Schrodinger python api.
If the current Schrodinger python version is less than the minimum, an Exception will be raised. If the current version is greater than the maximum, a warning will be issued. schrodinger. get_release_name ( ) → str [source] ¶
If you’re looking to integrate Google services into your website or application, you’ll need a Google API key. An API key is a unique identifier that allows you to access and use v... If SCHRODINGER_PYTHON_DEBUG is not set, returns WARNING. schrodinger.utils.log. get_logger (name: Optional [str] = None) → logging.Logger [source] ¶ A convenience function to call default_logging_config and return a logger object. schrodinger.utils.log. get_output_logger_handler → logging.Handler [source] ¶ Get the common handler used for ... 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 ...May 11, 2022 · class schrodinger.application.msv.seqio.SeqDAlignmentWriter [source] ¶. Bases: schrodinger.application.msv.seqio.BaseProteinAlignmentWriter. Class to write sequence and descriptors to seqd file. Each sequence is exported to a seqd file with name “<seq_name>_<chain_name>.seqd”. classmethod write(aln, …May 18, 2021 · 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. …
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 ...
How can I use my own Python libraries with the Schrödinger Python API ...Feb 22, 2022 · Source code for schrodinger. """ 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 …
The Desmond trajectories are saved in binary files and both DTR and XTC formats are supported. To read a trajectory: from schrodinger.application.desmond.packages import traj tr = traj.read_traj('foo_trj') # DTR format trajectory fr = tr[0] # first frame. Here tr is simply a python list of trajectory Frame objects.class 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) 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. 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 ...
Schrödinger Python API 2021-4 documentation » schrodinger.application.bioluminate.patch_utils.patch_finder module schrodinger.application.bioluminate.patch_utils.patch_finder. read_asl_file ( basename ) …
schrodinger.analysis.enrichment.metrics.calc_ActivesInNStar(adjusted_active_ranks, n_sampled_set) [source] ¶. Return the number of the known active ligands found in a given sample size. Parameters. adjusted_active_ranks ( list(int)) – Modified active ranks; each rank is improved by the number of preceding actives.
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 ). You’ve probably heard the term “annual percentage yield” used a lot when it comes to credit cards, loans and mortgages. Banks or investment companies use the annual percentage yiel...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 …class schrodinger.structutils.structalign.StructAlign¶ Bases: object. This is the class used to perform the structural alignment. This class will check at initialization time if Prime is installed by trying to import schrodinger.applications.ska and will fail if it’s not installed as nothing more can be done.class schrodinger.job.queue.ResourceHost(name: str, procs: int, resource: Optional[str] = None) ¶. Bases: object. Tracks the allowed number of processors for each resource on a given host. Use a ResourceHost object to specify a host for JobDJ that has processors reserved for jobs that request a specific resource.May 11, 2022 · 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.Implementation of ProteinSequence, Sequence, and StructureSequence class. StructureSequence allows iteration over all sequences in a given protein CT, and iteration over residues of each (in sequence order). schrodinger.protein.sequence.guess_seq_type(res_names) ¶. Takes an iterable of …
Note: If cm1a is turned on, enterMol calculates charges which is a fairly lengthy operation. :param handle: mmffld handle :param st: structure to assign atom types :param apply_mmlewis: whether to apply mmlewis to the incoming structure :raise AtomTypingFailure: if mmffld_enterMol() fails """ try: mmffld_assign = …Using the Schrödinger Python API ¶. This document can be accessed from the Schrödinger website at www.schrodinger.com/pythonapi. Contents ¶. … 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 ... 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 ... Oct 16, 2560 BE ... ... API - In Pharmacophore modeling, Phase ... Schrödinger Extensions for KNIME ... Python Script 1:1 (x4). Schrödinger Scripting. Executes a Python ...May 18, 2021 · def version_compatible (minimum, maximum): """ Check that the version is between minimum and maximum values. 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 version is greater than the …The self-consistent quantum-electrostatic (also known as Poisson-Schrödinger) problem is notoriously difficult in situations where the density of …
May 13, 2019 · Bases: schrodinger.structure._ReaderWriterContextManager. Provides a single iterator that reads structure from multiple files. Typical usage is idential to typical useage of the StructureReader class except that the class is instantiated with a python list of file names rather than a single file name.
