Iamkaant at 22:30, 6 October 2025

2025-10-06T22:30:36Z

← Older revision		Revision as of 22:30, 6 October 2025
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	== Installation ==		== Installation ==

	You can find the program in {{code\|/mnt/nfs/exa/work/ak87/UCSF/SCRIPTS/SHOW_STRUCTURES/align-2d-struct-highlight_interactive.py}}		You can find the program in <code>/mnt/nfs/exa/work/ak87/UCSF/SCRIPTS/SHOW_STRUCTURES/align-2d-struct-highlight_interactive.py</code>

	=== Requirements ===		=== Requirements ===

Iamkaant: added path to the program

2025-10-06T22:28:59Z

added path to the program

← Older revision		Revision as of 22:28, 6 October 2025
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	== Installation ==		== Installation ==

			You can find the program in {{code\|/mnt/nfs/exa/work/ak87/UCSF/SCRIPTS/SHOW_STRUCTURES/align-2d-struct-highlight_interactive.py}}

	=== Requirements ===		=== Requirements ===

Iamkaant: Created page with "= Interactive Molecular Structure Alignment Application = A PyQt5-based interactive tool for aligning and visualizing molecular analogs with customizable highlighting, transformations, and high-resolution export capabilities. == Table of Contents == * Installation * Quick Start * Features * User Interface * Workflows * File Formats * #Troubleshooting|Troubleshooting..."

2025-10-06T21:02:01Z

Created page with "= Interactive Molecular Structure Alignment Application = A PyQt5-based interactive tool for aligning and visualizing molecular analogs with customizable highlighting, transformations, and high-resolution export capabilities. == Table of Contents == * Installation * Quick Start * Features * User Interface * Workflows * File Formats * #Troubleshooting|Troubleshooting..."

New page

= Interactive Molecular Structure Alignment Application =

A PyQt5-based interactive tool for aligning and visualizing molecular analogs with customizable highlighting, transformations, and high-resolution export capabilities.

== Table of Contents ==

* [[#Installation|Installation]]
* [[#Quick Start|Quick Start]]
* [[#Features|Features]]
* [[#User Interface|User Interface]]
* [[#Workflows|Workflows]]
* [[#File Formats|File Formats]]
* [[#Troubleshooting|Troubleshooting]]
* [[#Tips and Best Practices|Tips and Best Practices]]

== Installation ==

=== Requirements ===

* Python 3.7 or higher
* RDKit (chemistry toolkit)
* PyQt5 (GUI framework)
* Pillow (image processing)

=== Step-by-Step Installation ===

==== Using Conda (Recommended) ====

<syntaxhighlight lang="bash">
# Create a new conda environment
conda create -n mol_aligner python=3.9

# Activate the environment
conda activate mol_aligner

# Install RDKit from conda-forge
conda install -c conda-forge rdkit

# Install PyQt5 and Pillow
conda install pyqt pillow
# Or using pip
pip install rdkit PyQt5 pillow
</syntaxhighlight>

'''Note:''' Installing RDKit via pip can be challenging on some systems. Conda installation is strongly recommended.

=== Platform-Specific Notes ===

==== macOS ====
* No additional steps required
* Font rendering uses system fonts (Helvetica, Arial)

==== Linux ====
* Install font packages for better rendering:
<syntaxhighlight lang="bash">
sudo apt-get install fonts-dejavu-core # Ubuntu/Debian
sudo yum install dejavu-sans-fonts # CentOS/RHEL
</syntaxhighlight>

==== Windows ====
* No additional steps required
* Arial font is used by default

== Quick Start ==

=== Launching the Application ===

<syntaxhighlight lang="bash">
python mol_aligner_app.py
</syntaxhighlight>

=== Basic Workflow ===

# '''Load molecules:''' Click "Browse File" and select your SDF or SMILES file
# '''Set reference:''' Enter the SMILES string of your reference/core structure
# '''Configure display:''' Set number of columns (default: 4) and font size (default: 24)
# '''Click "Load & Align":''' Molecules will be aligned and displayed
# '''Edit as needed:''' Select molecules, toggle highlights, rotate/mirror structures
# '''Export:''' Click "💾 Export High-Res PNG" to save your grid

