Schrödinger Python API

https://learn.schrodinger.com/public/python_api/2026-1/
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### Method: setup

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.matsci.permittivity.html

Prepares the environment before the job starts, including file transfers and logging setup.

```APIDOC
## Method: setup

### Description
Performs setup operations before job execution.

### Parameters
- **copy_infile** (bool) - Optional - Copy the input files to current folder
- **copy_additional_files** (bool) - Optional - Copy the additional files to current folder
- **more_files** (list of str) - Optional - List of customized files to copy
```

--------------------------------

### Start and Use Glide Server

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.glide.http_client.html

Example of starting a Glide server, waiting for it to be ready, performing a dock, and then stopping the server. Ensure the server is stopped after use.

```python
server = GlideServerManager({'GRIDFILE': 'grid.zip'})
server.start()
while not server.isReady():
    time.sleep(1)
poses = server.dock(st)
server.stop()
```

--------------------------------

### Run Lipinski Example Pipeline

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.seam.examples.lipinski.html

Execute the Lipinski example pipeline. This is the basic command to start the process.

```bash
$SCHRODINGER/run seam_example.py lipinski

```

--------------------------------

### Configure Passwordless SSH Setup

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.utils.sshconfig.html

This snippet demonstrates the complete process of setting up passwordless SSH. It finds or generates key pairs, checks their validity, configures the local SSH setup if necessary, and then installs the public key on a remote host.

```python
from schrodinger.utils import sshconfig

(priv_file, pub_file) = sshconfig.find_key_pair()
pub_key = sshconfig.check_key_pair(priv_file, pub_file)
if not pub_key:
    pub_key = sshconfig.configure_local_ssh_setup(priv_file, pub_file)
sshconfig.install_remote_pubkey("bobio", "rajagopa", "blah-blah", pub_key)

```

--------------------------------

### Run Haystack Example

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.seam.examples.haystack.html

Execute the haystack example workflow. This command initiates the example, demonstrating basic usage.

```bash
$SCHRODINGER/run seam_example.py haystack
```

--------------------------------

### Instantiate, Configure, and Start a Task

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.tasks.tasks.html

Instantiate a defined task, set its input parameters, start its execution, and wait for completion. Check the status and access the output.

```python
task = FooThreadTask()
task.input.x = 3
task.input.y = 4
task.start()
assert task.status is tasks.Status.RUNNING
task.wait()
assert task.status is tasks.Status.DONE
print(task.output)
```

--------------------------------

### DoFn Setup Method

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.transforms.combiners.html

The setup() method is called to prepare a DoFn instance for processing bundles. Initialize transient in-memory resources here, which can be disposed of in teardown().

```python
def setup(self):
    """Called to prepare an instance for processing bundles of elements.
    This is a good place to initialize transient in-memory resources, such as network connections. The resources can then be disposed in `DoFn.teardown`.
    """
    pass
```

--------------------------------

### Server Start Command

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.seam.viz.watcher.html

Command to start the seam pipeline visualization webserver.

```APIDOC
## Command Line Interface

### Description
Starts the webserver that serves the seam pipeline visualization web application.

### Usage
```bash
$SCHRODINGER/run python3 -m schrodinger.seam.viz.server start [path/to/local/seam]
```

### Parameters
#### Path Parameters
- **path/to/local/seam** (str) - Optional - The path to a local seam directory to visualize. If not provided, the server will look for seamwatcher directories.
```

--------------------------------

### Common Setup for Properties Tabs

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.jaguar.gui.tabs.properties_tab.html

Performs common setup procedures for all properties tabs.

```python
setup()
```

--------------------------------

### Example Properties Output

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.bioluminate.protein.protein.html

An example of the 'properties' output dictionary, showing calculated values for different energy and surface area metrics.

```python
properties = {
    'e_pot'         : 1573.4,
    'e_internal'    : 624.7,
    'e_interaction' : 994.8,
    'prime_energy'  : 744.2,
    'pka'           : 124.1,
    'sasa_polar',   : 3122.3,
    'sasa_nonpolar' : 271.1,
    'sasa_total'    : 3393.4
}
```

--------------------------------

### schrodinger.application.licensing.licserver.main.handle_quick_slm_setup

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.licensing.licserver.main.html

Handles the quick setup process for SLM (Schrodinger License Manager).

```APIDOC
## schrodinger.application.licensing.licserver.main.handle_quick_slm_setup

### Description
Handles the quick setup process for SLM.

### Method
Python Function

### Parameters
#### Request Body
- **_opt** (Namespace) - Required - Options namespace containing setup parameters.
```

--------------------------------

### schrodinger.autoinstall.prepare_os.setup_scratch_dir

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.autoinstall.prepare_os.html

Creates the tmp. /scratch directory and sets appropriate permissions if it doesn’t exist.

```APIDOC
## schrodinger.autoinstall.prepare_os.setup_scratch_dir

### Description
Creates the tmp. /scratch directory and sets appropriate permissions if it doesn’t exist.

### Method
(Not specified, likely a Python function call)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
- **logger** (logger) - Description: A logger instance for logging messages.
```

