### Install PDB2PQR from Source

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/getting.md

Install PDB2PQR by building from the source code. Navigate to the top-level directory of the source code and run this command.

```bash
pip install .
```

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

### Logger Setup

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/io.md

Function to set up the logging mechanism.

```APIDOC
## POST /pdb2pqr.io.setup_logger

### Description
Sets up the logger to output log files to the same directory as the PQR output file.

### Method
POST

### Endpoint
/pdb2pqr.io.setup_logger

### Parameters
#### Request Body
- **output_pqr** (str) - Required - The path to the PQR file.
- **level** (str) - Optional - The logging level (e.g., 'DEBUG', 'INFO'). Defaults to 'DEBUG'.

### Response
#### Success Response (200)
- **message** (str) - A confirmation message indicating the logger has been set up.

#### Response Example
```json
{
  "message": "Logger setup complete."
}
```
```

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

### Install PDB2PQR from Source (Editable Mode)

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/getting.md

For developers, install PDB2PQR in editable mode using this command from the top-level source directory. This allows for changes in the source code to be reflected immediately without reinstallation.

```bash
pip install -e .
```

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

### Install PDB2PQR via PIP

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/getting.md

Use this command to install the PDB2PQR package using pip. It is recommended to do this within a virtual environment.

```bash
pip install pdb2pqr
```

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

### Setup Molecular System

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/main.md

Initializes and sets up the molecular system for analysis, including parsing PDB records and definitions.

```APIDOC
## setup_molecule

### Description
Set up the molecular system.

### Method
Not specified (assumed to be a function call within a script)

### Endpoint
Not applicable (Python function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
* **pdblist** (*list*) – list of PDB records
* **definition** ([*Definition*](definitions.md#pdb2pqr.definitions.Definition)) – topology definition
* **ligand_path** (*str*) – path to ligand (may be None)

### Returns
(biomolecule object, definition object–revised if ligand was parsed, ligand object–may be None)

### Return type
([Biomolecule](biomolecule.md#pdb2pqr.biomolecule.Biomolecule), [Definition](definitions.md#pdb2pqr.definitions.Definition), Ligand)
```

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

### Get PDB2PQR Help

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/using/index.md

Command to display all available options and usage information for the PDB2PQR command-line tool.

```bash
pdb2pqr --help
```

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

### GET /io/get_definitions

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/io.md

Loads topology definition files for amino acids, nucleic acids, and patches.

```APIDOC
## GET /io/get_definitions

### Description
Load topology definition files.

### Parameters
#### Query Parameters
- **aa_path** (str) - Optional - likely location of amino acid topology definitions
- **na_path** (str) - Optional - likely location of nucleic acid topology definitions
- **patch_path** (str) - Optional - likely location of patch topology definitions

### Response
#### Success Response (200)
- **definitions** (object) - topology Definitions object.
```

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

### GET /io/get_pdb_file

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/io.md

Obtains a PDB file from a local path or the RCSB PDB webserver.

```APIDOC
## GET /io/get_pdb_file

### Description
Obtain a PDB file. First check the path given on the command line - if that file is not available, obtain the file from the PDB webserver.

### Parameters
#### Query Parameters
- **name** (str) - Required - name of PDB file (path) or PDB ID

### Response
#### Success Response (200)
- **file** (file) - file-like object containing PDB file
```

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

### GET /biomolecule/properties

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/biomolecule.md

Retrieves various properties of the biomolecule structure.

```APIDOC
## GET /biomolecule/properties

### Description
Retrieve metadata properties of the biomolecule including heavy atom counts, patch maps, and reference maps.

### Method
GET

### Endpoint
/biomolecule/properties

### Response
#### Success Response (200)
- **num_missing_heavy** (int) - Number of missing biomolecular heavy atoms
- **patch_map** (list) - Definition patch maps
- **reference_map** (dict) - Definition reference map
```

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

### pdb2pqr.quatfit.qfit

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/quatfit.md

Method for getting new atom coordinates from sets of reference and definition coordinates.

```APIDOC
## pdb2pqr.quatfit.qfit

### Description
Method for getting new atom coordinates from sets of reference and definition coordinates.

### Parameters
#### Path Parameters
- **numpoints** (int) - Required - the number of points in each list
- **refcoords** ([[float, float, float]]) - Required - list of reference coordinates
- **defcoords** ([[float, float, float]]) - Required - list of definition coordinates

### Response
- **Returns** (tuple) - (reference center, definition center, left rotation matrix)
```

