### Startup Selector

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/beans/MSketchPane

Displays a dialog for selecting a skin at startup.

```APIDOC
## POST /ui/startup-selector

### Description
Displays a dialog used at startup time to allow the user to select a skin.

### Method
POST

### Endpoint
`/ui/startup-selector`

### Parameters
None

### Request Example
(No request body for POST request)

### Response
#### Success Response (200)
No specific response body, indicates the startup selector dialog was shown.

#### Response Example
(No response body)
```

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

### Get Start Column (Java)

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/formats/documents/jchemexcel/StructureToJC4XL

Retrieves the starting column index for adding structures. This indicates the first column where structure data will be placed.

```java
int getStartColumn();
```

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

### Startup Selector Display

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/beans/MSketchPane

Displays a skin selector dialog at startup.

```APIDOC
## POST /startup/selector

### Description
This method is used at startup to display a skin selector dialog.

### Method
POST

### Endpoint
`/startup/selector`

### Parameters
This endpoint does not take any parameters.

### Request Example
```json
{
  "message": "Display startup selector"
}
```

### Response
#### Success Response (200)
This method returns void, indicating successful execution.

#### Response Example
```json
{
  "status": "success"
}
```
```

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

### Get Timing Information

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/clustering/Common

Retrieves timing information related to process execution. `getStartTime()` returns the start time, and `getElapsedTime()` returns the duration in milliseconds since the start time.

```java
public long getStartTime()
```

```java
public long getElapsedTime()
```

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

### Parameter: PRELOAD

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/sketch/SketchParameterConstants

Comma separated list of modules to preload at startup of the applet. Order modules determines which modules are loaded earlier and which ones are later.

```APIDOC
## PRELOAD Parameter

### Description
Comma separated list of modules to preload at startup of the applet. The order of modules determines the loading sequence.

### Identifier
`"preload"`

### See Also
- Constant Field Values
- Parameters and Events documentation
```

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

### Get Molecule Volume - Java

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Returns the calculated volume of the molecule.

```Java
public double getVolume()
```

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

### Parameter: BACKGROUNDLOAD_PRIORITY

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/sketch/SketchParameterConstants

Comma separated list of modules to preload at startup of the applet. Order modules determines which modules are loaded earlier and which ones are later.

```APIDOC
## BACKGROUNDLOAD_PRIORITY Parameter

### Description
Comma separated list of modules to preload at startup of the applet. The order of modules determines the loading sequence.

### Identifier
`"bgload"`

### See Also
- Constant Field Values
- Parameters and Events documentation
```

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

### Get Calculator Tags

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Returns the set of tags reported by this calculator.

```APIDOC
## Set<CalculatorTag> tags()

### Description
Returns the set of tags reported by this calculator.

### Method
`Set<CalculatorTag>`

### Endpoint
N/A (This is a method within a plugin class)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None
```

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

### MFont Constructor Details

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/struc/graphics/MFont

Detailed explanations for each MFont constructor.

```APIDOC
## MFont Constructor Details

### MFont(String family, int style, double size)
`public MFont(String family, int style, double size)`
Contructs a font.

* Parameters:
  * `family` - the family
  * `style` - the style
  * `size` - the size

### MFont(String str)
`public MFont(String str) throws IllegalArgumentException`
Parses a font from a string.

* Parameters:
  * `str` - the string to be converted

* Throws:
  * `IllegalArgumentException`

### MFont(MFont f)
`public MFont(MFont f)`
Copy constructor.

* Parameters:
  * `f` - the font to copy

### MFont(Font f)
`public MFont(Font f)`
Create a wrapper for the specified AWT font.

* Parameters:
  * `f` - the AWT font
```

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

### File Position Management

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/struc/MDocument

Methods for getting and setting the starting position of a document within an input file.

```APIDOC
## GET /api/position/start

### Description
Gets the starting position of this document in the input file.

### Method
GET

### Endpoint
/api/position/start

### Response
#### Success Response (200)
- **position** (long) - The starting position of the document in the file.

#### Response Example
```json
{
  "position": 123456789
}
```

## POST /api/position/start

### Description
Sets the starting position of this document in the input file.

### Method
POST

### Endpoint
/api/position/start

### Parameters
#### Request Body
- **off** (long) - Required - The new starting position.

### Request Example
```json
{
  "off": 987654321
}
```

### Response
#### Success Response (200)
- **message** (string) - Indicates successful setting of the start position.

#### Response Example
```json
{
  "message": "Start position set successfully."
}
```

## GET /api/position/end

### Description
Gets the ending position of this document in the input file.

### Method
GET

### Endpoint
/api/position/end

### Response
#### Success Response (200)
- **position** (long) - The ending position of the document in the file.

#### Response Example
```json
{
  "position": 123456789
}
```
```

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

### createVisitor Method

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/com/chemaxon/calculations/stereoanal/filters/cistrans/CisDoubleBondFilter

Constructs a specified visitor implementation for stereo centers.

```APIDOC
## createVisitor

### Description
Constructs the specified visitor implementation.

### Method
protected

### Endpoint
N/A

### Parameters
- **consumer** (Consumer<CisTransStereoCenter>) - Required - A consumer function to process CisTransStereoCenter objects.

### Request Example
```java
// Assuming 'consumer' is a defined Consumer<CisTransStereoCenter>
StereoCenterVisitor visitor = cisDoubleBondFilter.createVisitor(consumer);
```

### Response
#### Success Response (200)
- **StereoCenterVisitor** - The created visitor implementation.

#### Response Example
```json
{
  "visitor_type": "StereoCenterVisitor"
}
```
```

