3.3-resistor

This release corresponds to the version of RESISTOR described in the STAR Protocols publication. The attached archives contain the compiled binaries for running RESISTOR, and the source code corresponds to those binaries.

3.2.304

Hotfix that fixes null pointer exception "parameter file is null".

Fixes #173

Changes:

• e5da24f Merge branch 'main' of github.com:donaldlab/OSPREY3
• 29c8378 Fix typos
• 1350cb1 Use variable instead of literal in build.gradle.kts
• ef1fe9d Default to an empty array instead of a null array
• 06b63e8 Merge pull request #176 from donaldlab/hong_dev
• 5ae3d4f update JNA to 5.10.0 and add apple silicon JNA platform + compiled library
• da71d47 implement joinToClasspath() body
• 53f2abc Merge pull request #175 from donaldlab/jdk17
• 568c0f0 update to jdk17
• fceb43c add new javadoc functions to the pydoc renderer, and add translations to make the docs look more pythonic

See More

• 52d2fab implement java method argument lookups for the python documentation
• 308d1a7 update gradle to 7.3 for compatibility with JDK 17
• d779f5b improvements to the javadoc->pydoc translator thingy, like reading javadocs for individual method arguments
• e483013 update python docs generator to build links into the javadocs for java types
• d8394fc update to Kotlin 1.5.31 to work around compiler bug
• 3ae07e3 split code documentation generation into separate tasks
• ff6a2cc add generated kotlin docs to the hugo site
• b26ba5f add generated javadocs to hugo, move generated docs into a hugo module and out of the source tree
• 0fe045a remove huge theme from source tree, download and use as go module on-demand
• 2e6ea9c Fix nullpointer when not passing extra parameters to forcefield
• 1fad00c minor formatting changes to some documentation
• 5930ade WIP: new python API doc generator
• e7a2b62 add more troubleshooting tips for the osprey service deployment
• e1930ab add some troubleshooting info to the osprey service ops doc
• b07edb1 add some developer documentation for the osprey service

This list of changes was auto generated.

Incorporate latest bits

This is a beta release to allow users to try out the latest bits.

Changes:

• 68ce186 Fix precision-related bug that causes BBKStar to return sequences in wrong order if Kstar score is large enough.
• 0c4e9dc fix bug where the CudaConfEnergyCalculator tried to send empty batches to the batch minimization kernel, which Cuda apparently doesn't like
• e75b6f4 improve exception handling in CudaConfEcalc
• 0a1ba26 update CudaConfEcalc cmake files to work with cmake version 3.21.2, and add big fat warning to explain why compiling kernels with Cuda Toolkit v11 doesn't work
• bf0e06b Default to computing K* with int.MAX_SIZE
• 8504bed try to implement osprey-service-docker installer for OSX, but give up for now. it's not worth the trouble, docker isn't really supported on OSX anyway
• b472410 apparently storing huge files in the git repo is bad, and GitHub straight forbids it, so make build tools to store large build files on the dlab filesystem via SSH instead of directly in the repo
• 2dd78df Merge branch 'main' of github.com:donaldlab/OSPREY3 into main
• afb102f Add "savePdb" and molecule deprotonation command
• e4521ff add a service provider picker to the GUI