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

### SITE Class Initialization

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/pdb.md

Initializes the SITE class by parsing a line from a PDB file to extract information about a site.

```APIDOC
## SITE Class Initialization

### Description
Initializes the SITE class by parsing a line from a PDB file to extract information about a site.

### Method
__init__

### Parameters
#### Path Parameters
- **line** (str) - Required - The line containing PDB site information.

### Request Body
```
{
  "line": "string"
}
```

### Response
#### Success Response (200)
- **seq_num** (int) - Sequence number of the site.
- **site_id** (string) - Site name.
- **num_res** (int) - Number of residues comprising the site.
- **res_name1** (string) - Residue name for the first residue.
- **chain_id1** (string) - Chain identifier for the first residue.
- **seq1** (int) - Residue sequence number for the first residue.
- **ins_code1** (string) - Insertion code for the first residue.
- **res_name2** (string) - Residue name for the second residue.
- **chain_id2** (string) - Chain identifier for the second residue.
- **seq2** (int) - Residue sequence number for the second residue.
- **ins_code2** (string) - Insertion code for the second residue.
- **res_name3** (string) - Residue name for the third residue.
- **chain_id3** (string) - Chain identifier for the third residue.
- **seq3** (int) - Residue sequence number for the third residue.
- **ins_code3** (string) - Insertion code for the third residue.
- **res_name4** (string) - Residue name for the fourth residue.
- **chain_id4** (string) - Chain identifier for the fourth residue.
- **seq4** (int) - Residue sequence number for the fourth residue.
- **ins_code4** (string) - Insertion code for the fourth residue.

### Response Example
```json
{
  "seq_num": 1,
  "site_id": "A",
  "num_res": 1,
  "res_name1": "ARG",
  "chain_id1": "A",
  "seq1": 10,
  "ins_code1": " ",
  "res_name2": null,
  "chain_id2": null,
  "seq2": null,
  "ins_code2": null,
  "res_name3": null,
  "chain_id3": null,
  "seq3": null,
  "ins_code3": null,
  "res_name4": null,
  "chain_id4": null,
  "seq4": null,
  "ins_code4": null
}
```
```

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

### Run Web Server Tests

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/releases.md

Executes a comprehensive test suite against the production PDB2PQR web server.

```bash
make test-webserver
```

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

### GET /io/get_molecule

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/io.md

Retrieves molecular structure information from a PDB ID or file path.

```APIDOC
## GET /io/get_molecule

### Description
Get molecular structure information as a series of parsed lines.

### Parameters
#### Query Parameters
- **input_path** (str) - Required - structure file PDB ID or path

### Response
#### Success Response (200)
- **molecule_records** (list) - list of molecule records
- **is_cif** (bool) - Boolean indicating whether entry is CIF
```

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

### Water Optimization Class Initialization

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/hydrogens.md

Initializes the water optimization class with necessary parameters.

```APIDOC
## __init__ (residue, optinstance, routines)

### Description
Initialize the water optimization class.

### Parameters
#### Path Parameters
- **residue** (Residue) - Required - the residue to flip
- **optinstance** (OptimizationHandler) - Required - the optimization instance containing information about what to optimize
- **routines** (Debump) - Required - debumping routines object
```

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

### __init__(line)

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/pdb.md

Initializes the strand data structure by parsing a specific line from a PDB file.

```APIDOC
## __init__(line)

### Description
Initializes the object by parsing a line from a PDB file, mapping specific column ranges to class fields.

### Parameters
#### Request Body
- **line** (str) - Required - A string representing a line from a PDB file containing strand information.

### Fields
- **strand** (int) - Strand number (starts at 1).
- **sheet_id** (string) - Sheet identifier.
- **num_strands** (int) - Number of strands in the sheet.
- **init_res_name** (string) - Residue name of initial residue.
- **init_chain_id** (string) - Chain identifier of initial residue.
- **init_seq_num** (int) - Sequence number of initial residue.
- **init_i_code** (string) - Insertion code of initial residue.
- **end_res_name** (string) - Residue name of terminal residue.
- **end_chain_id** (string) - Chain identifier of terminal residue.
- **end_seq_num** (int) - Sequence number of terminal residue.
- **end_i_code** (string) - Insertion code of terminal residue.
- **sense** (int) - Sense of strand (0: first, 1: parallel, -1: anti-parallel).
- **cur_atom** (string) - Registration: Atom name in current strand.
- **curr_res_name** (string) - Registration: Residue name in current strand.
- **curChainId** (string) - Registration: Chain identifier in current strand.
- **curr_res_seq** (int) - Registration: Residue sequence number in current strand.
- **curr_ins_code** (string) - Registration: Insertion code in current strand.
- **prev_atom** (string) - Registration: Atom name in previous strand.
- **prev_res_name** (string) - Registration: Residue name in previous strand.
- **prevChainId** (string) - Registration: Chain identifier in previous strand.
- **prev_res_seq** (int) - Registration: Residue sequence number in previous strand.
- **prev_ins_code** (string) - Registration: Insertion code in previous strand.
```

