|Tags||Date||Developer||Last 200 Commit Logs|
| ||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 <firstname.lastname@example.org>
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)
| ||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)
Updated for IBM Poughkeepsie P8/P9 test cluster
* build.csh 1.134 (changed +15 -0)
| ||2018-05-04||johns||Corrected the non-page-aligned fallback safety check test condition for|
callers that fail to query the new molfile plugin API
read_timestep_pagealign_size() before their first call to read
* molfile_plugin/src/jsplugin.c 1.80 (changed +2 -3)
| ||2018-05-03||johns||Revised jsplugin to automatically use or disuse block/page-aligned|
kernel-bypass direct I/O depending on whether the caller has made
use of the new read_timestep_pagealign_size() entry point in the
VMD molfile plugin API, beginning with ABI version 17
* molfile_plugin/src/jsplugin.c 1.79 (changed +143 -15)
| ||2018-05-02||johns||Added first rev of molfile plugin for reading ORCA files. Still needs to be|
made more cross-platform portable and more broadly compilable with varying
* molfile_plugin/src/orcaplugin.C 1.1 (added +2494 -0)
Added plugin API read_timestep_pagealign_size, and revved ABI version to 18.
* include/vmdplugin.h 1.34 (changed +2 -2)
* include/molfile_plugin.h 1.110 (changed +2 -2)
| ||2018-04-28||johns||Made the PDBx plugin compatible with "old school" C++ compilers that arise|
on some platforms.
* molfile_plugin/src/pdbxplugin.C 1.22 (changed +35 -16)
| ||2018-04-27||johns||Draft molfile plugin API for read_timestep_pagealign_size()|
* include/molfile_plugin.h 1.109 (changed +25 -2)
| ||2018-04-25||ryanmcgreevy||Abinitio now restarts from prior failed or completed runs and appends all results to look like one run|
* modelmaker/rosetta_vmd.tcl 1.8 (changed +54 -9)
* modelmaker/rosetta_input_generator.tcl 1.2 (changed +4 -4)
* modelmaker/modelmaker.tcl 1.12 (changed +19 -19)
| ||2018-04-23||ryanmcgreevy||Fixed bug when calculating per residue cc|
* modelmaker/CCColor.tcl 1.3 (changed +1 -1)
| ||2018-04-20||jribeiro||Addition of the optional salts for structure preparation:|
CsCl MgCl2 CaCl2 ZnCl2 (already supported by the autoionize)
* qwikmd/qwikmd_func.tcl 1.64 (changed +26 -8)
* qwikmd/qwikmd.tcl 1.72 (changed +2 -2)
Typo correction in detecting Cesium (CES)
* autoionize/autoionizegui.tcl 1.14 (changed +3 -3)
| ||2018-04-19||jribeiro||Additional .qwikmd files loading mechanism using the "initial structure" selection|
entry and load button
* qwikmd/qwikmd.tcl 1.71 (changed +17 -7)
Make the deletion of the previous output folders more precise. Delete only
the files of the system to be replaced and leave the rest intact.
Lock the save button in the case of the preparation a QM/MM simulation
from a classical simulations
* qwikmd/qwikmd_func.tcl 1.63 (changed +4 -2)
* qwikmd/qwikmd.tcl 1.70 (changed +37 -21)
| ||2018-04-18||jribeiro||Change the QM Options from global (same options for all protocols) to QM options for each protocol.|
A combobox on the top of "QM Options" controls the target protocol.
Add the capability to load the orbitals for orca. The print commands are exemplary, working when Orca
ran with PM3. These commands need to be changed if another theory level is used.
General bugfixes and improvements.
