From a08ed1c2190e34c0d87a35c33de5ac0da26eb9d6 Mon Sep 17 00:00:00 2001
From: Pau Andrio <andriopau@gmail.com>
Date: Thu, 17 Oct 2024 14:15:23 +0200
Subject: [PATCH] Fix typing errors

---
 biobb_pmx/docs/source/command_line.md  | 46 +++++++++++++++++++-------
 biobb_pmx/pmxbiobb/pmxanalyse.py       |  1 -
 biobb_pmx/pmxbiobb/pmxligand_hybrid.py |  5 ++-
 3 files changed, 36 insertions(+), 16 deletions(-)

diff --git a/biobb_pmx/docs/source/command_line.md b/biobb_pmx/docs/source/command_line.md
index a05ca62..dd6bf80 100644
--- a/biobb_pmx/docs/source/command_line.md
+++ b/biobb_pmx/docs/source/command_line.md
@@ -13,18 +13,40 @@ Command:
 ```python
 pmxligand_hybrid -h
 ```
-    /Users/pau/mambaforge/envs/dev38/bin/pmxligand_hybrid: line 3: Module containing the PMX ligand_hybrid class and the command line interface.: command not found
-    /Users/pau/mambaforge/envs/dev38/bin/pmxligand_hybrid: line 4: import: command not found
-    /Users/pau/mambaforge/envs/dev38/bin/pmxligand_hybrid: line 5: import: command not found
-    from: can't read /var/mail/pathlib
-    /Users/pau/mambaforge/envs/dev38/bin/pmxligand_hybrid: line 7: import: command not found
-    /Users/pau/mambaforge/envs/dev38/bin/pmxligand_hybrid: line 8: import: command not found
-    from: can't read /var/mail/typing
-    from: can't read /var/mail/biobb_common.generic.biobb_object
-    from: can't read /var/mail/biobb_common.configuration
-    from: can't read /var/mail/biobb_common.tools.file_utils
-    /Users/pau/mambaforge/envs/dev38/bin/pmxligand_hybrid: line 15: syntax error near unexpected token `('
-    /Users/pau/mambaforge/envs/dev38/bin/pmxligand_hybrid: line 15: `class Pmxligand_hybrid(BiobbObject):'
+    usage: pmxligand_hybrid [-h] [-c CONFIG] --input_structure1_path INPUT_STRUCTURE1_PATH --input_structure2_path INPUT_STRUCTURE2_PATH --input_topology1_path INPUT_TOPOLOGY1_PATH --input_topology2_path INPUT_TOPOLOGY2_PATH --output_structure1_path OUTPUT_STRUCTURE1_PATH --output_structure2_path OUTPUT_STRUCTURE2_PATH --output_topology1_path OUTPUT_TOPOLOGY1_PATH --output_topology2_path OUTPUT_TOPOLOGY2_PATH --output_log_path OUTPUT_LOG_PATH [--input_scaffold1_path INPUT_SCAFFOLD1_PATH] [--input_scaffold2_path INPUT_SCAFFOLD2_PATH] [--input_pairs_path INPUT_PAIRS_PATH]
+    
+    Run PMX ligand hybrid module
+    
+    optional arguments:
+      -h, --help            show this help message and exit
+      -c CONFIG, --config CONFIG
+                            This file can be a YAML file, JSON file or JSON string
+      --input_scaffold1_path INPUT_SCAFFOLD1_PATH
+                            Path to the index of atoms to consider for the ligand structure 1
+      --input_scaffold2_path INPUT_SCAFFOLD2_PATH
+                            Path to the index of atoms to consider for the ligand structure 2
+      --input_pairs_path INPUT_PAIRS_PATH
+                            Path to the input atom pair mapping.
+    
+    required arguments:
+      --input_structure1_path INPUT_STRUCTURE1_PATH
+                            Path to the input ligand structure file 1
+      --input_structure2_path INPUT_STRUCTURE2_PATH
+                            Path to the input ligand structure file 2
+      --input_topology1_path INPUT_TOPOLOGY1_PATH
+                            Path to the input ligand topology file 1
+      --input_topology2_path INPUT_TOPOLOGY2_PATH
+                            Path to the input ligand topology file 2
+      --output_structure1_path OUTPUT_STRUCTURE1_PATH
+                            Path to the output ligand structure file 1
+      --output_structure2_path OUTPUT_STRUCTURE2_PATH
+                            Path to the output ligand structure file 2
+      --output_topology1_path OUTPUT_TOPOLOGY1_PATH
+                            Path to the output ligand topology file 1
+      --output_topology2_path OUTPUT_TOPOLOGY2_PATH
+                            Path to the output ligand topology file 2
+      --output_log_path OUTPUT_LOG_PATH
+                            Path to the log file
 ### I / O Arguments
 Syntax: input_argument (datatype) : Definition
 
diff --git a/biobb_pmx/pmxbiobb/pmxanalyse.py b/biobb_pmx/pmxbiobb/pmxanalyse.py
index 6a16941..e6af81d 100755
--- a/biobb_pmx/pmxbiobb/pmxanalyse.py
+++ b/biobb_pmx/pmxbiobb/pmxanalyse.py
@@ -5,7 +5,6 @@
 from typing import Optional
 from pathlib import Path
 import shutil
-from typing import Optional
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
 from biobb_common.tools import file_utils as fu
diff --git a/biobb_pmx/pmxbiobb/pmxligand_hybrid.py b/biobb_pmx/pmxbiobb/pmxligand_hybrid.py
index f7856aa..5781f1c 100755
--- a/biobb_pmx/pmxbiobb/pmxligand_hybrid.py
+++ b/biobb_pmx/pmxbiobb/pmxligand_hybrid.py
@@ -1,4 +1,4 @@
-# !/usr/bin/env python3
+#!/usr/bin/env python3
 
 """Module containing the PMX ligand_hybrid class and the command line interface."""
 import os
@@ -7,7 +7,6 @@
 import shutil
 import argparse
 from typing import Optional
-from typing import Optional
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
 from biobb_common.tools.file_utils import launchlogger
@@ -221,7 +220,7 @@ def pmxligand_hybrid(input_structure1_path: str, input_structure2_path: str, inp
                             output_topology_path=output_topology_path, output_atomtypes_path=output_atomtypes_path,
                             input_scaffold1_path=input_scaffold1_path, input_scaffold2_path=input_scaffold2_path,
                             input_pairs_path=input_pairs_path,
-                            properties=properties, **kwargs).launch()
+                            properties=properties).launch()
 
 
 def main():