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ChangeLog
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#===============================================================================
## Log of code changes in the POPScomp suite
## Adaptation to R-compatible output and FunPDBe starts at version 2.0
## Development of Shiny App starts at version 3.0
## Docker image released at version 3.1
#===============================================================================
- 3.2.2
Sun 26 Mar 12:28:23 BST 2023
Changed branch name 'master' to 'main', because that is now the
standard in GitHub and the CI failed.
Virtual instance updated to Ubuntu 22.04.2 LTS (GNU/Linux 5.15.0-1030-gcp x86_64)
Re-installation of R packages, POPSR and re-compilation of POPSC.
Mon Oct 25 17:20:19 BST 2021
runID now also dependent on PDBfile upload
- 3.2.1
Sat 28 Aug 12:13:14 BST 2021
Fixed non functional button 'Download All Results'.
Now a run ID is created as a digest of the system time whenever
the input parameters are modified. That run ID is used for the name of
the output directory and its zip file. It is also used for all other
downloaded files. That way files belonging to the same run are tied
together by a unique identifier.
- 3.1.8
Added "busyIndicator" from "shinysky" library to flag background computation.
- 3.1.7
Wed 23 Dec 09:30:46 GMT 2020
The Shiny interface fails when a (single-chain) protein has no chain name,
because the white space is interpreted as missing "chain" column.
This has now been corrected in POPS by inserting a '-' chain character.
- 3.1.6
Sun 20 Sep 18:18:55 BST 2020
Fixed multi-chain error; 'wait' switch for system calls
Fixed two bugs in 'dim' calls.
- 3.1.5
commit/e6c7a62d9d6bbaa2ee948e7c52edbdfed9612413
Removed sensitive file.
- 3.1.4
commit/8f96f1ca06c4928cce6f8bb4330588c131f11813
Improved initialisation.
- 3.1.3
commit/034ee1f0104474f644059fbc39c3c57562e3d90e
Improved initialisation and re-running of app.
- 3.1.2
Sat 22 Feb 09:20:46 GMT 2020
Zenodo DOI.
- 3.1.1
Wed 12 Feb 19:35:20 GMT 2020
Several bug fixes regarding paths and complex detection.
Public release of GitHub POPScomp.
- 3.1
Sun 9 Feb 10:25:43 GMT 2020
Implementation of POPScomp functionality completed.
- 3.0.6
Sun 2 Feb 19:00:11 GMT 2020
Added --routPrefix switch to identify POPSCOMP output.
- 3.0.5
Sat 1 Feb 21:45:36 GMT 2020
Added logo to Shiny interface.
Added download buttons to Shiny interface.
- 3.0.4
Sun 19 Jan 00:08:40 GMT 2020
Corrected output file names for --rout.
Previous names broke Shiny app.
- 3.0.3
Wed 15 Jan 10:01:58 GMT 2020
Makefile pipeline for large-scale run over PDBML.
Run over >150000 structures (all <4MB) of PDBML.
Validated output.
Uploaded output to FunPDBe server using 'lftp'.
- 3.0.2
Fri 20 Dec 10:00:19 GMT 2019
Made PDBML version memory clean; just DLL libraries flag problems in
valgrind, but that is likely a valgrind bug.
Added OpenMP support instead of MPI support, but requires code change.
topol.c:nonbonded memory allocation outside loop, for example
Removed MPI support
Changed to error exit=0 and empty <pdbID>.json output
- 3.0.1
Sat 23 Nov 15:34:37 GMT 2019
Fixed bug: Now PDB identifier is read correctly from XML file.
Removed HET atom matching until POPSCOMP functionality reinstated.
Added recognition of alternative locations: only 'A' sites accepted.
Corrected nucleotide residue matching.
Release of new POPScomp_PDBML data resource.
- 3.0
Mon 22 Apr 22:53:52 BST 2019
Launched POPScomp as R Shiny server popscomp.org:3838.
Development of POPSC and POPSR synchronised under
https://github.com/Fraternalilab/POPScomp.