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

### Get All Reactants - Java

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/reaction/Reactor

Retrieves all input reactants as an array of Molecule objects. This method is useful for getting a complete list of starting materials for a reaction. Requires JChem 5.5 or later.

```Java
public Molecule[] getReactants()
```

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

### Molecule File Position

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/struc/Molecule

APIs to get and set the start and end positions of a molecule within an input file.

```APIDOC
## GET /websites/apidocs_chemaxon/getEndPosition

### Description
Gets the end position of this molecule in the input file.

### Method
GET

### Endpoint
/websites/apidocs_chemaxon/getEndPosition

### Parameters
None

### Response
#### Success Response (200)
- **long** - the end position

#### Response Example
```json
12345
```

## POST /websites/apidocs_chemaxon/setEndPosition

### Description
Sets the end position of this molecule in the input file.

### Method
POST

### Endpoint
/websites/apidocs_chemaxon/setEndPosition

### Parameters
#### Request Body
- **off** (long) - Required - the end position

### Request Example
```json
{
  "off": 12345
}
```

### Response
#### Success Response (200)
- **void** - Operation successful

#### Response Example
```json
null
```
```

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

### Configuration and Initialization API

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/beans/MarvinPane

This section details methods for initializing UI components, handling property changes, and managing application-level configurations such as debug settings and resource loading.

```APIDOC
## Configuration and Initialization

### `initButton(AbstractButton b, ResourceBundle rc, String key)`

**Description**: Deprecated: Use `SwingUtil.initButton` instead.

**Method**: INIT

**Endpoint**: N/A (Method call within the application)

**Parameters**:
- **b** (AbstractButton) - Required - The button to initialize.
- **rc** (ResourceBundle) - Required - The resource bundle for localization.
- **key** (String) - Required - The key for the button's resource.

### `isExitCanceled()`

**Description**: Checks whether exiting is allowed or not.

**Method**: GET

**Endpoint**: N/A (Method call within the application)

**Parameters**: None

**Response**: 
#### Success Response (boolean)
- **Returns**: `true` if exiting is canceled, `false` otherwise.

### `isPrintEnabled()`

**Description**: Determines if the "File -> Print" menu item is enabled or not.

**Method**: GET

**Endpoint**: N/A (Method call within the application)

**Parameters**: None

**Response**: 
#### Success Response (boolean)
- **Returns**: `true` if print is enabled, `false` otherwise.

### `isSaveIniEnabled()`

**Description**: Automatically saves user settings to an initialization file.

**Method**: GET

**Endpoint**: N/A (Method call within the application)

**Parameters**: None

**Response**: 
#### Success Response (boolean)
- **Returns**: `true` if saving to initialization file is enabled, `false` otherwise.

### `propertyChange(PropertyChangeEvent ev)`

**Description**: Handles "ancestor" events or sets parameters if a bean property is changed.

**Method**: EVENT HANDLER

**Endpoint**: N/A (Method call within the application)

**Parameters**:
- **ev** (PropertyChangeEvent) - Required - The property change event.

### `readResources(Class<?> cl, String fname)`

**Description**: Reads resources from the specified file.

**Method**: READ

**Endpoint**: N/A (Method call within the application)

**Parameters**:
- **cl** (Class<?>) - Required - The class to load resources from.
- **fname** (String) - Required - The name of the resource file.

### `removeActionListener(ActionListener l)`

**Description**: Removes an action listener.

**Method**: REMOVE

**Endpoint**: N/A (Method call within the application)

**Parameters**:
- **l** (ActionListener) - Required - The action listener to remove.

### `setAtomNumberingType(int type)`

**Description**: Sets the atom numbering type.

**Method**: SET

**Endpoint**: N/A (Method call within the application)

**Parameters**:
- **type** (int) - Required - The type of atom numbering.

### `setEnabled(boolean b)`

**Description**: Enables or disables this component, depending on the value of the parameter b.

**Method**: SET

**Endpoint**: N/A (Method call within the application)

**Parameters**:
- **b** (boolean) - Required - `true` to enable, `false` to disable.

### `setPopupMenusEnabled(boolean b)`

**Description**: Allows popup menus.

**Method**: SET

**Endpoint**: N/A (Method call within the application)

**Parameters**:
- **b** (boolean) - Required - `true` to enable popup menus, `false` to disable.

### `setPrintEnabled(boolean b)`

**Description**: Sets whether the "File -> Print" menu item is enabled or not.

**Method**: SET

**Endpoint**: N/A (Method call within the application)

**Parameters**:
- **b** (boolean) - Required - `true` to enable print, `false` to disable.

### `setDebug(int debug)`

**Description**: Switches on the debug messages.

**Method**: SET

**Endpoint**: N/A (Method call within the application)

**Parameters**:
- **debug** (int) - Required - An integer value to control debug message level.

