I updated openforcefield from ver 0.5 to ver 0.6. ForceField of SMIRNOFF is also updated. I tried to use new version of OpenFF.At first, I calculated partial charge with semi empirical method ‘AM1-BCC’. Ambertools is used for the calculation, it is easy. Just finished, check the result. Nitrogen has the most negative charge and neighborContinue reading “Small molecule MD with openMM #MD #Openforcefield”
Tag Archives: python
Calculate free solvent accessible surface area #RDKit #Chemoinformatics
Recent version of rdkit has method to calculate FreeSASA.I never used the function so I used it. So I tried to use it. I calculated freeSASA with very simple molecules Phenol and hydroxy pyridine. To calculate FreeSASA, prepare raddii is needed. Now ready, let’s calculate FreeSASA. At first I expected that FreeSASA of pyridine isContinue reading “Calculate free solvent accessible surface area #RDKit #Chemoinformatics”
Make RGroup decompose table with old ver. RDKit #RDKit #Chemoinformatics
ObjectiveRecent version of RDKit has rdRGroupDecomposition module for R Group decomposition. You know, it is very useful module for SAR analysis. However this function is not implemented in old version of rdkit (i.e. rdkit for 32 bit windows). I would like to implement similar module for 32bit windows system. My approach with codeSo, I triedContinue reading “Make RGroup decompose table with old ver. RDKit #RDKit #Chemoinformatics”
Extract chemical information from patent data #pat-informatics #chemoinformatics
As you know, patent informatics is important for drug discovery project. And SureChembl is one of the dataset for chemical structures which are extracted from patent document by OCR. It is worth that it can freely available data source. I surprised that recently google patents provides chemical data too. It seems not fully cover allContinue reading “Extract chemical information from patent data #pat-informatics #chemoinformatics”
Useful package for descriptor calculation #chemoinformatics #rdkit
Descriptor calculation is an important task for chemoinfomatics. I often use rdkit to do it. And today I found very useful package for descriptor calculation which name is descriptorus. URL is below. https://github.com/bp-kelley/descriptastorus It is very easy to install the package. Just following command. After did it, I could use the package. By using theContinue reading “Useful package for descriptor calculation #chemoinformatics #rdkit”
Calculate solvent effect in Psi4 #psi4 #quantumchemistry
Recently I use not only chemoinformatics tools but also quantum chemistry tool, my favorite is Psi4. Psi4 has many options and plug-ins for quantum calculation. Most setting of calculation is vacuum, but it actually true. So considering the solvent around the molecules is important. Can psi4 perform calculation with solvent effect? Yes! PCMSolver is pluginContinue reading “Calculate solvent effect in Psi4 #psi4 #quantumchemistry”
Lead Optimization Mapper(LOMAP) for FEP calculation #chemoinformatics #RDKit #Networkx
Free energy perturbation (FEP) is useful method for Computer aid drug design. The method calculates energy difference between several similar molecules. And the system is closed system. To perform the calculation for several molecules. The efficient method of making molecules system is required. I found an interesting article today. The url is below.https://www.ncbi.nlm.nih.gov/pubmed/24072356 The authorsContinue reading “Lead Optimization Mapper(LOMAP) for FEP calculation #chemoinformatics #RDKit #Networkx”
Psikit update/Draw ESP, HOMO LUMO #RDKit #Chemoinformatics #quantumchemistry
I just updated psikit which is package for quantum-chemoinformatics ;) It can be installed from conda / pypi :) I added and updated new function for molecular property rendering. Current version of psikit can draw not only frontier orbital but also ESP and dual descriptor. Dual descriptor is calculated by psi4. What is dual descriptor?Continue reading “Psikit update/Draw ESP, HOMO LUMO #RDKit #Chemoinformatics #quantumchemistry”
Enumerate partial heteroaromatic rings in a molecule #RDKit #Chemoinformatics
I posted hetero shuffling before. It worked well but redundant. There is a nice code in RDKit UGM2017 material. URL is below. https://github.com/rdkit/UGM_2017/blob/master/Notebooks/Cole-Enumerate-Heterocycles.ipynb The code defined transformation with hard coding and seems nice. In case of real project, we sometime would like to do enumeration against partial substructure not all structure. I thought how toContinue reading “Enumerate partial heteroaromatic rings in a molecule #RDKit #Chemoinformatics”
Rotate molecule and visualize it #RDKit #Chemoinformatics
Some days ago, I found an interesting question in rdkit mailing list. The question is how to rotate molecule around an axis. I do not have any idea to do it. But RDKit has a function to do it. I read API and try to do it. rdMolTransforms.TransformConformer function can rotate molecue with transform matrix.Continue reading “Rotate molecule and visualize it #RDKit #Chemoinformatics”
