v0.2.0

docs/index.md

@@ -40,4 +40,20 @@
 Now, lazydock only support pypi install:  
 ```
 pip install lazydock
-```
+```
+
+
+## Contains
+
+### pymol utils - pml
+- [autodock](pml/autodock_utils.md): parse autodock results to pdb pose.  
+- [interaction](pml/interaction_utils.md): calculate interactions between receptor and poses.  
+- [server](pml/server.md): provide a server-client interface to communicate with pymol.  
+- [shader](pml/shader.md): provide a shader for pymol.  
+
+### pyroseeta utils - pyrt
+- [pose](pyrt/pose.md): provide a wrapper pose class to opt pose.  
+
+
+## release note
+- [0.2.0](release_note/0.2.0.md)

docs/pml/server.md

@@ -0,0 +1,102 @@
+# Overview
+This module provides a client-server architecture for interacting with PyMOL, a molecular visualization system. The `VServer` class runs on the server side, listening for connections and executing PyMOL commands sent by the client. The `VClient` class is used on the client side to send commands to the server. The `PymolAPI` class acts as a wrapper for PyMOL's API, providing a convenient interface for command execution.
+
+# Classes
+## `PymolAPI`
+### Description
+A wrapper class for PyMOL's API, allowing for the execution of PyMOL commands (`cmd`) or API functions (`api`) through a client-server architecture.
+
+### Methods
+#### `send_action(api: str, fn: str, *args, **kwargs) -> Any`
+##### Description
+Sends an action to the server to be executed.
+
+##### Parameters
+- `api`: The API type ('cmd' or 'api').
+- `fn`: The function name to execute.
+- `*args`: Positional arguments for the function.
+- `**kwargs`: Keyword arguments for the function.
+
+##### Returns
+- `Any`: The return value of the executed function.
+
+## `VServer`
+### Description
+A server class that listens for connections from clients and executes PyMOL commands sent by the clients.
+
+### Methods
+#### `copy_logs() -> List[str]`
+##### Description
+Copies the server logs.
+
+##### Returns
+- `List[str]`: A list of log strings.
+
+#### `copy_new_logs() -> List[str]`
+##### Description
+Copies new logs since the last check.
+
+##### Returns
+- `List[str]`: A list of new log strings.
+
+#### `_add_log(log: str, verbose: bool = False) -> None`
+##### Description
+Adds a log entry.
+
+##### Parameters
+- `log`: The log message.
+- `verbose`: Whether to print the log message.
+
+#### `_recvall(sock: socket.socket, count: int)`
+##### Description
+Receives all data from the socket.
+
+##### Parameters
+- `sock`: The socket object.
+- `count`: The number of bytes to receive.
+
+#### `_sendall(scok: socket.socket, data: bytes) -> None`
+##### Description
+Sends all data to the socket.
+
+##### Parameters
+- `scok`: The socket object.
+- `data`: The data to send.
+
+#### `_run_server() -> None`
+##### Description
+The main loop of the server, running in a separate thread, listening for connections and executing commands.
+
+## `VClient`
+### Description
+A client class that connects to the server and sends commands to be executed in PyMOL.
+
+### Methods
+#### `send_action(api: str, fn: str, *args, **kwargs) -> Any`
+##### Description
+Sends an action to the server to be executed.
+
+##### Parameters
+- `api`: The API type ('cmd' or 'api').
+- `fn`: The function name to execute.
+- `*args`: Positional arguments for the function.
+- `**kwargs`: Keyword arguments for the function.
+
+##### Returns
+- `Any`: The return value of the executed function.
+
+#### `sen_quit() -> None`
+##### Description
+Sends a quit command to the server and closes the connection.
+
+## Functions
+### `_test_server()`
+##### Description
+A test function to start the server and print logs.
+
+### `_test_client()`
+##### Description
+A test function to start the client, connect to the server, and execute a PyMOL command.
+
+# Main Execution
+The provided code includes a main execution block that starts both the server and client in separate processes, allowing for testing of the client-server architecture.

docs/pml/shader.md

@@ -0,0 +1,175 @@
+# Overview
+This module provides a set of classes and functions designed to coloring molecular in PyMOL. It includes classes to represent atoms and residues with associated data, and a `Shader` class to apply color gradients based on calculated interaction values.
+
+# Functions
+## `get_c_value()`
+### Description
+Retrieves the `c_value` for a `ShaderRes` instance. If `c_value` is not set, it calculates the sum of `c_values` of its atoms.
+
+### Parameters
+- None
+
+### Returns
+- `float`: The `c_value` of the residue.
+
+### Notes
+- The `c_value` is only recalculated if `atoms` is updated after the initial calculation.