* qwikmd/qwikmd_logText.tcl 1.18 (changed +57 -45)
* qwikmd/qwikmd_info.tcl 1.12 (changed +41 -1)
* qwikmd/qwikmd_func.tcl 1.62 (changed +813 -125)
* qwikmd/qwikmd_ballon.tcl 1.11 (changed +127 -1)
* qwikmd/qwikmd.tcl 1.69 (changed +913 -238)
* qwikmd/QMMM-Ann.conf 1.3 (changed +3 -3)
| ||2018-04-11||ryanmcgreevy||Workaround for rosetta bug where abinitio doesn't keep fixed part's sidechains fixed. for now, take fixed part from template and merge that with rosetta generated part.|
* modelmaker/rosetta_vmd.tcl 1.7 (changed +16 -0)
| ||2018-04-11||brendanbc1||Added ability to read PDB_model_num (the alt_loc field in vmd)|
from PDBx files.
* molfile_plugin/src/pdbxplugin.C 1.21 (changed +26 -1)
| ||2018-04-10||ryanmcgreevy||Analysis alignment now uses exact selection text of user and does not add backbone, so that users can align with only CA as an example. If aligned pdb already exists, skips doing alignment again. Will now overwrite formatted dcd so subsequent analysis runs can be done in same folder.|
* modelmaker/utilities.tcl 1.6 (changed +14 -13)
* modelmaker/rosetta_vmd.tcl 1.6 (changed +2 -2)
| ||2018-04-10||brendanbc1||Added ability to read spheres from PDB-Dev files.|
Fixed a string handling bug that could cause some fields to be truncated.
* molfile_plugin/src/pdbxplugin.C 1.20 (changed +218 -75)
| ||2018-04-06||brendanbc1||Added a check for PDB-Dev files and adds warning that support is|
experimental. Also adds warnings for missing PDBx fields that are required
in the PDBx spec.
Fixed memory leak and other memory related errors in delete_pdbxParser.
Improved string handling when reading headers to prevent buffer overflows.
Fixed errors in the way we were parsing special bonds.
Removed unused variables and renamed/reformated parts of the code for
* molfile_plugin/src/pdbxplugin.C 1.19 (changed +287 -162)
| ||2018-04-05||brendanbc1||Commit includes multiple bug fixes, and experimental support for PDB-Dev.|
Fixed an error handling bug that occurred when we couldn't find the number
of atoms in a file.
Fixed a buffer overflow that occured when special bond column names
were larger than expected, and added length checks to internal string
Fixed multiple memory leaks and uninitialized reads.
Added comments and renamed variables to improve readability.
* molfile_plugin/src/pdbxplugin.C 1.18 (changed +223 -157)
| ||2018-03-27||ryanmcgreevy||New model command options for sorting and modifying output structures|
* modelmaker/modelmaker.tcl 1.11 (changed +70 -4)
| ||2018-03-23||ryanmcgreevy||Added kmin and kmax options for python clustering|
* modelmaker/utilities.tcl 1.3 (changed +2 -2)
* modelmaker/rosetta_vmd.tcl 1.5 (changed +2 -2)
* modelmaker/modelmaker.tcl 1.10 (changed +23 -1)
Fixed naming for tmp input pdb and seq files in model command
* modelmaker/modelmaker.tcl 1.9 (changed +5 -5)
Python clustering now creates a pdb of each medoid
* modelmaker/utilities.tcl 1.5 (changed +20 -3)
Python clustering now creates dcds for each cluster
* modelmaker/utilities.tcl 1.4 (changed +21 -0)
| ||2018-03-08||johns||Rewrote the internals of the color scale bar plugin to generate color|
bars that will render with high quality in ray tracing engines, by
replacing line primitives with cylinders and color-per-vertex triangles.
* colorscalebar/pkgIndex.tcl 1.6 (changed +1 -1)
* colorscalebar/colorscalebar.tcl 1.26 (changed +34 -15)
* colorscalebar/Makefile 1.6 (changed +1 -1)
Updated multiseq to accept any current version of the colorscalebar plugin
* multiseq/multiseq.tcl 1.37 (changed +2 -2)
Updated the MRC/CCP4 plugint to correctly interpret non-IMOD tomograms
that use signed-byte voxel formats by checking the sign of 'amin' in the header.