```

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

### Get Hydrogen Bond Count - Java

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Returns the number of hydrogen bonds present in the molecule.

```Java
public int getHBondCount()
```

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

### createVisitor Method

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/com/chemaxon/calculations/stereoanal/filters/cistrans/CisTransDoubleBondFilter

Constructs a visitor implementation for processing cis-trans stereo centers.

```APIDOC
## createVisitor

### Description
Constructs the specified visitor implementation for processing cis-trans stereo centers.

### Method
POST

### Endpoint
/websites/apidocs_chemaxon/createVisitor

### Parameters
#### Query Parameters
- **consumer** (Consumer<CisTransStereoCenter>) - Required - A consumer function to process each cis-trans stereo center.

### Request Example
```json
{
  "consumer": "(stereoCenter) => console.log(stereoCenter)"
}
```

### Response
#### Success Response (200)
- **visitor** (StereoCenterVisitor) - The constructed visitor implementation.

#### Response Example
```json
{
  "visitor": "StereoCenterVisitor object"
}
```
```

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

### Get EFlows Starting From Atom

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/struc/graphics/MEFlow

Retrieves all electron flows (EFlows) that originate from a specified atom. This method is a specialized version of getEFlowsOfAtom.

```java
public static List<MEFlow> getEFlowsFromAtom(MolAtom atom)
// Returns: List of MEFlows, empty if no electron flow arrow is connected to the atom.
```

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

### Basic Aromatization Wrapper (Java)

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/com/chemaxon/overlap/io/StandardizerWrappers

Creates a StandardizerWrapper configured for basic aromatization. This is a convenient way to apply a common aromatization setting.

```java
public static StandardizerWrapper aromatizeBasic()
```

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

### Get Atom Distances - Java

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Calculates and returns the distance between two specified atoms within a molecule.

```Java
public double getDistance(int atom1, int atom2)
Returns the distance of 2 atoms.
Parameters:
    `atom1` - is the (0-based) index of the 1st atom     `atom2` - is the (0-based) index of the 2nd atom
```

```Java
public double getDistance(int[] atoms) throws PluginException
Returns the distance of 2 atoms.
Parameters:
    `atoms` - is the array containing (0-based) indexes of 2 atoms
Throws:
    `PluginException` - if atoms are not set properly
```

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

### Install MarvinSketch License (Java)

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/beans/MSketchPane

Demonstrates how to install a valid license for using the MSketchPane class. It involves obtaining a LicenseHandler instance and setting the license file path.

```java
LicenseHandler lm = LicenseHandler.getInstance();
lm.setLicenseFile(path_to_license_file);
```

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

### Get Steric Hindrance - Java

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Calculates the steric hindrance of a given atom based on covalent radii and distances.

```Java
public double getStericHindrance(int atom)
Calculates hindrance of an atom from covalent radii values and distances. The stericHindrance is related to the steric hindrance of the given atom.
Parameters:
    `atom` - index of the atom
```

