3.2.198

Changes:

• ae78a40 Add a --max-num-confs argument to CommandBindingAffinity
• 18d2e36 Add a residues property to the scans
• 4bde05a Add a scan function for mutation scanning
• d8aafc3 Merge branch 'develop' of https://github.com/gusennan/osprey into develop
• 06f4e0d Swap good 'ol K* back in instead of using BBK*
• 483e0cf change from draft releaseses to pre-releases
• 75e2177 Merge branch 'add-top-n-command' into develop
• c9fa6c4 Move merged classes into their project-specific locations
• 977158a Merge branch 'atom-pair-interactions' into develop
• 78e2b9d Add azure-pipline and gradle application support

See More

• 50d692c Add new functions to debug Atom-Atom energy calculations
• f906fe7 Remove unused abstract function in InterResBondingTemplate
• e6b45f3 Add a new runnable command for debugging Atom-Atom energy calculations
• 7f940e3 Add new functions to debug Atom-Atom energy calculations
• 21103b3 Remove unused abstract function in InterResBondingTemplate
• 9419e53 provide the jar:// filesystem for runtime images of OpenJDK14, so JPype works correctly
• 37bdbc7 Merge branch 'dlab-master' into develop
• db54971 remove upstream code
• 890a6b5 Add function to allow for arbitrary jvm args.
• beea5c6 Only print python versions on --info or higher
• 1081182 update python example for new compiled conformation spaces, and fix conf space migration bugs in the java code
• f7dfb41 add additional help info for CLI
• 2f4334d Swap BBK* for K* traditional in CommandBindingAffinity
• 9d1cb72 Merge master into develop
• 696bef2 Bring gusennan/master up to date with donaldlab/master
• 1ad5db3 fix NPE in SOFEA when not using ConfDB
• 7101b11 update lfs pointer line endings
• 0803bb5 post rebase cleanup
• 360f142 Add CUDA bins
• c2a6830 Add working version of binding affinity via file specification
• 42d06a8 Unset the steric shell so all residues are considered in efunc
• ddcdb1a Move verifyInput to right position
• 01b1259 Auto stash before merge of "develop" and "origin/develop"
• f6d6b9b do the entropy and enthalpy calculation in using parallel streams
• 16fa902 Add Continuous flexibility and Gpu support
• c61d2f9 Add command to print information about design
• 9db5100 Add runtime checks for design intention consistency.
• 16c4f51 Update big math to 2.3.0
• d308f18 Use big math for log function instead of self-implementation
• 992c8ca Update Thermodynamic Conf Listener to calculate correct bounds
• bbeea7f Add AutoValue library for simple tuples
• 2d9b639 Redo residue numbering to include chain
• 9ddc46f Remove Jeff's Coordinates and add in extraTemplates
• 4e807ee Incorporate bounds on entropy and enthalpy
• 8f04326 Ignore unknown properties on Residue class
• c5decdf Fix some typos
• dc0dd31 add ff14SB files
• 66fe524 update README
• 2b19495 add README
• b45c0f0 add tpie jar to repo
• 9a0a8d6 remove unnecessary out parameter
• d5ebcba Add the name parameter of Molecule back in
• f6be547 add toml jar
• 0866b34 add command to limit number of confs evaluated
• 814160b add templates from jeff
• 373d115 add flags for debugging energy and thermodynamics
• 2f96da0 fix build
• 005ad95 add energy conf listener
• d7e55d7 add hie, hip, hid to AminoAcid enum
• 1876af5 add memory debugging
• b6e1a7b add ThermodynamicsConfListener.java
• b45da80 Add comments, clean up CommandPartitionFunction
• 03e4bb1 add some comments
• 91a3a5c clean up Gradient Descent PFunc
• a8a3af8 comment through partition function calculation
• 55ce7b2 update stability design
• 6836a94 Refactor common options into an abstract class.
• baecef0 Add a CLI
• 2e6473d remove GradientDescentMARKStarPfunc.java
• 3af7e88 Complete commenting GradientDescentPFunc.java
• c5214ca Remove programming languages and non-CI tests
• c368769 Use BBKStar instead of traditional KStar
• 96d1936 update jcuda and gradle version
• de597d4 Merge pull request #124 from donaldlab/float_dihedrals
• 9e3cbbc Merge branch 'master' into float_dihedrals
• e27d8e0 Read in dihedrals as floats
• d5c99a0 Add EnergiedConfQueue class as a container for ordered conformations.
• bf9877c Add CLI arguments for printing ensembles
• 218f35b update command
• dfcddee Add message that design is valid when checking design in stability command
• c5c4e38 Take the first template that matches.
• e0c6c98 post rebase cleanup
• 623920b Add CUDA bins
• c4223a1 Add working version of binding affinity via file specification
• 4825bc5 Unset the steric shell so all residues are considered in efunc
• 81e1fdb Move verifyInput to right position
• 31029fc Auto stash before merge of "develop" and "origin/develop"
• 33c839d do the entropy and enthalpy calculation in using parallel streams
• 649c40f Add Continuous flexibility and Gpu support
• 9d29385 Add command to print information about design
• d4622e2 Add runtime checks for design intention consistency.
• b227080 Update big math to 2.3.0
• f3cef52 Use big math for log function instead of self-implementation
• 3fd7fa1 Update Thermodynamic Conf Listener to calculate correct bounds
• c5ea581 Add AutoValue library for simple tuples
• 2f74b97 Redo residue numbering to include chain
• 1f13832 Remove Jeff's Coordinates and add in extraTemplates
• c276292 Incorporate bounds on entropy and enthalpy
• ab91f90 Ignore unknown properties on Residue class
• d140ac3 Fix some typos
• eceb814 add ff14SB files
• 5c0df4c update README
• f1024c7 add README
• f0e4eda add tpie jar to repo
• 94b5a8f remove unnecessary out parameter
• 40a068b Add the name parameter of Molecule back in
• 54360de add toml jar
• 18041b9 add command to limit number of confs evaluated
• 5affb79 add templates from jeff
• fbfc2be add flags for debugging energy and thermodynamics
• 6f4cd45 fix build
• 5e40fd6 add energy conf listener
• 6b4675f add hie, hip, hid to AminoAcid enum
• ac4511b add memory debugging
• 792802f add ThermodynamicsConfListener.java
• 833bd05 Add comments, clean up CommandPartitionFunction
• 2df3834 add some comments
• e10e946 clean up Gradient Descent PFunc
• 35bb8be comment through partition function calculation
• cb862b9 update stability design
• d3741ad Refactor common options into an abstract class.
• d381587 Add a CLI
• dc8ff74 remove MARKStar.java
• 9140448 remove GradientDescentMARKStarPfunc.java
• a8b3782 Complete commenting GradientDescentPFunc.java
• eb4f42c Remove programming languages and non-CI tests

This list of changes was auto generated.