--------------------------------

### Get Starting SASA Values

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.bioluminate.methionine_oxidation.html

Calculates the initial Solvent Accessible Surface Area (SASA) for specified residues in a starting structure.

```python
schrodinger.application.bioluminate.methionine_oxidation.get_starting_sasas(_start_st : Structure_, _resids : list[str]_)
```

--------------------------------

### Get Installed Hostfile Path

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.job.jobcontrol.html

Retrieves the pathname of the schrodinger.hosts file from the most recent previous installation directory. If a root directory is provided, it searches within that path; otherwise, it uses standard installation locations.

```python
schrodinger.job.jobcontrol.get_installed_hostfiles()
```

--------------------------------

### schrodinger.autoinstall.prepare_os.run

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.autoinstall.prepare_os.html

Main routine to prepare the OS by installing required packages and Nvidia drivers.

```APIDOC
## schrodinger.autoinstall.prepare_os.run

### Description
Main routine to prepare the OS by installing required packages and Nvidia drivers.

### Method
(Not specified, likely a Python function call)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
- **os_enum** (OperatingSystem_) - Description: The operating system enum.
- **os_version_str** (str) - Description: The full OS version string (e.g., ‘ubuntu 22.04’).
- **schrodversion** (str) - Description: The version of the Schrodinger suite.
- **ngpu** (int) - Description: The number of GPUs, which determines if Nvidia drivers are installed.
- **tmpdir** (str) - Description: The temporary directory for downloads.
```

--------------------------------

### schrodinger.autoinstall.jobserver_install.run

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.autoinstall.jobserver_install.html

Main routine to set up the Job Server and its host configuration.

```APIDOC
## schrodinger.autoinstall.jobserver_install.run

### Description
Main routine to set up the Job Server and its host configuration.

### Method
(Not specified, likely a Python function call)

### Endpoint
(Not applicable, this is a Python module function)

### Parameters
#### Path Parameters
(None)

#### Query Parameters
(None)

#### Request Body
(None)

### Request Example
(Not applicable, this is a Python module function)

### Response
#### Success Response (200)
(Not specified, likely returns None or status)

#### Response Example
(Not applicable)
```

--------------------------------

### setup()

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.jaguar.gui.tabs.molecule_tab.html

Performs tab-specific initialization. This method should be defined in subclasses if initialization is needed.

```APIDOC
## setup()

### Description
Perform tab specific initialization. This function should be defined in subclasses if initialization is needed.
```

--------------------------------

### get_mag_hubbu() Function

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.matsci.espresso.utils.html

Gets starting magnetization and Hubbard U parameters from an atom.

```APIDOC
## get_mag_hubbu() Function

### Description
Get starting magnetization and Hubbard U parameters from atom property. If not present, return the default.

### Parameters
- **atom** (schrodinger.structure._StructureAtom) - Atom from which values are taken
- **decimals** (int) - Number of decimals to round to (default: 10)

### Returns
- **MagElement namedtuple**: Tuple of starting magnetization and Hubbard parameters.
```

--------------------------------

### GET /get_element

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.matsci.espresso.utils.html

Cleans an element name by removing trailing digits often associated with starting magnetization.

```APIDOC
## GET /get_element

### Description
Get element name with the removed digits from atom type.

### Method
GET

### Parameters
#### Query Parameters
- **element** (str) - Required - Element name with potential digits.

### Response
#### Success Response (200)
- **element** (str) - Element without digits
```

--------------------------------

### schrodinger.application.licensing.licserver.main.handle_install

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.licensing.licserver.main.html

Manages the installation process for the license server.

```APIDOC
## schrodinger.application.licensing.licserver.main.handle_install

### Description
Handles the ‘install’ subcommand.

### Method
Python Function

### Parameters
#### Request Body
- **_opt** (Namespace) - Required - Options namespace containing installation parameters.
```

--------------------------------

### run

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.autoinstall.suite_install.html

Main routine for the suite installation process.

```APIDOC
## run

### Description
Main routine to orchestrate the installation process.

### Parameters
- **isource** (str) - Required - The source of the installation.
- **isource_type** (str) - Required - The type of the installation source.
- **version** (str) - Required - The version of the suite to install.
- **ipath** (str) - Required - The target installation path.
- **tmpdir** (str) - Required - The temporary directory to use during installation.
```

--------------------------------

### Get Grid and Radius Values

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.matsci.freevolume.html

Retrieves grid and radius values for properties on a structure that start with a specified base string.

```APIDOC
## GET /api/freevolume/grid_radius

### Description
Get all the grid and radius values for properties on the structure that begin with the given base string.

### Method
GET

### Endpoint
/api/freevolume/grid_radius

### Parameters
#### Query Parameters
- **struct** (schrodinger.structure.Structure) - Required - The structure to extract the properties from
- **propbase** (str) - Required - The starting string for properties to search for

### Response
#### Success Response (200)
- **dict** - Keys are GridRadius instances, values are the property value for that set of grid/radius values.

### Response Example
```json
{
  "example": "{\"GridRadius1\": value1, \"GridRadius2\": value2}"
}
```
```