== Features ==

=== Core Features ===

* '''Molecular Alignment:''' Automatically aligns analogs based on Maximum Common Substructure (MCS)
* '''Interactive Highlighting:''' Click atoms to toggle highlights on/off
* '''Structure Transformations:''' Rotate (90°) and mirror structures while keeping atom labels readable
* '''Flexible Display:''' Adjustable grid columns (1-10) and font sizes (16-48pt)
* '''Property Display:''' Show any molecular property as label (Catalog ID, Price, MW, LogP, etc.)
* '''High-Resolution Export:''' Export publication-quality PNG at 300 DPI

=== Supported File Formats ===

==== Input Files ====

* '''SDF (Structure Data File):''' .sdf extension
* '''SMILES:''' .smi or .smiles extension

==== SMILES File Format ====

Tab or space-delimited format:
<syntaxhighlight lang="text">
SMILES_STRING Catalog_ID Property1 Property2
c1ccccc1 Benzene 10.50 150.2
CCO Ethanol 5.00 78.1
</syntaxhighlight>

* First column: SMILES string (required)
* Second column: Catalog ID (optional, defaults to "Mol_N")
* Additional columns: Any properties you want to display

==== SDF Files ====

Standard SDF format with properties embedded:
* Catalog ID
* Price, USD
* Molecular Weight
* LogP
* Any custom properties

== User Interface ==

=== Main Window Components ===

==== 1. Toolbar ====

{| class="wikitable"
! Button !! Function !! Shortcut
|-
| '''✏️ Edit Highlights Mode''' || Toggle between selection and atom editing modes || Click to toggle
|-
| '''📝 Atom List...''' || Open dialog with checkboxes for all atoms || -
|-
| '''Reset Highlights''' || Restore original highlights (non-matching atoms) || -
|-
| '''Clear All Highlights''' || Remove all highlights || -
|-
| '''Rotate ↻ 90°''' || Rotate selected molecule 90° clockwise || -
|-
| '''Rotate ↺ 90°''' || Rotate selected molecule 90° counter-clockwise || -
|-
| '''Mirror Horizontal ↔''' || Flip selected molecule left-to-right || -
|-
| '''Mirror Vertical ↕''' || Flip selected molecule top-to-bottom || -
|-
| '''💾 Export High-Res PNG''' || Save grid as high-resolution image || -
|-
| '''Reset Selected''' || Reset all transformations for selected molecule || -
|}

==== 2. Input Section ====

* '''File:''' Path to SDF or SMILES file
* '''Browse File:''' Open file dialog
* '''Reference:''' SMILES string of reference structure
* '''Columns:''' Number of columns in grid (1-10)
* '''Load & Align:''' Process and display molecules

==== 3. Label Settings ====

* '''Font Size:''' Dropdown with sizes 16-48pt
* '''Second Line:''' Dropdown to select which property to display
** "Catalog ID only" - single line label
** Any property from your file

==== 4. Grid Display ====

* Scrollable area showing aligned molecules
* Click molecule to select (blue border)
* In Edit Mode: Click atoms to toggle highlights

==== 5. Status Bar ====

* Shows current operation status
* Displays MCS statistics after loading
* Shows atom selection feedback

=== Visual Feedback ===

* '''Selection:''' Blue border (3px) around selected molecule
* '''Default:''' Gray border (1px) around unselected molecules
* '''Edit Mode:''' Info banner turns blue, cursor becomes crosshair
* '''Selection Mode:''' Gray info banner, cursor is pointing hand
* '''Highlights:''' Light green circles around highlighted atoms

== Workflows ==

=== Workflow 1: Basic Structure Alignment ===

'''Goal:''' Align a series of molecular analogs and highlight variable regions

# Prepare your data:
#* SDF file with multiple analogs
#* Reference SMILES (the core scaffold)
# Launch the application
# Click "Browse File" and select your SDF
# Enter reference SMILES in "Reference" field
# Set "Columns" to desired value (e.g., 4 for 4×N grid)
# Click "Load & Align"
# Review alignment:
#* Status bar shows MCS statistics
#* Green highlights show atoms different from reference
# Export: Click "💾 Export High-Res PNG"

=== Workflow 2: Custom Highlight Editing ===

'''Goal:''' Manually adjust which atoms are highlighted

'''Method 1: Direct Atom Clicking'''
# Load and align molecules (see Workflow 1)
# Click "✏️ Edit Highlights Mode" button in toolbar
# Click directly on atoms to toggle highlights on/off
# Status bar confirms each atom toggle
# Click "✏️ Edit Highlights Mode" again to exit

