|Tags||Date||Developer||Last 200 Commit Logs|
| ||2019-10-17||johns||Added draft experimental direct I/O plugin timestep read APIs for|
high performance random access out-of-core trajectory I/O supporting
both OS kernel bypass and GPU-Direct I/O implementations.
* include/molfile_plugin.h 1.112 (changed +20 -1)
| ||2019-10-11||jribeiro||Delete charmmprev unused variable that was causing some issues with the deletion of topology files.|
* qwikmd/qwikmd_func.tcl 1.70 (changed +0 -1)
Delete legacy bond list updating call
* molefacture/molefacture_gui.tcl 1.72 (changed +3 -5)
Improvements to the hydrogen atoms deletion when the bond order is changed
* molefacture/molefacture_edit.tcl 1.17 (changed +21 -3)
Re-format and correction to some comments
* molefacture/molefacture_geometry.tcl 1.25 (changed +3 -2)
Re-wrote the text message in the info window when trying to select or modifying molecules anchor atoms.
* molefacture/molefacture_internals.tcl 1.53 (changed +1 -2)
| ||2019-10-08||jribeiro||Bugfix for the creation of mutation/protonation state combobox selector to clean the array, and not unset the array.|
* qwikmd/qwikmd_func.tcl 1.69 (changed +1 -1)
| ||2019-10-07||jribeiro||Add giff images to be used as motion indicators (arrows to expand and collapse GUI' frames). These images should be used instead of the unicode characters to prevent missing characters.|
Update QwikMD code to use the arrow giff images
* qwikmd/qwikmd_func.tcl 1.68 (changed +1 -1)
* qwikmd/qwikmd.tcl 1.82 (changed +46 -31)
* qwikmd/arrow_right.gif 1.1 (added binary)
* qwikmd/arrow_down.gif 1.1 (added binary)
Fix typo in the name of the lipid parameter file name.
* namdgui/namdgui.tcl 1.39 (changed +2 -2)
| ||2019-10-04||jribeiro||Bugfix for the patches adding atoms to two residues and the atomArray resizing routine. The solution was to keep a record of the patch name applied to the residue. If the record is empty of the patch name is different from the record, then resize atoms array (if needed).|
* psfgen/src/topo_mol_struct.h 1.23 (changed +2 -1)
* psfgen/src/topo_mol.c 1.64 (changed +34 -26)
Delete commented-out code and update the comments for the previous bugfix (adding atoms to two different residues)
* psfgen/src/topo_mol.c 1.65 (changed +4 -5)
| ||2019-10-01||jribeiro||Bugfix for the calculation of the scaling factor used to place the colinear lone pairs.|
* psfgen/src/topo_mol.c 1.63 (changed +10 -1)
| ||2019-09-17||mariano||Fixed parsing of hess.log to correct for systems larger than 10 atoms.|
Fixed output file name to be 'hess_job2_internal.hess'.
* fftk/fftk_QMORCA.tcl 1.2 (changed +10 -9)
| ||2019-09-17||jribeiro||Added a comment about psfgen_static_init function called by namd during the start-up process|
* psfgen/src/tcl_psfgen.c 1.88 (changed +4 -1)
| ||2019-09-17||johns||Updated psfplugin to correctly write out 10-character records for CHARMM|
EXTended format, and corrected some C++isms that worked their way into
src comments, etc. The new code uses ternary expressions to select
the right fprintf() format specifier when the CHARMM EXTended output mode
* molfile_plugin/src/psfplugin.c 1.84 (changed +41 -28)
| ||2019-09-13||jribeiro||Fix the writing of extended psf files to be compatible with CHARMM. The patch implements the 10 characters number in the "!N" header sections for the extended psf file format. Patch sent Joshua Vermaas.|
* psfgen/src/topo_mol_output.c 1.44 (changed +16 -14)
| ||2019-09-05||jribeiro||Update the version number to 2.0|
* molefacture/pkgIndex.tcl 1.9 (changed +1 -1)
* molefacture/molefacture.tcl 1.110 (changed +2 -2)
* molefacture/doc/index.html 1.21 (changed +1 -1)
* molefacture/Makefile 1.12 (changed +1 -1)
| ||2019-09-05||johns||Updated ffTK version numbers to 2.0.|
* fftk/pkgIndex.tcl 1.4 (changed +1 -1)
* fftk/fftk.tcl 1.15 (changed +2 -2)
* fftk/doc/index.html 1.19 (changed +6 -6)
* fftk/Makefile 1.8 (changed +1 -1)
| ||2019-09-03||johns||Updated pre-built binary docs PDF.|
* psfgen/doc/ug.pdf 1.3 (changed binary)
| ||2019-08-27||johns||Corrected ffTK Makefile to add files to the distrib target.|
* fftk/Makefile 1.7 (changed +1 -1)
Corrected hard-coded psfgen version dependency to 2.0
* solvate/solvate.tcl 1.65 (changed +2 -2)
Updated ffTK plugin that Mariano and Giuseppe have revised to add
abstractions that support multiple tools for quantum chemistry
calculations used in parameter development.
* fftk/fftk_guiProcs.tcl 1.48 (changed +23 -23)
* fftk/fftk_guiInterface.tcl 1.48 (changed +370 -188)
* fftk/fftk_distort.tcl 1.5 (changed +3 -2)
* fftk/fftk_SharedFcns.tcl 1.16 (changed +66 -1)
* fftk/fftk_QMORCA.tcl 1.1 (added +1689 -0)
* fftk/fftk_QMGaussian.tcl 1.1 (added +1457 -0)
* fftk/fftk_GeomOpt.tcl 1.10 (changed +25 -143)
* fftk/fftk_GenZMatrix.tcl 1.16 (changed +32 -547)
* fftk/fftk_GenDihScan.tcl 1.14 (changed +30 -153)
* fftk/fftk_GenBonded.tcl 1.20 (changed +16 -92)
* fftk/fftk_DihOpt.tcl 1.23 (changed +32 -108)
* fftk/fftk_Configuration.tcl 1.3 (changed +1 -1)
* fftk/fftk_ChargeOpt_ESP.tcl 1.2 (changed +154 -119)
* fftk/fftk_ChargeOpt.tcl 1.27 (changed +53 -146)
* fftk/fftk_BuildPar.tcl 1.19 (changed +1 -1)
* fftk/fftk_BondAngleOpt.tcl 1.21 (changed +37 -31)
* fftk/fftk.tcl 1.14 (changed +8 -4)
Updated hard-coded psfgen version dependency for psfgen 2.0
* networkview/networkView.tcl 1.11 (changed +2 -2)
* networkview/adjacencyMatrix.tcl 1.8 (changed +2 -2)
| ||2019-08-21||jribeiro||Added the warning for setting the vpbonds to 0 when preparing simulations for NAMD 2.13 containing lone pairs and Drude particles.|
* psfgen/doc/ug_psfgen.tex 1.22 (changed +1 -1)
| ||2019-08-13||ryanmcgreevy||Changed ReMDFF map generation to create initial unblurred map separately, avoiding issues with trying to apply a guassian with sigma 0|
* mdff/mdff_gui.tcl 1.48 (changed +9 -4)
Changed ssrestraint balloon tooltip proc name to avoid conflicts with actual ssrestraint proc
* mdff/mdffgui_balloon.tcl 1.2 (changed +1 -1)
* mdff/mdff_gui.tcl 1.47 (changed +1 -1)
| ||2019-08-09||jribeiro||Set the psfgen version to 2.0|
* psfgen/src/tcl_psfgen.c 1.87 (changed +3 -3)
* psfgen/src/pkgIndex.tcl 1.26 (changed +1 -1)
Update the psfgen version in the Makefile
* psfgen/Makefile 1.18 (changed +1 -1)
| ||2019-08-09||johns||Switched psfgen to use the new code paths by default.|
* psfgen/Makefile 1.17 (changed +1 -1)
| ||2019-08-06||jribeiro||Added Brian Radak to the authors' list|
* psfgen/doc/ug_macros.tex 1.15 (changed +2 -2)
Deleted the declaration of topo_mol_lonepair_t *lonepairList in the topo_mol_segment_t structure since it was not being used.
* psfgen/src/topo_mol_struct.h 1.21 (changed +1 -17)
Implemented safety checks to prevent the use of the molfile plugin to write structures with lone pairs and drude particles until the plugins are updated. Also prevented the use of writenamdbin for structures containing drude particles. Since the lone pairs are treated as atoms at the pdb level, and there is no extra field to add to the file (alpha and thole), we can use this command to write structures with lone pairs.
* psfgen/src/topo_mol_struct.h 1.22 (changed +6 -1)
* psfgen/src/topo_mol_pluginio.c 1.59 (changed +13 -1)
* psfgen/src/topo_mol_output.c 1.43 (changed +16 -1)
* psfgen/src/topo_mol.c 1.62 (changed +12 -2)
* psfgen/src/psf_file_extract.c 1.40 (changed +5 -1)
| ||2019-08-02||jribeiro||The first version of the updated documentation.|
* psfgen/doc/ug_psfgen.tex 1.21 (changed +105 -1)
* psfgen/doc/ug_macros.tex 1.14 (changed +3 -2)
Update the plugin version on the webpage.