--------------------------------

### Get Command-Line Flags

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.matsci.deswidgets.html

Retrieves command-line flags and their values for simulation setup. Ensure EXEC and infile_path are defined in your environment.

```python
cmd = [EXEC, infile_path]
cmd += rs_widget.getCommandLineFlag()
```

--------------------------------

### schrodinger.autoinstall.jobserver_install.setup_jsc

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.autoinstall.jobserver_install.html

Sets up the Job Server Controller (JSC), including user creation, command execution, and service configuration.

```APIDOC
## schrodinger.autoinstall.jobserver_install.setup_jsc

### Description
Sets up the Job Server Controller (JSC). This involves creating users, running the `jsc_admin setup-server` command, configuring file permissions, setting up the `jobserverd.service`, and enabling necessary feature flags.

### Method
(Not specified, likely a Python function call)

### Endpoint
(Not applicable, this is a Python module function)

### Parameters
#### Path Parameters
(None)

#### Query Parameters
(None)

#### Request Body
(None)

### Request Example
(Not applicable, this is a Python module function)

### Response
#### Success Response (200)
(Not specified, likely returns None or status)

#### Response Example
(Not applicable)
```

--------------------------------

### setup(app)

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.infra.epydoc_to_sphinx.html

Hooks up the process_docstring function to the Sphinx application instance.

```APIDOC
## setup(app)

### Description
Hooks up `process_docstring` so it can convert all docstrings. This function is called automatically by Sphinx.

### Parameters
- **app** (sphinx.Sphinx) - Required - The currently running Sphinx instance.
```

--------------------------------

### Get Owner Chain of Params

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.models.parameters.html

Returns a list of param owners starting from the top-level param and ending with self. This helps trace the hierarchy of nested parameters.

```python
`foo.bar.atom.coord.ownerChain()` will return `[foo, bar, atom, coord]` where every item is a concrete param.
`Foo.bar.atom.coord.x.ownerChain()` will return `[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]` where every item is an abstract params. 

```

--------------------------------

### Get Segment Indices from Chain

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.bioluminate.antibody.assembly_yaml.html

Determines the start and end indices for a segment within a chain, based on the domain key. Used for FV or FAB region alignment.

```python
schrodinger.application.bioluminescent.antibody.assembly_yaml.get_segment_indices(_chain_dict : Dict[str, Any]_, _domain_key : str_) -> Tuple[int, int]
```

--------------------------------

### setUpDirs()

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.matsci.thermo_correction_utils.html

Sets up the necessary directories for thermochemical calculations.

```APIDOC
## setUpDirs()

### Description
Set up the directories.

### Method
N/A (Function)

### Endpoint
N/A

### Parameters
None

### Request Example
None

### Response
#### Success Response (200)
None

#### Response Example
None

### Raises
**ThermoCorrectionException** – if there is an issue
```

--------------------------------

### CarbonCount PTransform Example

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.transforms.template.starter.html

A PTransform that counts carbon atoms in molecules. This demonstrates exposing a major data-parallel task as a composite PTransform, as recommended by the Beam style guide.

```python
class CarbonCount(PTransform):
    """A PTransform that counts the number of carbon atoms in each molecule in the input PCollection."""
    def expand(self, molecule_pcoll):
        pass
```

--------------------------------

### schrodinger.autoinstall.jobserver_install.setup_hosts_file

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.autoinstall.jobserver_install.html

Sets up the hosts.yml file for the Job Server, defining available compute resources.

```APIDOC
## schrodinger.autoinstall.jobserver_install.setup_hosts_file

### Description
Sets up the hosts.yml file for the Job Server. This file defines the compute resources available to the Schrodinger suite.

### Method
(Not specified, likely a Python function call)

### Endpoint
(Not applicable, this is a Python module function)

### Parameters
#### Path Parameters
(None)

#### Query Parameters
(None)

#### Request Body
(None)

### Request Example
(Not applicable, this is a Python module function)

### Response
#### Success Response (200)
(Not specified, likely returns None or status)

#### Response Example
(Not applicable)
```

--------------------------------

### run

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.autoinstall.slm_install.html

Main routine to set up the Schrodinger License Manager.

```APIDOC
## run

### Description
Main routine to set up the Schrodinger License Manager.

### Method
Not applicable (Python function)

### Endpoint
Not applicable (Python function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```python
# Example usage (assuming parameters are defined)
# run(ipath='/path/to/schrodinger', hostname='license.server.com', licsource='license_file.txt')
```

### Response
#### Success Response (200)
None (function modifies system state)

#### Response Example
None
```

--------------------------------

### Get Segment ASL for Domain

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.bioluminate.antibody.assembly_yaml.html

Generates the segment ASL string for a specified range of residues within a domain. Requires the list of residues and the alignment start and end indices.

```python
schrodinger.application.bioluminescent.antibody.assembly_yaml.get_segment_asl(_resids : List[str]_, _align_start_index : int_, _align_end_index : int_) -> str
```

--------------------------------

### start

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.jaguar.gui.base_panel.html

Launches a Jaguar job using the current panel settings.

```APIDOC
## POST start

### Description
Launch the job. Note that updateAndCheckMmJag must be run before this function to update and validate self._jag_input.

