fixed active sites

lmdu · Jun 19, 2024 · dc3a26f · dc3a26f
1 parent 86d8797
commit dc3a26f
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Showing 8 changed files with 44 additions and 8 deletions.
diff --git a/docs/_static/green.png b/docs/_static/green.png
diff --git a/docs/_static/poseinter.png b/docs/_static/poseinter.png
diff --git a/docs/docking.rst b/docs/docking.rst
@@ -61,7 +61,7 @@ Go to **Run** menu -> **AutoDock4** to start AutoDock4 docking. You will be prom
 
 .. note::
 
-	How to select receptor and ligand preparation tools (view `Molecular Preparation`_). How to set parameters for AutoDock4 (view `Autodock4 Settings`_)
+	How to select receptor and ligand preparation tools (view **Molecular Preparation** section). How to set parameters for AutoDock4 (view **Global Settings** -> **Autodock4 Settings** section)
 
 Run AutoDock Vina
 ~~~~~~~~~~~~~~~~~
@@ -78,7 +78,9 @@ Go to **Run** menu -> **AutoDock Vina** to start Autodock Vina. You will be prom
 
 #. Click **OK** to start docking tasks.
 
-How to select receptor and ligand preparation tools (view `Molecular Preparation`_). How to set parameters for AutoDock Vina (view `Autodock Vina Settings`_)
+.. note::
+
+	How to select receptor and ligand preparation tools (view **Molecular Preparation** section). How to set parameters for AutoDock Vina (view **Global Settings** -> **Autodock Vina Settings** section)
 
 Run QuickVina-W
 ~~~~~~~~~~~~~~~
@@ -95,12 +97,14 @@ Go to **Run** menu -> **QuickVina-W** to start QuickVina. You will be prompted w
 
 #. Click **OK** to start docking tasks.
 
-How to select receptor and ligand preparation tools (view `Preparation Tools`_). How to set parameters for QuickVina-W (view `QuickVina Settings`_)
+.. note::
+
+	How to select receptor and ligand preparation tools (view **Preparation Tools** section). How to set parameters for QuickVina-W (view **Global Settings** -> **QuickVina Settings** section)
 
 Fix Receptor
 ------------
 
-Sometimes, your receptor PDB file may have some problems during molecular docking. You can use `PDBFixer <https://github.com/openmm/pdbfixer>`_ or `PDB2PQR <https://github.com/Electrostatics/pdb2pqr>`_ to fix the PDB file. The parameter settings can be found in `PDBFixer Settings`_ and `PDB2PQR Settings`_.
+Sometimes, your receptor PDB file may have some problems during molecular docking. You can use `PDBFixer <https://github.com/openmm/pdbfixer>`_ or `PDB2PQR <https://github.com/Electrostatics/pdb2pqr>`_ to fix the PDB file. The parameter settings can be found in **Gobal Settings** -> **PDBFixer Settings** and **PDB2PQR Settings**.
 
 .. rst-class:: wy-text-center
 

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -81,6 +81,12 @@ Go to `https://qvina.github.io/ <https://qvina.github.io/>`_ page, and then clic
 
 #. Go to `https://github.com/lmdu/dockey/releases <https://github.com/lmdu/dockey/releases>`_ page, click on ``Dockey-version-ubuntu.deb`` to download it. Then double click the downloaded installer to install the program following the on-screen instructions.
 
+#. You can also install Dockey using command line tool like this:
+
+	.. code:: shell
+
+		sudo dpkg -i Dockey-version-ubuntu.deb
+
 #. Or, you can click on ``Dockey-version-ubuntu.AppImage`` to download it and run it like this:
 
 	.. code:: shell

diff --git a/docs/pose.rst b/docs/pose.rst
@@ -80,11 +80,31 @@ You can click one pose in best pose table or job pose table to view the 3D struc
 Preset Active Binding Sites
 ---------------------------
 
-You can right click a receptor in molecular list and then go to menu **Preset Active Binding Sites** to open a dialog. You can select several residues as active binding sites to see whether ligands can be docked to them. If the ligand can be docked to preset binding sites, the pose in table will has green background color.
+Before starting docking, you can right click a receptor in molecular list and then go to menu **Preset Active Binding Sites** to open a dialog. You can select several residues as active binding sites to see whether ligands can be docked to them. If the ligand can be docked to preset binding sites, the pose in table will has green background color.
+
+.. rst-class:: wy-text-center
+
+	|posegreen|
+
+You can right click the pose with green background, and go to **view details** to view interactions.
+
+.. rst-class:: wy-text-center
+
+	|poseinter|
+
 
 .. |bestpose| image:: _static/bestpose.png
+
 .. |jobpose| image:: _static/jobpose.png
+
 .. |posemenu| image:: _static/posemenu.png
 	:width: 250
+
 .. |poseview| image:: _static/poseview.png
+	:width: 500
+
+.. |posegreen| image:: _static/posegreen.png
+	:width: 500
+
+.. |poseinter| image:: _static/poseinter.png
 	:width: 500
diff --git a/docs/settings.rst b/docs/settings.rst
@@ -95,4 +95,10 @@ Go to **Edit** -> **Global Settings** -> **PDB2PQR** -> to set parameters for PD
 	:width: 500
 
 .. |meekolig| image:: _static/meekolig.png
-	:width: 500
+	:width: 500
+
+.. |pdbfixer| image:: _static/pdbfixer.png
+	:width: 500
+
+.. |pdb2pqr| image:: _static/pdb2pqr.png
+	:width: 500
diff --git a/src/config.py b/src/config.py
@@ -19,7 +19,7 @@
 
 DOCKEY_VERSION = "1.0.0"
 
-DOCKEY_BUILD = "240612"
+DOCKEY_BUILD = "240619"
 
 COMPAT_VERSION = "1.0.0"
 

diff --git a/src/table.py b/src/table.py
@@ -1365,7 +1365,7 @@ def view_details(self):
 
 		if pose.actives:
 			rows = []
-			for active in pose.actives.split(','):
+			for active in pose.actives.split(';'):
 				itype, chain, res, num = active.split(':')
 				rows.append("<tr><td>{}</td><td>{}</td><td>{}</td><td>{}</td></tr>".format(
 					itype, chain, res, num