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DEPTH-FIRST
A Workbench for Machine Learning in Chemistry. October 26th 2020. Kick the tires on a short, hackable aqueous solubility predictor built from a DeepChem graph convolutional network. Read More→. AN INTRODUCTION TO THE CHEMDRAW CDXML FORMAT An Introduction to the ChemDraw CDXML Format 2021-04-07T17:00:00Z. Although it receives relatively little attention in cheminformatics, ChemDraw may be the most important piece of software in chemistry. GETTING STARTED WITH RDKIT AND JUPYTER Getting Started with RDKit and Jupyter 2020-08-17T17:00:00Z. RDKit is a cheminformatics toolkit with bindings for Python. It's packed with functionality, deployed within multiple open source projects, and is widely-used in machine learning applications. RDKit can also be difficult to install. This article discusses the problem and a method for using RDKit within Jupyter notebooks. GRAPHS IN RUST: AN INTRODUCTION TO PETGRAPH MATCHED MOLECULAR PAIRS Matched Molecular Pairs. The well-known medicinal chemistry practice of pairwise structural comparison has been formalized as Matched Molecular Pair (MMP) analysis. One definition calls an MMP a pair of molecules "that differ only by a particular, well-defined, structural transformation." Often a measured property of some kind is associatedTHE SDFILE FORMAT
A COMPREHENSIVE TREATMENT OF AROMATICITY IN THE SMILESSEE MORE ONDEPTH-FIRST.COM
RUST FOR CHEMINFORMATICS SIXTY-FOUR FREE CHEMISTRY DATABASES Sixty-Four Free Chemistry Databases. October 11th 2011. The open Web offers a rich collection of diverse chemical data sources - if you know where to look. It's been over four years since I wrote the previous post in this series describing some emerging chemical databases, and a lot has happened in this space. The time seems rightfor an update.
HACKING PUBCHEM
DEPTH-FIRST
A Workbench for Machine Learning in Chemistry. October 26th 2020. Kick the tires on a short, hackable aqueous solubility predictor built from a DeepChem graph convolutional network. Read More→. AN INTRODUCTION TO THE CHEMDRAW CDXML FORMAT An Introduction to the ChemDraw CDXML Format 2021-04-07T17:00:00Z. Although it receives relatively little attention in cheminformatics, ChemDraw may be the most important piece of software in chemistry. GETTING STARTED WITH RDKIT AND JUPYTER Getting Started with RDKit and Jupyter 2020-08-17T17:00:00Z. RDKit is a cheminformatics toolkit with bindings for Python. It's packed with functionality, deployed within multiple open source projects, and is widely-used in machine learning applications. RDKit can also be difficult to install. This article discusses the problem and a method for using RDKit within Jupyter notebooks. GRAPHS IN RUST: AN INTRODUCTION TO PETGRAPH MATCHED MOLECULAR PAIRS Matched Molecular Pairs. The well-known medicinal chemistry practice of pairwise structural comparison has been formalized as Matched Molecular Pair (MMP) analysis. One definition calls an MMP a pair of molecules "that differ only by a particular, well-defined, structural transformation." Often a measured property of some kind is associatedTHE SDFILE FORMAT
A COMPREHENSIVE TREATMENT OF AROMATICITY IN THE SMILESSEE MORE ONDEPTH-FIRST.COM
RUST FOR CHEMINFORMATICS SIXTY-FOUR FREE CHEMISTRY DATABASES Sixty-Four Free Chemistry Databases. October 11th 2011. The open Web offers a rich collection of diverse chemical data sources - if you know where to look. It's been over four years since I wrote the previous post in this series describing some emerging chemical databases, and a lot has happened in this space. The time seems rightfor an update.
