.jobserver.get_log_dir(ssh: paramiko.client.SSHClient, hostname: str) [source] ¶. Returns the complete path of the directory to access log files of processes being managed by supervisord in the remote host.May 10, 2564 BE ... The PyMOLWiki – which is maintained by the community and by Schrödinger ... Concepts | Settings | Selections | Commands | A.P.I. | Launching | ...Calculate Enrichment from Virtual Screening ¶. The `analysis.enrichment`_ helps to calculate enrichments based on known actives and the number of decoys in screen. from schrodinger.analysis.enrichment import calculator efcalc = calculator.Calculator( actives = "my_actives.txt", # Active titles, one per line. results = "screen_results.mae ... schrodinger.application.jaguar.input module. ¶. Functions and classes for reading and creating Jaguar input files. It allows setting and querying of keyword values in Jaguar input &gen sections and also provides an interface to some of the mmjag library. The JaguarInput class also provides for the running of jobs. 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 …The self-consistent quantum-electrostatic (also known as Poisson-Schrödinger) problem is notoriously difficult in situations where the density of …在最高级别上，Schrödinger Python API提供了一个基本的分子结构类，并允许与Maestro和Schrödinger计算产品进行编程交互。. 您可以使用它来自动化工作流程并扩展我们软件的核心功能。. 本文档提供了API的概述，但没有提供类和函数API文档中给出的详细级别。. 它的 ...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 …May 11, 2022 · This is the top level package for all Schrodinger modules. The main modules of interest are schrodinger.structure and the ones in the schrodinger.structutils package. The Python Module Overview included with the Schrodinger distribution gives an expository introduction to the Schrodinger …Using the Schrödinger Python API ¶. This document can be accessed from the Schrödinger website at www.schrodinger.com/pythonapi. Contents ¶. …May 11, 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. Atom objects are accessed from the list-like scVariables: ORIGIN (enum.Enum) – Possible sequence 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.jaguar.input module. ¶. Functions and classes for reading and creating Jaguar input files. It allows setting and querying of keyword values in Jaguar input &gen sections and also provides an interface to some of the mmjag library. The JaguarInput class also provides for the running of jobs. schrodinger.application.jaguar.input module. ¶. Functi AIMpy: A Python code to solve Schr ̈odinger-like equations with The Asymptotic Iteration Method. Mesut Karakoc ̧∗. Department of Physics, Faculty of Science, …Python API · Design of a Highly Selective ... Ready to release the power of digital chemistry? Contact us · Schrödinger ... Copyright © 2024 Schrödinger, Inc. Atom objects are accessed from the list-like schrodinge
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 ).Python API · Design of a Highly Selective ... Ready to release the power of digital chemistry? Contact us · Schrödinger ... Copyright © 2024 Schrödinger, Inc. 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.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.job.jobcontrol module. ¶. Core job control for python. There are currently four major sections of this module - “Job database,” “Job launching,” “Job backend,” and “Job hosts.”. The job database section deals with getting info about existing Jobs, the job launching section deals with starting up a subjob, and the ...
Oct 20, 2022 · Cookbook. ¶. This cookbook aims to give short, self-contained, runnable code samples to perform common tasks that would be assembled into a larger script. This document is a work in progress. Our Python API is extremely extensive and we’ll continue to add to the recipes here each release. All the code …schrodinger.application.jaguar.input module. ¶. Functions and classes for reading and creating Jaguar input files. It allows setting and querying of keyword values in Jaguar input &gen sections and also provides an interface to some of the mmjag library. The JaguarInput class also provides for the running of jobs.…
Reader Q&A - also see RECOMMENDED ARTICLES & FAQs. This is the top level package for all Schrodinger modules. The . Possible cause: May 11, 2022 · The two most important concepts are the.
LiveDesign is a flexible, cloud-based informatics and analysis environment for your biologics discovery team. Streamline workflows with centralized access to all … 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.rdkit.filtering.keep_top_n(products, nkeep, nsample, prop, reverse=False) ¶. A generator that yields only the best nkeep molecules out of the first nsample molecules in products, compared by prop. By default, the highest values of prop are kept; when reverse is true, the lowest values are kept instead.
May 11, 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.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 …
You can use the same commands you would type in the M May 18, 2021 · schrodinger.structutils.interactions package. ¶. Detect interactions between structures using the same underlying rules as maestro. Currently has functions to detect pi-pi interactions, pi-cation interactions, salt … Schrödinger wrote Jobcontrol instead of using off the she Atom objects are accessed from the list-like schroding The length of the list is equal to the number of the input values. Each value ranges from 0 to (number of output clusters-1). Used by the unit test to verify that the clustering works correctly. getClusteredValues() ¶. Return a list of clustered values. Outer list represents clusters, each item (cluster) will consist of one or more input values. Feb 8, 2021 · Bases: schr 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 ... Feb 8, 2021 · Introductischrodinger.application.jaguar.input module. ¶. FunMay 11, 2022 · This is the top level package for The schrodinger.project module provides access to Structures in a Maestro project. Properties of the Structure entry can be accessed from the property dictionary using the mae file data name. For example, the Glide score of a docked pose may be accessed as: glide_score = st.property['r_i_glide_gscore'] 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 Specific Modules. MacroModel. schrodinger.application.jaguar.input module. ¶. Functions and c According to the Smithsonian National Zoological Park, the Burmese python is the sixth largest snake in the world, and it can weigh as much as 100 pounds. The python can grow as mu...May 9, 2023 · 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. Need a Django & Python development company in Plano? Read r[ How can I use my own Python libraries with the SSee the API documentation for more details on the p 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 SMARTS patterns. Either nonzero or grid must be supplied but not both. :type surface_color: str or `schrodinger.structutils.color.Color` :param surface_color: The color of the surface. If a string, must be a color name recognized by the Color class. :type name: str :param name: The name of the surface - shows in Maestro's Manage Surfaces dialog under Surface ...