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

### MObject Methods

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/struc/MObject

A comprehensive list of instance and abstract methods for interacting with MObject instances.

```APIDOC
## MObject Methods

### Method Summary

**Instance Methods:**

- **`addAttributeKeys(List<String> l)`** (`void`)
  - Description: Adds the attribute names to the specified list.

- **`addCdataAttributeKeys(List<String> l)`** (`void`)
  - Description: Adds attribute names to the specified list.

- **`addNotify(MDocument doc)`** (`void`)
  - Description: Called when the object is added to a document.

- **`checkValidity(MDocument doc, Collection<MolAtom> invec)`** (`boolean`)
  - Description: Is it a valid object in the document?

- **`clearProperties()`** (`void`)
  - Description: Removes all properties from this MObject.

- **`clone()`** (`MObject`)
  - Description: Creates a clone.

- **`connectToSgroupOfAtom(SuperatomSgroup sg, MolAtom a)`** (`void`)
  - Description: Connects to a sgroup of an atom.

- **`containsAtom(MolAtom a)`** (`boolean`)
  - Description: Checks if the object contains the specified atom reference.

- **`containsPoint(DPoint3 p, CTransform3D trot)`** (`boolean`)
  - Description: Checks if the object contains the specified point.

- **`containsPropertyKey(String key)`** (`boolean`)
  - Description: Returns true if this MObject has a mapping for the specified property key.

- **`distanceFrom(double x, double y)`** (`double`)
  - Description: Gets the 2D distance from the specified point.

- **`finishCloning(MDocument olddoc, MDocument newdoc)`** (`void`)
  - Description: Finish cloning a document.

- **`fixClonedPoints(MObject[] objarr0, MObject[] objarr, int i)`** (`void`)
  - Description: Sets the parent object for this object.

- **`getAttribute(String s)`** (`String`)
  - Description: Gets the value of an attribute.

- **`getBackground()`** (`Color`)
  - Description: Gets the background color of the object.

- **`getColor()`** (`Color`)
  - Description: Gets the color of the object.

- **`getContainerMObject(MDocument doc)`** (`MObject`)
  - Description: Gets the container MObject.

- **`getLineColor()`** (`Color`)
  - Description: Gets the line color of the object.

- **`getPointRef(int i, CTransform3D trot)`** (`MPoint`)
  - Description: Gets a reference to a point of the object.

- **`getPointRefCount()`** (`int`)
  - Description: Gets the number of point references.

- **`getProperty(String key)`** (`Object`)
  - Description: Returns the property value to which the specified property key is mapped at this MObject, or null if this MObject has no mapping for this property key.

- **`hasBackground()`** (`boolean`)
  - Description: Can the object have a background?

- **`hasColor()`** (`boolean`)
  - Description: Can the object have a color (non-line and non-background)?

- **`hasLineColor()`** (`boolean`)
  - Description: Can the object have a line color?

- **`isChildOf(MObject o)`** (`boolean`)
  - Description: Is this object a children of another one?

- **`isEmpty()`** (`boolean`)
  - Description: An object may become empty if all the children are removed.

- **`isInternalSelectable()`** (`boolean`)
  - Description: Is it a selection only internal object?

- **`isReactionArrow(MoleculeGraph mol)`** (`boolean`)
  - Description: Checks if it is a reaction arrow.

- **`isSelectableNow()`** (`boolean`)
  - Description: Is the object selectable now?

- **`isSelected()`** (`boolean`)
  - Description: Is the object selected?

- **`isTransformable()`** (`boolean`)
  - Description: Is it a transformable object?

- **`propertyCount()`** (`int`)
  - Description: Returns the number of property (property key - property value) mappings of this MObject.

- **`propertyKeySet()`** (`Set<String>`)
  - Description: Returns a set view of the property keys of this MObject.

- **`propertySet()`** (`Set<Map.Entry<String,Object>>`)
  - Description: Returns a collection view of the properties (property key - property value mappings) of this MObject.

- **`putProperty(String key, Object value)`** (`void`)
  - Description: Associates the specified value with the specified key at this MObject.

- **`removeAtom(MolAtom atom)`** (`void`)
  - Description: Removes the atom from the corresponding molecule object.

- **`removeChild(MObject o)`** (`void`)
  - Description: Removes a child object.

- **`removeNotify(MDocument doc)`** (`void`)
  - Description: Called when the object is removed from a document.

- **`removeProperty(String key)`** (`Object`)
  - Description: Removes the mapping for this property key from this MObject if present.

- **`replaceAtom(MolAtom orig, MolAtom a)`** (`void`)
  - Description: Replaces a contained atom with another one.

- **`setAttribute(String s, String v)`** (`void`)
  - Description: Sets the value of an attribute.

- **`setBackground(Color c)`** (`void`)
  - Description: Sets the background color of the object.

- **`setColor(Color c)`** (`void`)
  - Description: Sets the color of the object.

- **`setLineColor(Color c)`** (`void`)
  - Description: Sets the color of the object.

- **`setSelected(boolean s)`** (`void`)
  - Description: Selects or unselects the object.

- **`toString()`** (`String`)
  - Description: Returns a string representation of the object.

**Abstract Methods:**

- **`calcCenter(DPoint3 p, CTransform3D t)`** (`abstract void`)
  - Description: Calculates the geometrical center.

- **`distanceFrom(double x, double y, CTransform3D t)`** (`abstract double`)
  - Description: Gets the 2D distance from the specified point.

- **`getPoint(int i)`** (`abstract MPoint`)
  - Description: Gets a point of the object.

- **`getPointCount()`** (`abstract int`)
  - Description: Gets the number of points.

**Static Methods:**

- **`makeColor(String s)`** (`protected static Color`)
  - Description: Creates a Color object from a string representation.
```

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

### BCUTParameters Constructors

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/descriptors/BCUTParameters

Provides information on how to instantiate BCUTParameters objects, either with default values, from a configuration file, or from an XML configuration string.

```APIDOC
## Constructors

### `BCUTParameters()`

**Description**: Creates an empty object. Initializes parameters to default values.

**Method**: `public BCUTParameters()`

### `BCUTParameters(File configFile)`

**Description**: Creates a new object based on a given configuration file.

**Method**: `public BCUTParameters(File configFile)`

**Parameters**:
- `configFile` (File) - XML configuration file

**Throws**:
- `MDParametersException` - missing or bad XML configuration

### `BCUTParameters(String XMLconfig)`

**Description**: Creates a new object based on a given configuration string.

**Method**: `public BCUTParameters(String XMLconfig)`

**Parameters**:
- `XMLconfig` (String) - XML configuration string

**Throws**:
- `MDParametersException` - missing or bad XML configuration
```

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

### Get Atom Angles - Java

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Calculates and returns the angle formed by three specified atoms within a molecule.

```Java
public double getAngle(int atom1, int atom2, int atom3)
Returns the angle of 3 atoms.
Parameters:
    `atom1` - is the (0-based) index of the 1st atom     `atom2` - is the (0-based) index of the 2nd atom     `atom3` - is the (0-based) index of the 3rd atom
```

```Java
public double getAngle(int[] atoms) throws PluginException
Returns the angle of 3 atoms.
Parameters:
    `atoms` - is the array containing (0-based) indexes of 3 atoms
Throws:
    `PluginException` - if atoms are not set properly
```

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

### Get Molecular Energy - Java

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Returns the calculated energy of a molecular conformer using different force fields.

```Java
public double getDreidingEnergy()
Returns the energy of the conformer.
```

```Java
public double getMMFF94Energy()
Returns the MMFF94 energy of the structure (default: kcal/mol).
Since:
    Marvin 5.4
```

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

### MElectron Constructors

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/struc/graphics/MElectron

Details on how to instantiate an MElectron object.

```APIDOC
## Constructors

### MElectron(DPoint3 p, MolAtom atom)

**Description**: Creates an MElectron with a specified point and associated atom.

**Method**: `public MElectron(DPoint3 p, MolAtom atom)`

### MElectron()

**Description**: Creates a default MElectron object.
```