- 2.3
Sat 18 Aug 15:47:57 BST 2018
master branch: adding capability to read gzipped files
configure.ac checks presence of zlib (system) library
HET residues and atoms are output with original names
HET nucleotides are now recognised by N3 (instead of P)
- 2.2
Sat 18 Aug 15:48:07 BST 2018
PDBML branch: PDBML formatted files can be read as input
configure.ac checks presence of libxml2 (system) library
- 2.1
Sat 24 Feb 15:27:07 GMT 2018
json branch: Implementation of JSON output for Elixir in the branch 'json'.
https://github.com/DaveGamble/cJSON
- 2.0
Sun 15 Oct 23:32:59 BST 2017
Rout branch: Making the transition to R-based post-processing of SASA data
in branch 'Rout'.
- 1.8.1
Thu Jul 21 15:18:43 BST 2016
Added Calpha to bSASA calculation
- 1.8.0
Mon Jun 13 00:11:54 BST 2016
New feature: Output of a nearest neighbour list between
distinct chains, where only the contact residue with the shortest
distance is listed. The default output is 'interface.out'.
To enable with the switch --intefaceOut.
- 1.7.0
Fri Jun 3 11:35:12 BST 2016
New feature: Output of the buried SASA (bSASA).
Assuming SASA is calculated for residue 'i',
bSASA is summed only over side-chain atoms to form bSASA_phil and
bSASA_phob, depending upon the hydrophilic or hydrophobic
nature of the contacting atom. bSASA default output is 'popsb.out'.
- 1.6.5
Sat May 28 17:17:42 BST 2016
Bug fix: Now considering PDB format column
'27 AChar Code for insertion of residues'.
- 1.6.4.
Sun Apr 12 12:59:43 BST 2015
Corrected output annotatation and format of %SASA to Q(SASA).
Changed output format of molecule SASA.
- 1.6.3
Sun Apr 12 12:59:08 BST 2015
Few weeks ago, changed wrong return status back to zero.
- 1.6.2
Wed Nov 6 17:48:11 GMT 2013
Added suggestion if no bonds are found: use '--coarse'.
Now exiting when the same atom is used for distance calculations because
of atom clashes. This leads to segmentation faults otherwise.
- 1.6.1
Tue Oct 8 15:15:03 BST 2013
Bug fix for 20130925: Relative residue SASA returned as 'nan'.
'neli.out' not linked by web server.
Bug fix for 20130806: Web server gives error code for Se and S_ hetero atoms.
Modified output headers for consistency.
- 1.6.0
Sat Mar 2 09:32:54 GMT 2013
MPI version.
- 1.5.5
Fri Sep 28 13:40:34 BST 2012
Added --enable-debug and --enable-profiling configure options.
- 1.5.4
Thu May 31 18:12:10 BST 2012
Removed bug in %SASA calculation.
- 1.5.3
Wed May 2 18:40:55 BST 2012
Modified trajectory SASA calculation: now the output goes to a separate
file for each trajectory structure and the output per structure is
using the same parameter settings as the main output.
- 1.5.2
Tue Oct 25 15:20:21 BST 2011
Bug fix: surface calculation works now for coarse grained.
- 1.5.1
Thu Oct 13 16:28:15 BST 2011
Added fractional SASA to output.
- 1.5.0
Mon Sep 26 11:11:57 BST 2011
Added computation of solvation free energies.
- 1.4.0
Thu Aug 4 18:20:46 BST 2011
Added printout of date-time and command line argument values.
Mon Apr 4 16:35:16 BST 2011
POPS is now under Git control.
Created branch 'trajectory'.
Added trajectory input. A GROMOS96 trajectory is provided with switch --traj
and POPS* is performed on each frame. The total SASA output is listed
in pops.traj.out.
- 1.3.2 : released
Tue Mar 15 16:38:37 GMT 2011
Command line argument rProbe was not used in program, but the constant_sasa
value instead. Fixed that, but segmentation faults appeared for rProbe > 4.
Increased allocation of topol->neighbourState and topol->neighbourPar
to 1024 and added assertion '< 1024' to neighbour list construction.
- 1.3.1 : released 07.03.11
Fri Mar 4 14:46:37 GMT 2011
Modified output of neighbour list to match the PDB numbering.