* psfgen/doc/index.html 1.13 (changed +1 -1)
| ||2019-08-02||johns||Added macro to permit compilation on Win32|
* psfgen/src/pdb_file_extract.c 1.16 (changed +2 -1)
Eliminate warnings about potentially uninitialized vars.
* psfgen/src/topo_mol.c 1.61 (changed +2 -2)
Eliminated more uninitialized variable warnings
* psfgen/src/charmm_parse_topo_defs.c 1.18 (changed +9 -11)
* psfgen/src/topo_defs.h 1.11 (changed +7 -7)
| ||2019-08-01||jribeiro||Bug fix on the command delatom and fixed all the references to the dihedral atoms the during the writing process.|
* psfgen/src/topo_mol_pluginio.c 1.57 (changed +10 -10)
* psfgen/src/topo_mol_output.c 1.41 (changed +13 -9)
* psfgen/src/topo_mol.c 1.59 (changed +22 -45)
Continuing to silence compiler warnings on the "new" psfgen version
* psfgen/src/topo_mol.c 1.60 (changed +8 -30)
* psfgen/src/tcl_psfgen.c 1.86 (changed +7 -9)
* psfgen/src/psf_file_extract.c 1.39 (changed +3 -3)
Deletion of the unused static_assert_int_is_32_bits variable
* psfgen/src/topo_mol_output.c 1.40 (changed +1 -2)
* psfgen/src/psf_file_extract.c 1.37 (changed +2 -3)
* psfgen/src/pdb_file_extract.c 1.15 (changed +3 -3)
Elimination of the compiler warnings from Hydrogen mass repartition code, and assume default values correctly. The command assumes now the form of "hmassrepart dowater 1/0 mass [float numer]". The arguments are optional, and the default values are 0 for dowater and 3.024 for (hydrogen target) mass. Elimination of the variable "i" as a flag for whether the mass value was defined in the command.
* psfgen/src/tcl_psfgen.c 1.85 (changed +57 -45)
Fix the compiler warning messages on psf_file_extract functions.
* psfgen/src/psf_file_extract.c 1.38 (changed +10 -8)
* psfgen/src/psf_file.h 1.9 (changed +10 -2)
Include prototype declaration of the topo_defs_anisotropy function in the topo_defs.h
* psfgen/src/topo_defs.h 1.10 (changed +7 -2)
Include prototype declaration of the topo_mol_set_drude_xyz function in the topo_mol.h
* psfgen/src/topo_mol.h 1.14 (changed +7 -1)
Silencing compiler warnings on the new psfgen version
* psfgen/src/topo_mol_pluginio.c 1.58 (changed +8 -8)
Use the proper definition of atomtype with drude in the case of charmm psf file format
* psfgen/src/topo_mol_output.c 1.42 (changed +9 -2)
| ||2019-07-30||jribeiro||Anisotropy section of the psf files is now being parsed and loaded in the readpsf command.|
* psfgen/src/topo_mol_struct.h 1.20 (changed +5 -5)
* psfgen/src/topo_defs_struct.h 1.11 (changed +5 -5)
* psfgen/src/psf_file_extract.h 1.9 (changed +11 -0)
* psfgen/src/psf_file_extract.c 1.36 (changed +128 -8)
* psfgen/src/psf_file.c 1.16 (changed +49 -4)
Fix to the parsing and units conversion of the angles and dihedrals from the lone pair section. The distance, angles, and dihedrals are now float opposing to double, as this precision is enough for these quantities. The same change should be employed throughout the code in the areas where double is not necessary.
* psfgen/src/topo_mol_struct.h 1.19 (changed +5 -5)
* psfgen/src/topo_mol_output.c 1.39 (changed +4 -5)
* psfgen/src/psf_file_extract.h 1.8 (changed +7 -2)
* psfgen/src/psf_file_extract.c 1.35 (changed +18 -10)
Fixed some code formatting issues
* psfgen/src/topo_mol_pluginio.c 1.56 (changed +4 -4)
* psfgen/src/topo_mol.c 1.57 (changed +6 -4)
Set drude coordinates from the pdb when loading a psf and pdb containing drude particles. The coordinates from the drude are loaded from pdb either using the command coordpdb or the readpsf <> pdb <>. The other mechanisms to load structures are not yet up to date as molfile, psfgen, and NAMD binary files need to agree on how to store all this information. This is valid for reading and writing. Safety checks still need to be implemented to avoid segmentation fault if the user decides to use those mechanisms with drude.
* psfgen/src/topo_mol.c 1.58 (changed +27 -0)
* psfgen/src/pdb_file_extract.c 1.14 (changed +21 -1)
| ||2019-07-29||jribeiro||Continue to add read-in functionality for drude forcefield and lone pairs. The atoms are now filtered in the case of being lone pairs or drude particles. The bonds between these particles and their hosts may be present in the psf file. In this case, the bonds are not read from the psf, but they can be restored if the vpbonds option is set to 1 (default value) in the psfgen script.|
* psfgen/src/topo_mol_struct.h 1.18 (changed +29 -16)
* psfgen/src/topo_mol_pluginio.c 1.55 (changed +2 -2)
* psfgen/src/topo_mol_output.c 1.38 (changed +23 -17)
* psfgen/src/topo_mol.c 1.56 (changed +27 -20)
* psfgen/src/tcl_psfgen.c 1.84 (changed +2 -2)
* psfgen/src/psf_file_extract.c 1.34 (changed +18 -4)
Fix the printout of the dihedrals and impropers when using the molfile plugin.
* psfgen/src/topo_mol_pluginio.c 1.54 (changed +20 -16)
Include the chain ID info extracted from the pdb when using the command readpsd <> pdb <> command.
Fix the out-of-bounds references when deleting dihedrals and impropers
Beginning of the implementation of the read of structures containing drude particles and lone pairs.
The compiler messages will be addressed after the read-in functionality is complete.
* psfgen/src/topo_mol_output.c 1.37 (changed +7 -11)
* psfgen/src/topo_mol.c 1.55 (changed +34 -15)
* psfgen/src/topo_defs.c 1.20 (changed +3 -2)
* psfgen/src/psf_file_extract.h 1.7 (changed +18 -6)
* psfgen/src/psf_file_extract.c 1.33 (changed +230 -23)
* psfgen/src/psf_file.c 1.15 (changed +43 -8)
| ||2019-07-29||johns||Change plugin name for amira plugin as pointed out by Joao|
* molfile_plugin/src/amiraplugin.C 1.3 (changed +1 -1)
| ||2019-07-25||ryanmcgreevy||Removed old -allframes option from sim, a holdover from when this command used volmap. This functionality should be added back in the future.|
* mdff/mdff_sim.tcl 1.4 (changed +2 -2)
| ||2019-07-24||johns||Added Makefile for the JSON package.|
* json/Makefile 1.1 (added +23 -0)
Added TclLib pure-script JSON parser to the plugins tree to ease
implementation of particular web-based structure/forcefield query interfaces.
* json/pkgIndex.tcl 1.1 (added +12 -0)
* json/json_write.tcl 1.1 (added +190 -0)
* json/json.tcl 1.1 (added +325 -0)
* json/README 1.1 (added +6 -0)
* json/ChangeLog 1.1 (added +145 -0)
Added copyright and revision control headers to psfgen source files.
They should have been there all along, but they were missing. The headers
make it obvious what version was the basis for user-submitted patches
and the like, so they are helpful even aside from documentation/comments
that describe the source code purpose/structure etc.
* psfgen/src/topo_mol_struct.h 1.17 (changed +19 -0)
* psfgen/src/topo_mol_pluginio.h 1.9 (changed +19 -0)
* psfgen/src/topo_mol_pluginio.c 1.53 (changed +20 -0)
* psfgen/src/topo_mol_output.h 1.6 (changed +22 -2)
* psfgen/src/topo_mol_output.c 1.34 (changed +19 -0)
* psfgen/src/topo_mol.h 1.11 (changed +19 -0)
* psfgen/src/topo_mol.c 1.50 (changed +20 -0)
* psfgen/src/topo_defs_struct.h 1.10 (changed +19 -0)
* psfgen/src/topo_defs.h 1.9 (changed +19 -0)
* psfgen/src/topo_defs.c 1.18 (changed +19 -0)
* psfgen/src/tcl_psfgen.c 1.81 (changed +19 -0)
* psfgen/src/tcl_main.c 1.7 (changed +19 -0)
* psfgen/src/stringhash.h 1.3 (changed +19 -0)
* psfgen/src/stringhash.c 1.3 (changed +19 -0)
* psfgen/src/psfgen.h 1.8 (changed +26 -12)
* psfgen/src/psf_file_extract.h 1.6 (changed +19 -0)
* psfgen/src/psf_file_extract.c 1.32 (changed +20 -0)
* psfgen/src/psf_file.h 1.8 (changed +19 -0)
* psfgen/src/psf_file.c 1.14 (changed +20 -1)
* psfgen/src/pdb_file_extract.h 1.4 (changed +19 -0)
* psfgen/src/pdb_file_extract.c 1.12 (changed +20 -0)
* psfgen/src/pdb_file.h 1.3 (changed +14 -2)
* psfgen/src/pdb_file.c 1.6 (changed +15 -3)
* psfgen/src/memarena.h 1.3 (changed +19 -0)
* psfgen/src/memarena.c 1.4 (changed +19 -0)
* psfgen/src/hasharray.h 1.3 (changed +19 -0)
* psfgen/src/hasharray.c 1.5 (changed +19 -0)
* psfgen/src/extract_alias.h 1.2 (changed +19 -0)
* psfgen/src/extract_alias.c 1.2 (changed +19 -0)
* psfgen/src/charmm_parse_topo_defs.h 1.3 (changed +19 -0)
* psfgen/src/charmm_parse_topo_defs.c 1.17 (changed +19 -0)
* psfgen/src/charmm_file.h 1.4 (changed +19 -0)
* psfgen/src/charmm_file.c 1.4 (changed +19 -0)
Added the JSON package to the build.