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

### Residue Initialization and Methods

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/aa.md

Details on how to initialize a Residue object and the methods available for managing its atoms.

```APIDOC
## Residue Class

### `__init__(atoms, ref)`

Initialize a Residue object.

#### Parameters
* **atoms** (list[Atom]) - A list of `Atom` objects to be stored in this object.
* **ref** (DefinitionResidue) - The reference object for the residue. Used to convert from the alternate naming scheme to the main naming scheme.

### `add_atom(atom)`

Add an atom to the residue. Overrides the existing `add_atom` to include the link to the reference object.

#### Parameters
* **atom** (Atom) - The atom to add to the residue.

### `create_atom(atomname, newcoords)`

Create a water atom. Note the HETATM field.

#### Parameters
* **atomname** (str) - The name of the atom to be added.
* **newcoords** (list[float, float, float]) - The coordinates for the new atom.

### `water_residue_names`

A class variable containing a list of common water residue names.

* Value: `['HOH', 'WAT']`
```

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

### EXPDTA Record Initialization

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/pdb.md

Initializes the EXPDTA record to identify the experimental technique used for the structure.

```APIDOC
## __init__(line)

### Description
Initialize by parsing an EXPDTA PDB line.

### Parameters
#### Request Body
- **line** (str) - Required - Line with PDB class

### Data Fields
- **technique** (string) - The experimental technique(s) with optional comment
```

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

### Run PDB2PQR Command Line

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/using/index.md

Basic command to run PDB2PQR from the command line. Specify options like force field, input PDB file path, and output PQR file path. The input path can be a PDB ID for automatic retrieval.

```bash
pdb2pqr [options] --ff={forcefield} {path} {output-path}
```

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

### SLTBRG Class Initialization

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/pdb.md

Initializes the SLTBRG class by parsing a line from a PDB file to define salt bridges.

```APIDOC
## SLTBRG Class Initialization

### Description
Initializes the SLTBRG class by parsing a line from a PDB file to define salt bridges.

### Method
__init__

### Parameters
#### Path Parameters
- **line** (str) - Required - The line containing PDB salt bridge information.

### Request Body
```
{
  "line": "string"
}
```

### Response
#### Success Response (200)
- **name1** (string) - Atom name of the first atom in the salt bridge.
- **alt_loc1** (string) - Alternate location indicator for the first atom.
- **res_name1** (string) - Residue name of the first atom.
- **chain_id1** (string) - Chain identifier of the first atom.
- **res_seq1** (int) - Residue sequence number of the first atom.
- **ins_code1** (string) - Insertion code of the first atom.
- **name2** (string) - Atom name of the second atom in the salt bridge.
- **alt_loc2** (string) - Alternate location indicator for the second atom.
- **res_name2** (string) - Residue name of the second atom.
- **chain_id2** (string) - Chain identifier of the second atom.
- **res_seq2** (int) - Residue sequence number of the second atom.
- **ins_code2** (string) - Insertion code of the second atom.
- **sym1** (string) - Symmetry operator for the first atom.
- **sym2** (string) - Symmetry operator for the second atom.

### Response Example
```json
{
  "name1": "CB",
  "alt_loc1": " ",
  "res_name1": "ARG",
  "chain_id1": "A",
  "res_seq1": 10,
  "ins_code1": " ",
  "name2": "CD",
  "alt_loc2": " ",
  "res_name2": "ASP",
  "chain_id2": "A",
  "res_seq2": 15,
  "ins_code2": " ",
  "sym1": " ",
  "sym2": " "
}
```
```

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

### Test PDB2PQR with Coverage.py and Pytest

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/getting.md

Run basic tests for PDB2PQR using Coverage.py and Pytest. Execute this command from the top level of the source directory. Add the --run-long option for more extensive testing.

```bash
coverage run -m pytest
```

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

### Format code with Ruff

Source: https://github.com/electrostatics/pdb2pqr/blob/main/CONTRIBUTING.md

Use these commands in the project root to automatically fix imports and format the codebase.

```bash
# in the project root directory
ruff check --select I --fix .
ruff format .
```

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

### Input Class

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/inputgen.md

Represents an entire APBS input file, containing PQR file information, electrostatic calculations, and print statements.

```APIDOC
## `pdb2pqr.inputgen.Input` Class

### Description
Each object of this class is one APBS input file.

### Method
`__init__`

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
* **pqrpath** (str) - path to PQR file
* **size** (Psize) - parameter sizing object
* **method** (str) - solution method (e.g., mg-para, mg-auto, etc.)
* **asyncflag** (bool) - perform an asynchronous parallel focusing calculation
* **istrng** - ionic strength/concentration (M)
* **potdx** (bool) - whether to write out potential information in DX format

### NOTE
This assumes you have already run psize, either by `size.run_psize(...)()` or `size.parse_string(...)()` followed by `size.set_all()`.

### Methods
#### `dump_pickle()`
Make a Python pickle associated with the APBS input parameters.

#### `print_input_files(output_path)`
Generate the input file(s) associated with this object.

* **Parameters:**
  **output_path** (str) - location for generated files

### Request Example
None

### Response
None
```