### Response
#### Success Response (200)
- **job** (schrodinger.job.jobcontrol.Job) - A job object for the launched job
```

--------------------------------

### Example: Get Consensus Waters

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.bioluminate.protein.protein.html

Demonstrates how to find all consensus water molecules between two protein structures using a 2 Angstrom distance cutoff. Requires importing StructureReader and protein modules.

```python
from schrodinger.structure import StructureReader
from schrodinger.application.bioluminate import protein

pt = maestro.project_table_get()
```

--------------------------------

### Access Structure Atoms

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.structure.html

Access individual atoms by index (starting from 1), delete atoms, get the total number of atoms, or iterate over all atoms in a structure. Avoid modifying the atom list while iterating.

```python
# Access an atom (indices start at 1)
atomobj = st.atom[n]
```

```python
# Delete an atom
del st.atom[n]
```

```python
# Find the number of atoms
len(st.atom)
```

```python
# Iterate over all atoms
for atom in st.atom:
    take_some_action(atom)
```

--------------------------------

### Get Next Customer Facing Name

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.matsci.msutils.html

Generates the next sequential name based on a given name. For example, 'xx' becomes 'xx (1)' and 'xx (n)' becomes 'xx (n + 1)'.

```python
schrodinger.application.matsci.msutils.get_next_name(_name_)
```

--------------------------------

### Initialize and Use InputConfig

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.inputconfig.html

Demonstrates how to initialize an InputConfig object with specifications and access configuration values.

```python
list_of_specs = ["NUM_RINGS = integer(min=1, max=100, default=1)"]
config = InputConfig(filename, list_of_specs)
if config['NUM_RINGS'] > 4:
    do_something()
```

--------------------------------

### schrodinger.seam.examples.haystack Module

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.seam.examples.haystack.html

A pedagogical example workflow to demonstrate how logging and works with seam. The workflow creates a collection of strings, most of which are “haystalk” and a few of which are “needle”. The workflow then processes each item in the collection, sleeping for a fixed amount of time for each “haystalk”/”needle” and aggregating them into lists. To get a sense of how logging works, run this example and read the README found in the generated “seam/logs” directory.

```APIDOC
## Basic Usage

### Description
Runs the haystack example workflow with default settings.

### Command
```bash
$SCHRODINGER/run seam_example.py haystack
```

## Parallelized Usage with Jobserver

### Description
Runs the haystack example workflow in parallel using a jobserver, with a specified sleep time per stalk.

### Command
```bash
$SCHRODINGER/run seam_example.py haystack –per-stalk-sleep-time 0.001 -HOST localhost:8
```
```

--------------------------------

### Instantiate and configure a pipeline stage

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.pipeline.stage.html

Demonstrates how to create a stage instance, assign keywords, define input objects, and execute the stage.

```python
stageobj = YourStage(<stagename>)

# Add keywords:

stageobj['NUM_RINGS'] = 2
stageobj['UNIQUEFIELD'] = 's_m_title'

# Add input objects:
# ligand_files is list of file names
ligandsobj = pipeio.Structures(ligand_files)
stageobj.setInput(1, 'INPUT1', ligandsobj)

# Tell the stage where to save it's output:
stageobj.setOutputName(1, 'OUTPUT')

# Integers (1) are position numbers.
# INPUT1 is the name of the input object

# Run the stage:

outputs = stageobj.run()
```

--------------------------------

### ThompsonSampler setUpOutputFiles() Method

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.building_block_exploration.bb_explorer_run_thompson_sampling.html

Sets up the necessary output files for the Thompson sampling job.

```APIDOC
## setUpOutputFiles ThompsonSampler

### Description
Sets up the job by creating and registering required output files.

### Method
POST

### Endpoint
/setup_output_files

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (200)
- **message** (str) - Confirmation message that output files have been set up.

#### Response Example
```json
{
  "message": "Output files created and registered."
}
```
```

--------------------------------

### Start Method Decorator

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.ui.qt.appframework2.appmethods.html

Decorator for the ‘Start’ method, used to define the behavior when the panel starts.

```APIDOC
## schrodinger.ui.qt.appframework2.appmethods.start

### Description
Decorator for the ‘Start’ method. This method is called when the panel is initiated.

### Method
Decorator

### Endpoint
N/A (Decorator function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
#### Success Response (200)
None

#### Response Example
None
```

--------------------------------

### License Installation

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.licensing.licadmin.html

Functions for installing licenses.

```APIDOC
## schrodinger.application.licensing.licadmin.handle_install_action(_opts_)

### Description
Install a license in the license directory. If a license key is given, download the license from Netsuite, first.