* Makefile 1.144 (changed +2 -1)
Added the rest of the JSON package src files.
* json/json_write.test 1.1 (added +213 -0)
* json/json_write.pcx 1.1 (added +47 -0)
* json/json_write.man 1.1 (added +97 -0)
* json/json.test 1.1 (added +225 -0)
* json/json.pcx 1.1 (added +31 -0)
* json/json.man 1.1 (added +96 -0)
Commented problematic code in the hydrogen mass repartitioning command
processing (potentially uninitialized data) and eliminated
unused variables causing compiler warnings. Clearly more valgrind runs
are needed to find uninitialized data issues like these.
* psfgen/src/tcl_psfgen.c 1.83 (changed +13 -10)
Continued cleanup of compiler warnings, addressing missing includes for
required function prototypes, and so on.
* psfgen/src/topo_mol_output.c 1.36 (changed +9 -16)
* psfgen/src/topo_mol.c 1.53 (changed +35 -44)
Continued cleanup of compiler warnings, etc.
* psfgen/src/topo_mol.c 1.54 (changed +4 -7)
Corrected many portability, syntactic, and code style issues.
* psfgen/src/topo_mol.c 1.49 (changed +6 -8)
Corrected misspelled macro #ifdef check that led to bad function prototypes
* psfgen/src/topo_mol.h 1.12 (changed +3 -3)
Eliminated compiler warnings, misc cleanup.
* psfgen/src/topo_defs.c 1.19 (changed +6 -17)
Eliminated compiler warnings, unused variables, and unprototyped
functions due to lack of proper include files.
* psfgen/src/topo_mol.c 1.52 (changed +3 -10)
Elimination of compiler warnings
* psfgen/src/tcl_psfgen.c 1.82 (changed +4 -5)
Further corrections of the is_xxx() helper routine fctn prototypes.
* psfgen/src/topo_mol.h 1.13 (changed +4 -3)
Misc cleanup to eliminate compiler warnings
* psfgen/src/topo_mol.c 1.51 (changed +5 -5)
* psfgen/src/pdb_file_extract.c 1.13 (changed +3 -6)
Ongoing cleanup and elimination of compiler warnings
* psfgen/src/topo_mol_output.c 1.35 (changed +15 -24)
Replaced the old hash table implementation in psfgen with the current
one from VMD, which is also used by all of the plugins, for consistency.
The new version has better-doxygenized source comments (though still
in need of improvement), and is also updated with macros to handle the
namespace management needs of statically-linked plugins, e.g., the
molfile plugins so we don't encounter namespace collisions from multiple
plugins or other libs that contain the same hash table symbols.
* psfgen/src/hash.h 1.2 (changed +53 -21)
* psfgen/src/hash.c 1.2 (changed +67 -50)
| ||2019-07-23||johns||Continuing cleanup of illegal and non-portable syntax.|
* psfgen/src/topo_mol.c 1.44 (changed +19 -18)
Corrected C++ syntax that worked its way into code that should be
strict ANSI C.
* psfgen/src/topo_defs.c 1.16 (changed +6 -4)
* psfgen/src/charmm_parse_topo_defs.c 1.16 (changed +4 -6)
Corrected C++ syntax that worked its way into code that should be
strict ANSI C. Noted non-portable variable size local array allocation.
* psfgen/src/topo_mol.c 1.43 (changed +40 -49)
Corrected many portabilit, syntactic, and code style issues.
Commented on many locations where integer constants are used for
return codes without comments, these should all get replaced by
symbolic constants/enums/macros instead.
* psfgen/src/topo_mol.c 1.47 (changed +24 -21)
Corrected many portability, syntactic, and code style issues.
* psfgen/src/topo_defs.c 1.17 (changed +5 -0)
Ongoing correction of syntactic issues in psfgen.
* psfgen/src/topo_mol.c 1.46 (changed +62 -54)
Ongoing corrections to psfgen for ANSI C compliance
* psfgen/src/topo_mol.c 1.45 (changed +36 -24)
Orrected many portability, syntactic, and code style issues.
* psfgen/src/topo_mol_output.c 1.33 (changed +2 -1)
* psfgen/src/tcl_psfgen.c 1.80 (changed +31 -35)
Replaced non-portable/illegal dynamic array size construct with portable code.
* psfgen/src/topo_mol.c 1.48 (changed +3 -5)
| ||2019-07-23||gumbart||Changed readpsf / coordpdb lines to one line readpsf ___ pdb ___|
original version fails to read coordinates when segnames
in pdb are truncated and do not match those in psf
* solvate/solvate.tcl 1.64 (changed +9 -7)
* autoionize/autoionize.tcl 1.28 (changed +4 -3)
| ||2019-07-18||jribeiro||Skip residues evaluation without topology to be submitted to the cgenff until the cgenffcaller plugin is available. This allows the user to export the topologies, psf, and pdb files without being prompted with the error that the cgenff (server or local copy) is not defined correctly.|
* molefacture/molefacture_internals.tcl 1.52 (changed +10 -7)
| ||2019-07-17||jribeiro||Initialize atoms' lone pair and drude fields|
* psfgen/src/topo_mol_pluginio.c 1.52 (changed +9 -0)
* psfgen/src/psf_file_extract.c 1.31 (changed +8 -7)
| ||2019-07-16||jribeiro||The first psfgen version to pass the test suite; the hydrogen mass repartition (both in a small and half of a million atom structures) tests, and the build of the addictive charmm36 and drude force field with lone pairs and drude particles. As noticed before, there is still room for improvement in the data structure (avoiding the use of double and lone pair and drude information for all atoms); and also for speed up. Psfgen is now compiling with the molfile plugin and using it to generate js files (the other file formats can also be produced this way). The read-in of structures with lone pairs and drude particles will be developed next. Need to check if VMD still adds the space in the atoms' names with three characters when generating js files. This forces a while loop in the functions is_hydrogen and is_oxygen.|
* psfgen/src/topo_mol_struct.h 1.16 (changed +5 -0)
* psfgen/src/topo_mol_pluginio.c 1.51 (changed +41 -44)
* psfgen/src/topo_mol_output.c 1.32 (changed +27 -20)
* psfgen/src/topo_mol.c 1.42 (changed +598 -152)
* psfgen/src/topo_defs.c 1.15 (changed +1 -1)
* psfgen/src/psf_file_extract.h 1.5 (changed +23 -0)
* psfgen/src/psf_file_extract.c 1.30 (changed +24 -7)
* psfgen/src/psf_file.h 1.7 (changed +10 -0)
* psfgen/src/psf_file.c 1.13 (changed +39 -2)
| ||2019-07-10||jribeiro||Adding missing molefacture_balloontext.tcl to the VMFILES list of the Makefile|
* molefacture/Makefile 1.11 (changed +1 -1)
| ||2019-07-09||jribeiro||Remove the json parser package dependency from molefacture.|
* molefacture/molefacture.tcl 1.109 (changed +1 -2)
| ||2019-07-02||jribeiro||Allow the import of topologies with halogens, but only if no lone pairs are detected. This ensures compatibility with the CHARMM36 pre-lone pairs in the halogens.|
* molefacture/molefacture_internals.tcl 1.51 (changed +10 -3)
* molefacture/molefacture_gui.tcl 1.71 (changed +14 -2)
* molefacture/molefacture.tcl 1.108 (changed +9 -9)
| ||2019-07-01||jribeiro||Create a new mechanism to store and retrieve the parameters read by the plugin. Now there is a global list that stores all the parameters fed by the user, and upon reading, there is handlerID that is returned. This handlerID points to the position of the topology in the global list. In this way, the program calling this plugin does not need to store the topologies but queries the readcharmmpar plugin for individual components of the topologies. The overhaul is not complete. Further modifications will need to happen, especially changing the arguments of the procs to accept the handlerID instead of the full digested parameters.|
* readcharmmpar/readcharmmpar.tcl 1.21 (changed +51 -2)
Small changes and corrections to the documentation page
* molefacture/doc/index.html 1.20 (changed +24 -20)
Update plugin version
* readcharmmpar/readcharmmpar.tcl 1.22 (changed +2 -2)
* readcharmmpar/pkgIndex.tcl 1.8 (changed +1 -1)
* readcharmmpar/Makefile 1.10 (changed +1 -1)
| ||2019-06-28||jribeiro||Add message of "*Terminal Patches not supported" in the patches entry label|
* qwikmd/qwikmd.tcl 1.81 (changed +2 -2)
Fix bug in gui after detecting the presence of the cgenffcaller plugin
* molefacture/molefacture_gui.tcl 1.70 (changed +2 -2)
Fix hotkey definition for move fragments
* molefacture/molefacture_gui.tcl 1.69 (changed +1 -1)
Fix protein builder bug
* molefacture/molefacture_internals.tcl 1.50 (changed +1 -1)
* molefacture/molefacture_builder.tcl 1.41 (changed +1 -1)
Update the index.html of the Molefacture web page
* molefacture/doc/index.html 1.19 (changed +276 -59)
Update the plugin webpage according to the new version
* molefacture/doc/molefacture.png 1.5 (changed +316 -355)
* molefacture/doc/icons/translate.png 1.1 (added binary)
* molefacture/doc/icons/select_atom.png 1.1 (added binary)
* molefacture/doc/icons/rotate.png 1.1 (added binary)
* molefacture/doc/icons/move_frag.png 1.1 (added binary)
* molefacture/doc/icons/move_atom.png 1.1 (added binary)
* molefacture/doc/icons/duplicate_sel.png 1.1 (added binary)
* molefacture/doc/icons/del_bond.png 1.1 (added binary)
* molefacture/doc/icons/del_atom.png 1.1 (added binary)
* molefacture/doc/icons/bond_order.png 1.1 (added binary)
* molefacture/doc/icons/add_hydrogen.png 1.1 (added binary)
* molefacture/doc/icons/add_bond.png 1.1 (added binary)
* molefacture/doc/icons/add_atom.png 1.1 (added binary)
| ||2019-06-28||johns||Added rough draft initial placeholder data structures for|
alchemical free energy information in trajectory files.