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

### MViewPane.makeHelpMenu(Container) Replacement

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/deprecated-list

As of Marvin 3.4, `MarvinPane.addHelpMenu(java.awt.Container)` should be used instead of `MViewPane.makeHelpMenu(Container)`.

```APIDOC
## MViewPane.makeHelpMenu(Container)

### Description
As of Marvin 3.4, `MarvinPane.addHelpMenu(java.awt.Container)` should be used instead.

### Method
(Deprecated)

### Endpoint
N/A (Class Method)

### Parameters
- **container** (Container) - Description of the container parameter.

### Request Example
```java
MViewPane.makeHelpMenu(myContainer);
```

### Response
N/A
```

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

### Molecule Iterator (Final)

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/io/MDocSource

Gets a final molecule iterator for the document source, starting at the current position. Only one iterator can be created per MolImporter.

```APIDOC
## GET /websites/apidocs_chemaxon/getMoleculeIterator

### Description
Gets a molecule iterator for this document source. The iterator starts at the current position. Only one iterator can be created for one MolImporter.

### Method
GET

### Endpoint
/websites/apidocs_chemaxon/getMoleculeIterator

### Parameters
None

### Request Example
None

### Response
#### Success Response (200)
- **moleculeIterator** (MoleculeIterator) - The molecule iterator.

#### Response Example
```json
{
  "moleculeIterator": "<molecule_iterator_object>"
}
```

### Throws
- **UnsupportedOperationException** - if an iterator was created before
```

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

### Get Atom Dihedrals - Java

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Calculates and returns the dihedral angle defined by four specified atoms within a molecule.

```Java
public double getDihedral(int atom1, int atom2, int atom3, int atom4)
Returns the dihedral of 4 atoms.
Parameters:
    `atom1` - is the (0-based) index of the 1st atom     `atom2` - is the (0-based) index of the 2nd atom     `atom3` - is the (0-based) index of the 3rd atom     `atom4` - is the (0-based) index of the 4th atom
```

```Java
public double getDihedral(int[] atoms) throws PluginException
Returns the dihedral of 4 atoms.
Parameters:
    `atoms` - is the array containing (0-based) indexes of 4 atoms
Throws:
    `PluginException` - if atoms are not set properly
```

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

### Initialize Action (Java)

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/beans/MarvinPane

Initializes an Action with resources, a key, and an accelerator. This method is deprecated as of Marvin 3.3.1 and replaced by SwingUtil.initAction. It requires an Action, a ResourceBundle, a key, and a KeyStroke.

```Java
@Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public static void initAction(Action action, ResourceBundle rc, String key, KeyStroke accel)
Deprecated, for removal: This API element is subject to removal in a future version.
as of Marvin 3.3.1, replaced by SwingUtil.initAction 

Parameters:
    `action` - the action     `rc` - the resources     `key` - name of the resource     `accel` - the accelerator or null 

Since:
    Marvin 3.3
```

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

### MSketchPane Constructors

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/beans/MSketchPane

Constructors for initializing the MSketchPane.

```APIDOC
## Constructors

### `MSketchPane()`

Constructs the sketcher.

### `MSketchPane(UserSettings settings)`

Constructs the sketcher with the specified user settings object.

### `MSketchPane(UserSettings settings, boolean loadtmpl)`

Constructs the sketcher with the specified user settings object and template loading option.

### `MSketchPane(UserSettings settings, boolean loadtmpl, JComponent parent)`

Constructs the sketcher with the specified user settings object, template loading option, and parent component.
```

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

### Get Molecular Formula

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/calculations/ElementalAnalyser

Calculates the molecular formula as a string listing all atom types and their occurrences. Example: C6H6 for benzene.

```java
public String formula()
```

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

### StandardizerActionFactory Builder Configuration (Java)

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/standardizer/StandardizerActionFactory

This example demonstrates how to build a StandardizerActionFactory using its Builder class. It includes adding Chemaxon's default configuration, user-defined configurations, and pre-configured transformations. Error handling for missing user-defined configurations is also shown. This method is suitable for initializing the factory with various action definitions.

```java
StandardizerActionFactory.Builder builder = new StandardizerActionFactory.Builder();
builder.add(StandardizerTest.class.getResourceAsStream(StandardizerActionFactory.DEFAULT_CONFIGURATION_PATH));
try {
    builder.add(DotfileUtil.open(StandardizerActionFactory.USER_DEFINED_STANDARDIZERCONFIG_XML));
} catch (IOException e) {
    // no user defined standardizer configuration found
}
builder.add(StandardizerTest.class.getResourceAsStream(StandardizerActionFactory.PRE_CONFIGURED_TRANSFORMATIONS));
StandardizerActionFactory factory = builder.build();
```

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

### Get EFlows Associated with Atom

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/struc/graphics/MEFlow

Returns all electron flows (EFlows) that either start from or point to a given atom. If no EFlows are connected, an empty list is returned.

```java
public static List<MEFlow> getEFlowsOfAtom(MolAtom atom)
// Parameters: atom - the sink or source atom
// Returns: List of EFlows, empty if no EFlow starts from this atom and no EFlow ends to this atom.
```