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

### SOURCE Class Initialization

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/pdb.md

Initializes the SOURCE class by parsing a line from a PDB file to describe the source of a biological molecule.

```APIDOC
## SOURCE Class Initialization

### Description
Initializes the SOURCE class by parsing a line from a PDB file to describe the source of a biological molecule.

### Method
__init__

### Parameters
#### Path Parameters
- **line** (str) - Required - The line containing PDB source information.

### Request Body
```
{
  "line": "string"
}
```

### Response
#### Success Response (200)
- **source** (string) - Identifies the source of the macromolecule in a token: value format.

### Response Example
```json
{
  "source": "ORGANISM: Homo sapiens (Human)"
}
```
```

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

### Run PDB2PQR Suite

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/run.md

Executes the PDB2PQR suite for biomolecular electrostatics calculations.

```APIDOC
## pdb2pqr.run.run_pdb2pqr

### Description
Run the PDB2PQR Suite

### Method
Not specified (assumed to be a function call within a Python environment)

### Parameters
- **pdblist** (list) - Description not specified
- **my_biomolecule** (object) - Description not specified
- **my_definition** (object) - Description not specified
- **options** (object) - Description not specified
- **is_cif** (boolean) - Description not specified
```

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

### Test PDB2PQR with Pytest

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/getting.md

Run basic tests for PDB2PQR using Pytest. Execute this command from the top level of the source directory. Add the --run-long option for more extensive testing.

```bash
python -m pytest
```

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

### Ligand Data Structures and Utilities

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/ligand.md

Provides access to constants and classes for handling ligand information, including element groups, non-bonded electrons, radii, and valence data, as well as MOL2 file parsing.

```APIDOC
## PDB2PQR Ligand Module Constants

### `pdb2pqr.ligand.ELEMENT_BY_GROUP`

Groups of the periodic table.

### `pdb2pqr.ligand.NONBONDED_BY_TYPE`

Numbers of non-bonded electrons for Sybyl-type atoms. Adapted from [https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540100804](https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540100804) (Table I).

### `pdb2pqr.ligand.RADII`

Radii for different atom types. When using these tables, the most specific Sybyl atom type should be used first and then the generic element should be used.

### `pdb2pqr.ligand.VALENCE_BY_ELEMENT`

Valence electrons by element.

### `pdb2pqr.ligand.VALENCE_BY_GROUP`

Numbers of valence electrons for the groups of the periodic table.

## `pdb2pqr.ligand.mol2` Module

Support molecules in Tripos MOL2 format.

For further information look at (web page exists: 25 August 2005):
[http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0](http://www.tripos.com/index.php?family=modules,SimplePage,,,&page=sup_mol2&s=0)

### Class: `pdb2pqr.ligand.mol2.Mol2Atom`

MOL2 molecule atoms.

#### `__init__()`

Initializes a `Mol2Atom` object.

#### `assign_radius(primary_dict, secondary_dict)`

Assign radius to atom.

* **Parameters:**
  * **primary_dict** (*dict*) – primary dictionary of radii indexed by atom type or element
  * **secondary_dict** (*dict*) – backup dictionary for radii not found in primary dictionary

#### Property: `bond_order`

Total number of electrons in bonds with other atoms.

* **Returns:** total number of electrons in bonds with other atoms
* **Return type:** int

#### Property: `bonded_atom_names`

Bonded atom names.

* **Returns:** bonded atom names
* **Return type:** list

#### Property: `coords`

Coordinates.

* **Returns:** coordinates
* **Return type:** numpy.ndarray

#### `distance(other)`

Get distance between two atoms.

* **Parameters:**
  * **other** ([*Mol2Atom*](#pdb2pqr.ligand.mol2.Mol2Atom)) – other atom for distance measurement
* **Returns:** distance
* **Return type:** float

#### Property: `element`

Element for this atom (uppercase).

* **Returns:** element for this atom
* **Return type:** str

#### Property: `formal_charge`

Formal charge for this atom.

* **Returns:** formal charge for this atom
* **Return type:** int

#### Property: `num_bonded_heavy`

Number of heavy atoms bonded to this atom.

* **Returns:** number of heavy atoms
* **Return type:** int

#### Property: `num_bonded_hydrogen`

Number of hydrogen atoms bonded to this atom.

* **Returns:** number of hydrogen atoms
* **Return type:** int

### Class: `pdb2pqr.ligand.mol2.Mol2Bond`

MOL2 molecule bonds.

#### `__init__(atom1, atom2, bond_type, bond_id=0)`

Initialize bond.

* **Parameters:**
  * **atom1** (*str*) – name of first atom in bond
  * **atom2** (*str*) – name of second atom in bond
  * **bond_type** (*int*) – type of bond: 1 (single), 2 (double), or ar (aromatic)
  * **bond_id** (*int*) – integer ID of bond

#### Property: `atom_names`

Get atom names in bond.

* **Returns:** tuple with names of atoms in bond.
* **Return type:** (str, str)
```