See More

• 2c23fa6 fix edge cases and bugs in the user settings system and handling of service providers
• 0906924 fix edge-cases where Netty doesn't exit cleanly when trying to start a local service but failed
• 80446ea implement installer/uninstaller for osprey service docker image
• f4610b9 dockerize osprey service, add HTTPs support, add multi-version support
• a03a9d0 make NodeProcessor threads in COFFEE recover from errors getting nodes from NodeDB
• 7ac63dd add useful toString() method to PartitionFuction.Values
• 9c7937a fix bug when converting AssignedCoords with small molecule to old-style molecule, fixes #172
• 170d1b6 change version file to osprey-version
• e8a41b0 fix bug in conf space builder where two wild-type fragments had the same id
• eed36e5 change SeqDB precision defaults to prevent pfunc stalls in some cases
• a1ff6a8 abort coffee pfunc calculations if any precision errors are found
• e0cbde5 fix issues with build.properties not being written correctly
• 988b200 add missing imageOutputDir option to jpackage builds
• b8ee97b Change postgres table names to lower camelcase
• 82a8bbc Added simple test for sander coordinate parsing, fixed regex to really fix bug.
• e4d2b8e Fixed bug caused by Sander overwriting coordinate whitespace delimiter with a - symbol on negative coordinates.
• 42c2fd2 Add a more descriptive error message when atom coords not found
• d00ed4d Fixed bug in BigExp with infinity comparison
• 2d112a5 Save TPIE in the lib dir
• a115ebf change openjdk package to include jpackage
• 4bbae1e fix NodeDB bugs when switching sequences (was causing large performance issues), update tests, improve stats and logging, and also other minor quality of life improvements
• daeaae2 Merge branch 'main' into java16
• 6c82167 Add a new CLI
• eb480ad expose new COFFEE stats reporting options in python API
• 39a106d clear node performance data (used to score/rank nodes) when nodedb gets cleared
• c28bc6c add options to report stats for node processing
• 276d0f1 Update to JDK16, Gradle 7
• 6cc15af RLimit fields should be public
• 26ad755 add some tools to monitor memory usage particularly in a SLURM environment
• 64106bb get rid of custom Duration class, apparently the Java runtime library already has one
• 68e8c66 fix a data race in the new distributed z matrix calculator
• 0d2520b make sure the case of residue types in SeqSpace positions are handled consistently
• 6d66e08 add a new regression test to check tightness of conformation energy bounds
• 1496fe5 update to a new version of the BigDecimalMath library to get a fix for a concurrency issue
• 5cf3514 convert another JCuda exception into a GPUs-not-present signal
• 903fb40 add some debugging code (commented out) for looking into forcefield issues
• 7448449 fix a bug where the K* director for COFFEE was saving ensembles when it wasn't supposed to
• 90ec7e0 add a detailed test to check forcefield atoms pairs for a test conf space, and update tests with new compiled conf spaces
• e03d8b2 Update to Java 16
• 495cc84 fix bug in conf space compiler that sometimes omitted forcefield atom pairs between different molecules
• 51978b5 add a timeout to pfunc calculations in K*, since sometimes loose bounds can cause pfunc calculations to take WAY longer than we'd like, but we still want to get through all the sequences
• db0bdd9 add workaround for edge case in tools that call amber (single-residue polymers)
• 8035fd6 update to new kludge version, to fix binary incompatibility with newer kotlinc (inline/value classes)
• 9a77b84 fix edge case in Mol2 persistence
• 4242574 switch ClusterZMatrix from a static work partition to a dynamic one, to hopefully make the calculation much less prone to timeout errors on large jobs
• 7a77488 fix integer encoding errors when using byte buffers
• 0a4d82d improve error handling and reporting in cuda conf energy calculator, and add better error messages for common error cases
• eb5fef3 add extra guidance on memory allocations in SLURM example script
• 17f2db3 cleanup log output for K* COFFEE director
• 67dc1be cleanup residue analysis code in AssignedCoords.toMol() and make errors more descriptive
• 8cd67c9 fix bug in conf space compiler that was recording PDB metadata incorrectly, causing later errors when trying to write PDB files
• a74a956 work around a bug in Ktor (possibly) to fix an issue with the conf space compiler
• a31527a fix bug when reading conf space files
• 8349606 update kotlin/ktor/serialization library versions to (hopefully) fix a concurrency bug in the osprey service
• 6ce8006 try to debug a non-deterministic bug, but fail, so just add more logging instead
• d71f2a1 fix bug in copying dihedral angle motions when copying conf spaces
• 094aac8 fix .gitignore file to stop filtering out amber binaries
• e1715d6 start a skeleton for the statically-generated documentation website, based on hugo and pydoc-markdown
• 3e095ce make an example script for running K*+COFFEE on a SLURM cluster
• 79fc2a5 make Python API and example script for a bounded-memory version of K* that uses COFFEE
• 2bb6863 update the example conf space to contain the wild-type sequence, otherwise we can't use stability thresholds in K* designs
• fae0034 make writing conf space files deterministic, ie don't let unordered hash tables cause things to be written in quasi-random orders
• ca16901 remove duplicated file
• e75c42c implement a K* director for COFFEE
• 1b268d6 fix bug in build script when starting from a clean clone from the repo
• 5ba999c Trigger builds on commits to main rather than master
• c04a51e fix bug where serialization/deserialization trips with energy matrices weren't saving the constant energy term
• 8f435eb implement Python API for K* designs using the new conf space tools, also make K* designs NOT resume by default
• cbac634 move conformation library selection to its own tool, to make it possible to load conflibs before creating wild-type conformations, which avoids an issue where wild-type conformations have no motions, because conflibs haven't been loaded yet.
• c05c20d...