Visualize pharmacophore with RDKit #RDKit #Pymol #Chemoinformatics
Some years ago, I wrote a post about how to communicate pymol and RDKit. In the post, I demonstrated how to visualize Phamarcophore in rdkit. And recently I got a query about the post and think about more efficient way.What I want to write in the post is new approach to visualize pharmacophore with RDKit.Continue reading “Visualize pharmacophore with RDKit #RDKit #Pymol #Chemoinformatics”
New functionality of psikit #Chemoinformatics #RDKit #Psi4
Happy new year! ‘Akemashite Omedetou Gozaimasu’ in Japanese! I and @kzfm_ -san are developing a library which uses a rdkit & psi4 named psikit. You can find brief introduction the concept following URL.http://blog.kzfmix.com/entry/1536978824 Today I added new function that can calculate RESP charge of give molecule. RESP charge means ‘Restraints for Deriving Atomic Charges’. DetailsContinue reading “New functionality of psikit #Chemoinformatics #RDKit #Psi4”
Make interactive chemical space plot in jupyter notebook #cheminformatics #Altair
I often use seaborn for data visualization. With the library, user can make beautiful visualization. BTW, today I tried to use another library that can make interactive plot in jupyter notebook. Name of the library is ‘altair’. https://altair-viz.github.io/index.html The library can be installed from pip or conda and this package based vega and vega-lite. VegaContinue reading “Make interactive chemical space plot in jupyter notebook #cheminformatics #Altair”
Build stacking Classification QSAR model with mlxtend #chemoinformatics #mlxtend #RDKit
I posed about the ML method named ‘blending’ somedays ago. And reader recommended me that how about try to use “mlxtend”. When I learned ensemble learning package in python I had found it but never used. So try to use the library to build model. Mlxtend is easy to install and good document is providedContinue reading “Build stacking Classification QSAR model with mlxtend #chemoinformatics #mlxtend #RDKit”
Vote Vote Vote #chemoinformatics
Somedays ago, I posted about ensemble classification method named ‘blending’. The method is not implemented in scikit-learn. So I am implementing the function now. By the way, scikit-learn has an ensemble classification method named ‘VotingClassifer’. https://scikit-learn.org/stable/modules/generated/sklearn.ensemble.VotingClassifier.html#sklearn.ensemble.VotingClassifier Following explanation from sklearn document. The idea behind the VotingClassifier is to combine conceptually different machine learning classifiers andContinue reading “Vote Vote Vote #chemoinformatics”
Visualize pharmacophore in RDKit #RDKit
RDKit has pharmacophore feature assignment function. The function can retrieve molecular features based on pre-defined ph4core. And RDKit IPythonconsole can draw molecules on ipython notebook. Today I tried to visualize ph4core on notebook. Code is very simple. First, load feature definition. Then calculate pharmacophore. And compute 2D cordes. Next I defined drawing function. To highlightContinue reading “Visualize pharmacophore in RDKit #RDKit”
Generate possible list of SMLIES with RDKit #RDKit
In the computer vision, it is often used data augmentation technique for getting large data set. On the other hand, Canonical SMILES representations are used in chemoinformatics area. RDKit UGM in last year, Dr. Esben proposed new approach for RNN with SMILES. He expanded 602 training molecules to almost 8000 molecules with different smiles representationContinue reading “Generate possible list of SMLIES with RDKit #RDKit”
Tracking progress of machine learning #MachineLearning
To conduct machine learning it is needed to optimize hyper parameters. For example scikit-learn provides grid search method. And you know there are several packages to do that such as hyperopt or gyopt etc. How do you mange builded models? It is difficult for me. Recently I am interested in mlflow . MLflow is anContinue reading “Tracking progress of machine learning #MachineLearning”
Ensemble learning with scikit-learn and XGBoost #machine learning
I often post about the topics of deep learning. But today I would like to post about ensemble learning. There are lots of documents describes Ensemble learning. And I think following document is very informative for me. Kaggle Ensembling Guide I interested one of the method, named ‘blending’. Regarding above URL, the merit of ‘blending’Continue reading “Ensemble learning with scikit-learn and XGBoost #machine learning”
convert rdkit mol object to schrodinger’s mol object #RDKit #Chemoinformatics
I posted a memo about how to read maestro file format from RDKit. It means that rdkitter can use “mae” format from RDKit. ;-) BTW, schrodinger’s site provides API for python. I would like to know the way to communicate rdkit from schrodinger python API. https://www.schrodinger.com/pythonapi I read the API in lunch break and testedContinue reading “convert rdkit mol object to schrodinger’s mol object #RDKit #Chemoinformatics”
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