### Method
POST

### Endpoint
/schrodinger/application/licensing/licadmin/handle_install_action

### Parameters
#### Request Body
- **_opts_** (object) - Required - Options for the install action.
```

```APIDOC
## schrodinger.application.licensing.licadmin.install_remote_server_license(_lic_server_address_)

### Description
Generate a license file pointing to a remote server, and install it in the license directory.

### Method
POST

### Endpoint
/schrodinger/application/licensing/licadmin/install_remote_server_license

### Parameters
#### Request Body
- **_lic_server_address_** (str) - Required - The address of the license server, in the form “port@host”.
```

```APIDOC
## schrodinger.application.licensing.licadmin.install_netsuite_license(_key_)

### Description
Download a license from Netsuite using the given key, and install it in the license directory.

### Method
POST

### Endpoint
/schrodinger/application/licensing/licadmin/install_netsuite_license

### Parameters
#### Request Body
- **_key_** (str) - Required - The license key to use for downloading from Netsuite.
```

--------------------------------

### PkaPage initSetUp Method

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.jaguar.gui.input_tab_widgets_pka.html

Creates and initializes widgets from the UI module. Subclasses should use this to set up subwidgets and connect signals.

```python
initSetUp()
```

--------------------------------

### GET /getBasisForEid

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.jaguar.gui.input_tab_widgets.html

Get the basis set for the specified entry id.

```APIDOC
## GET /getBasisForEid

### Description
Get the basis set for the specified entry id. If there are per-atom basis sets specified for the structure, the per_atom_name will be returned.

### Method
GET

### Parameters
#### Query Parameters
- **eid** (str) - Required - The entry id
- **per_atom_name** (str) - Required - The name to return if per-atom basis sets are specified

### Response
#### Success Response (200)
- **basis** (Basis or str) - The basis set name, or per_atom_name if per-atom basis sets are specified
```

--------------------------------

### Prestart Method

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.ui.qt.appframework2.appmethods.html

Placeholder method, potentially for actions before the start method is executed.

```APIDOC
## schrodinger.ui.qt.appframework2.appmethods.prestart

### Description
Placeholder method, potentially for actions before the start method is executed.

### Method
Function

### Endpoint
N/A

### Parameters
None

### Request Example
None

### Response
#### Success Response (200)
None

#### Response Example
None
```

--------------------------------

### run

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.autoinstall.slurm_install.html

Main routine to install and configure SLURM and its integration.

```APIDOC
## run

### Description
Main routine to install and configure SLURM and its integration.

### Parameters
- **vslurm** (str) - Required - The version of SLURM to install.
- **vschrod** (str) - Required - The version of the Schrodinger suite.
- **ipath** (str) - Required - The installation path for the Schrodinger suite.
- **os_enum** (OperatingSystem) - Required - The detected operating system.
- **os_version_str** (str) - Required - The full OS version string (e.g., ‘rocky 8’).
- **hostname** (str) - Required - The hostname of the machine.
- **ncpu** (int) - Required - The number of CPU cores.
- **ngpu** (int) - Required - The number of GPUs.
- **liccheck** (bool) - Required - A boolean to enable license checking features.
- **tmpdir** (str) - Required - The temporary directory for downloads and compilation.
```

--------------------------------

### schrodinger.application.jaguar.script_dir

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.jaguar.html

Return the script directory under the Jaguar installation that has python scripts installed.

```APIDOC
## schrodinger.application.jaguar.script_dir

### Description
Return the script directory under the Jaguar installation that has python scripts installed.

### Method
GET

### Endpoint
/schrodinger/application/jaguar/script_dir

### Response
#### Success Response (200)
* **script_directory** (string) - The absolute path to the Jaguar script directory.
```

--------------------------------

### GET /

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.glide.http_server.html

Access the root path to get an HTML form for testing the server.

```APIDOC
## GET /

### Description
Serves an HTML form that can be used for testing the Glide HTTP Server directly from a web browser.

### Method
GET

### Endpoint
/

### Response
#### Success Response (200)
- **html_form** (string) - The HTML content of the testing form.
```

--------------------------------

### Setup Job Queue

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.matsci.equilibrium_md.html

Configures and sets up the job queue for managing multiple jobs.

```python
setUpQue()
```

--------------------------------

### Initialize and Configure EsolInput

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.jaguar.esol_input.html

Demonstrates creating an EsolInput instance, setting keyword values, iterating through them, and handling invalid keyword assignments.

```python
input = EsolInput()
# Set user-defined values
input.setValue('integerKW', 3)
input.setValue('floatKW', '7.0')
input.setValue('stringKW', 'foo')

# Print all keyword/value pairs.
for keyword in input:
    print "keyword '%s' has value %s" % (keyword, input[keyword])

# Handling the case of trying to set an unsupported keyword
try:
    input['mykeyword'] = 'value'
except WorkflowKeywordException as e:
    print e.allowed_keywords
```

--------------------------------

### Installation Check Utilities

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.utils.installation_check.html

Utilities for checking installation requirements and handling package management.

```APIDOC
## schrodinger.utils.installation_check.get_distro_package()

### Description
Returns the distro package to use for package requirements check handling the special case for distros.

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/get_distro_package

### Response
#### Success Response (200)
- **package_name** (str) - The name of the distro package.

### Response Example
{
  "package_name": "ubuntu-package-name"
}

## schrodinger.utils.installation_check.get_requirements_url()

### Description
Retrieves the URL for requirements.

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/get_requirements_url

### Response
#### Success Response (200)
- **url** (str) - The URL for requirements.

### Response Example
{
  "url": "http://example.com/requirements.txt"
}

## schrodinger.utils.installation_check.ensure_logfile(_output_dir =None_)

### Description
Context manager for adding a logfile to LOGGERS. Ensures that multiple nested entries into the context manager only add one logfile.

