This repo will no longer be maintained, please visit https://github.com/milvus-io/bootcamp/tree/master/solutions/molecular_similarity_search.

MolSearch

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Requirements

• Milvus CPU

• postgres

• RDKit

Deploy

1. Run Milvus Docker

This demo uses Milvus-0.10.4-CPU，please refer to https://milvus.io/docs/v0.10.4/milvus_docker-cpu.md。

# Start Milvus
$ docker run -d --name milvus_cpu_0.10.4 \
-p 19530:19530 \
-p 19121:19121 \
-v /home/$USER/milvus/db:/var/lib/milvus/db \
-v /home/$USER/milvus/conf:/var/lib/milvus/conf \
-v /home/$USER/milvus/logs:/var/lib/milvus/logs \
-v /home/$USER/milvus/wal:/var/lib/milvus/wal \
milvusdb/milvus:0.10.4-cpu-d120220-e72454

2. Run molsearch-webserver docker

$ docker run -td -p 35001:5000 -e "MILVUS_HOST=192.168.1.85" -e "MILVUS_PORT=19530" -e "PG_HOST=192.168.1.85" -e "PG_PORT=5432" zilliz/molsearch-webserver:0.2.0

The description for parameters:

3. Run molsearch-webclient docker

$ docker run -td -p 8001:80 -e API_URL=http://192.168.1.85:35001  zilliz/molsearch-webclient:0.1.0

Note: Please update 192.168.1.85 to the IP address of the Milvus docker.

4. Import data to Milvus

Import '.smi' data into Milvus, where the first column is smiles and the second column is the id number, for example:

o1c(C(O)CNC(C)(C)C)cc2c1c(CC(=O)OC(C)(C)C)ccc2 10001

# Run the following command under the script directory
$ cd script
$ python insert_data.py -f test_1w.smi

The data is from pubchem and zinc, which extracted 10,000 pieces of data.

You can enter the IP and port where molsearch-webclient is launched in your browser.

192.168.1.85:8001

How to use

MolSearch is an open source molecular search software based on Milvus and MolView, which has six main feature: editor, chemical formula, molecular search, tool classes, 3D model, Jmol tools.

Drawing structural formulas

Top toolbar

• Trash: clear the entire canvas
• Eraser: erase atoms, bonds or the current selection
• Undo/redo: undo or redo your recent changes
• Selection tools: all these tool can be used to drag the current selection or individual atoms and bonds. You can add/remove atoms and bonds to the selection by clicking them. If you have selected a separate fragment, you can rotate it by dragging an atom in the selection. You can delete the selection using the DEL key or using the eraser tool. Each tool has different behavior for the right mouse button:
  • Drag: move the entire molecule (you can already use the left mouse button for this)
  • Rectangle select: select atoms and bonds using a rectangular selection area
  • Lasso select: select atoms and bonds by drawing a freehand selection area
• Color mode: display atoms and bonds using colors
• skeleton mode: displays all C and H atoms instead of skeletal display
• Center: centers the whole molecule
• Clean: cleans the structural formula using an external service
• to 3D: converts the structural formula into a 3D model

Left toolbar

• Bonds: pick one of the bond types (single, double, triple, up, down) and add or modify bonds
• Fragments: pick one of the fragments (benzene, cyclopropane, etc.) and add fragments
• Chain: create a chain of carbon atoms
• Charge: increment (+) or decrement (-) the charge of atoms

Right toolbar

In this toolbar you can select from a number of elements, you can also pick an element from the periodic table using the last button. You can use the element to create new atoms or modify existing atoms.

Finding structures

You can load molecules, just type what you are looking for and a list of available molecules will appear.

Search

These functions allow you to perform some advanced searches through the database using the structural formula from the sketcher.

1. Similarity search: search for compounds with a similar structural formula
2. Substructure search: search for compounds with the current structure as subset
3. Superstructure search: search for compounds with the current structure as superset

Tools

The Tools menu contains several utility functions which are listed below.

• Structural formula image: sketcher snapshot (PNG with alpha channel)
• 3D model image: model snapshot (PNG)
• MOL file: exports a MDL Molfile from the 3D model (common molecules)

Information card

This collects and displays information about the structural formula.

3D Model

The Model menu contains some general functions for the 3D model.

Reset

This function sets the model position, zoom and rotation back to default.

Representation

You can choose from a list of different molecule representations including; ball and stick, stick, van der Waals spheres, wireframe and lines. Macromolecules are automatically drawn using ribbons.

Background

You can switch between a black, gray or white background. The default background is black (exported images from GLmol or ChemDoodle have a transparent background)

Engines

You can choose from three different render engines: GLmol, Jmol and ChemDoodle. GLmol is used as default render engine. GLmol and ChemDoodle are based on WebGL, a browser technology to support 3D graphics. If WebGL is not available in your browser, Jmol will be used for all rendering.

MolSearch automatically switches to:

1. Jmol if you execute functions from the Jmol menu
2. GLmol if you load macromolecules (due to significant higher performance)
3. ChemDoodle if you load a crystal structure (GLmol cannot render crystal structures)

Jmol tools

The Jmol menu offers some awesome Jmol-only functions and calculations.

Clear

Clears all executed calculations and measurements.

High Quality

Enables High Quality rendering in Jmol (enabled by default on fast devices) When turned off, anti-aliasing is disabled and the model is drawn using lines while transforming it.

Calculations

You can perform the following Jmol calculations in Jmol:

• MEP surface lucent/opaque: calculates and projects molecular analysis software electrostatic potential on a translucent or opaque van der Waals surface
• Charge: calculates and projects atomic charge as text label and white to atom color gradient
• Bond dipoles: calculates and draws individual bond dipoles
• Overall dipole: calculates and draws net bond dipole
• Energy minimization: executes an interactive MMFF94 energy minimization (note that this function only executes a maximum of 100 minimization steps at a time)

Measurement

You can measure distance, angle and torsion using Jmol. You can activate and deactivate one of these measurement types via the Jmol menu.

• Distance distance between two atoms in nm
• Angle angle between two bonds in degrees
• Torsion torsion between four atoms in degrees

Note that in some cases, the resolved 3D model is only an approach of the real molecule, this means you have to execute an Energy minimization in order to do reliable measurements.