* include/molfile_plugin.h 1.111 (changed +48 -3)
| ||2019-06-26||johns||Enable both plugin-based I/O and also the new psfgen internal implementation|
path when building huge structures.
* psfgen/Makefile.pluginio 1.4 (changed +2 -1)
| ||2019-06-25||jribeiro||Add the icons for the buttons of the new Molefacure interface. There are two versions of the same image, one for Linux and Windows, and the other "_mac.gif" for MacOS. This is necessary as tk 8.5 does not show the text of the radiobuttons when the "-indicatoron false" option is set. The Mac version of the icons has the text included in the image itself.|
* molefacture/lib/icons/translate_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/translate_selected.gif 1.1 (added binary)
* molefacture/lib/icons/translate_mac.gif 1.1 (added binary)
* molefacture/lib/icons/translate.gif 1.1 (added binary)
* molefacture/lib/icons/selectatom_sel_mac.gif 1.1 (added binary)
* molefacture/lib/icons/selectatom_sel.gif 1.1 (added binary)
* molefacture/lib/icons/selectatom_mac.gif 1.1 (added binary)
* molefacture/lib/icons/selectatom.gif 1.1 (added binary)
* molefacture/lib/icons/rotate_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/rotate_selected.gif 1.1 (added binary)
* molefacture/lib/icons/rotate_mac.gif 1.1 (added binary)
* molefacture/lib/icons/rotate.gif 1.1 (added binary)
* molefacture/lib/icons/move_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/move_selected.gif 1.1 (added binary)
* molefacture/lib/icons/move_mac.gif 1.1 (added binary)
* molefacture/lib/icons/move_frag_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/move_frag_selected.gif 1.1 (added binary)
* molefacture/lib/icons/move_frag_mac.gif 1.1 (added binary)
* molefacture/lib/icons/move_frag.gif 1.1 (added binary)
* molefacture/lib/icons/move.gif 1.1 (added binary)
* molefacture/lib/icons/duplicate_mac.gif 1.1 (added binary)
* molefacture/lib/icons/duplicate.gif 1.1 (added binary)
* molefacture/lib/icons/delete_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/delete_selected.gif 1.1 (added binary)
* molefacture/lib/icons/delete_mac.gif 1.1 (added binary)
* molefacture/lib/icons/delete_bond_mac.gif 1.1 (added binary)
* molefacture/lib/icons/delete_bond.gif 1.1 (added binary)
* molefacture/lib/icons/delete.gif 1.1 (added binary)
* molefacture/lib/icons/bond_order_mac.gif 1.1 (added binary)
* molefacture/lib/icons/bond_order.gif 1.1 (added binary)
* molefacture/lib/icons/arrow_right.gif 1.1 (added binary)
* molefacture/lib/icons/arrow_down.gif 1.1 (added binary)
* molefacture/lib/icons/add_hydrogen_mac.gif 1.1 (added binary)
* molefacture/lib/icons/add_hydrogen.gif 1.1 (added binary)
* molefacture/lib/icons/add_bond_mac.gif 1.1 (added binary)
* molefacture/lib/icons/add_bond.gif 1.1 (added binary)
* molefacture/lib/icons/add_atom_selected_mac.gif 1.1 (added binary)
* molefacture/lib/icons/add_atom_selected.gif 1.1 (added binary)
* molefacture/lib/icons/add_atom_mac.gif 1.1 (added binary)
* molefacture/lib/icons/add_atom.gif 1.1 (added binary)
Declare missing array ate the namespace level
* qwikmd/qwikmd.tcl 1.79 (changed +1 -0)
Molefacture redesign. The molefacture interface was completely redesigned to become more interactive and easy to use. Many features, like FEP and Nucleic Acid Builder, were hidden to reduce complexity while the new interface was being developed. These features will be re-implemented one at the time in the subsequent versions.
The new version is not based on xbgf files, as the molecule is designed in memory, and export to files only when necessary.
Instead of 3 different lists (atom, bonds, and angles), there is now only one table listing the atoms and its information (name, type, element, etc.). The bonds, angles, and dihedrals are detected automatically while the atoms are selected, and can be manipulated using the sliders in the respective GUI sections.
Molefacture can use Open Babel (obminimize command) or NAMD to minimize the structure being modeled. In the case of NAMD, CHARMM36 Force Field is used, and the user can submit the new molecule to the CGenFF server to fetch the topologies and parameters. TODO: The direct connection between VMD and CGenFF server (cgenffcaller plugin) is not yet distributed until the user authentication mechanism is defined. Once this is established, the plugin will be included in the VMD distribution, and the user will be able to submit to the server from directly within VMD. Until then, one has to this manually, or use the local version of CGenFF.
Many new functions were added, like adding independent fragments and bond them together; creating ring and chain "skeletons" made up of carbon atoms that can be decorated and modified for faster drafting of molecules, and an "Undo" button to go back to previous states in the modeling process.
This plugin will have more porpuses than just creating molecules, and the interface is planned to be modulated using the left panel (atom's table) by making this panel a notebook with tabs, in which each tab serves a different purpose. Example of one of these porpuses is the selection of the different partitions of a drug part of an alchemical transformation.
* molefacture/molefacture_state.tcl 1.22 (changed +266 -111)
* molefacture/molefacture_internals.tcl 1.49 (changed +2045 -1163)
* molefacture/molefacture_gui.tcl 1.68 (changed +3522 -1166)
* molefacture/molefacture_geometry.tcl 1.24 (changed +364 -288)
* molefacture/molefacture_edit.tcl 1.16 (changed +321 -118)
* molefacture/molefacture_builder.tcl 1.40 (changed +1222 -418)
* molefacture/molefacture_balloontext.tcl 1.1 (added +64 -0)
* molefacture/molefacture.tcl 1.106 (changed +1032 -82)
Update the definition of the amino acid fragments to ensure compatibility with the new Molefacture version.
* molefacture/lib/amino_acids/THR.mfrag 1.2 (changed +1 -1)
* molefacture/lib/amino_acids/PRO.mfrag 1.5 (changed +0 -3)
* molefacture/lib/amino_acids/GLY-end.mfrag 1.6 (changed +1 -3)
Update the definition of the fragments to ensure compatibility with the new Molefacture version.
* molefacture/lib/basemol/cyclooctane.mfrag 1.2 (changed +12 -36)
* molefacture/lib/basemol/cyclohexane.mfrag 1.2 (changed +8 -26)
* molefacture/lib/basemol/cycloheptane.mfrag 1.2 (changed +11 -32)
Update the definition of the fragments to ensure compatibility with the new Molefacture version. Add the carbonyl fragment
* molefacture/lib/fragments/frag.mdb 1.5 (changed +1 -1)
* molefacture/lib/fragments/cyclooctane.frag 1.2 (changed +11 -34)
* molefacture/lib/fragments/cycloheptane.frag 1.2 (changed +12 -32)
* molefacture/lib/fragments/carbonyl.mfrag 1.1 (added +11 -0)
Update version number.
