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Sunday, 9 August 2015. MMFF Partial Charges Improvements in CDK. Some time last year Mark Williamson. Brought to my attention discrepancies in CDK's MMFF partial charge calculation. Investigating further it seemed to mainly be a problem with atom typing. There were two existing classes that could assigned MMFF atom types using a combination of a decision tree and string matching hose codes. The 761 molecules from the MMFF94 Validation Suite. Apart from improving atom type assignments the charge assignmen...

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Efficient Bits | efficientbits.blogspot.com Reviews
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Sunday, 9 August 2015. MMFF Partial Charges Improvements in CDK. Some time last year Mark Williamson. Brought to my attention discrepancies in CDK's MMFF partial charge calculation. Investigating further it seemed to mainly be a problem with atom typing. There were two existing classes that could assigned MMFF atom types using a combination of a decision tree and string matching hose codes. The 761 molecules from the MMFF94 Validation Suite. Apart from improving atom type assignments the charge assignmen...
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Efficient Bits | efficientbits.blogspot.com Reviews

https://efficientbits.blogspot.com

Sunday, 9 August 2015. MMFF Partial Charges Improvements in CDK. Some time last year Mark Williamson. Brought to my attention discrepancies in CDK's MMFF partial charge calculation. Investigating further it seemed to mainly be a problem with atom typing. There were two existing classes that could assigned MMFF atom types using a combination of a decision tree and string matching hose codes. The 761 molecules from the MMFF94 Validation Suite. Apart from improving atom type assignments the charge assignmen...

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efficientbits.blogspot.com efficientbits.blogspot.com
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Efficient Bits: January 2014

http://www.efficientbits.blogspot.com/2014_01_01_archive.html

Saturday, 11 January 2014. New SMILES behaviour - generating (CDK 1.5.4). In the previous post. I outline the changes to SMILES. Parsing in the Chemistry Development Kit (CDK). The original plan was to have several posts detailing the changes but in the end it was more practical to put this in a single release note document (available: here. Although the key changes to SMILES Generation are summarised in the release notes I thought it would be worth touching on some details. Existing SMILES generation API.

2

Efficient Bits: September 2014

http://www.efficientbits.blogspot.com/2014_09_01_archive.html

Friday, 12 September 2014. The latest release of the CDK (1.5.8) includes a new generator for rendering structure diagrams. A detailed introduction to configuring the new generator is available on the CDK wiki. ChEBI's current entity of the month. Will be used to demonstrate the sizing. Three parameters that are important in the overall sizing of depictions. These are the. Which are all registered as. Is not needed if we allow our diagram to be fitted automatically. Is set during diagram generation.

3

Efficient Bits: December 2014

http://www.efficientbits.blogspot.com/2014_12_01_archive.html

Tuesday, 30 December 2014. CDK Release 1.5.10. CDK 15.10 has been released and is available from sourceforge ( download here. And the Maven central repository (XML 1). This release follows very shortly after 1.5.9 and is the first release available from the central maven repository. This means there is now no need to include a custom repo when using the library in downstream projects (XML 1). The short release notes ( 1.5.10-Release-Notes. Wednesday, 24 December 2014. CDK Release 1.5.9. Repository url ht...

4

Efficient Bits: February 2014

http://www.efficientbits.blogspot.com/2014_02_01_archive.html

Wednesday, 19 February 2014. CDK now built using Maven. At 13 years and 4 months the Chemistry Development Kit. CDK) is reasonably mature for a software project. Over the years there have been many changes in development practices as the code base evolved. This post is a departure for the usual algorithms and performance tests and looks at a recent and major change in the CDK development process. On Monday, Egon, Nina and I made the final alterations that changed the build system from Ant. Summarises the...

5

Efficient Bits: December 2013

http://www.efficientbits.blogspot.com/2013_12_01_archive.html

Wednesday, 18 December 2013. New SMILES behaviour - parsing (CDK 1.5.4). It's been a while since the last CDK development release. Over 4 months). The CDK 1.5.4 will be released in the next few days and has a lot of improved functionality. This is the first of several posts expanding on the functionality and detailing some design decisions. One major overhaul has been the handling of the SMILES. Atom-typing / Implicit hydrogen counts. Atom-typing is no longer performed, this mirrors the behaviour of the ...

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Efficient Bits

Sunday, 9 August 2015. MMFF Partial Charges Improvements in CDK. Some time last year Mark Williamson. Brought to my attention discrepancies in CDK's MMFF partial charge calculation. Investigating further it seemed to mainly be a problem with atom typing. There were two existing classes that could assigned MMFF atom types using a combination of a decision tree and string matching hose codes. The 761 molecules from the MMFF94 Validation Suite. Apart from improving atom type assignments the charge assignmen...

efficientbits.com efficientbits.com

Efficient Bits

Thoughts on making software by Jamie da Silva. 7/10 - Newtonsoft.Json.dll 6.x is installed in the GAC by an application on the dev server MSBuild no longer copys Newtonsoft.Json.dll during build. Build does not fail because old copies are in output folders. 8/11 - Newtonsoft.Json.dll 7.x is added…. A Simple Order Process with Azure WebJobs. The Velocity Origin Story. I guess these days it's probably not as amazing to others as it seems to me. That I can be sitting in my home office in New Jersey and ...

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