* molfile_plugin/src/ccp4plugin.C 1.43 (changed +28 -9)
| ||2018-03-07||johns||Blue Waters has an extra login node now.|
* build.csh 1.133 (changed +1 -0)
| ||2018-03-06||johns||Applied Ying-Chih's new version of parseFEP that corrects errors that had|
started cropping up in the latest test versions of VMD.
* parsefep/pkgIndex.tcl 1.10 (changed +1 -1)
* parsefep/parseFEP.tcl 1.16 (changed +419 -83)
* parsefep/Makefile 1.10 (changed +1 -1)
Begin addressing DCD plugin limitations with respect to 2-billion atom simulations
* molfile_plugin/src/dcdplugin.c 1.80 (changed +28 -25)
Updated CCP4/MRC map reader plugin to properly handle density maps with
several billion voxels in them.
* molfile_plugin/src/ccp4plugin.C 1.42 (changed +11 -10)
| ||2018-03-02||jribeiro||Allow creating QM regions with -1 < charges > +1 with MOPAC, but still giving|
* qwikmd/qwikmd_func.tcl 1.61 (changed +3 -2)
* qwikmd/qwikmd.tcl 1.68 (changed +3 -2)
| ||2018-03-01||ryanmcgreevy||Fixed bug in ssanalysis if only 1 struct. turn off evaluate_ss_analysis for now because gnuplot is causing a variety of issues and may no longer be needed.|
* modelmaker/ss_analysis.tcl 1.3 (changed +1 -1)
* modelmaker/rosetta_vmd.tcl 1.4 (changed +2 -10)
Joao's gnuplot fix
* modelmaker/ss_analysis.tcl 1.4 (changed +3 -6)
Quick_mdff now works with multiple maps and new gridpdb selection text. removed last mention of juan cluster code
* modelmaker/utilities.tcl 1.2 (changed +0 -25)
* modelmaker/modelmaker.tcl 1.8 (changed +32 -8)
| ||2018-02-28||ryanmcgreevy||Ss analysis no longer launches another vmd|
* modelmaker/rosetta_vmd.tcl 1.3 (changed +12 -10)
| ||2018-02-27||ryanmcgreevy||Added optional output prefix for fragment files|
* modelmaker/modelmaker.tcl 1.7 (changed +9 -0)
| ||2018-02-26||jribeiro||Add qmbondscheme option to QwikMD GUI|
* qwikmd/qwikmd_logText.tcl 1.17 (changed +3 -1)
* qwikmd/qwikmd_info.tcl 1.11 (changed +10 -1)
* qwikmd/qwikmd_func.tcl 1.60 (changed +9 -1)
* qwikmd/qwikmd.tcl 1.67 (changed +23 -1)
| ||2018-02-22||johns||Added 'bfeestimator' plugin directory to the build.|
* Makefile 1.142 (changed +3 -1)
Added BFE estimator
* doc/index.html 1.106 (changed +1 -0)
Added BFE estimator docs
* bfeestimator/doc/index.html 1.1 (added +89 -0)
* bfeestimator/doc/Fig2.jpg 1.1 (added binary)
* bfeestimator/doc/Fig1.jpg 1.1 (added binary)
Added Chris Chipot's BFE estimator example input files
* bfeestimator/doc/Example.zip 1.1 (added binary)
Added Chris Chipot's binding free energy estimator plugin.