* qwikmd/qwikmd.tcl 1.80 (changed +2 -2)
* qwikmd/pkgIndex.tcl 1.5 (changed +1 -1)
* qwikmd/Makefile 1.9 (changed +1 -1)
* paratool/pkgIndex.tcl 1.9 (changed +1 -1)
* paratool/paratool.tcl 1.111 (changed +2 -2)
* paratool/doc/index.html 1.9 (changed +1 -1)
* paratool/Makefile 1.15 (changed +1 -1)
* molefacture/pkgIndex.tcl 1.8 (changed +1 -1)
* molefacture/molefacture.tcl 1.107 (changed +2 -2)
* molefacture/Makefile 1.10 (changed +1 -1)
* idatm/pkgIndex.tcl 1.2 (changed +1 -1)
* idatm/idatm.tcl 1.19 (changed +2 -2)
* idatm/doc/index.html 1.3 (changed +1 -1)
* idatm/Makefile 1.4 (changed +1 -1)
* autopsf/pkgIndex.tcl 1.14 (changed +1 -1)
* autopsf/doc/tech.html 1.3 (changed +1 -1)
* autopsf/doc/index.html 1.14 (changed +1 -1)
* autopsf/autopsf.tcl 1.149 (changed +2 -2)
* autopsf/Makefile 1.22 (changed +1 -1)
| ||2019-06-25||johns||Revised write_js_timestep() to ensure that it will always succeed,|
regardless whether the caller provides page-aligned block-multiple-sized
memory buffers or not. Since write performance is generally far less
critical than read performance, two I/O calls (each) are used to
write out the Timestep coordinate and PBC unit cell blocks in
page-multiple-sized records on disk. We use a persistent zero-filled
buffer in the jshandle data structure to write the necessary padding bytes.
* molfile_plugin/src/jsplugin.c 1.81 (changed +32 -6)
| ||2019-06-24||jribeiro||Fix typo: '#' missing from in the comment.|
* autopsf/autopsf.tcl 1.148 (changed +2 -2)
Improvement of the ring detection using atomselection instead of moltoptools. moltoptools doesn't work for nanotubes.
make_bond now uses the bond list and bond order from the atomselection and not the one in memory. It is important to get the correct indexing when the atom's index is not consecutive.
As far as I am aware, only the new Molefacture uses this plugin.
* idatm/idatm.tcl 1.18 (changed +133 -42)
Prevent QwikMD from deleting molecules loaded before opening QwikMD. Update the Gui to use tktooltip and infobuttons plugin. Separate the GUI design from the declaration of long commands. Use a condensed atomselection in a single representation to represent the residues selected either on the "Manipulation Window" or in the OpenGL window, instead of creating individual representations per selected residue. Small Improvements and bug fix.
Add the interface between QwikMD and Molefacture. QwikMD can now export un-parameterized molecule to Molefacture. When Molefacture "apply to the parent," loads the information to the "Edit Atom" window of QwikMD. Although this works, one needs to make it more bulletproof.
* qwikmd/qwikmd_func.tcl 1.67 (changed +297 -71)
* qwikmd/qwikmd.tcl 1.78 (changed +1155 -1076)
Protect the filenames from spaces in the path. Enforce the detection of the first residue of the segment, so single residue segments are identified correctly.
* autopsf/autopsf.tcl 1.147 (changed +8 -8)
Reate a new mechanism to store and retrieve the topology read by the plugin. Now there is a global list that stores all the topologies fed by the user, and upon reading, there is handlerID that is returned. This handlerID points to the position of the topology in the global list. In this way, the program calling this plugin does not need to store the topologies but queries the readcharmmtop plugin for individual components of the topologies. The overhaul is not complete. Further modifications will need to happen, especially changing the arguments of the procs to accept the handlerID instead of the full digested topology.
* readcharmmtop/readcharmmtop.tcl 1.19 (changed +52 -4)
Update the plugin to use the new readcharmmtop plugin interface.
* qwikmd/qwikmd_func.tcl 1.66 (changed +3 -3)
* qwikmd/qwikmd.tcl 1.77 (changed +3 -2)
* paratool/paratool_topology.tcl 1.30 (changed +3 -2)
* paratool/paratool_readwrite.tcl 1.43 (changed +7 -4)
* paratool/paratool_components.tcl 1.35 (changed +5 -2)
* paratool/paratool.tcl 1.110 (changed +18 -8)
| ||2019-06-18||johns||Sync up psfgen plugin I/O Makefile with the Makefile for normal builds.|
* psfgen/Makefile.pluginio 1.3 (changed +3 -1)
| ||2019-06-07||ryanmcgreevy||Tooltips now use the new tktooltip plugin.|
* mdff/mdff_gui.tcl 1.46 (changed +44 -66)
| ||2019-06-07||johns||Added cv_dashboard, infobutton, and tktooltip plugins to the build|
* Makefile 1.143 (changed +4 -1)
Added info.gif to build
* infobutton/Makefile 1.2 (changed +1 -1)
Added initial infobutton Makefile
* infobutton/Makefile 1.1 (added +23 -0)
Added initial rev of infobutton plugin for use by QwikMD and MDFF plugins
* infobutton/pkgIndex.tcl 1.1 (added +16 -0)
* infobutton/infobutton.tcl 1.1 (added +148 -0)
* infobutton/info.gif 1.1 (added +10 -0)
Added initial tktooltip Makefile
* tktooltip/Makefile 1.1 (added +23 -0)
Added initial version of tktooltip plugin for use by QwikMD and MDFF plugins
* tktooltip/tktooltip.tcl 1.1 (added +47 -0)
* tktooltip/pkgIndex.tcl 1.1 (added +16 -0)
| ||2019-06-04||ryanmcgreevy||Added tooltip text for labels of main tab of MDFF GUI, MDFF Setup, to aid users in understanding the purpose of each option.|
* mdff/pkgIndex.tcl 1.7 (changed +1 -1)
* mdff/mdffgui_balloon.tcl 1.1 (added +162 -0)
* mdff/mdff_gui.tcl 1.45 (changed +70 -0)
* mdff/Makefile 1.7 (changed +2 -2)
| ||2019-05-31||johns||Updated cv_dashboard with a fix for the launch issue I previously reported.|
* cv_dashboard/cv_dashboard_main.tcl 1.2 (changed +1 -1)
* cv_dashboard/cv_dashboard.tcl 1.2 (changed +6 -4)
| ||2019-05-22||johns||Added cv_dashboard templates to the plugin tree|
* cv_dashboard/templates/moving_frame_of_reference.in 1.1 (added +25 -0)
* cv_dashboard/templates/components/tilt.in 1.1 (added +13 -0)
* cv_dashboard/templates/components/spinangle.in 1.1 (added +13 -0)
* cv_dashboard/templates/components/selfcoordnum.in 1.1 (added +11 -0)
* cv_dashboard/templates/components/rmsd.in 1.1 (added +12 -0)
* cv_dashboard/templates/components/orientation.in 1.1 (added +20 -0)
* cv_dashboard/templates/components/inertia.in 1.1 (added +11 -0)
* cv_dashboard/templates/components/hbond.in 1.1 (added +11 -0)
* cv_dashboard/templates/components/gyration.in 1.1 (added +11 -0)
* cv_dashboard/templates/components/groupcoord.in 1.1 (added +15 -0)
* cv_dashboard/templates/components/distancez.in 1.1 (added +16 -0)
* cv_dashboard/templates/components/distancexy.in 1.1 (added +16 -0)
* cv_dashboard/templates/components/distancevec.in 1.1 (added +14 -0)
* cv_dashboard/templates/components/distancepairs.in 1.1 (added +14 -0)
* cv_dashboard/templates/components/distanceinv.in 1.1 (added +15 -0)
* cv_dashboard/templates/components/distancedir.in 1.1 (added +13 -0)
* cv_dashboard/templates/components/distance.in 1.1 (added +13 -0)
* cv_dashboard/templates/components/dipolemagnitude.in 1.1 (added +10 -0)
* cv_dashboard/templates/components/dipoleangle.in 1.1 (added +16 -0)
* cv_dashboard/templates/components/dihedralPC.in 1.1 (added +12 -0)
* cv_dashboard/templates/components/dihedral.in 1.1 (added +19 -0)
* cv_dashboard/templates/components/coordnum.in 1.1 (added +20 -0)
* cv_dashboard/templates/components/angle.in 1.1 (added +17 -0)
* cv_dashboard/templates/colvar_extended.in 1.1 (added +36 -0)
* cv_dashboard/templates/colvar_analysis.in 1.1 (added +38 -0)
* cv_dashboard/templates/colvar.in 1.1 (added +37 -0)
Added new colvars cv_dashboard plugin to the plugin tree.
* cv_dashboard/pkgIndex.tcl 1.1 (added +16 -0)
* cv_dashboard/cv_dashboard_plots.tcl 1.1 (added +290 -0)
* cv_dashboard/cv_dashboard_main.tcl 1.1 (added +473 -0)
* cv_dashboard/cv_dashboard_editor.tcl 1.1 (added +395 -0)
* cv_dashboard/cv_dashboard.tcl 1.1 (added +286 -0)
* cv_dashboard/README.md 1.1 (added +52 -0)
* cv_dashboard/Makefile 1.1 (added +22 -0)
| ||2019-04-24||jribeiro||As the drude particles are never stored as atoms in the atomArray, it is necessary to make a first pass through all atoms in the residue to update the atomid (additional increment for drude particles on the host) before starting printing any information to the psf file. This was not being done previously, and it is now fixed. The need to duplicate the atomid update before printing to any file (psf, pdb or namdbin) would be avoided if the write commands were somehow communicating and setting a global variable when the atomids were first assigned. Not implemented yet.|
Fix the exclusion declaration as for every particle is necessary to have an entry, even for drude and lone pairs (0 as default).