### Method
USE

### Endpoint
/schrodinger/utils/installation_check/ensure_logfile

## schrodinger.utils.installation_check.main()

### Description
Run installation check.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/main

### Response
#### Success Response (200)
- **exit_code** (int) - The exit code of the installation check.

### Response Example
{
  "exit_code": 0
}

## schrodinger.utils.installation_check.cd(_path_)

### Description
Change directory.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/cd

#### Parameters
##### Path Parameters
- **path** (str) - Required - The directory path to change to.

## schrodinger.utils.installation_check.get_host_entries(_args_)

### Description
Get all the host entries (jobcontrol.Host objects) from the hosts file. If no -test arguments were given, return them all. If -test arguments were given, return entries whose names are given by those arguments and which are present in the hosts file (warn on absent ones).

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/get_host_entries

#### Parameters
##### Query Parameters
- **args** (list) - Optional - Test arguments to filter host entries.

### Response
#### Success Response (200)
- **host_entries** (list) - A list of host entries.

### Response Example
{
  "host_entries": [
    {
      "name": "host1",
      "address": "192.168.1.1"
    }
  ]
}

## schrodinger.utils.installation_check.run_test_jobs(_entries_ , _launch_dir ='.'_, _duration =10_, _timeout =None_)

### Description
Run testapp jobs using a list of host entries (jobcontrol.Host objects). Return a list of all jobids, succeeded and failed, that were run.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/run_test_jobs

#### Parameters
##### Request Body
- **entries** (list) - Required - A list of host entries (jobcontrol.Host objects).
- **launch_dir** (str) - Optional - The directory to launch jobs from. Defaults to ".".
- **duration** (int) - Optional - The duration of the test jobs in seconds. Defaults to 10.
- **timeout** (int) - Optional - The timeout for the test jobs in seconds.

### Request Example
{
  "entries": [
    {
      "name": "host1",
      "address": "192.168.1.1"
    }
  ],
  "launch_dir": "/tmp",
  "duration": 20,
  "timeout": 60
}

### Response
#### Success Response (200)
- **job_ids** (list) - A list of job IDs.

### Response Example
{
  "job_ids": ["job123", "job456"]
}

## schrodinger.utils.installation_check.get_postmortem_command(_jobids : List[str]_) → List[str]

### Description
Return correct postmortem command.

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/get_postmortem_command

#### Parameters
##### Query Parameters
- **jobids** (List[str]) - Required - A list of job IDs.

### Response
#### Success Response (200)
- **command** (List[str]) - The postmortem command.

### Response Example
{
  "command": ["postmortem", "--jobid", "job123"]
}

## schrodinger.utils.installation_check.run_postmortem(_jobids_)

### Description
Run postmortem for a given set of jobids, log the results into the “postmortem.log”.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/run_postmortem

#### Parameters
##### Request Body
- **jobids** (List[str]) - Required - A list of job IDs.

### Request Example
{
  "jobids": ["job123", "job456"]
}

## schrodinger.utils.installation_check.https_session(_max_retries =5_)

### Description
Creates an HTTPS session with retry capabilities.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/https_session

#### Parameters
##### Query Parameters
- **max_retries** (int) - Optional - Maximum number of retries for the session. Defaults to 5.

### Response
#### Success Response (200)
- **session_id** (str) - An identifier for the HTTPS session.

### Response Example
{
  "session_id": "sess_abc123"
}

## schrodinger.utils.installation_check.download_linux_packages_requirement(_sess : Session_, _file_to_download : str_) → str

### Description
Download the given file using the given requests session to a temporary location and return the path.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/download_linux_packages_requirement

#### Parameters
##### Request Body
- **sess** (Session) - Required - The requests session object.
- **file_to_download** (str) - Required - The file to download.

### Request Example
{
  "sess": "sess_abc123",
  "file_to_download": "packages.txt"
}

### Response
#### Success Response (200)
- **file_path** (str) - The path to the downloaded file.

### Response Example
{
  "file_path": "/tmp/packages.txt"
}

## schrodinger.utils.installation_check.env_update_and_run(_cmd : List_) → CompletedProcess

### Description
Run bash script in an isolated environment.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/env_update_and_run

#### Parameters
##### Request Body
- **cmd** (List[str]) - Required - The command to run.

### Request Example
{
  "cmd": ["bash", "./script.sh"]
}

### Response
#### Success Response (200)
- **completed_process** (CompletedProcess) - The result of the completed process.

### Response Example
{
  "completed_process": {
    "returncode": 0,
    "stdout": "Output from script.",
    "stderr": ""
  }
}

## schrodinger.utils.installation_check.test_deps()

### Description
Determine if we have required packages to satisfy the suite dependencies. If test fails, raises RuntimeError with suggestion on how to fix.