HACKING PUBCHEM
DEPTH-FIRST
A Workbench for Machine Learning in Chemistry. October 26th 2020. Kick the tires on a short, hackable aqueous solubility predictor built from a DeepChem graph convolutional network. Read More→.ABOUT THE AUTHOR
About the Author. Richard L. Apodaca is a chemist living in La Jolla, California. His company, Metamolecular, solves chemical information problems through software products and consulting services. E-mail: rich.apodaca@gmail.com Online: Twitter; GitHub. Education and Work. Founder at Metamolecular, LLC; Medicinal Chemist at Johnson & Johnson Pharmaceutical Research &THE SDFILE FORMAT
The SDfile Format Updated 2020-07-22T19:00:00Z. Chemical datasets often need to be exchanged with high fidelity. A number of file formats enabling such exchange can be found in the wild but the most common by far is the structure-data file (SDfile, aka "SD File," "SDfile," or "SDF").
MATCHED MOLECULAR PAIRS Matched Molecular Pairs. The well-known medicinal chemistry practice of pairwise structural comparison has been formalized as Matched Molecular Pair (MMP) analysis. One definition calls an MMP a pair of molecules "that differ only by a particular, well-defined, structural transformation." Often a measured property of some kind is associated RETURNING RUST ITERATORS Returning Rust Iterators. Rust iterators are fundamental to the language and can be found in a variety of contexts. Consuming iterators returned from functions in the standard library and crates is straightforward. Eventually, however, you'll want to return iterators from your own functions. This article discusses the majorapproaches to this
GRAPHS IN RUST: INTRODUCING GAMMA Graphs are used heavily within cheminformatics, a field concerned with the collection, storage, and retrieval of information about substances. Most cheminformatics systems use a library for manipulating molecular structures. Such a library is known as a "cheminformatics toolkit" or just "toolkit." At the core of every cheminformatics toolkit CHEMCELL - EASILY CONVERT NAMES AND CAS NUMBERS TO ChemCell - Easily Convert Names and CAS Numbers to Chemical Structures in Excel 2010-11-01T00:00:00.000Z. Note: the same functionality described in this article is now available on Google Spreadsheets.. Chemical databases often start as a list of names or Chemical Abstracts Service (CAS) Registry numbers contained in an Excel spreadsheet. But as more and more expectations get placed HACKING PUBCHEM: DIRECT ACCESS WITH FTP Hacking PubChem: Direct Access with FTP 2006-09-29T00:00:00.000Z. A previous article in the Hacking PubChem series pointed out that the entire PubChem database can be downloaded via FTP.This article shows how simple tools written in Ruby can be used to efficiently process the massive amount of data on PubChem's FTP-server. WHICH PROGRAMMING LANGUAGE SHOULD I LEARN AS A CHEMIST Which Programming Language Should I Learn as a Chemist? 2012-06-12T00:00:00.000Z. Reddit Chemistry hosts an interesting discussion about which programming language is most useful to learn as a chemist. This is an important question as chemists everywhere come face-to-face with the worst job market on record.Combining a good chemistry background with a useful skill such as FREE ACCESS TO ACS PUBLICATIONS AND WHY YOU CAN'T HAVE IT As early as 2008, ACS Publications has had a policy in place of allowing unlimited free access to certain journal content. As reported by ACS LiveWire in 2008: For example, ACS Articles on Request enables authors to freely distribute their articles in the forum of their choosing. Dana Roth, Chemistry Librarian at Caltech, describes theprogram
DEPTH-FIRST
A Workbench for Machine Learning in Chemistry. October 26th 2020. Kick the tires on a short, hackable aqueous solubility predictor built from a DeepChem graph convolutional network. Read More→. AN INTRODUCTION TO THE CHEMDRAW CDXML FORMAT An Introduction to the ChemDraw CDXML Format 2021-04-07T17:00:00Z. Although it receives relatively little attention in cheminformatics, ChemDraw may be the most important piece of software in chemistry. GETTING STARTED WITH RDKIT AND JUPYTER Getting Started with RDKit and Jupyter 2020-08-17T17:00:00Z. RDKit is a cheminformatics toolkit with bindings for Python. It's packed with functionality, deployed within multiple open source projects, and is widely-used in machine learning applications. RDKit can also be difficult to install. This article discusses the problem and a method for using RDKit within Jupyter notebooks. GRAPHS IN RUST: AN INTRODUCTION TO PETGRAPH MATCHED MOLECULAR PAIRS Matched Molecular Pairs. The well-known medicinal chemistry practice of pairwise structural comparison has been formalized as Matched Molecular Pair (MMP) analysis. One definition calls an MMP a pair of molecules "that differ only by a particular, well-defined, structural transformation." Often a measured property of some kind is associatedTHE SDFILE FORMAT
A COMPREHENSIVE TREATMENT OF AROMATICITY IN THE SMILESSEE MORE ONDEPTH-FIRST.COM
RUST FOR CHEMINFORMATICS SIXTY-FOUR FREE CHEMISTRY DATABASES Sixty-Four Free Chemistry Databases. October 11th 2011. The open Web offers a rich collection of diverse chemical data sources - if you know where to look. It's been over four years since I wrote the previous post in this series describing some emerging chemical databases, and a lot has happened in this space. The time seems rightfor an update.