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

### MSketchPane Instance Methods

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/beans/MSketchPane

Instance methods for interacting with the MSketchPane.

```APIDOC
## Instance Methods

### `addPropertyChangeListener(String propertyName, PropertyChangeListener listener)`

Adds a `PropertyChangeListener` for a specific property.

### `centralizeMoleculeDisplay()`

Puts the molecule into the center of the display.

### `clearHistory()`

Resets the undo queue.

### `doPaste()`

Invokes the Paste action.

### `getAutoScale()`

Returns the autoscale property.

### `getBoundRectSize()`

Gets the size of the bounding rectangle.

### `getCanvasComponent()`

Determines the canvas component of MarvinSketch.

### `getCommonActions()`

Deprecated. Use alternative methods for common actions.

### `getDocument()`

Gets the document.

### `getImage(double scale)`

Gets the canvas contents as an image using a scale factor.

Examples:
To get an image with a scale factor equivalent to 100% magnification: `getImage(getDefaultScale());`
To get an image with the actual scale factor: `getImage(getScale());`

### `getImage(Dimension size)`

Gets the canvas contents as an image scaled to fit in the specified rectangle.

### `getMag()`

Deprecated, for removal: Replaced by `getScale()` as of Marvin 2.8.1.

### `getMergedst()`

Gets the merge distance.

### `getMol()`

Returns a clone of the current molecule on the canvas.

### `getMol(String fmt)`

Gets the molecule in a specified text format.

### `getMolPanel()`

Returns the underlying panel.

### `getMrvWithSettings()`

Deprecated, for removal: Use `getMol(String)` instead.

### `getObjectAtPointer()`

Gets the object at the mouse pointer.

### `getPiece(String fmt)`

Gets the current molecule piece in the specified format.

### `getReactionSupport()`

Checks if reaction drawing is supported.

### `getScale()`

Returns the scale factor of the current magnification.

### `getSelection()`

Gets a clone of the current selection.

### `getSimpView()`

Deprecated, for removal: Replaced by `isBondDraggedAlong()` as of Marvin 3.5.

### `getSketchMode()`

Gets the current sketching mode.

### `getStickdst()`

Gets the sticking distance.

### `getUndo()`

Gets the maximum undo depth.

### `isBondDraggedAlong()`

Checks if the currently used bond is shown at the mouse cursor.

### `isCloseEnabled()`

Determines if the _File- >Close_ menu item is enabled.

### `isConfirmExit()`

Gets whether the confirmation dialog will appear upon exit.

### `isLoadedMolModified()`

Determines whether the original molecule loaded is modified.

### `isReactionErrorVisible()`

Deprecated, for removal: This method is deprecated and has no replacement as of Version 5.3.2.

### `isValenceErrorVisible()`

Checks if valence errors are highlighted.

### `propertyChange(PropertyChangeEvent ev)`

Handles property change events.

### `readExternal(ObjectInput in)`

Restores the object's state.

### `redo()`

Invokes a redo command.

### `setAutoScale(boolean as)`

Sets the autoscale property.

### `setBondDraggedAlong(boolean v)`

Sets the visibility of the currently used bond at the mouse cursor.

### `setCloseEnabled(boolean b)`

Sets the accessibility of the _Close_ menu item in the _File_ menu.

### `setConfirmExit(boolean b)`

Sets whether to display the confirmation dialog about exiting.

### `setDisabledGroupTypes(List<String> disabledGroupTypes)`

Sets the disabled group types.

### `setDocument(MDocument doc)`

Sets the document.

### `setMag(double m)`

Deprecated, for removal: Replaced by `setScale(double)` as of Marvin 2.8.1.

### `setMergedst(double d)`

Sets the merge distance.

### `setMol(Molecule m)`

Sets the molecule.

### `setMol(Molecule m, boolean init)`

Deprecated, for removal: Use `setMol(Molecule)` instead.

### `setMol(File f, String opts)`

Sets the molecule from a file with specified options.
```

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

### Get Calculation Remark

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Retrieves the remark associated with a calculation. If no result types are set, it returns the remark; otherwise, it returns null.

```APIDOC
## GET /websites/apidocs_chemaxon/getRemark

### Description
Returns the calculation remark. If no results (no result types) are set, it returns the remark; otherwise, it returns `null`.

### Method
GET

### Endpoint
/websites/apidocs_chemaxon/getRemark

### Parameters

#### Query Parameters
N/A

#### Request Body
N/A

### Request Example
N/A

### Response
#### Success Response (200)
- **remark** (string) - The calculation remark or null.

#### Response Example
```json
{
  "remark": "Calculation completed successfully."
}
```
or
```json
{
  "remark": null
}
```
```

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

### Get Lowest Energy Conformer - Java

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Retrieves the lowest energy conformer of a molecule. This method is part of the molecule manipulation utilities.

```Java
public Molecule getLowestEnergyConformer()
Returns the lowest energy conformer of the molecule.
```

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

### createVisitor Method

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/com/chemaxon/calculations/stereoanal/filters/atrop/KnownAtropFilter

Constructs a visitor implementation for processing atropisomeric stereo centers.

```APIDOC
## createVisitor Method

### Description
Constructs the specified visitor implementation for processing atropisomeric stereo centers. This method is inherited from `AbstractStereoFilter`.

### Method
protected

### Endpoint
N/A

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
- **consumer** (Consumer<AtropStereoCenter>) - Required - A consumer function to process each `AtropStereoCenter`.

### Request Example
```json
{
  "consumer": "(atropCenter) => console.log(atropCenter)"
}
```

### Response
#### Success Response (200)
- **visitor** (StereoCenterVisitor) - A `StereoCenterVisitor` implementation.

#### Response Example
```json
{
  "visitor": "StereoCenterVisitor object"
}
```
```