3.2.213

Changes:

• f5b765f Merge pull request #148 from donaldlab/kstar-task-context
• 31a83c3 Pass the TaskContext as a parameter to the partition function creation.
• 7f1fc31 fix bug with python pip tasks in the Gradle script
• 264f4ac Merge pull request #145 from donaldlab/144-idx-out-of-bounds
• 3b79d74 Only submit score tasks when there are actually conformations to score.
• 3515b31 Merge pull request #141 from donaldlab/azure-fix
• 4e51caa specify to look in the root project for the AZURE_BUILD_ID property
• 13931cf Atom pair interactions (#139)
• 9419e53 provide the jar:// filesystem for runtime images of OpenJDK14, so JPype works correctly
• 890a6b5 Add function to allow for arbitrary jvm args.

See More

• 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
• 1ad5db3 fix NPE in SOFEA when not using ConfDB
• de597d4 Merge pull request #124 from donaldlab/float_dihedrals
• 9e3cbbc Merge branch 'master' into float_dihedrals
• e27d8e0 Read in dihedrals as floats

This list of changes was auto generated.

3.2.203

Changes:

• 523202c Add --scan-flex-dist as a binding affinity parameter.
• cb13874 Merge branch '144-idx-out-of-bounds' into develop
• 3b79d74 Only submit score tasks when there are actually conformations to score.
• 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*
• 3515b31 Merge pull request #141 from donaldlab/azure-fix
• 4e51caa specify to look in the root project for the AZURE_BUILD_ID property

See More

• 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
• 13931cf Atom pair interactions (#139)
• 78e2b9d Add azure-pipline and gradle application support
• 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...

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...

3.2.172

Changes:

• 9419e53 provide the jar:// filesystem for runtime images of OpenJDK14, so JPype works correctly
• 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
• 1ad5db3 fix NPE in SOFEA when not using ConfDB
• de597d4 Merge pull request #124 from donaldlab/float_dihedrals
• 9e3cbbc Merge branch 'master' into float_dihedrals
• e27d8e0 Read in dihedrals as floats

This list of changes was auto generated.

3.2.101

The big news in this release is that we've packaged the JRE with the binaries, meaning you don't have to have java already installed on your system to run Osprey. Additionally, this release contains a number of bug fixes. The detailed changes from the last published release are below.

Changes:

• 3595d64 Add Azure Pipelines CI/CD and use python -m pip instead of pip executable
• ead5ce0 Set up CI with Azure Pipelines
• ed0049d Revert "Merge pull request #121 from donaldlab/confTableFactory"
• 3c07fba Merge pull request #121 from donaldlab/confTableFactory
• cd5db8d Add builder for ConfTable for Andy
• 0fd9b21 The return of listBackboneVoxels expects one element
• 3947ec5 Merge pull request #119 from donaldlab/bug-115
• 79621fb Make field public
• 4dc5f7e Merge pull request #118 from donaldlab/bug-114
• a690121 Don't attempt to serialize EPICMatrices