* psfgen/src/topo_mol_output.c 1.31 (changed +74 -45)
| ||2019-04-22||jribeiro||Fix lone pairs initialization|
* psfgen/src/topo_mol.c 1.40 (changed +6 -2)
Fix the units of the colinear lone pairs. Initialize lone pair counter. Fix the line counter of the improper psf section
* psfgen/src/topo_mol_output.c 1.30 (changed +42 -35)
Re-do the initialization of the atom's lone pair flag and pointer
* psfgen/src/topo_mol.c 1.41 (changed +9 -3)
| ||2019-04-18||jribeiro||Fix missing initialization of the numaniso counter (counter of the anisotropy definitions) and the aniso pointer of the residues.|
* psfgen/src/psf_file_extract.c 1.28 (changed +2 -1)
Fix the dihedral and improper definitions based on the new data structure. TODO: the communication between psfgen and molfile plugin is still to be tested and developed. molfile plugin is still not capable of writing psf files for drude force field. The atoms section' columns Alpha and Thole are missing, as well as the sections NUMLP and NUMANISO.
* psfgen/src/topo_mol_pluginio.c 1.50 (changed +47 -2)
Fix the inclusion of psfgen.h so the PSFGENLOGFILE is defined and the messages can be saved to a log file.
* psfgen/src/tcl_main.c 1.6 (changed +4 -0)
Implementation of the parsing and assignment of the anisotropy definitions for the drude force field. These definitions are stored at the residue level, opposing the storage of bonds (e.g.) at the atom level.
Although there is not an explicit DELETE ANISOTROPY in the CHARMM, everytime an atom is deleted from a residue containing anisotropy definitions, all entries are checked. If the deleted atom is declared in an anisotropy definition, this entry is eliminated as well. There only one exception which is present in the toppar_drude_nucleic_acid_2017c.str, where one DELETE ANISOTROPY is found, but the same entry is re-define a few lines below this call - not sure if this is a mistake in the str file.
When comparing the psf files generated by psfgen and CHARMM, psfgen add the anisotropy defined in patches at the beginning of the aniso list of the first residue called in the patch. CHARMM places them at the end of the NUMANISO section.
Not much effort was put into the evaluation of the quality of the rtf and str files being read, as the drude force field doesn't have a lot of people developing their own topologies. This need to be worked out.
Regarding the drude force field and lone pairs, the read-in of psf/pdb files containing drude and lone pairs still need to be implemented.
Molfile plugin cannot write psf files containing drude and lone pairs yet.
* psfgen/src/topo_mol_struct.h 1.15 (changed +22 -1)
* psfgen/src/topo_mol_output.c 1.29 (changed +247 -16)
* psfgen/src/topo_mol.c 1.39 (changed +133 -12)
* psfgen/src/topo_defs_struct.h 1.9 (changed +26 -0)
* psfgen/src/topo_defs.h 1.8 (changed +1 -1)
* psfgen/src/topo_defs.c 1.14 (changed +116 -19)
* psfgen/src/psfgen.h 1.7 (changed +9 -0)
* psfgen/src/psf_file_extract.c 1.29 (changed +1 -1)
* psfgen/src/charmm_parse_topo_defs.c 1.15 (changed +43 -8)
Set the VPBONDS (virtual particle bonds) = 1 by default, so the bonds between the drude particles and their host, and the lone pairs and their host are printed in the bonds section of the psf file.
Fix the traverse of the atomArray array in the tcl_segment to increment the index i instead of incrementing the pointer itself.
Added the psfgen_kill_mol function call before returning TCL_ERROR.
* psfgen/src/tcl_psfgen.c 1.79 (changed +25 -16)
| ||2019-04-12||jim||Fix to velnamdbin log message by Brian Radak from NAMD repository|
Author: Brian Radak <email@example.com>
Date: Thu Aug 10 11:02:00 2017 -0500
Fix output error when writing velnamdbin
A modest output error was added when psfgen was modified to write
velnamdbin files as a secondary option for writenamdbin. The buffer
was simply being overwritten by the velnamdbin message rather than
first being printed to stdout. This is now fixed.
To reiterate, this only affected the message sent to stdout, the
actual files were of course being written as intended. I just
happened to be checking this carefully when I noticed the message
was not appearing.
* psfgen/src/tcl_psfgen.c 1.78 (changed +4 -1)
| ||2019-04-08||jribeiro||Bug fix in the extraction of dihedral from psf|
* psfgen/src/psf_file_extract.c 1.26 (changed +1 -4)
Delete duplicated output line with number of atoms
* psfgen/src/topo_mol_output.c 1.27 (changed +0 -2)
Fix the charge of the drude particle host atom
* psfgen/src/topo_mol_output.c 1.28 (changed +7 -2)
Implementation of hydrogen mass repartition in psfgen (patch by Brian Radak). This command assumes that a segment was already built, wither by segment command or read-in a psf&pdb/namdbin files. The mass of the hydrogen atoms are increased to the target mass (default 3.024), and the mass of the heavy atom is subtracted (heavy_atom_mass - hydrogen_mass - target_mass)
Hydrogen mass repartition syntax:"hmassrepart dowater/nowater (default nowater) <target mass (default 3.024)" - e.g. hmassrepart dowater 3.024
Command not documented yet.
* psfgen/src/topo_mol.h 1.10 (changed +5 -0)
* psfgen/src/topo_mol.c 1.38 (changed +14 -0)
* psfgen/src/tcl_psfgen.c 1.77 (changed +141 -0)
Initialize lone-pairs and drude fields when reading a psf file. The read-in functions are still not finalized but needed to fix this part to implement the mass repartition sent by Brian Radak
* psfgen/src/psf_file_extract.c 1.27 (changed +10 -0)
| ||2019-04-03||jribeiro||Initial implementation of lone pairs (lp) and drude particles. Here the lone pairs, like in the topology files (rtf/str) are treated as atoms with an additional structure topo_mol_lonepair_t. The structure has the values for distance, angle (in case of linear lp is used as scale), dihedral and a array of atoms - lp's host at which the lp is bonded and two other atoms that form the angle and dihedral that allow placing the particle. The linear lp has only one host and one additional atom to define the direction. As the declaration of bonds in lps is optional, psfgen ignores the ones read in rtf and generates them during the writing process if the command "vpbonds 1" (command not documented yet) is executed before the command writepsf. Ignoring the lp bonds makes is This same command also prints the bonds between the drude particles and their hosts. If "vpbonds 0", neither drude or lone pairs bonds are printed to the psf file.|
The drude particles are just store as additional info (alpha, thole, and type) in the host atom. The particle is generated when writing to the psf file, and it is never stored in the atomArray array.
The function to guess the lone pair's coordinates is the same as to guess the atom's coordinates from the IC card of atoms, only the order of the atoms is reversed. This follows the same logic of CHARMM and NAMD (which have the same functions to place particles .)
The implementation is not finished yet. So far, the !NUMLP and !NUMANISO sections are not being printed, and the read-in psf and PDB files are not implemented. The read-in will be actually the last one to be implemented, once the data structures changes are stable. The data structure may be changed rather soon to avoid have 2 doubles (alpha and thole) and 1 char* (drude type) that are never used, which is the case of additive force-field.
The variable lonepairList at the segment level (topo_mol_segment_t struct) will store lp pointers in the segment, in the additive force-field mode (if no drude particle is detected). This is quite useful as in the additive case we can have millions of atoms and a few lps. In this case, storing the pointers to this particles make it faster to address them instead of search in the atomArray. This is not implemented yet.
* psfgen/src/topo_mol_struct.h 1.14 (changed +60 -1)
* psfgen/src/topo_mol_output.c 1.26 (changed +228 -32)
* psfgen/src/topo_mol.c 1.37 (changed +474 -38)
* psfgen/src/topo_defs_struct.h 1.8 (changed +67 -6)
* psfgen/src/topo_defs.h 1.7 (changed +26 -0)
* psfgen/src/topo_defs.c 1.13 (changed +101 -2)
* psfgen/src/tcl_psfgen.c 1.76 (changed +40 -7)
* psfgen/src/psfgen.h 1.6 (changed +4 -0)
* psfgen/src/charmm_parse_topo_defs.c 1.14 (changed +178 -1)
New command to save the psfgen messages to a file (psfgen_logfile <filename>) and close the file (psfgen_logfile close), instead of printing to the console. This command allows to use several log files in the same psfgen session, but only one file can be opened at the time. This might be useful to store the messages of the different sections of the script to separate files.
Command not documented yet.