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

### Setting Parameters for MarvinPane (Java)

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/beans/MarvinPane

Illustrates how to set the parameter string for a MarvinPane, which configures various aspects of the molecular visualization and editing. This must be called before other property setting methods.

```java
molPanel.setParams("rows=2\n" +
"cols=2\n" +
"layout0=:2:2:M:1:0:1:1:c:b:1:1:L:0:0:1:1:c:n:0:1\n" +
"param0=:M:100:100:L:10b\n" +
"\n" +
"# MarvinSketch properties also have to be specified here for the\n" +
"# sketcher windows that can be launched using Edit/Structure.\n" +
"extrabonds=arom,wedge\n");
```

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

### Get Current Parametrized Metric Threshold

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/descriptors/MDParameters

Retrieves the threshold value that is currently set for the active parametrized metric. This value is used in user interfaces to guide beginners.

```java
public float getThreshold()

```

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

### Get Warning Message

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Retrieves a warning message if the lowest energy conformer calculation was unsuccessful or aborted by the user, otherwise returns null.

```APIDOC
## GET /websites/apidocs_chemaxon/getWarningMessage

### Description
Returns a warning message if the lowest energy conformer calculation was unsuccessful or aborted by the user, `null` otherwise.

### Method
GET

### Endpoint
/websites/apidocs_chemaxon/getWarningMessage

### Parameters

#### Query Parameters
N/A

#### Request Body
N/A

### Request Example
N/A

### Response
#### Success Response (200)
- **warningMessage** (string) - A warning message or null.

#### Response Example
```json
{
  "warningMessage": "Conformer calculation was aborted by the user."
}
```
or
```json
{
  "warningMessage": null
}
```
```

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

### PFParameters Constructors

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/descriptors/PFParameters

Provides details on how to create and initialize PFParameters objects.

```APIDOC
## Constructors

### `PFParameters()`

**Description:** Creates an empty Pharmacophore Fingerprint parameter object.

### `PFParameters(File configFile)`

**Description:** Creates a new Pharmacophore Fingerprint parameter object based on a given configuration file.

**Parameters:**
#### Path Parameters
- **configFile** (File) - Required - The configuration file to load parameters from.

### `PFParameters(String XMLconfig)`

**Description:** Creates a new Pharmacophore Fingerprint parameter object based on a given XML configuration string.

**Parameters:**
#### Path Parameters
- **XMLconfig** (String) - Required - The XML configuration string to load parameters from.
```

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

### Plugin Management and Configuration

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/com/chemaxon/calculations/gui/PluginFactory

This section describes how Chemaxon plugins are managed, including their keys, configuration loading, parameter panels, and options panes. It also outlines the process for creating parameter panels and setting initial values.

```APIDOC
## Plugin Configuration and Management

### Description
Provides an overview of how Chemaxon plugins are defined, configured, and managed. This includes the structure of plugin keys, the process of loading configuration XML and property files, and the mechanisms for creating and accessing parameter panels and options panes.

### Method
N/A (Conceptual Overview)

### Endpoint
N/A (Conceptual Overview)

### Parameters
#### Plugin Key Format
`key=$<plugin class name>$$<menu>$<mnemonics>$<group>$<groupmnemonic>$<NOPARAMS>`
- The first character after '=' is a delimiter.
- `plugin class name` is mandatory; others are optional.

#### Configuration Loading
1. Configuration XML search in CLASSPATH: `plugin/<plugin name>Parameters.xml`.
2. If XML not found, plugin fetches its panel via `plugin.getParameterPanel()`.

#### Initial Parameter Values
- Loaded from `$HOME/chemaxon/<plugin name>Parameters.properties` (Windows) or `$HOME/.chemaxon/<plugin name>Parameters.properties` (UNIX/Linux).
- If not found, defaults are used from configuration XML or `plugin.getParameterPanel()`.

### Request Example
N/A

### Response
N/A
```

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

### Manage File Position (Java)

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/struc/MDocument

Provides methods to get and set the starting position of the document within an input file. This is useful for managing file I/O and document referencing.

```Java
public long getStartPosition()
Gets the starting position of this document in the input file. 
Returns:
    the starting position
```

```Java
public void setStartPosition(long off)
Sets the starting position of this document in the input file. 
Parameters:
    `off` - the starting position
```