See More

• bd3ede8 Merge pull request #117 from donaldlab/cats-multiple-regions
• 887be63 Allow multiple CATS backbone flexible regions
• 94dcf73 Merge branch 'python-debug'
• d134a53 Add the ability to attach to a java debugger while using Python script
• 8cc5e48 remove references to dev tools that aren't part of osprey
• 959b9ed refactor new compiled ConfEnergyCalculator interface to remove any dependency on TaskExecutors
• d176dbd add benchmarks for energy matrix calculation
• d42875b start to benchmark the new energy calculators
• 0c8a303 add the "v2" template coords to the resources
• 9211cd8 add stability filter to MinLMFE criterion for SOFEA
• 3c6f418 optimize SOFEA thread synchronization a bit
• 821770b fix a subtle concurrency bug in SOFEA
• 8c0b54b debug forcefield code, update the compiled conf spaces
• 5c6d684 update the Python scripts to the new K*/BBK*/Pfunc APIs, and integrate the sequence analysis into all K*/BBK* examples
• c811868 fix issues with tests, so real bugs aren't hidden in failed test noise:
• af0a93a fix PartitionFunction interface to match better with modern pfunc implementations, update BBK* to support compiled conf spaces, and also fix a zillion little bugs introduced by the recent cluster changes
• 617c7ed Merge branch 'cluster'
• 49f3ff7 support SSBOND and CONECT records when writing PDBs
• b277156 integrate with SLURM to get cluster info
• 6fec087 update K* to work with cluster parallelism
• 99f6b22 give the task contexts lifetimes, and let the cluster synchronize on them, so nodes can share results of cluster computations
• 7431439 get emat and pfunc calculation working over the cluster
• a154ebb refactor the cluster/parallelism/ecalc implementation to suck less
• a423db0 oh right, we require JDK 11+ now, so let the Java compiler use the new features
• a4ff228 integrate cluster code with Parallelism system, implement tasks running with context, and get lab code working with energy calculator
• fcaaafd implement a properly load-balanced task executor service, instead of the randomized one that Hazelcast comes with by default.
• 3d8fca8 try to get cluster parallelism working with Hazelcast
• 21251a5 fix build issues in windows
• ad039c6 more tweaks to readme
• 52e3207 update readme
• 085b27f try to fix travis issues: still getting weird errors with setup tools, try to install setuptools before other python packages
• 3818190 try to fix travis issues: explicitly install python 2 and 3, and install packages via pip for both
• 148bb0a try to fix travis issues: install python3-pip
• 675e6b9 try to fix travis issues: go back to apt-get instead of apt
• 2d19f71 print OS/platfor info in Osprey preamble
• 7033390 try to fix travis build issues
• e5072fe improve build support for python 2 and 3
• 6459595 update the gdrive upload script to catch the new filenames
• dd07fc6 bump version to 3.2
• 36a1a9c add support for Python3!
• 220aace update TravisCI to build against OpenJDK11
• 7a33437 update filename references to avoid compound extension names, because mac
• 6237725 add auto-generated docs for newer classes
• 09d9f9f update build system to bundle the JRE, so we can develop with any JDK we want
• 6acd1dc rename files to use new non-compound extensions
• fb4778e warn developers that they'll need at least a v11 JDK now to compile osprey, fix issues with JVM memory reporting, and add a test to (hopefully) catch future JVM memory reporting issues.
• 21c4583 Merge remote-tracking branch 'origin/master'
• 3d9a50f Port fix to UpdatingEnergyMatrix bug in master for MARK* design runs.
• 124a671 propagating fixes from Nate
• d931e0b Fix bug in script.
• 6c04e51 Update example script to pass in (newly mandatory) confEcalcRigid parameter for BBK* runs.
• 00d1359 Using PartitionFunctionFactory.makeConfSearchFactory to make confSearchFactories in the event that they're needed to compute bounds.
• 6659e0d fix bug where compiled conf spaces make positions in seq spaces that aren't actually mutable
• 0e4e1db update F98Y example with more continuous flexibility
• 3ee34a8 update conf spaces to the new format
• 3ed4bde implement molecule dihedral angles in the "static" atoms, so we can eg add continuous flexibility to small molecule ligands
• a99c1d4 Use the provided ConfSpaceInfo's ConfSearchFactory if it's not null.
• 8300eab Modify SequenceAnalyzer to use a static method from PartitionFunctionFactory to generate the ConfSearchFactory.
• 49ef10b update to new conf space and compiled conf space formats
• f8b7b1c implement molecule rotations and translations in the new compiled conf space format, also update all the compiled conf spaces to the new format
• 1e7a393 make the SequenceAnalyzer a little nicer, make it work with compiled conf spaces, and update the example K* script to use it
• 278e494 implement conversion of AssignedCoords instances to Molecule instances, using new metadata in the compiled conf spaces, also update testing,example compiled conf spaces to new format
• ac36c30 rough draft of a python script for a K* design using the new conf spaces
• c37106f fix issues with GradientDescentPfunc and conf spaces with no design positions, also cleanup a bit and use BigMath for more consistent precision and performance
• 5636cc7 fix issues with: conf spaces with no design positions, including static-static energies in conformation scores,energies printing large BigDecimals
• 3b33849 let CPUConfEnergyCalculator instances share a single thread pool, but still handle resource cleanup correctly
• 41d140d refactor K* to also support the new compiled conf spaces and get it all working correctly.
• 159544b Build energyMatrix and confSearchFactory from scratch in SequenceAnalyzer to support BBK* runs that don't create a confSearchFactory.
• 179263d consume new binary format for compiled conf spaces, and start to work on tests for K*
• fa33695 update to new compiled conf space format from the GUI
• d288542 test confecalc adapter on pfunc calculation
• 061a524 integrate CPUConfEnergyCalculator with parallelism system
• 3407341 integrate new compiled conf spaces with A* and GMECFinder
• db8e134 start integrating the new ConfSpace and its related energy calculators with the existing ConfEnergyCalculator system, ...

v3.2 beta 1

This release of the Osprey Python library is a beta version of the new conformation space system created by the GUI.

This time, there are operating system-specific distributions, since Osprey now contains its own Java Runtime Environment (JRE). Meaning, It's no longer necessary to install Java before using Osprey.

Also, we've added support for Python 3, so be sure to download the file that corresponds to not just your operating system, but also your Python environment, either 2 or 3.

Version 3.1 release candidate 1

This release incorporates performance improvements and bug fixes made over the past year.