HACKING PUBCHEM
DEPTH-FIRST
A Workbench for Machine Learning in Chemistry. October 26th 2020. Kick the tires on a short, hackable aqueous solubility predictor built from a DeepChem graph convolutional network. Read More→. AN INTRODUCTION TO THE CHEMDRAW CDXML FORMAT An Introduction to the ChemDraw CDXML Format 2021-04-07T17:00:00Z. Although it receives relatively little attention in cheminformatics, ChemDraw may be the most important piece of software in chemistry. GETTING STARTED WITH RDKIT AND JUPYTER Getting Started with RDKit and Jupyter 2020-08-17T17:00:00Z. RDKit is a cheminformatics toolkit with bindings for Python. It's packed with functionality, deployed within multiple open source projects, and is widely-used in machine learning applications. RDKit can also be difficult to install. This article discusses the problem and a method for using RDKit within Jupyter notebooks. GRAPHS IN RUST: AN INTRODUCTION TO PETGRAPH MATCHED MOLECULAR PAIRS Matched Molecular Pairs. The well-known medicinal chemistry practice of pairwise structural comparison has been formalized as Matched Molecular Pair (MMP) analysis. One definition calls an MMP a pair of molecules "that differ only by a particular, well-defined, structural transformation." Often a measured property of some kind is associatedTHE SDFILE FORMAT
A COMPREHENSIVE TREATMENT OF AROMATICITY IN THE SMILESSEE MORE ONDEPTH-FIRST.COM
RUST FOR CHEMINFORMATICS SIXTY-FOUR FREE CHEMISTRY DATABASES Sixty-Four Free Chemistry Databases. October 11th 2011. The open Web offers a rich collection of diverse chemical data sources - if you know where to look. It's been over four years since I wrote the previous post in this series describing some emerging chemical databases, and a lot has happened in this space. The time seems rightfor an update.
HACKING PUBCHEM
DEPTH-FIRST
A Workbench for Machine Learning in Chemistry. October 26th 2020. Kick the tires on a short, hackable aqueous solubility predictor built from a DeepChem graph convolutional network. Read More→.ABOUT THE AUTHOR
About the Author. Richard L. Apodaca is a chemist living in La Jolla, California. His company, Metamolecular, solves chemical information problems through software products and consulting services. E-mail: rich.apodaca@gmail.com Online: Twitter; GitHub. Education and Work. Founder at Metamolecular, LLC; Medicinal Chemist at Johnson & Johnson Pharmaceutical Research &THE SDFILE FORMAT
The SDfile Format Updated 2020-07-22T19:00:00Z. Chemical datasets often need to be exchanged with high fidelity. A number of file formats enabling such exchange can be found in the wild but the most common by far is the structure-data file (SDfile, aka "SD File," "SDfile," or "SDF").