* psfgen/src/tcl_psfgen.c 1.75 (changed +145 -0)
* psfgen/src/tcl_main.c 1.5 (changed +17 -0)
* psfgen/src/psfgen.h 1.5 (changed +6 -0)
These commits start a series of changes that aim to improve psfgen's performance and implement CHARMM lone pairs and drude particles.
The data structure of the atoms in the molecule was changed from a linked list to an array (atomArray). Using an array brings a lot of advantages, including access the atom using the index that it appears in the topology, and not having walk all the list, comparing atom's name to find an atom every time it is needed. The index is valid as long as the topology is not defining patches and the residue was not changed (e.g., with deletions of a patch). In the cases where the residue was changed, we need to rely on the previous way to find atoms, by searching for its name in the residue. The atoms are still continuous, without gaps even when an atom is deleted, and the array has a null pointer at the end. When a patch is applied, the final number is tested, and if needed, the size of the array is expanded using realloc. To delete atoms, the pointers of the array are re-arranged to close the gap left by the deleted atom.
The dihedral and improper data structure were also changed, as now, instead of saving the same information in all the atoms that compose the dihedral or improper, including in the atom being used as index 0 of the definition, the atom being defined (e.g. index 0 of the dihedral) is not stored in the variable, the rest of the atoms are stored. This speeds up when going through the dihedrals and improper to be written to the psf file. The same changes in the angle data structure didn't return considerable time improvements, so it was left the same. One may want to apply the same logic to all data structures (angle, cmap, and exclusions) in the future. The bonds data structure was kept the same, as the atoms need to be accessible in both orders randomly, which make having the information about both atoms all the time beneficial.
The dihedral detection (auto-dihedral) also changed. Instead of using the angles to find the dihedral, now the bonds are used (fewer atoms to check - faster), and the atomid is used like in VMD, as the bonded atom has to have an id bigger than the previous to be considered.
To compile psfgen with the new changes, one has to add NEWPSFGEN as a compiler flag. Another flag was added for profiling purposes, NOIO. Add NOIO flag to the compiler, and the file printing events will be avoided.
Several comments were added throughout the code.
* psfgen/src/topo_mol_struct.h 1.13 (changed +129 -60)
* psfgen/src/topo_mol_pluginio.c 1.49 (changed +140 -3)
* psfgen/src/topo_mol_output.c 1.25 (changed +325 -0)
* psfgen/src/topo_mol.c 1.36 (changed +2102 -343)
* psfgen/src/topo_defs_struct.h 1.7 (changed +126 -2)
* psfgen/src/topo_defs.c 1.12 (changed +160 -0)
* psfgen/src/tcl_psfgen.c 1.74 (changed +38 -4)
* psfgen/src/psfgen.h 1.4 (changed +6 -0)
* psfgen/src/psf_file_extract.c 1.25 (changed +65 -5)
* psfgen/src/pkgIndex.tcl 1.25 (changed +1 -2)
| ||2019-03-28||jribeiro||Bug fix during the check for spaces in the definition of QM package installation path|
* qwikmd/qwikmd.tcl 1.76 (changed +2 -1)
| ||2019-03-06||ryanmcgreevy||Added basic segmentation interface to MapTools GUI. Since we use the -separate_groups option there to load the segmented maps as subvolumes of the original map, new volid selection menus have been added for both the main map and secondary map (for binary ops). Every command has been updated to use the sub volume volid where applicable.|
* mdff/mdff_gui.tcl 1.44 (changed +155 -45)
| ||2019-02-27||ryanmcgreevy||Added a save button for the main Map Tools mapmol which calls the new voltool write command to save the map to a file. Removed the auto-save dialog box popup from the commands with output options, since now a user can save the map directly.|
* mdff/mdff_gui.tcl 1.43 (changed +22 -20)
| ||2019-02-20||ryanmcgreevy||Added threshold option to the density load box to be used with the griddx command. This is especially useful now that the Map Tools GUI gives an interactive histogram plot, making it easier for threshold determination.|
* mdff/mdff_gui.tcl 1.40 (changed +16 -5)
Added threshold to saved settings and moved all Map Tools settings to their own namespace, since we don't have to worry about saving them because of their interactive nature.
* mdff/mdff_gui.tcl 1.42 (changed +136 -131)
Fixed incorrectly copied variable name, causing trace headaches
* mdff/mdff_gui.tcl 1.41 (changed +1 -1)
Fixed possibly long-standing bug where top was being used in an atomselect command instead of the molid variable, resulting in errors if the -mol option was used during restrain
* chirality/chirality.tcl 1.29 (changed +2 -2)
| ||2019-02-15||ryanmcgreevy||New Map Tools tab of the MDFF GUI provides a front end to the new Voltool commands for volumetric data manipulation, including an interactive multiplot based histogram, of which a command line version was also added to the mdff plugin.|
* mdff/mdff_map.tcl 1.5 (changed +7 -8)
* mdff/mdff_gui.tcl 1.39 (changed +790 -2)
| ||2019-02-15||jribeiro||Bug fix for initialization of checkbuttons without textvariable defined on Mac and Windows|
* qwikmd/qwikmd.tcl 1.75 (changed +4 -3)
| ||2019-02-14||jribeiro||Bug fix when QwikMD window was closed and an analysis tab is selected|
* qwikmd/qwikmd.tcl 1.74 (changed +7 -6)
| ||2019-02-14||johns||Started rewriting the pdbxplugin low-level parsing routines to allow them|
to handle the much more general formatting used by the IHM extensions.
Began implementing skeletal parsing of IHM cross link and cross link
The previous code skipped record types that contained string data of
various kinds, but this is not really an acceptable situation since it
breaks parsing of various types of IHM data, and it would mean that
parsing of the more general variants of mmCIF won't work either.
A general note about the previous code is that it wasn't written in a
very modular or extensible way, so some redesign is going to be required
to eliminate the sort of "cut and paste" parser code growth that occured
during early development.
* molfile_plugin/src/pdbxplugin.C 1.26 (changed +313 -15)
| ||2019-02-12||johns||Began revising the experimental Integrative Hybrid Modeling (IHM) features|
of the PDBx plugin to facilitate adding support for several more of the
IHM record types and to prepare for revisions to the molfile plugin
data structures to begin facilitating native handling of IHM data going
* molfile_plugin/src/pdbxplugin.C 1.25 (changed +48 -14)
| ||2019-02-11||johns||Minor revisions for self-consistency, code formatting, and readability.|
* molfile_plugin/src/pdbxplugin.C 1.24 (changed +201 -137)
| ||2019-02-08||johns||Pdbxplugin: Changed default behavior of the PDBx plugin to assign the|
PDBx type field to the VMD atom name field so we get CA atoms and others
labelled as VMD expects them to be per the original PDB file format
and variants thereof.
* molfile_plugin/src/pdbxplugin.C 1.23 (changed +12 -4)
| ||2019-02-07||johns||Added lmplugin and orcaplugin to the optional plugin compilation list.|
In principle, the ORCA plugin should be able to be enabled by default
after further testing/revisions have made it bulletproof.
The Lattice Microbes plugin has dependencies on both HDF5, and recursively
also on some compression libraries, so that means it can't be compiled if
we don't have the dependencies compiled and available.
* molfile_plugin/Makefile 1.132 (changed +2 -2)
Allow the DCD plugin to optionally skip checking the Fortran record
lengths against the system size, to permit easy recovery of files that only
have a single corrupted record length value. This is now unified with the
existing code to disable record length checks for systems with more than
2^30 atoms for similar reasons, to allow user-disabling of checking via
the VMDDCDNOCHECKRECLEN environment variable.
* molfile_plugin/src/dcdplugin.c 1.86 (changed +8 -3)
| ||2019-02-04||jribeiro||Prevent errors when no protein, nucleic or glycan molecules are present during structure check|
* qwikmd/qwikmd_func.tcl 1.65 (changed +5 -1)
| ||2019-01-29||johns||Continued correcting ORCA plugin helper functions that had the wrong|
* molfile_plugin/src/orcaplugin.C 1.5 (changed +12 -8)
Continued rewrite of ORCA plugin to address portability and
robustness issues. Corrected uninitialized state flag used
to track whether the ORCA log files were in units of Angstroms or Bohr.
* molfile_plugin/src/orcaplugin.C 1.4 (changed +156 -136)
| ||2019-01-10||ryanmcgreevy||Modified new histogram command to use voltool and fixed bug with multiplot x axis. Changed every remaining use of volutil to voltool. Removed -deprecate options for sim and cc. mdff plugin is now entirely independent from volutil.|
* mdff/xmdff_phenix.tcl 1.9 (changed +2 -2)
* mdff/mdff_sim.tcl 1.3 (changed +6 -46)
* mdff/mdff_map.tcl 1.4 (changed +95 -50)
* mdff/mdff_gui.tcl 1.38 (changed +1 -1)
* mdff/mdff_correlation.tcl 1.3 (changed +11 -72)
* mdff/mdff.tcl 1.7 (changed +4 -2)
* mdff/README_REMDFF.txt 1.2 (changed +1 -1)
| ||2018-12-17||johns||Updated comments to clarify what versions of Psipred the plugin has|
been successfully tested with after the latest update.