'''Method 2: Atom List Dialog'''
# Load and align molecules
# Click a molecule to select it
# Click "📝 Atom List..." in toolbar
# Check/uncheck atoms in the list
# Use "Select All", "Select None", or "Invert" buttons
# Click "OK" to apply

'''Method 3: Bulk Operations'''
# Select a molecule
# Click "Reset Highlights" to restore original highlights
# Click "Clear All Highlights" to remove all highlights

=== Workflow 3: Structure Transformations ===

'''Goal:''' Adjust molecule orientation for better visual comparison

# Load and align molecules
# Click a molecule to select it (blue border appears)
# Apply transformations:
#* '''Rotate:''' Click "Rotate ↻ 90°" or "Rotate ↺ 90°"
#* '''Mirror:''' Click "Mirror Horizontal ↔" or "Mirror Vertical ↕"
# Transformations can be combined:
#* Example: Rotate 90° + Mirror Horizontal
# '''Important:''' Atom labels remain upright and readable
# To undo: Click "Reset Selected"

=== Workflow 4: Customizing Labels ===

'''Goal:''' Display specific molecular properties

# Load molecules with properties
# After loading, check "Second Line" dropdown
#* It auto-populates with available properties
# Select desired property:
#* "Catalog ID only" - single line
#* "Price, USD" - shows price
#* "Molecular Weight" - shows MW
#* Any other property from your file
# Adjust "Font Size" for readability (try 32 or 36)
# Changes apply immediately to all molecules
# Export preserves your settings

=== Workflow 5: Publication-Quality Export ===

'''Goal:''' Create high-resolution image for papers/presentations

# Complete your analysis (alignment, highlights, labels)
# Configure display:
#* Font Size: 32-40pt for publication
#* Second Line: Choose relevant property
#* Columns: Adjust for best layout
# Click "💾 Export High-Res PNG"
# Choose save location
# Result:
#* 700×700 pixels per molecule (2× display size)
#* 300 DPI resolution
#* Fonts scaled 2× for clarity
#* All transformations and highlights preserved

== File Formats ==

=== Creating SMILES Files ===

'''Basic format:'''
<syntaxhighlight lang="text">
c1ccccc1 Benzene 10.50
c1ccc(O)cc1 Phenol 15.20
c1ccc(N)cc1 Aniline 18.00
</syntaxhighlight>

'''With multiple properties:'''
<syntaxhighlight lang="text">
SMILES ID Price MW LogP
c1ccccc1 BEN-001 10.50 78.11 2.13
c1ccc(O)cc1 PHE-002 15.20 94.11 1.46
c1ccc(N)cc1 ANI-003 18.00 93.13 0.90
</syntaxhighlight>

'''Naming convention:'''
* Use .smi or .smiles extension
* Tab or space-delimited
* First column must be valid SMILES
* Comments: Lines starting with # are ignored

=== SDF File Properties ===

The application reads all properties from SDF files. Common properties:

* '''Catalog ID''' - Molecule identifier
* '''Price, USD''' - Pricing information
* '''Molecular Weight''' - Calculated or experimental MW
* '''LogP''' - Partition coefficient
* '''SMILES''' - SMILES representation
* '''Custom properties''' - Any field in your SDF

'''Tip:''' Use RDKit to add custom properties to SDF:

<syntaxhighlight lang="python">
from rdkit import Chem

mol = Chem.MolFromSmiles('c1ccccc1')
mol.SetProp('Catalog ID', 'BEN-001')
mol.SetProp('Price, USD', '10.50')
mol.SetProp('Custom Property', 'Value')

writer = Chem.SDWriter('output.sdf')
writer.write(mol)
writer.close()
</syntaxhighlight>

== Troubleshooting ==

=== Performance Issues ===

==== Slow loading with many molecules ====

* MCS calculation is O(n) for n molecules
* For >100 molecules, expect 10-30 second load time
* Timeout is 10 seconds per molecule for MCS

== License ==
(c) Claude and Andrii

Interactive Molecular Structure Alignment App for QSAR - Revision history

Iamkaant at 22:30, 6 October 2025

Iamkaant: added path to the program