* bfeestimator/pkgIndex.tcl 1.1 (added +16 -0)
* bfeestimator/bfee.tcl 1.1 (added +1787 -0)
* bfeestimator/Makefile 1.1 (added +23 -0)
| ||2018-02-20||ryanmcgreevy||Added fragments command for using local fragment picker and removing Robetta webserver dependence|
* modelmaker/modelmaker.tcl 1.6 (changed +56 -0)
| ||2018-02-15||ryanmcgreevy||Changed default cccolor selection from all to protein and noh|
* modelmaker/modelmaker.tcl 1.5 (changed +2 -2)
* modelmaker/CCColor.tcl 1.2 (changed +4 -4)
| ||2018-02-02||ryanmcgreevy||Modelmaker model usage info no longer shows get_empty_density info|
* modelmaker/modelmaker.tcl 1.4 (changed +1 -1)
| ||2018-02-01||ryanmcgreevy||Fixed pdb2seq output and model usage info|
* modelmaker/modelmaker.tcl 1.3 (changed +5 -4)
| ||2018-02-01||johns||Updated plugin build scripts for final ORNL Summit system|
* build.csh 1.132 (changed +3 -1)
| ||2018-01-31||ryanmcgreevy||Fixed cluster alignment code path and added modelmaker interface for modeller scripts|
* modelmaker/ss_analysis.tcl 1.2 (changed +150 -65)
* modelmaker/rosetta_vmd.tcl 1.2 (changed +11 -10)
* modelmaker/modelmaker.tcl 1.2 (changed +109 -2)
* modelmaker/model-single.py 1.2 (changed +8 -34)
* modelmaker/Makefile 1.1 (added +29 -0)
| ||2018-01-26||johns||Added documentation files for modelmaker|
* modelmaker/doc/index.md 1.1 (added +22 -0)
* modelmaker/doc/_config.yml 1.1 (added +7 -0)
First version of the modelmaker plugin
* modelmaker/utilities.tcl 1.1 (added +467 -0)
* modelmaker/ss_analysis.tcl 1.1 (added +502 -0)
* modelmaker/rosetta_vmd.tcl 1.1 (added +534 -0)
* modelmaker/rosetta_scoring_wrapper.tcl 1.1 (added +300 -0)
* modelmaker/rosetta_input_generator.tcl 1.1 (added +872 -0)
* modelmaker/pkgIndex.tcl 1.1 (added +14 -0)
* modelmaker/modelmaker.tcl 1.1 (added +1788 -0)
* modelmaker/model-single.py 1.1 (added +83 -0)
* modelmaker/makepsf.tcl 1.1 (added +184 -0)
* modelmaker/helix-turn-cc.tcl 1.1 (added +124 -0)
* modelmaker/find_selection.tcl 1.1 (added +227 -0)
* modelmaker/clusterK.py 1.1 (added +195 -0)
* modelmaker/clash_selection.tcl 1.1 (added +13 -0)
* modelmaker/align2d.py 1.1 (added +37 -0)
* modelmaker/README.md 1.1 (added +81 -0)
* modelmaker/CCColor.tcl 1.1 (added +156 -0)
| ||2018-01-10||jribeiro||Bug Fix on the declaration of the Temperature when preparing simulations|
from previous simulations performed with QwikMD
* qwikmd/qwikmd_func.tcl 1.59 (changed +7 -4)
| ||2018-01-09||jribeiro||Use vec operations to calculate mean and standard deviation|
* qwikmd/qwikmd_func.tcl 1.58 (changed +30 -28)
| ||2018-01-08||johns||Corrected command line parameter count check on the graphene plugin to|
accept 6 parameters rather than a minimum of 8.
* nanotube/pkgIndex.tcl 1.7 (changed +1 -1)
* nanotube/gui.tcl 1.8 (changed +2 -2)
* nanotube/graphene.tcl 1.10 (changed +2 -2)
* nanotube/Makefile 1.7 (changed +1 -1)
| ||2017-12-29||jribeiro||Fix issue with copying files on Mac returned by the glob command|
* qwikmd/qwikmd.tcl 1.66 (changed +4 -3)
| ||2017-12-28||jribeiro||Prevent issues finding the original pdb file when stored in folders|
with space characters
* qwikmd/qwikmd.tcl 1.65 (changed +7 -7)
| ||2017-12-21||johns||Added fftk_ChargeOpt_ESP.tcl to the distrib target|
* fftk/Makefile 1.6 (changed +1 -1)
Updated alascan plugin dependency version number for new parsefep
* alascanfep/alascan.tcl 1.2 (changed +1 -1)
| ||2017-12-18||johns||Updated version of ParseFEP from Chris Chipot and colleagues.|
The new version improves FEP analysis performance by a factor of ten or so.
