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https://github.com/zilliztech/molsearch

An opensource molecule analyze software
https://github.com/zilliztech/molsearch

Last synced: about 1 year ago
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An opensource molecule analyze software

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README 

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

# MolSearch



[English](README.md) | [中文版](CN_README.md)



# Requirements 



- ### [Milvus CPU](https://milvus.io/docs/v0.10.4/milvus_docker-cpu.md)



- ### 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:



| Parameter                     | Description                                                  |

| ----------------------------- | ------------------------------------------------------------ |

| -p 35001:5000                 | -p specifies pot mapping between the host and the image.     |

| -e "MILVUS_HOST=192.168.1.85" | -e specifies the system parameter mapping between the host and the image. Pease update `192.168.1.25` to the IP address of the Milvus docker. |

| -e "MILVUS_PORT=19530"        | Update `19530` to the port of Milvus docker.                 |



## 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



```bash

# Run the following command under the script directory

$ cd script

$ python insert_data.py -f test_1w.smi

```



> The data is from  [pubchem](ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/SDF) and [zinc](http://zinc.docking.org/tranches/home/), which extracted 10,000 pieces of data.



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



```bash

192.168.1.85:8001

```



# How to use



MolSearch is an open source molecular search software based on [Milvus](https://github.com/milvus-io/milvus) and [MolView](https://github.com/molview/legacy), which has six main feature: editor, chemical formula, molecular search, tool classes, 3D model, Jmol tools.



![img](./pic/molsearch.png)



## Drawing structural formulas



### Top toolbar



![img](./pic/draw1.png)            



- **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



![](./pic/draw2.png)             



- **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



![](./pic/draw3.png)



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



 ![](./pic/load.png)



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.