+
+# Classes
+## `ShaderAtom`
+### Description
+A data class representing an atom in a molecular model with properties such as model, chain, residue index, element, and an optional `c_value` for coloring.
+
+### Members
+- `model`: The model name.
+- `chain`: The chain identifier.
+- `resi`: The residue index.
+- `elem`: The element type.
+- `index`: The atom index.
+- `c_value`: An optional float value associated with the atom.
+- `alpha`: An optional float representing the opacity.
+
+## `ShaderRes`
+### Description
+A data class representing a residue in a molecular model, containing a list of `ShaderAtom` instances and optional `c_value` and `alpha` properties.
+
+### Methods
+#### `get_c_value()`
+##### Description
+Retrieves the `c_value` for the residue. If not set, it calculates the sum of `c_values` of its atoms.
+
+##### Parameters
+- None
+
+##### Returns
+- `float`: The `c_value` of the residue.
+
+### Members
+- `atoms`: A list of `ShaderAtom` instances.
+- `c_value`: An optional float value associated with the residue.
+- `alpha`: An optional float representing the opacity.
+
+## `ShaderValues`
+### Description
+A class to manage and retrieve `c_values` for chains, residues, and atoms in a molecular model.
+
+### Methods
+#### `get_c_value(chain: str, resi: int, atom_index: int = None) -> float`
+##### Description
+Retrieves the `c_value` for a specified chain, residue, and optionally an atom.
+
+##### Parameters
+- `chain`: The chain identifier.
+- `resi`: The residue index.
+- `atom_index`: The optional atom index.
+
+##### Returns
+- `float`: The `c_value` for the specified atom or residue.
+
+#### `get_all_c_values(level: str = 'res') -> list`
+##### Description
+Retrieves all `c_values` for the specified level (residue or atom).
+
+##### Parameters
+- `level`: The level of detail ('res' for residue, 'atom' for atom).
+
+##### Returns
+- `list`: A list of tuples containing model, chain, residue index, atom index (if applicable), alpha, and `c_value`.
+
+#### `from_interaction_df(df: Union[str, pd.DataFrame], model: str, sum_axis: int = 0) -> ShaderValues`
+##### Description
+Loads `c_values` from an interaction data frame.
+
+##### Parameters
+- `df`: The data frame or path to the data frame.
+- `model`: The model name.
+- `sum_axis`: The axis along which to sum the data frame.
+
+##### Returns
+- `ShaderValues`: The instance itself after loading the data.
+
+## `Shader`
+### Description
+A class to apply color gradients to molecular models in PyMOL based on `c_values`.
+
+### Methods
+#### `get_col_from_c_value(c_value: float) -> (tuple, str)`
+##### Description
+Returns the RGBA color and a color name for a given `c_value`.
+
+##### Parameters
+- `c_value`: The `c_value` for which to generate the color.
+
+##### Returns
+- `tuple`: The RGBA color.
+- `str`: The color name.
+
+#### `_get_rgba_col_name(c_value: float, _col_name: str = None, _cmd = None) -> (tuple, str)`
+##### Description
+Generates the RGBA color and a color name for a given `c_value`, storing it globally if it doesn't exist.
+
+##### Parameters
+- `c_value`: The `c_value` for which to generate the color.
+- `_col_name`: An optional predefined color name.
+- `_cmd`: The PyMOL command module.
+
+##### Returns
+- `tuple`: The RGBA color.
+- `str`: The color name.
+
+#### `create_colors_in_pml(values: ShaderValues, level: str = 'res', names: List[str] = None, _cmd = None)`
+##### Description
+Creates colors in PyMOL for each `c_value` in the provided `ShaderValues`.
+
+##### Parameters
+- `values`: The `ShaderValues` instance.
+- `level`: The level of detail ('res' for residue, 'atom' for atom).
+- `names`: An optional list of predefined color names.
+- `_cmd`: The PyMOL command module.
+
+#### `auto_scale_norm(c_values)`
+##### Description
+Automatically scales the normalization based on the provided `c_values`.
+
+##### Parameters
+- `c_values`: A list of `c_values` to use for scaling.
+
+#### `apply_shader_values(values: ShaderValues, level: str = 'res', auto_detect_vlim: bool = True, alpha_mode: str = None, _cmd = None)`
+##### Description
+Applies the shader values to a molecular model in PyMOL.
+
+##### Parameters
+- `values`: The `ShaderValues` instance.
+- `level`: The level of detail ('res' for residue, 'atom' for atom).
+- `auto_detect_vlim`: Whether to automatically detect the color limits.
+- `alpha_mode`: An optional transparency mode for PyMOL.
+- `_cmd`: The PyMOL command module.