This version also corrects a bug in the Bennett-Acceptance Ratio (BAR)
module that had affected prior versions.
* parsefep/pkgIndex.tcl 1.9 (changed +1 -1)
* parsefep/parseFEP.tcl 1.15 (changed +1409 -1583)
* parsefep/doc/index.html 1.8 (changed +2 -2)
* parsefep/Makefile 1.9 (changed +1 -1)
| ||2017-12-15||gumbart||Added link to parmed for conversion to Amber-style files|
* fftk/doc/index.html 1.18 (changed +3 -2)
| ||2017-12-13||gumbart||Added support for RESP calculations used in the Amber force field.|
* fftk/fftk_guiProcs.tcl 1.47 (changed +304 -14)
* fftk/fftk_guiInterface.tcl 1.46 (changed +781 -83)
* fftk/fftk_ChargeOpt_ESP.tcl 1.1 (added +434 -0)
* fftk/fftk.tcl 1.13 (changed +2 -1)
* fftk/doc/index.html 1.17 (changed +125 -40)
| ||2017-12-06||jribeiro||Typos Correction|
* qwikmd/qwikmd_logText.tcl 1.16 (changed +3 -3)
| ||2017-11-21||jribeiro||Add missing close brackets|
* runante/runante.tcl 1.22 (changed +3 -3)
| ||2017-11-15||jribeiro||Add mdProtInfo array to the save file, when the qwikmd file is saved|
without prepare the simulation.
* qwikmd/qwikmd_func.tcl 1.57 (changed +2 -2)
| ||2017-11-03||gumbart||Fixed a parsing error for gaussian|
* qmtool/qmtool_readwrite.tcl 1.60 (changed +2 -1)
| ||2017-10-27||johns||Corrected leaked title string and temporary atom parsing strings in|
vaspposcarplugin, reported by Thomas Holder.
* molfile_plugin/src/vaspposcarplugin.c 1.10 (changed +6 -4)
Corrected mismatched parameter to strstr() in vaspoutcarplugin, reported
by Thomas Holder.
* molfile_plugin/src/vaspoutcarplugin.c 1.10 (changed +3 -3)
Fix a memory leak of temporary path strings in the MSMS plugin reported
by Thomas Holder.
* molfile_plugin/src/msmsplugin.C 1.14 (changed +3 -1)
Updated MSMS plugin version number.
* molfile_plugin/src/msmsplugin.C 1.15 (changed +2 -2)
| ||2017-10-25||jribeiro||Correction the shift in the time axis when plotting the QMEnergies due to the double|
print of the Energies by NAMD.
Addition of the printing of the QMEnergies analysis info in the infoMD file
* qwikmd/qwikmd_logText.tcl 1.15 (changed +20 -6)
* qwikmd/qwikmd_func.tcl 1.56 (changed +18 -18)
* qwikmd/qwikmd.tcl 1.64 (changed +15 -5)
| ||2017-10-24||jribeiro||Addition of the functions and checkbutton to plot electrostatic energies|
Correction the shift in the time axis when plotting the energies due to the NAMD
double printing of some timesteps in the log file
* qwikmd/qwikmd_logText.tcl 1.14 (changed +8 -5)
* qwikmd/qwikmd_func.tcl 1.55 (changed +17 -2)
* qwikmd/qwikmd_ballon.tcl 1.10 (changed +5 -1)
* qwikmd/qwikmd.tcl 1.63 (changed +89 -17)
| ||2017-10-23||jribeiro||Regenerate the pdb structure and the tempMol molecule|
if a mutation is performed. If a mutation is performed
on the N-terminal of a protein chain, re-evaluate the N-terminal patch
* autopsf/autopsf.tcl 1.146 (changed +23 -10)
| ||2017-10-17||johns||Changed ffTK GUI scripts to use Unix linefeed text formatting to prevent|
future issues with CVS diffing changes.