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

### File Testing Utilities

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/io.md

Utility functions for testing the existence and location of forcefield and other files.

```APIDOC
## POST /pdb2pqr.io.test_dat_file

### Description
Tests for the existence of a forcefield dat file, checking various name permutations.

### Method
POST

### Endpoint
/pdb2pqr.io.test_dat_file

### Parameters
#### Request Body
- **name** (str) - Required - The name of the dat file.

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

#### Response Example
```json
{
  "path": "/path/to/forcefield.dat"
}
```

#### Error Response (404)
- **error** (str) - "FileNotFoundError: file not found"

#### Error Example
```json
{
  "error": "FileNotFoundError: file not found"
}
```
```

```APIDOC
## POST /pdb2pqr.io.test_for_file

### Description
Tests for the existence of a file with a given name and type, checking various name permutations.

### Method
POST

### Endpoint
/pdb2pqr.io.test_for_file

### Parameters
#### Request Body
- **name** (str) - Required - The name of the file.
- **type_** (str) - Required - The type of the file.

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

#### Response Example
```json
{
  "path": "/path/to/somefile.txt"
}
```

#### Error Response (404)
- **error** (str) - "FileNotFoundError: if file not found"

#### Error Example
```json
{
  "error": "FileNotFoundError: if file not found"
}
```
```

```APIDOC
## POST /pdb2pqr.io.test_names_file

### Description
Tests for the existence of a .names file, which contains XML mapping information.

### Method
POST

### Endpoint
/pdb2pqr.io.test_names_file

### Parameters
#### Request Body
- **name** (str) - Required - The name of the forcefield.

### Response
#### Success Response (200)
- **path** (str) - The path to the found .names file.

#### Response Example
```json
{
  "path": "/path/to/forcefield.names"
}
```

#### Error Response (404)
- **error** (str) - "FileNotFoundError: file not found"

#### Error Example
```json
{
  "error": "FileNotFoundError: file not found"
}
```
```

```APIDOC
## POST /pdb2pqr.io.test_xml_file

### Description
Tests for the existence of an XML file, checking various name permutations.

### Method
POST

### Endpoint
/pdb2pqr.io.test_xml_file

### Parameters
#### Request Body
- **name** (str) - Required - The name of the dat file.

### Response
#### Success Response (200)
- **path** (str) - The path to the found XML file.

#### Response Example
```json
{
  "path": "/path/to/forcefield.xml"
}
```

#### Error Response (404)
- **error** (str) - "FileNotFoundError: file not found"

#### Error Example
```json
{
  "error": "FileNotFoundError: file not found"
}
```
```

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

### Mol2Bond Class Initialization

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/ligand.md

Initializes a MOL2 molecule bond object. Bonds are defined between two atoms with a specified bond type and ID.

```python
class pdb2pqr.ligand.mol2.Mol2Bond(atom1, atom2, bond_type, bond_id=0):
    def __init__(self, atom1, atom2, bond_type, bond_id=0):
        pass
```

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

### PDB2PQR psize Class: Psize

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/psize.md

Class for parsing input files and suggesting settings for grid calculations.

```APIDOC
## `class` pdb2pqr.psize.Psize

Class for parsing input files and suggesting settings.

### `__init__(cfac=1.7, fadd=20.0, space=0.5, gmemfac=200, gmemceil=400, ofrac=0.1, redfac=0.25)`

Initialize the Psize object.

#### Parameters:
* **cfac** (float) - factor by which to expand molecular dimensions to get coarse grid dimensions.
* **fadd** (float) - amount (in Angstroms) to add to molecular dimensions to get the fine grid dimensions.
* **space** (float) - desired fine mesh resolution (in Angstroms).
* **gmemfac** (float) - number of bytes per grid point required for a sequential multigrid calculation.
* **gmemceil** (float) - maximum memory (in MB) allowed for sequential multigrid calculation. Adjust this value to force the script to perform faster calculations (which require more parallelism).
* **ofrac** (float) - overlap factor between mesh partitions in parallel focusing calculation.
* **redfac** (float) - the maximum factor by which a domain dimension can be reduced during focusing.

### `parse_input(filename)`

Parse input structure file in PDB or PQR format.

#### Parameters:
* **filename** (str) - string with path to PDB- or PQR-format file.

### `parse_lines(lines)`

Parse the PQR/PDB lines.

#### Parameters:
* **lines** ([str]) - PDB/PQR lines to parse.

### `parse_string(structure)`

Parse the input structure as a string in PDB or PQR format.

#### Parameters:
* **structure** (str) - input structure as string in PDB or PQR format.

### `run_psize(filename)`

Parse input PQR file and set parameters.

#### Parameters:
* **filename** (str) - path of PQR file.

### `set_all()`

Set up all of the things calculated individually above.

### `set_center(maxlen, minlen)`

Compute molecular center.

#### Parameters:
* **maxlen** ([float, float, float]) - maximum molecule lengths.
* **minlen** ([float, float, float]) - minimum molecule lengths.

#### Returns:
center of molecule

#### Return type:
[float, float, float]

### `set_coarse_grid_dims(mol_length)`

Compute coarse mesh lengths.

#### Parameters:
* **mol_length** ([float, float, float]) - input molecule lengths.

#### Returns:
coarse grid dimensions

#### Return type:
[float, float, float]

### `set_fine_grid_dims(mol_length, coarse_length)`

Compute fine mesh lengths.

#### Parameters:
* **mol_length** ([float, float, float]) - input molecule lengths.
* **coarse_length** ([float, float, float]) - coarse grid lengths.

#### Returns:
fine grid lengths

#### Return type:
[float, float, float]

### `set_fine_grid_points(fine_length)`

Compute mesh grid points, assuming 4 levels in multigrid hierarchy.

#### Parameters:
* **fine_length** ([float, float, float]) - lengths of the fine grid.

#### Returns:
number of grid points in each direction

#### Return type:
[int, int, int]

### `set_focus(fine_length, nproc, coarse_length)`

Calculate the number of levels of focusing required for each processor subdomain.

#### Parameters:
* **fine_length** ([float, float, float]) - fine grid length.
* **nproc** ([int, int, int]) - number of processors in each dimension.
* **coarse_length** ([float, float, float]) - coarse grid length.

### `set_length(maxlen, minlen)`

Compute molecular dimensions, adjusting for zero-length values.

#### Parameters:
* **maxlen** ([float, float, float]) - maximum dimensions from molecule.
* **minlen** ([float, float, float]) - minimum dimensions from molecule.

#### Returns:
molecular dimensions

#### Return type:
[float, float, float]
```