MATCHED MOLECULAR PAIRS Matched Molecular Pairs. The well-known medicinal chemistry practice of pairwise structural comparison has been formalized as Matched Molecular Pair (MMP) analysis. One definition calls an MMP a pair of molecules "that differ only by a particular, well-defined, structural transformation." Often a measured property of some kind is associated RETURNING RUST ITERATORS Returning Rust Iterators. Rust iterators are fundamental to the language and can be found in a variety of contexts. Consuming iterators returned from functions in the standard library and crates is straightforward. Eventually, however, you'll want to return iterators from your own functions. This article discusses the majorapproaches to this
GRAPHS IN RUST: INTRODUCING GAMMA Graphs are used heavily within cheminformatics, a field concerned with the collection, storage, and retrieval of information about substances. Most cheminformatics systems use a library for manipulating molecular structures. Such a library is known as a "cheminformatics toolkit" or just "toolkit." At the core of every cheminformatics toolkit CHEMCELL - EASILY CONVERT NAMES AND CAS NUMBERS TO ChemCell - Easily Convert Names and CAS Numbers to Chemical Structures in Excel 2010-11-01T00:00:00.000Z. Note: the same functionality described in this article is now available on Google Spreadsheets.. Chemical databases often start as a list of names or Chemical Abstracts Service (CAS) Registry numbers contained in an Excel spreadsheet. But as more and more expectations get placed HACKING PUBCHEM: DIRECT ACCESS WITH FTP Hacking PubChem: Direct Access with FTP 2006-09-29T00:00:00.000Z. A previous article in the Hacking PubChem series pointed out that the entire PubChem database can be downloaded via FTP.This article shows how simple tools written in Ruby can be used to efficiently process the massive amount of data on PubChem's FTP-server. WHICH PROGRAMMING LANGUAGE SHOULD I LEARN AS A CHEMIST Which Programming Language Should I Learn as a Chemist? 2012-06-12T00:00:00.000Z. Reddit Chemistry hosts an interesting discussion about which programming language is most useful to learn as a chemist. This is an important question as chemists everywhere come face-to-face with the worst job market on record.Combining a good chemistry background with a useful skill such as FREE ACCESS TO ACS PUBLICATIONS AND WHY YOU CAN'T HAVE IT As early as 2008, ACS Publications has had a policy in place of allowing unlimited free access to certain journal content. As reported by ACS LiveWire in 2008: For example, ACS Articles on Request enables authors to freely distribute their articles in the forum of their choosing. Dana Roth, Chemistry Librarian at Caltech, describes theprogram
Depth-First
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MOLECULAR ASSEMBLY INDEXJune 4th 2021
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STANDARD INCHI
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FAST HYDROGEN COUNTING IN SMILESFebruary 10th 2021
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ABSTRACT SYNTAX TREES FOR SMILESDecember 14th 2020
Designing a suite of power tools for SMILES manipulation in Rust.Read More→
A WORKBENCH FOR MACHINE LEARNING IN CHEMISTRYOctober 26th 2020
Kick the tires on a short, hackable aqueous solubility predictor built from a DeepChem graph convolutional network.Read More→
SMILES READING PERFORMANCE: RDKIT VS CHEMCOREOctober 19th 2020
Rust and C++/Python cheminformatics toolkits face off on a core task.Read More→
START SEEING VALENCE AND CORE ELECTRONSOctober 12th 2020
Inexpensive molecular validation through simple integer arithmetic.Read More→
RUNNING A SMILES VALIDATION BENCHMARK Updated October 5th 2020 Cleaner cheminformatics datasets begin with standards.Read More→
EDMONDS' BLOSSOM ALGORITHM PART 1: CAST OF CHARACTERSSeptember 28th 2020
Understanding a classic algorithm in graph theory that remainsrelevant today.
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INTERACTIVE RUST IN A REPL AND JUPYTER NOTEBOOK WITH EVCXRSeptember 21st 2020
Explore Rust and its libraries with immediate feedback.Read More→
GETTING STARTED WITH DEEPCHEMSeptember 14th 2020
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SAYING NO TO BROWSER UI FRAMEWORKSSeptember 7th 2020
Why the winning move in the JavaScript UI framework game may be not toplay.
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SMILES VALIDATION IN THE BROWSERAugust 24th 2020
A Project using Rust and WebAssembly.Read More→
GETTING STARTED WITH RDKIT AND JUPYTERAugust 17th 2020
Quickly set up an environment for cheminformatics and machine learningexperimentation.
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PYTHON EXTENSIONS IN PURE RUST WITH PYO3August 10th 2020
Avoid a lot of manual labor when creating Python wrappers.Read More→
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