* fftk/fftk_guiProcs.tcl 1.46 (changed +2720 -2720)
* fftk/fftk_guiInterface.tcl 1.45 (changed +4555 -4555)
Set elements using topotools if not found in PDB
* fftk/fftk_guiProcs.tcl 1.45 (changed +9 -1)
| ||2017-10-11||jribeiro||Complete the addition of the validation process of the "Ignore Interactive|
* qwikmd/qwikmd.tcl 1.62 (changed +12 -21)
QM/MM bug fix in the declaration of Temperature in the case of the first protocol
is not a Minimization (binvelocities and temperature declared at the same time)
Add new validation of the status to the "ignore interactive foreces" button (disable)
if MDFF is selected since MDFF does not use this option
* qwikmd/qwikmd_func.tcl 1.54 (changed +3 -3)
* qwikmd/qwikmd.tcl 1.61 (changed +18 -3)
| ||2017-10-11||johns||Updated the list of parameter and stream files to be included by default|
to favor CHARMM36 since other plugins such as AutoPSF are now using CHARMM36
* namdgui/pkgIndex.tcl 1.9 (changed +1 -1)
* namdgui/namdgui.tcl 1.38 (changed +9 -4)
* namdgui/Makefile 1.5 (changed +1 -1)
| ||2017-10-06||jribeiro||Add the "Ignore Interactive Forces" checkbutton to control the IMD keyword|
"IMDignoreForces". Allow or ignore forces applied during a "Live View"
* qwikmd/qwikmd_func.tcl 1.53 (changed +16 -4)
* qwikmd/qwikmd_ballon.tcl 1.9 (changed +8 -1)
* qwikmd/qwikmd.tcl 1.60 (changed +25 -4)
| ||2017-09-08||jribeiro||Use unique number to flag the selected atoms (-9999) to be checked|
* structurecheck/structurecheck.tcl 1.9 (changed +7 -8)
| ||2017-09-07||jribeiro||Use the variable user4 to mark the atoms selected. This avoid the use|
of very long atomselections passed to the other plugins that create
more atoms selections based on this original selection
* structurecheck/structurecheck.tcl 1.8 (changed +11 -1)
| ||2017-08-30||johns||Correct logic for freeing output buffers when index-selected coordinate|
frames are used and page-aligned page-multiple buffers are used by plugins.
* catdcd/catdcd.c 1.6 (changed +3 -3)
Incorporated a patch for the parm7 parser from Robin Betz that
corrects the parm7 plugin's handling of the atomic number field in the
input prmtop file instead of using mass field to guess what element
each atom is. This previously caused problems when VMD was passed
a prmtop where the hydrogens have had their masses repartitioned
(for a faster simulation timestep). Updated the plugin minor version number.
* molfile_plugin/src/parm7plugin.C 1.35 (changed +5 -2)
* molfile_plugin/src/ReadPARM7.h 1.33 (changed +19 -1)
Updated catdcd to version 5.2
* catdcd/catdcd.c 1.7 (changed +2 -2)
* catdcd/README 1.6 (changed +4 -0)
* catdcd/Makefile 1.12 (changed +1 -1)
Updated psfgen to meet requirements for out-of-core I/O with trajectory
file formats that need page-aligned page-multiple memory buffers to support
direct unbuffered I/O for atomic coordinates. Updated the psfgen version
number to 1.7.
* psfgen/src/topo_mol_pluginio.c 1.48 (changed +55 -3)
* psfgen/src/tcl_psfgen.c 1.73 (changed +2 -2)
* psfgen/src/pkgIndex.tcl 1.24 (changed +1 -1)
* psfgen/doc/ug.pdf 1.2 (changed binary)
* psfgen/Makefile 1.16 (changed +1 -1)
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