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

### DBREF Record Initialization

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/pdb.md

Initializes the DBREF record, which provides cross-reference links between PDB sequences and database entries.

```APIDOC
## __init__(line)

### Description
Initialize by parsing a DBREF PDB line.

### Parameters
#### Request Body
- **line** (str) - Required - Line with PDB class

### Data Fields
- **id_code** (string) - ID code of this entry
- **chain_id** (string) - Chain identifier
- **seq_begin** (int) - Initial sequence number
- **insert_begin** (string) - Initial insertion code
- **seq_end** (int) - Ending sequence number
- **insert_end** (string) - Ending insertion code
- **database** (string) - Sequence database name
- **db_accession** (string) - Sequence database accession code
- **db_id_code** (string) - Sequence database identification code
- **db_seq_begin** (int) - Initial sequence number of database segment
- **db_ins_begin** (string) - Insertion code of initial residue
- **dbseq_end** (int) - Ending sequence number of database segment
- **db_ins_end** (string) - Insertion code of ending residue
```

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

### build_parser

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/psize.md

Constructs the argument parser for the psize module.

```APIDOC
## build_parser()

### Description
Build argument parser for the module.

### Response
- **Returns** (argparse.ArgumentParser) - argument parser
```

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

### main Function

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/inputgen.md

The main driver function for the input generation process.

```APIDOC
## `pdb2pqr.inputgen.main()` Function

### Description
Main driver

### Method
`main`

### Parameters
None

### Request Example
None

### Response
None
```

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

### Lint code with Ruff

Source: https://github.com/electrostatics/pdb2pqr/blob/main/CONTRIBUTING.md

Run essential and optional lints to ensure code quality before submission.

```bash
# The essential lints must pass
ruff check --config ruff_essential.toml .
# Follow the optional lints as much as possible
ruff check .
```

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

### pdb2pqr.quatfit.find_coordinates

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/quatfit.md

Driver for the quaternion file to obtain coordinates for a new atom.

```APIDOC
## pdb2pqr.quatfit.find_coordinates

### Description
Provide the coordinates as inputs and obtain the coordinates for the new atom as output.

### Parameters
#### Path Parameters
- **numpoints** (int) - Required - the number of points in each list
- **refcoords** ([[float, float, float]]) - Required - the reference coordinates
- **defcoords** ([[float, float, float]]) - Required - the definition coordinates
- **defatomcoords** ([[float, float, float]]) - Required - the definition coordinates for the atom to be placed in the reference frame

### Response
- **Returns** ([[float, float, float]]) - the coordinates of the new atom in the reference frame
```

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

### Execute Long Test Suite

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/releases.md

Runs PDB2PQR tests on a large set of PDB files, with an optional environment variable to limit the number of tests.

```bash
export TESTNUM=50; make test-long
```