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

### StrucFPConfig Constructors and Methods

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/sss/screen/StrucFPConfig

Documentation for the StrucFPConfig class, including its constructors and methods for configuration management.

```APIDOC
## StrucFPConfig

### Description
Utility class for assembling and parsing structural FP configurations.

Since: JChem 3.1

### Constructor Summary

| Constructor    | Description             |
|----------------|-------------------------|
| `StrucFPConfig()` | Initializes StrucFPConfig. |

### Method Summary

| Modifier and Type | Method                      | Description                                                       |
|-------------------|-----------------------------|-------------------------------------------------------------------|
| `String`          | `getConfig()`               | Creates a configuration string according to the internal values.    |
| `List<Molecule>`  | `getMolecules()`            | Gets the Molecule objects for the keys.                           |
| `List<String>`    | `getMolStrings()`           | Gets the original strings for the keys.                           |
| `int`             | `getNumberOfIntegersNeeded()` | Indicates the number of 32 bit units needed to store the fingerprint. |
| `int`             | `getNumberOfKeys()`         | Indicates the number of structural keys.                          |
| `boolean`         | `getSmartsMode()`           | Indicates if molecule strings should be interpreted as SMARTS.    |
| `void`            | `parseConfig(String config)`| Parses a text configuration, and sets internal values accordingly. |
| `void`            | `readMolecules(InputStream input, boolean smartsMode)` | Reads the structures from a stream.                               |
| `void`            | `setMolStrings(List<String> strings, boolean smartsMode)` | Sets the original strings for the keys.                           |

### Method Details

#### `StrucFPConfig()`

**Description:** Initializes StrucFPConfig.

**Method:** Constructor

**Endpoint:** N/A

#### `getConfig()`

**Description:** Creates a configuration string according to the internal values.

**Method:** GET

**Endpoint:** N/A

**Returns:**
- `String`: the configuration string.

#### `getMolecules()`

**Description:** Gets the Molecule objects for the keys.

**Method:** GET

**Endpoint:** N/A

**Returns:**
- `List<Molecule>`: an ArrayList containing Molecule objects.

#### `getMolStrings()`

**Description:** Gets the original strings for the keys.

**Method:** GET

**Endpoint:** N/A

**Returns:**
- `List<String>`: an ArrayList containing String objects.

#### `getNumberOfIntegersNeeded()`

**Description:** Indicates the number of 32 bit units needed to store the fingerprint.

**Method:** GET

**Endpoint:** N/A

**Returns:**
- `int`: the number of ints needed to accommodate all keys.

Since: JChem 5.0

#### `getNumberOfKeys()`

**Description:** Indicates the number of structural keys.

**Method:** GET

**Endpoint:** N/A

**Returns:**
- `int`: the number of structural keys.

Since: JChem 5.0

#### `getSmartsMode()`

**Description:** Indicates if molecule strings should be interpreted as SMARTS.

**Method:** GET

**Endpoint:** N/A

**Returns:**
- `boolean`: `true`, if strings should be interpreted as SMARTS.

#### `parseConfig(String config)`

**Description:** Parses a text configuration, and sets internal values accordingly.

**Method:** POST

**Endpoint:** N/A

**Parameters:**
#### Query Parameters
- **config** (String) - Required - the configuration

#### Throws:
- `MolFormatException`: if the importer encounters a problem

#### `readMolecules(InputStream input, boolean smartsMode)`

**Description:** Reads the structures from a stream.

**Method:** POST

**Endpoint:** N/A

**Parameters:**
#### Query Parameters
- **input** (InputStream) - Required - the input stream
- **smartsMode** (boolean) - Required - indicates if the molecule strings should be interpreted as SMARTS.

#### Throws:
- `IOException`: if the inputstream encounters a problem

#### `setMolStrings(List<String> strings, boolean smartsMode)`

**Description:** Sets the original strings for the keys.

**Method:** POST

**Endpoint:** N/A

**Parameters:**
#### Query Parameters
- **strings** (List<String>) - Required - the list of molecule strings
- **smartsMode** (boolean) - Required - indicates if the molecule strings should be interpreted as SMARTS.

#### Throws:
- `MolFormatException`

### Inherited Methods from `java.lang.Object`
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`
```

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

### Get First Hit Time (Java)

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/jchem/db/JChemSearch

Retrieves the time taken to retrieve the first hit, measured from the start of screening, in milliseconds.

```java
public long getFirstHitTime()
```

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

### Get Molecule Projection Properties - Java

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/marvin/calculations/GeometryPlugin

Retrieves various properties related to the calculated molecule projections, such as minimal and maximal projection areas and radii.

```Java
public double getMinimalProjectionArea()
Returns the minimal projection area in Angstrom^2.
See Also:
    
      * `setCalculateMoleculeProjections(boolean)`
```

```Java
public double getMaximalProjectionArea()
Returns the maximal projection area in Angstrom^2.
See Also:
    
      * `setCalculateMoleculeProjections(boolean)`
```

```Java
public double getMinimalProjectionRadius()
Returns the radius of the circle surrounding the minimal projection in Angstrom.
See Also:
    
      * `setCalculateMoleculeProjections(boolean)`
```

```Java
public double getMaximalProjectionRadius()
Returns the radius of the circle surrounding the maximal projection in Angstrom.
See Also:
    
      * `setCalculateMoleculeProjections(boolean)`
```

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

### Initialize Standardizer and Standardize Molecule (Java)

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/standardizer/Standardizer

A simple Java example demonstrating how to initialize the Standardizer with an XML configuration file and then standardize a molecule.

```java
Standardizer standardizer = new Standardizer(new File("standardize.xml"));
standardizer.standardize(molecule);
```

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

### Get Dot-Disconnected Molecular Formula

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/calculations/ElementalAnalyser

Calculates the dot-disconnected molecular formula for multifragment molecules. Example: C7H5O2.Na for sodium benzoate. Introduced in Marvin 4.0.5.

```java
public String dotDisconnectedFormula()
```

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

### Constructor

Source: https://apidocs.chemaxon.com/jchem/developer/beans/api/chemaxon/struc/MPropertyContainer

Creates an empty property container.

```APIDOC
## Constructor MPropertyContainer

### Description
Creates an empty property container.

### Method
CONSTRUCTOR

### Endpoint
N/A

### Parameters
None

### Request Example
```
new MPropertyContainer()
```

### Response
N/A
```