Hello,
Can anyone can help me how can I use" multicomponent hydrogen bond propensity" feature in mercury and relate them to python in order to export data if there any confomer have passed the cocrystal or not?
thanks alot for your time.
For "multicomponent hydrogen bond propensity" feature in Mercury s/w and relate it to Python for exporting data, follow these steps:
1. Install Mercury: First, download and install the Mercury software, which is a crystallographic visualization and analysis program developed by the Cambridge Crystallographic Data Centre (CCDC). Ensure that you have a valid license for Mercury.
2. Load the Cocrystal Structure: Open Mercury and load the cocrystal structure you want to analyze. You can import the crystal structure from a file or retrieve it from a crystallographic database using the appropriate options in Mercury.
3. Calculate Multicomponent Hydrogen Bond Propensity: In Mercury, go to the "Calculations" menu and select "H-Bond Propensity." Choose the "Multicomponent" option to calculate the hydrogen bond propensity of the system. This analysis will evaluate the propensity of hydrogen bonding between different components of the cocrystal.
4. Analyze the Results: After the calculation is complete, Mercury will display the results of the multicomponent hydrogen bond propensity analysis. You can explore and visualize the hydrogen bonding patterns within the cocrystal structure using the interactive interface provided by Mercury.
5. Export Data to Python: To export the data for further analysis in Python, you can utilize the scripting capabilities of Mercury. In Mercury, go to the "Calculations" menu and select "Scripting." Write a script to extract the relevant data, such as the hydrogen bond propensities of each conformer, and export it to a file format compatible with Python, such as a CSV file.
6. Import Data in Python: In your Python environment, read the exported data file (e.g., CSV) using appropriate libraries such as pandas. Load the data into a DataFrame or any suitable data structure for further analysis.
7. Analyze Conformer Pass/Fail: Based on your specific criteria for determining whether a conformer has passed or failed the cocrystal, perform the necessary calculations or comparisons using the hydrogen bond propensity data in Python. You can define thresholds or rules to classify conformers and generate the desired output indicating the pass/fail status.
Good luck
Mohammad Imam
Good afternoon,
thank you so much for your reply.
I was wondering if you can tell me if have you tried on your structure as well?
because the CCDC video that I attached for you, looks like a different way.
I am struggling to understand that cause I have to run on my own structure.
How to: Run the Multi-Component Hydrogen Bond Propensity (HBP) script in the CSD Python API - YouTube
HELLO,
please let me know how can I add a new coformer (there are no data on CCDC) in order to design cocrystal in mercury?
is that ok to sketch a molecule in mercury and save it as an MOL file and use it as coformer in cocrystal prediction?or I have to use another way?
thank you so much for your help.
follow these steps:
1. Obtain the crystal structure of the coformer: If there are no crystallographic data available for the coformer, you will need to obtain its crystal structure through experimental techniques such as X-ray crystallography or by performing quantum mechanical calculations.
2. Generate a .cif file: Once you have the crystal structure of the coformer, you need to convert it into a CIF (Crystallographic Information File) format. You can use software such as Mercury or the program used to determine the crystal structure to generate the .cif file.
3. Prepare the coformer in Mercury: Open Mercury and go to the "File" menu. Choose "Import -> Crystal" to import the .cif file of the coformer. This will load the coformer's crystal structure into Mercury.
4. Set up the cocrystal design: In Mercury, you can set up the cocrystal design by going to the "Design" menu and choosing "Cocrystal Design." This will open a dialog box where you can specify the coformer and the active molecule (the compound you want to form a cocrystal with).
5. Perform the cocrystal design calculations: After setting up the cocrystal design parameters, you can start the calculations by clicking the "Start" button in the dialog box. Mercury will perform the necessary calculations to generate potential cocrystal structures based on the coformer and active molecule.
6. Analyze the results: Once the calculations are complete, you can analyze the generated cocrystal structures using Mercury's visualization and analysis tools. You can examine the intermolecular interactions, packing motifs, and other relevant properties to evaluate the feasibility and stability of the cocrystal structures.
Good luck
import pandas as pd
# Read exported data
data = pd.read_csv("exported_data.csv")
# Define a threshold value for passing the cocrystal test
threshold = 0.5
# Filter conformers that passed the test
passing_conformers = data[data["HydrogenBondPropensity"] > threshold]
# Export passing conformers to a new CSV file
passing_conformers.to_csv("passing_conformers.csv", index=False)
Muhammad Sohaib
Hello,
thank you for your kind reply.
could you please let me know what are the commands and how can I import them?
thanks alot
you can explore python libraries to deal with this module and functionality.
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