* psipred/psipred.tcl 1.7 (changed +5 -3)
| ||2018-12-15||johns||Added HDF5 build configs for LINUXAMD64 target|
* build.csh 1.136 (changed +6 -1)
Allow compilation of the ORCA plugin on Linux and MacOS for testing
of recent revisions to make it more C++03 friendly.
* molfile_plugin/Makefile 1.131 (changed +26 -1)
Applied Thomas Albers' diff to eliminate references to a fourth set of weights.
The first pass uses as input parameters the scoring matrix and three
weights, but multiseq (in psipred::calculateSecondaryStructure) hands it
four. Elsewhere (in psipred::checkPackageConfiguration) Multiseq
explicitly checks for the fourth weight.
With the change to eliminate the fourth set of weights, Psipred-3.21 works
* psipred/psipred.tcl 1.5 (changed +2 -5)
Revised HDF5 linkage parameter passing
* build.csh 1.137 (changed +6 -2)
* psipred/psipred.tcl 1.6 (changed +2 -2)
| ||2018-12-14||johns||Added build rules for the Orca plugin. It won't get added to the standard|
list of dependencies until the last portability issues have been resolved.
* molfile_plugin/Makefile 1.128 (changed +10 -1)
Added build rules for the latest Lattice Microbes plugin.
Since it depends on the HDF5 libraries, it will get compiled whenever
the HDF5 build variables are set, but not otherwise, just like the
plugins that have dependencies on NetCDF, Tcl, Expat, etc...
* molfile_plugin/Makefile 1.129 (changed +73 -49)
Added further build rules for plugins that depend on HDF5
* molfile_plugin/Makefile 1.130 (changed +42 -18)
Julio's first round of portability updates to Max's Orca plugin to
allow compilation w/ C++03.
* molfile_plugin/src/orcaplugin.C 1.2 (changed +116 -65)
New heavily revised version of Lattice Microbes plugin from Tyler Earnest
* molfile_plugin/src/lmplugin.C 1.1 (added +899 -0)
Newer Lattice Microbes plugin from Tyler Earnest, which has been adapted
to require far fewer external dependencies, leaving just HDF5, and able to
compile on C++03 toolchains.
* molfile_plugin/src/lmplugin.C 1.2 (changed +269 -195)
Orcaplugin: Pulled in Max's matrix class for the time being,
and started dealing with all of the compilation problems related to use
of particular C++11 features that are not universally available.
* molfile_plugin/src/orcaplugin.C 1.3 (changed +255 -16)
Tyler's updated version of the Lattice Microbes plugin
with misc refactoring, corrected RDME particle positioning, and
better error handling.
* molfile_plugin/src/lmplugin.C 1.3 (changed +592 -380)
|fftk-1-2-0||2018-12-13||gumbart||Updated a few variable names to use the Configuration namespace.|
* fftk/fftk_guiInterface.tcl 1.47 (changed +4 -4)
| ||2018-12-12||johns||Added missing typecasts to allow C++ compilation|
* molfile_plugin/src/qmplugin.h 1.25 (changed +3 -3)
Corrected missing typecasts for memory allocations provided by
calloc() and realloc().
* molfile_plugin/src/qmplugin.h 1.24 (changed +10 -10)
| ||2018-11-28||jribeiro||Parsing the charge penalties from stream files coming from CGenFF server|
* readcharmmtop/readcharmmtop.tcl 1.18 (changed +12 -4)
| ||2018-11-06||ryanmcgreevy||Updated griddx command to use new voltool pot command to generate potentials in a single step, speeding up the potential generation especially for large maps.|
* mdff/mdff_map.tcl 1.3 (changed +7 -3)
| ||2018-11-06||johns||Updated the Multiseq help URLs to point to Zan's new lab page URLs.|
* seqedit/seqedit_widget_select.tcl 1.9 (changed +2 -2)
* seqedit/seqedit_widget.tcl 1.18 (changed +2 -2)
* seqedit/metric_signatures.tcl 1.5 (changed +2 -2)
* seqedit/metric_percentid.tcl 1.6 (changed +2 -2)
* seqedit/metric_mutualinfo.tcl 1.5 (changed +2 -2)
* seqedit/metric_insertions.tcl 1.5 (changed +2 -2)
* seqedit/metric_element.tcl 1.5 (changed +2 -2)
* seqedit/metric_conservation.tcl 1.5 (changed +2 -2)
* seqedit/consensus_builder.tcl 1.4 (changed +2 -2)
* seqdata/seqdata_temperature.tcl 1.5 (changed +2 -2)
* networkview/doc/index.html 1.6 (changed +1 -2)
* multiseqdialog/multiseqdialog.tcl 1.13 (changed +2 -2)
* multiseq/multiseq.tcl 1.38 (changed +4 -4)
* multiseq/doc/index.html 1.10 (changed +2 -2)
* multiseq/colormap_vmd.tcl 1.7 (changed +2 -2)
* libbiokit/metric.tcl 1.5 (changed +2 -2)
* libbiokit/libbiokit_profcombine.tcl 1.4 (changed +2 -2)
* libbiokit/libbiokit_entropy.tcl 1.4 (changed +2 -2)
| ||2018-11-01||gumbart||Added NewDefinition flag to Geom keyword for Gaussian,|
which is needed to delete old ICs before setting new ones
* fftk/fftk_GenBonded.tcl 1.19 (changed +2 -2)
| ||2018-10-22||johns||Updated version of the dipole watcher plugin to facilitate|
optionally updating atom selections at each new timestep
* dipwatch/pkgIndex.tcl 1.4 (changed +1 -1)
* dipwatch/doc/index.html 1.3 (changed +3 -2)
* dipwatch/dipwatch.tcl 1.6 (changed +46 -20)
| ||2018-10-02||johns||Cleanup fctn header|
* molfile_plugin/src/dcdplugin.c 1.85 (changed +3 -3)
Pretty up the line-wrapped list of files
* modelmaker/Makefile 1.2 (changed +6 -6)
| ||2018-10-01||johns||Corrected console diagnostic message and eliminated overly broad scoping|
of "readlen" variable in favor of direct numeric comparison of bytes read
from low level readv() call.
* molfile_plugin/src/dcdplugin.c 1.83 (changed +5 -7)
Revised the DCD plugin to allow it to read trajectories that contain
more than 2^30 atoms, which requires ignoring the Fortran I/O markers
that are only 32-bits in size, and therefore contain I/O size values
that are either truncated or wrapped around. Revised some of the arithmetic
associated with fixed and unfixed atom memory allocations to use long integer
types to avoid integer wraparound.
* molfile_plugin/src/dcdplugin.c 1.84 (changed +43 -23)
| ||2018-09-27||jribeiro||Extend the search of dihedral angles to the combinatorial number of possible angles formed by more than two atoms bonded to a central atom. Addition of the proc to calculate the factorial number necessary to support the dihedral search|
* utilities/utilities.tcl 1.13 (changed +48 -20)
| ||2018-09-25||jribeiro||Prevent the env variable to QWIKMDTMPDIR cease to exist on windows by cleaning it with '""'. Set it to -1|
* qwikmd/qwikmd.tcl 1.73 (changed +4 -2)
| ||2018-09-12||ryanmcgreevy||Updated all relevant MDFF commands to use new Voltool commands instead of volutil internally. Front end usage remains unchanged|
* mdff/mdff_sim.tcl 1.2 (changed +38 -21)
* mdff/mdff_map.tcl 1.2 (changed +36 -28)
* mdff/mdff_gui.tcl 1.37 (changed +0 -1)
* mdff/mdff_correlation.tcl 1.2 (changed +68 -41)
* mdff/mdff_check.tcl 1.4 (changed +3 -3)
| ||2018-09-07||johns||Cranked DCD plugin minor version in light of periodic cell handling changes.|
* molfile_plugin/src/dcdplugin.c 1.82 (changed +2 -2)
DCD plugin will now express non-periodic unit cells with cell side
lengths of zero. In the distant past there was some sort of issue with
PBC side lengths of zero, but this must be handled properly by now or
fixed if not, since we will eventually also need to support
partially-periodic unit cells arising from the newer revs of NAMD's MSM.
* molfile_plugin/src/dcdplugin.c 1.81 (changed +3 -3)
| ||2018-08-16||gumbart||Fixed a potential memory leak in bond/angle optimization|
* fftk/fftk_distort.tcl 1.4 (changed +10 -5)
* fftk/fftk_BondAngleOpt.tcl 1.20 (changed +17 -27)
|siggraph2018||2018-07-31||johns||Improve numerical behavior of the solvate overlap check for non-standard|
* solvate/solvate.tcl 1.63 (changed +2 -2)
| ||2018-07-09||jribeiro||Prevent using torsion plot above the 5000 residues because it is too slow|
* structurecheck/structurecheck.tcl 1.10 (changed +7 -3)
| ||2018-07-03||jribeiro||Correct html header, deleting ParseFEP reference|
* bfeestimator/doc/index.html 1.2 (changed +2 -2)
| ||2018-06-20||johns||Corrected build paths for IBM Poughkeepsie center cluster|
* build.csh 1.135 (changed +4 -4)
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