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/test_deps

### Response
#### Success Response (200)
- **status** (str) - Indicates if dependencies are met.

### Response Example
{
  "status": "Dependencies met."
}

## schrodinger.utils.installation_check.get_installation_check_commands()

### Description
Returns a map of diagnostic commands with key: command description, value: args list.

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/get_installation_check_commands

### Response
#### Success Response (200)
- **commands** (dict) - A dictionary of diagnostic commands.

### Response Example
{
  "commands": {
    "Check disk space": ["df", "-h"]
  }
}

## schrodinger.utils.installation_check.run_installation_check(_output_dir ='.'_) 

### Description
Runs diagnostic commands and writes output in the directory specified. Note: licadmin will write the license - info file in the current directory, not in output_dir. We may want to remove the output_dir argument and leave it to the caller to cd to the correct directory.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/run_installation_check

#### Parameters
##### Query Parameters
- **output_dir** (str) - Optional - The directory to write output files to. Defaults to ".".

### Response
#### Success Response (200)
- **message** (str) - A message indicating the completion of the check.

### Response Example
{
  "message": "Installation check completed. Output written to ./"
}

## schrodinger.utils.installation_check.print_installation_check(_output_file= <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>_)

### Description
Runs diagnostic commands and writes output to the single file specified. This will not run licadmin to avoid generating any extraneous files.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/print_installation_check

#### Parameters
##### Query Parameters
- **output_file** (file) - Optional - The file to write output to. Defaults to stdout.

### Response
#### Success Response (200)
- **message** (str) - A message indicating the completion of the check.

### Response Example
{
  "message": "Installation check output printed to stdout."
}

## schrodinger.utils.installation_check.queue_inst_file(_queue_name_ , _filename_)

### Description
Gets the installation file for a given queue name and filename.

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/queue_inst_file

#### Parameters
##### Query Parameters
- **queue_name** (str) - Required - The name of the queue.
- **filename** (str) - Required - The name of the file.

### Response
#### Success Response (200)
- **file_content** (str) - The content of the installation file.

### Response Example
{
  "file_content": "File content here..."
}

## schrodinger.utils.installation_check.queue_orig_dir(_queue_name_)

### Description
Gets the original directory for a given queue name.

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/queue_orig_dir

#### Parameters
##### Query Parameters
- **queue_name** (str) - Required - The name of the queue.

### Response
#### Success Response (200)
- **directory_path** (str) - The path to the original directory.

### Response Example
{
  "directory_path": "/path/to/original/queue/dir"
}

## schrodinger.utils.installation_check.queue_orig_file(_queue_name_ , _filename_)

### Description
Gets the original file for a given queue name and filename.

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/queue_orig_file

#### Parameters
##### Query Parameters
- **queue_name** (str) - Required - The name of the queue.
- **filename** (str) - Required - The name of the file.

### Response
#### Success Response (200)
- **file_content** (str) - The content of the original file.

### Response Example
{
  "file_content": "Original file content here..."
}

## schrodinger.utils.installation_check.queue_config_diffs()

### Description
Return a collection of diffs of config and template queue files (original version from the installation vs what’s in the user’s queues dir).

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/queue_config_diffs

### Response
#### Success Response (200)
- **diffs** (list) - A list of configuration file diffs.

### Response Example
{
  "diffs": [
    {
      "file": "queue.conf",
      "diff": "--- a/queue.conf\n+++ b/queue.conf\n@@ -1 +1 @@\n-Option1=Value1\n+Option1=NewValue1"
    }
  ]
}

## schrodinger.utils.installation_check.queue_config_file_pairs()

### Description
Return a list of pairs of config/template queue files to be compared, and a list of warnings. A pair is one file from the user’s installation and the original version of the same file (from the ‘orig’ subdirectory). A warning is produced whenever the ‘orig’ subdirectory is not found, or when a user’s or original file that should be present, is not.

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/queue_config_file_pairs

### Response
#### Success Response (200)
- **pairs** (list) - A list of file pairs for comparison.
- **warnings** (list) - A list of warnings encountered.

### Response Example
{
  "pairs": [
    {
      "user_file": "/path/to/user/queue.conf",
      "original_file": "/path/to/orig/queue.conf"
    }
  ],
  "warnings": [
    "Original subdirectory not found for queue type X."
  ]
}

## schrodinger.utils.installation_check.queue_config_files_diff(_inst_filepath_ , _orig_filepath_)

### Description
Return a diff (list of strings) of two config/template queue files.

### Method
GET

### Endpoint
/schrodinger/utils/installation_check/queue_config_files_diff

#### Parameters
##### Query Parameters
- **inst_filepath** (str) - Required - The file path of the installation config file.
- **orig_filepath** (str) - Required - The file path of the original config file.