Nov 10, 2022 · 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.Aug 2, 2023 · Schrödinger Python API 2023-3 documentation » schrodinger.maestro package; schrodinger.maestro package ...schrodinger.structutils.analyze module — Schrödinger Python API 2022-2 documentation. schrodinger.structutils.analyze module ¶. Functions for …schrodinger.application.aacg.utils.is_aacg_ffio_struct(st_ffio) ¶. Checks whether the ‘aa2mr.py’ string is present in the ‘s_ffio_name’ property of the ffio block (if present). schrodinger.application.aacg.utils.is_aacg_cms_file(cms_file_name) ¶. Checks whether the ‘aa2mr.py’ string is present in the ‘s_ffio_name’ property of ...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 ...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 …Oct 4, 2563 BE ... Schrödinger and Gross-Pitaevskii equations. ... The ParaView Python API gives full access to its data analysis and visualization capabilities.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 …Parameters: sequence (str) – Amino acid sequence of the peptide to be built.; secondary_structure (enum SECONDARY_STRUCTURE) – A description of how the secondary structure can be set.; ss_seq (list) – If the secondary structure is Custom then this is sequence of secondary structure codes - one per residue; angles – If the secondary …
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 …
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 …
May 18, 2021 · def version_compatible (minimum, maximum): """ Check that the version is between minimum and maximum values. 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 version is greater than the …\n. gauss_empty.gif - a Gaussian wave packet moving across an empty potential function (no electromagnetic field, 0 gravity) \n. gauss_sin.gif - a Gaussian wave …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.Using the Schrödinger Python API ¶. This document can be accessed from the Schrödinger website at www.schrodinger.com/pythonapi. The full API …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 ... 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. Parameters: sequence (str) – Amino acid sequence of the peptide to be built.; secondary_structure (enum SECONDARY_STRUCTURE) – A description of how the secondary structure can be set.; ss_seq (list) – If the secondary structure is Custom then this is sequence of secondary structure codes - one per residue; angles – If the secondary …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 Desmond trajectories are saved in binary files and both DTR and XTC formats are supported. To read a trajectory: from schrodinger.application.desmond.packages import traj tr = traj.read_traj('foo_trj') # DTR format trajectory fr = tr[0] # first frame. Here tr is simply a python list of trajectory Frame objects.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. 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 ... AIMpy: A Python code to solve Schr ̈odinger-like equations with The Asymptotic Iteration Method. Mesut Karakoc ̧∗. Department of Physics, Faculty of Science, …
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 should be up to date …class 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) 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 Instagram:https://instagram. narragansett streetlike some larb crossword cluetaylor swift concert tickets tampaultimate guitar offerings crossword Python API · Design of a Highly Selective ... Ready to release the power of digital chemistry? Contact us · Schrödinger ... Copyright © 2024 Schrödinger, Inc. driving fast memejabletv The Desmond trajectories are saved in binary files and both DTR and XTC formats are supported. To read a trajectory: from schrodinger.application.desmond.packages import traj tr = traj.read_traj('foo_trj') # DTR format trajectory fr = tr[0] # first frame. Here tr is simply a python list of trajectory Frame objects.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. petite nude gif Schrödinger Python API 2022-2 documentation » schrodinger.analysis.enrichment.plotter module Functions and classes for plotting enrichment job outputs. e.g. basic Sensitivity v 1-Specificity plots, etc.Feb 8, 2021 · schrodinger.application.desmond.meta.get_meta_cfg_filename (meta_def) ¶ Returns the name of the kerseq and cvseq files given a metadynamics definition file :param meta_def: The content of definition file for collective variables. :param model: topology file.