+
+#### `apply_shader_values_to_selection(selection, c_value: float = None, alpha: float = 1.0, alpha_mode: str = None, _cmd = None)`
+##### Description
+Applies the shader values to a specific selection in PyMOL.
+
+##### Parameters
+- `selection`: The selection to which the shader values will be applied.
+- `c_value`: An optional `c_value` for the color.
+- `alpha`: The opacity level.
+- `alpha_mode`: An optional transparency mode for PyMOL.
+- `_cmd`: The PyMOL command module.
+
+#### `apply_shader_values_to_sele(select_expression: str, c_value: float = None, alpha: float = 1.0, alpha_mode: str = None, _cmd = None)`
+##### Description
+Applies the shader values to a selection expression in PyMOL.
+
+##### Parameters
+- `select_expression`: The selection expression to which the shader values will be applied.
+- `c_value`: An optional `c_value` for the color.
+- `alpha`: The opacity level.
+- `alpha_mode`: An optional transparency mode for PyMOL.
+- `_cmd`: The PyMOL command module.
+
+#### `__repr__(self)`
+##### Description
+Returns a string representation of the `Shader` instance.
+
+##### Returns
+- `str`: The string representation.

docs/release_notes/0.2.0.md

@@ -0,0 +1,53 @@
+<!--
+ * @Date: 2024-09-04 21:34:10
+ * @LastEditors: BHM-Bob [email protected]
+ * @LastEditTime: 2024-09-04 21:41:45
+ * @Description: 
+-->
+2024/9/4 21:31:18
+
+
+## Focus on  
+1. Add pml.shader and pml.server sub-module
+
+
+## What's New  
+- addon: add lazydock\pml\shader.py  
+- addon: lazydock\pml\server.py  
+- addon: add lazydock_pymol_plugin\lazy_plot.py  
+- addon: lazydock_pymol_plugin\__init__.py: extend new cmd: start_lazydock_server  
+- addon: lazydock\pml\shader.py: ShaderValues: add method from_interaction_df  
+- addon: lazydock\pml\shader.py: Shader: add __repr__ method  
+- addon: lazydock\pml\shader.py: Shader: add method auto_scale_norm, apply_shader_values_to_selection, apply_shader_values_to_sele  
+
+
+## Minor Addon
+- minor-addon: lazydock\pml\shader.py: Shader: apply_shader_values: add alpha_mode argument  
+- minor-addon: lazydock\pml\shader.py: Shader: support global_name2col and norm  
+- minor-addon: lazydock\pml\server.py: add data-length to enssure server can read all data  
+- minor-addon: lazydock\pml\shader.py: add _cmd option  
+- minor-addon: lazydock\pml\server.py: VClient: send_action: support return the return value of an action  
+- minor-addon: lazydock_pymol_plugin\__init__.py: start_lazydock_server: add start log  
+
+
+## BUG-FIX  
+- fix-bug: lazydock\pml\shader.py: from_interaction_df: skip first row now  
+- fix-bug: lazydock\pml\shader.py: fix _cmd argument passing  
+
+
+## CODE-FIX 
+- fix-code: lazydock\pml\interaction_utils.py: add __all__  
+- fix-code: lazydock_pymol_plugin\main.py: GUILauncher: add lazy_plot_tab  
+- fix-code: lazydock_pymol_plugin\lazy_plot.py: move pymol import to dev code  
+
+
+## Remove  
+None or a little.  
+
+
+## Other Changes  
+None or a little.   
+
+
+## Details  
+**完整的更新日志**: https://gitee.com/bhm-bob/LazyDock/commits/v0.2.0   

docs/source/conf.py

@@ -1,7 +1,7 @@
 '''
 Date: 2024-08-24 22:24:47
 LastEditors: BHM-Bob [email protected]
-LastEditTime: 2024-08-27 10:30:53
+LastEditTime: 2024-09-04 21:43:47
 Description: 
 '''
 # Configuration file for the Sphinx documentation builder.
@@ -12,8 +12,8 @@
 copyright = '2024, BHM-Bob'
 author = 'BHM-Bob G'
 
-release = '0.1.0'
-version = '0.1.0'
+release = '0.2.0'
+version = '0.2.0'
 
 # -- General configuration
 

lazydock/__version__.py

@@ -2,8 +2,8 @@
 __title__ = "lazydock"
 __description__ = "Lazy Dock"
 __url__ = "https://github.com/BHM-Bob/LazyDock"
-__version__ = "0.1.0"
-__build__ = "20240827_0"
+__version__ = "0.2.0"
+__build__ = "20240904_0"
 __author__ = "BHM-Bob G"
 __author_email__ = "[email protected]"
 __license__ = "MIT"