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

### Water Optimization Methods

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/hydrogens.md

Provides methods for completing, finalizing, and attempting optimizations for water residues.

```APIDOC
## Water Optimization Methods

### Description
Methods for completing, finalizing, and attempting optimizations for water residues.

### complete()

#### Description
Complete the water optimization process.

### finalize()

#### Description
Finalize a water residue. Try to minimize conflict with nearby atoms by building away from them. Called when LPs are still present so as to account for their bonds.

### try_acceptor(acc, donor)

#### Description
The main driver for adding an LP to an optimizeable residue.

#### Parameters
##### Path Parameters
- **donor** (Atom) - Required - hydrogen bond donor
- **acc** (Atom) - Required - hydrogen bond acceptor

#### Returns
- **bool** - indication of whether addition was successful

### try_both(donor, acc, accobj)

#### Description
Attempt to optimize both the donor and the acceptor. If one is fixed, we only need to try one side. First try to satisfy the donor - if that's successful, try to satisfy the acceptor. An undo may be necessary if the donor is satisfied and the acceptor isn’t.

#### Parameters
##### Path Parameters
- **donor** (Atom) - Required - hydrogen bond donor
- **acc** (Atom) - Required - hydrogen bond acceptor
- **accobj** (Flip) - Required - a Flip-like hydrogen bond structure object

#### Returns
- **bool** - indication of whether hydrogen was added

### try_donor(donor, acc)

#### Description
Add hydrogen to an optimizable residue.

#### Parameters
##### Path Parameters
- **donor** (Atom) - Required - hydrogen bond donor
- **acc** (Atom) - Required - hydrogen bond acceptor

#### Returns
- **bool** - indication of whether addition was successful
```

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

### CRYST1 Record Initialization

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/pdb.md

Initializes the CRYST1 record by parsing a PDB line to extract unit cell dimensions and space group information.

```APIDOC
## __init__(line)

### Description
Initialize by parsing a CRYST1 PDB line.

### Parameters
#### Request Body
- **line** (str) - Required - Line with PDB class

### Data Fields
- **a** (float) - a (Angstroms)
- **b** (float) - b (Angstroms)
- **c** (float) - c (Angstroms)
- **alpha** (float) - alpha (degrees)
- **beta** (float) - beta (degrees)
- **gamma** (float) - gamma (degrees)
- **space_group** (string) - Space group
- **z** (int) - Z value
```

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

### Run PDB2PQR Tests

Source: https://github.com/electrostatics/pdb2pqr/blob/main/tests/README.md

Execute all tests for the PDB2PQR project using pytest. Note that some tests can take a significant amount of time to complete.

```bash
$ python -m pytest
```

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

### Biomolecule Class Initialization

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/biomolecule.md

Initializes a Biomolecule object using a list of parsed PDB lines and a topology definition.

```APIDOC
## __init__ Biomolecule

### Description
Initialize using parsed PDB file

### Parameters
* **pdblist** (*list*) – list of objects from `pdb` from lines of PDB file
* **definition** ([*Definition*](definitions.md#pdb2pqr.definitions.Definition)) – topology definition object
```

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

### DefinitionHandler Class

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/definitions.md

Handles XML file content parsing for topology definitions.

```APIDOC
## DefinitionHandler Class

### Description
Handles definition XML file content parsing.

### Methods
- **characters(text)**: Parse text data in XML.
- **endElement(name)**: End XML element parsing. Raises KeyError for invalid names or RuntimeError for format issues.
- **startElement(name, _)**: Start XML element parsing.
```

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

### Mol2Atom Class Initialization

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/ligand.md

Initializes a MOL2 molecule atom object. This class represents atoms within a MOL2 file.

```python
class pdb2pqr.ligand.mol2.Mol2Atom:
    def __init__(self):
        pass
```

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

### pdb2pqr.ligand.mol2.Mol2Molecule

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/ligand.md

Methods for managing Tripos MOL2 molecule structures, including parsing, charge assignment, and structural analysis.

```APIDOC
## pdb2pqr.ligand.mol2.Mol2Molecule

### Description
Represents a Tripos MOL2 molecule and provides methods to parse files, assign charges/radii, and identify structural features like torsions and rings.

### Methods
- **assign_charges()**: Assign charges to atoms in molecule.
- **assign_parameters(primary_dict, secondary_dict)**: Assign charges and radii to atoms in molecule.
- **assign_radii(primary_dict, secondary_dict)**: Assign radii to atoms in molecule.
- **find_atom_torsions(start_atom)**: Set the torsion angles that start with this atom.
- **find_new_rings(path, rings, level=0)**: Find new rings in molecule.
- **parse_atoms(mol2_file)**: Parse @<TRIPOS>ATOM section of file.
- **parse_bonds(mol2_file)**: Parse @<TRIPOS>BOND section of file.
- **read(mol2_file)**: Routines for reading MOL2 file.
- **rotate_to_smallest(path)**: Rotate cycle path so that it begins with the smallest node.
- **set_rings()**: Set all rings in molecule.
- **set_torsions()**: Set all torsions in molecule.
```

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

### Ligand Module API

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/extending.md

API endpoints for handling ligand structures and properties.

```APIDOC
## Ligand API

### Description
Provides functionalities for processing ligand data, including atom radius assignment.

### Methods
- `pdb2pqr.ligand` (module level)
- `Mol2Atom.assign_radius()`
```

