Schrodinger python api.

The Python function passes the bounding box of Python 3D graphics objects to Maestro. schrodinger.maestro.maestro. hover_callback_add ( callback_func ) [source] ¶ Adds a Python function to be called each time the mouse rests over an atom in the Workspace.Introduction ¶. At the highest level, the Schrödinger Python API provides a base molecular structure class and allows for programmatic interaction with Maestro … 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. This function returns a ‘dict’ object. The keys are CT index (‘full_system’ CT’s index is 0, component CT’s index starts from 1), and the values are list of selected atoms of the corresponding component CT. schrodinger.application.desmond.cms.calc_average_vdw_coeff(struc) ¶. Calculates and …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 …

Schrödinger Python API 2023-3 documentation » schrodinger.maestro package; schrodinger.maestro package¶ Unusable placeholder for schrodinger.maestro. 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.

Package 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 Schrodinger Python API.In today’s digital landscape, businesses are constantly seeking ways to streamline their operations and enhance their productivity. One popular solution that many organizations are...

Using the Schrödinger Python API ¶. This document can be accessed from the Schrödinger website at www.schrodinger.com/pythonapi. Contents ¶. …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...See the API documentation for more details on the properties and methods of the Structure class. First we’ll set up a structure for what follows. “st” for “structure” is commonly used to name Structure instances. >>> from schrodinger import structure >>> from schrodinger.test import mmshare_data_file >>> st = structure.StructureReader ...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.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. ¶. 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.

Python API · Design of a Highly Selective ... Schrödinger · Platform · Products · Life Science · Materials Science · Pipeline · Dow...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. …The modified residue will have all the same properties as the standard one (hydophobicity, charge, etc.) but its long code (ie, its PDB residue name) will differ, and if a tuple of (string, string) is provided, both its long code and short code will differ. :param variants: list of (`ResidueType`, list of string or (string,string)) :returns: a ...schrodinger.forcefield.common. generate_partial_charges (st: schrodinger.structure._structure.Structure, version: pymmlibs.OPLSVersion = 16) [source] ¶ Generates partial charges for a given structure. Results will be stored in the PARTIAL_CHARGE_PROP atom-level property. Parameters. st – Structure for which … 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 ascending/descending ...

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.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 ...The self-consistent quantum-electrostatic (also known as Poisson-Schrödinger) problem is notoriously difficult in situations where the density of …The Python Module Overview included with the Schrodinger distribution gives an expository introduction to the Schrodinger Python API. It is available at … Bases: schrodinger.structure._io._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. select_atom_comp (asl) ¶. Returns a list of lists. Each list element contains a list of atom indices of the corresponding component CT. get_restrain ¶ set_restrain (restrain_list) ¶ ` restrain_list’ must be a list. Each element must be a list of ` Restrain’ objects.. clear_restrainSchrödinger Python API 2021-3 documentation ... # This is Python version of get_num_rotors from ligparse_utils.c # > must explicitly exit to not count rotors, each bond is # > considered rotatable as the default # If rings are not specified, determine the rings and sort by connection: ...

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.

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 () 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. 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. 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 ...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)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.

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 …

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...

In today’s fast-paced digital landscape, businesses are constantly looking for ways to streamline their processes and improve efficiency. One tool that has become increasingly popu...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 ()Module to rename the residues in a given protein sequence either incrementally or based on a given template protein sequence. schrodinger.protein.renumber_residues.renumber_residues(seq, start=1, increment=1, preserve_icode=False) ¶. Renumbers the residues so that the first residue gets the ‘start’ … 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. 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.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 ... Schrödinger Python API 2023-3 documentation » schrodinger.maestro package; schrodinger.maestro package¶ Unusable placeholder for schrodinger.maestro. 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 …Strip any ACE & NMA caps, and add an OXT cap. schrodinger.protein.nonstandard_residues.find_atom(st, name) ¶. Find the atom with the given PDB name. None is returned if no such atom is present. schrodinger.protein.nonstandard_residues.flip_isomer(st) ¶. Invert the isomerism of the …

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.For the most common chart types (XY Chart & 3D Chart), LightningChart Python has two programming APIs for creating visualizations. With the declarative API, you … schrodinger.application.desmond.meta.generate_meta_cfg (meta_def, model) ¶ Generate part of the config file for metadynamics simulation :param meta_def: The content of definition file for collective variables. :param model: topology file. :type meta_def: sea.Sea object :type model: cms.Cms object :return a string. Strip any ACE & NMA caps, and add an OXT cap. schrodinger.protein.nonstandard_residues.find_atom(st, name) ¶. Find the atom with the given PDB name. None is returned if no such atom is present. schrodinger.protein.nonstandard_residues.flip_isomer(st) ¶. Invert the isomerism of the …Instagram:https://instagram. look over there gifbest electric razorwalgreens lynn lane broken arrow oktransformers toys wiki Generate a structural interaction fingerprint for the given ligand with id. The receptor_region parameter is a list of receptor atom numbers corresponding to the receptor residues that are to be considered as interacting with the ligand. No other residues will be considered (their bits in the fingerprint will all be 0). stipper gifeuropean dates How can I use my own Python libraries with the Schrödinger Python API ...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 ... stores at woodburn outlet mall 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 ...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 ...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 …