- 1.3.0 : released 01.02.2011
Tue Feb 1 20:26:48 GMT 2011
Addded modified cutoff for 'P' atoms in coarse grained mode.
Improved warning for format error and added format examples to README.
- 1.2.4 : released 22.10.2010
Thu Oct 21 08:26:45 BST 2010
Added check for non-standard residue types for all ATOM entries,
not only for CA/P atoms.
Thu Jan 21 13:20:44 GMT 2010
Added GROMOS atom types to 'atomgroup_data.h'.
Added output file name to stdout.
Fri Dec 11 13:42:24 GMT 2009
Added external variable 'status' which is the return value of 'main',
to indicate 0=error-free, -1=warning or 1=error.
- 1.2.3
Fri Dec 4 15:53:17 GMT 2009
Modified default behaviour for short atoms.
Fri Dec 4 12:19:49 GMT 2009
Added correction function 'standardise_name'
to 'getpdb.c' routines to deal with atom name deviations.
- 1.2.2
Mon Oct 12 18:08:53 BST 2009
Added pattern matching for HETATM residues and
improved treatment of HETATM entries in SASA calculation.
- 1.2.1
Wed Sep 30 00:47:31 BST 2009
Added O1 and O2 C-terminal atoms (not PDB style).
Thu Sep 3 13:24:30 BST 2009
Updated configure.ac to current Automake style.
Sat Aug 22 20:28:28 BST 2009
Corrected number of atoms of DT from 22 to 21
Wed Jun 24 16:43:09 BST 2009
Removed duplicated 'input file' line in output.
- 1.2.0
Mon May 25 10:58:40 BST 2009
Changed compilation to GNU Build System
- 1.1.5
Thu Jan 29 16:46:16 GMT 2009
Modified 'atomgroup_data.h' to match the new 'sasa_data.h'.
Thu Jan 29 14:09:33 GMT 2009
Adaptation to modified vector library functions and addition of 'argpdb.h' header.
Thu Jan 29 11:22:47 GMT 2009
Ticket #6 'POPSc fails with DNA : 1DSZ.pdb'
PDB format 3.0 defines DNA residues as DC, DG, DA, DT, DU and DI and
replaces the '*' in saccharide atom names with '''.
Added residues DI (2'-DEOXYINOSINE-5'-MONOPHOSPHATE) and I (INOSINIC ACID).
Residue DN and N seem to be obsolete, but are kept for backward compatibility.
Added residue definitions for unknown polymer residue UNK and
unknown ligand residue UNL.
Wed Dec 17 15:08:55 GMT 2008
Added '--padding' option.
Wed Dec 17 14:30:25 GMT 2008
Added '--silent' and '--noHeaderOut' options.
Fri Dec 12 17:15:37 GMT 2008
Modified 'README' as main page of Doxygen output.
Fri Dec 12 16:07:28 GMT 2008
Added '--noTotalOut' option
- 1.1.4
Wed Dec 3 00:10:04 GMT 2008
Ticket#3 'nan' result for ASTRAL-SCOP domains
'd1bd8__' and 'd1gsma1'. This is caused by too short atom distances, which
create 'circular' diheder angles. Addded error handling for that case:
"Problematic conformation at atom 1168
Error: Check input structure for too short atom distances!"
Exits with error code 1.
- 1.1.3
Fri Oct 24 14:25:26 BST 2008
Added atom group code.
Fri Oct 24 14:24:56 BST 2008
Added neighbour list output.
- 1.1.2
Tue Jul 15 16:02:33 BST 2008
Returns error code 2 if too few (<2)
atoms, bonds, angles or torsions. Updated README.
- 1.1.1
Tue Jul 8 00:37:47 BST 2008
Correction in residue assignment to chains.
- 1.1.0
Sun Jun 29 13:08:19 BST 2008
Added 'chainOut' option.
Sun Jun 29 11:57:41 BST 2008
Modified 'atomOut' format.
Sat Jun 28 15:05:34 BST 2008
Adjusted aromatic ring parameters.
Sat Jun 28 13:34:11 BST 2008
Parameter GLY C changed from 1.90 to 1.72.
- 1.0.0
Mon May 12 18:58:53 BST 2008
first release for testing.
#===============================================================================