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

### pdb2pqr.pdb.PDB

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/pdb.md

Represents a PDB entry, initialized by parsing a line.

```APIDOC
## PDB Class

### Description
Represents a PDB entry, initialized by parsing a line.

### Method
__init__

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Request Example
None

### Response
None

### Error Handling
None
```

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

### Reading QCD Files

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/io.md

Functions for reading data from QCD files.

```APIDOC
## POST /pdb2pqr.io.read_qcd

### Description
Reads data from a QCD file (UHDB QCARD format).

### Method
POST

### Endpoint
/pdb2pqr.io.read_qcd

### Parameters
#### Request Body
- **qcd_file** (file) - Required - A file object ready for reading as text.

### Response
#### Success Response (200)
- **atoms** (list) - A list of atoms read from the file.

#### Response Example
```json
{
  "atoms": [
    {
      "serial": 1,
      "name": "CA",
      "residue_name": "ALA",
      "chain_id": "A",
      "residue_id": 1,
      "insertion_code": "",
      "x": 1.0,
      "y": 2.0,
      "z": 3.0,
      "occupancy": 1.0,
      "temperature_factor": 20.0,
      "element": "C",
      "charge": 0.5
    }
  ]
}
```
```

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

### Flip Class for Flippable Residues

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/hydrogens.md

Manages the optimization of flippable residues, including initialization, completion, and state finalization.

```APIDOC
## Class: pdb2pqr.hydrogens.structures.Flip

### Description
The holder for optimization of flippable residues.

### Methods

#### __init__(residue, optinstance, routines)

Initialize a potential flip. Rather than flipping the given residue back and forth, take each atom that would be flipped and pre-flip it, making a new `*FLIP` atom in its place.

* **Parameters:**
  * **residue** (*Residue*) – the residue to flip
  * **optinstance** (*OptimizationHandler*) – the optimization instance containing information about what to optimize
  * **routines** (*Debump*) – debumping routines object

#### complete()

Complete the flippable residue optimization. Call the [`finalize()`](#pdb2pqr.hydrogens.structures.Flip.finalize) function, and then rename all `FLIP` atoms back to their standard names.

#### finalize()

Finalize a flippable group back to its original state. Since the original atoms are now `*FLIP`, it deletes the `*` atoms and renames the `*FLIP` atoms back to `*`.

#### fix_flip(bondatom)

Remove atoms if hydrogen bond has been found for specified atom. If bondatom is of type `*FLIP`, remove all `*` atoms, otherwise remove all `*FLIP` atoms.

* **Parameters:**
  * **bondatom** (*Atom*) – atom to flip

#### try_acceptor(acc, donor)

Add a lone pair to an optimizable residue.

* **Parameters:**
  * **acc** (*Atom*) – hydrogen bond acceptor
  * **donor** (*Atom*) – hydrogen bond donor
* **Returns:** indication of whether addition was successful
* **Return type:** bool
```

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

### Input Generation API

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/extending.md

API endpoints for generating input files for PDB2PQR.

```APIDOC
## Input Generation API

### Description
Provides functionalities for initializing and managing input data for PDB2PQR calculations.

### Methods
- `Elec._init_()`
- `Input.dump_pickle()`
```

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

### Main Functionality API

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/extending.md

Core API endpoints for PDB2PQR main functionalities.

```APIDOC
## Main API

### Description
Core functionalities of PDB2PQR, including argument parsing, water removal, file format conversions, and printing PDB/PQR files.

### Methods
- `build_main_parser()`
- `drop_water()`
- `dx_to_cube()`
- `non_trivial()`
- `print_pdb()`
- `print_pqr()`
- `transform_arguments()`
```

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

### pdb2pqr.cif.keywds

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/cif.md

Handles the KEYWDS block in CIF files, returning parsed CONECT objects and any unparsed data.

```APIDOC
## pdb2pqr.cif.keywds(block)

### Description
Handle KEYWDS block.

### Parameters
#### Path Parameters
- **block** (str) – PDBx data block

### Returns
(array of pdb.conect objects, array of things that did not parse)

### Return type
([[pdb.CONECT](pdb.md#pdb2pqr.pdb.CONECT)], [str])
```

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

### Run PDB2PKA

Source: https://github.com/electrostatics/pdb2pqr/blob/main/docs/source/api/run.md

Executes the PDB2PKA tool to determine protonation states of proteins.

```APIDOC
## pdb2pka.run.run_pdb2pka

### Description
Run PDB2PKA

### Method
Not specified (assumed to be a function call within a Python environment)

### Parameters
- **ph** (float) - Description not specified
- **force_field** (string) - Description not specified
- **pdb_list** (list) - Description not specified
- **ligand** (string) - Description not specified
- **pdb2pka_params** (object) - Description not specified
```