### Response
#### Success Response (200)
- **diff** (list) - A list of strings representing the diff.

### Response Example
{
  "diff": [
    "Line 1 changed.",
    "Line 2 added."
  ]
}

## schrodinger.utils.installation_check.log_banner(_logger_)

### Description
Log the basic information.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/log_banner

#### Parameters
##### Request Body
- **logger** (Logger) - Required - The logger object.

## schrodinger.utils.installation_check.check_running_as_root(_logger_)

### Description
Produce a warning if we are running as root.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/check_running_as_root

#### Parameters
##### Request Body
- **logger** (Logger) - Required - The logger object.

## schrodinger.utils.installation_check.parse_args(_args =None_)

### Description
Parse cmdline arguments.

### Method
POST

### Endpoint
/schrodinger/utils/installation_check/parse_args

#### Parameters
##### Query Parameters
- **args** (list) - Optional - A list of arguments to parse.

### Response
#### Success Response (200)
- **parsed_args** (dict) - The parsed command line arguments.

### Response Example
{
  "parsed_args": {
    "verbose": true
  }
}

```

--------------------------------

### Get Dimers In Structure

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.matsci.clusterstruct.html

Gets a Dimer object for every dimer in the provided structure.

```APIDOC
## POST /get_dimers_in_structure

### Description
Gets a Dimer object for every dimer in struct.

### Method
POST

### Endpoint
/get_dimers_in_structure

### Parameters
#### Request Body
- **struct** (schrodinger.structure.Structure) - Required - The structure object containing the dimers to find
- **cell** (schrodinger.infra.structure.DistanceCell) - Optional - The distance cell to use for finding dimers
- **pbc** (schrodinger.infra.structure.PBC) - Optional - The PBC object used to create the distance cell
- **distance** (float) - Optional - The distance to use in creating a distance cell if none is provided
- **struct_index** (int) - Optional - An index for the structure that is providing these dimers. This is passed to the Dimer class and can be used by calling routines to track Dimers from different structures.
- **heavy_only** (bool) - Optional - Use only heavy atoms when determining dimers
- **by_com** (bool or ComInfo) - Optional - If True, create the info needed to find neighbors by center of mass instead of atom distance. If ComInfo, this is the pre-calculated data to use for center of mass distance. If False, do not find neighbors by center of mass. heavy_only is ignored if by_com is not False.

### Raises
- **RuntimeError** - If neither cell nor distance are provided

### Response
#### Success Response (200)
- **list of Dimer** - A Dimer object for each dimer that molecule forms

#### Response Example
{
  "example": "[Dimer object]"
}
```

--------------------------------

### PolarizabilitySubTab setup Method

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.jaguar.gui.tabs.properties_tab.html

Defines connections between widgets in the Polarizability sub-tab.

```python
def setup():
    """
    This function is used to define connections between widgets in this sub tab. 
    """
```

--------------------------------

### initSetUp()

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.livedesign.export_map_manager.html

Creates a widget from `ui` and stores it in `ui_widget`. Suggested subclass use: create and initialize subwidgets, and connect signals.

```APIDOC
## initSetUp()

### Description
Creates a widget from `ui` and stores it in `ui_widget`. Suggested subclass use: create and initialize subwidgets, and connect signals.

### Method
N/A (Method definition)

### Endpoint
N/A

### Parameters
N/A

### Request Example
N/A

### Response
N/A

### Response Example
N/A
```

--------------------------------

### Install Local Entitlement License

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.application.licensing.licserver.install.html

Installs a local entitlement license file from a NetSuite key. The license is valid for specified machine IDs and is installed to a specified directory or the first writable directory found.

```APIDOC
## POST /install_local_entitlement_from_key

### Description
Installs a local entitlement license file from a NetSuite key. The license will be valid for the specified machine IDs. The file will be installed to license_dir if specified, or else the first writable directory from search_path().

### Method
POST

### Endpoint
/install_local_entitlement_from_key

### Parameters
#### Query Parameters
- **_key** (str) - Required - license key string
- **_license_dir** (str | None) - Optional - directory to write the license file (or None to use default)
- **_hostnames** (list[str]) - Required - list of hostnames, sent for informational purposes
- **_machine_ids** (list[str]) - Required - list of machine IDs that the license will be valid for
- **_netsuite_info** (dict | None) - Optional - info about the key, if already known, to avoid another call to netsuite. Otherwise, will be queried.
- **_logger** (logging.Logger | None) - Optional - logger to use for messages

### Response
#### Success Response (200)
- **path** (str) - path to the written license file

### Errors
- **BadLicenseInputError** - if the contents are not a recognized format
- **WrongFileType** - if the contents are not a local-entitlement file
- **LicenseVerificationError** - if the entitlement could not be validated
- **NetsuiteError** - if querying or validating the key fails
- **NoWritableDirectoryError** - if no license directory can be written to
- **LicenseError** - otherwise
```

--------------------------------

### setup_slm

Source: https://learn.schrodinger.com/public/python_api/2026-1/api/schrodinger.autoinstall.slm_install.html

Sets up the Schrodinger License Manager (SLM) using `licadmin`. This function handles both license files (`txt`) and license keys.

```APIDOC
## setup_slm

### Description
Sets up the Schrodinger License Manager (SLM) using `licadmin`. This function handles both license files (`txt`) and license keys.

### Method
Not applicable (Python function)

### Endpoint
Not applicable (Python function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
```python
# Example usage (assuming logger and other parameters are defined)
# setup_slm(ipath='/path/to/schrodinger', licsource='license_file.txt', hostname='license.server.com', logger=my_logger)
```

### Response
#### Success Response (200)
None (function modifies system state)

#### Response Example
None
```
Tokens:
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