Molby - A Molecular Modeling Software

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- Document for the LAMatrix class was written.
- Document for the collaboration with other quantum chemistry softwares was written.
- Mbsf files now retain sigmas for the crystallographic parameters (imported from CIF).
- New Ruby commands: Molecule#fit_coordinates, Molecule#amend_by_symmetry, Molecule#set(get)_view_center, Molecule#hidden_atoms, Molecule#set_hidden_atoms, Molecule#charge, Kernel#lookup_menu
- When the MM parameters are edited from the bond/angle table, the force constant can be guessed by Universal Force Field (UFF).
- The MM parameters can now be specified by explicit atom indices.
- Other bug fixes (see the change log).
- The release format of the Mac executable is changed from dmg to zip.

- Features of Molecule#cell and Molecule#box are modified so that the handling of the sigma values of the cell parameters looks more consistent.
- Mbsf format now retains anisotropic parameters and sigma (for crystallographic data)
- Crash during creating bonds when ellipsoid display is on is fixed.
- Ruby: Molecule#fit_coordinates is implemented.
- LAMatrix#new, #zero, #submatrix now accept arguments in 'column,row' order.
- MM forces are updated after 'run(0)'
- Load/save mbsf files were broken when atom type variants were used for atom types with 3 or 4 characters. Fixed.
- The order of parameters in cmd_edit_local_parameter_in_mainview dialog was inconsistent. Fixed. Also fixed Ruby exception in UFF guess dialog.
- Molecule#transform, rotate, invert, etc. are now aware of symmetry related atoms. That is, the symmetry operation is updated so that the atoms are also symmetry related after transformation.
- Ruby: AtomRef#symop can now be set from script.
- Ruby: Molecule#amend_by_symmetry is implemented.
- Ruby: Molecule#set(get)_view_translation is now obsolete and replaced by set(get)_view_center.
- The order of the anisotropic thermal parameters is changed to 'b11, b22, b33, b12, b13, b23'. Inconsistency in some of the codes is fixed. TODO: when symmetry expansion is done, the anisotropic thermal parameters should be correctly converted.
- Ruby: Molecule#hidden_atoms and Molecule#set_hidden_atoms are implemented.
- The order of columns for MD parameters in the bond/angle/dihedral tables are changed, so that the columns appear in the same order as in the parameter table.
- UFF parameter guess is implemented.
- Molecule#neutralize was not working correctly. Fixed, and Molecule#charge was implemented.
- The load/unload global parameters dialog is sometimes out of the screen. Fixed.
- Windows version does not display last build date in the about dialog. Fixed.
- Parameters now can be specified by using both explicit indices and atom types, like '7-ca-8'.
- Parameter editing is improved.
- Restructure MolAction.c.
- Atom range specification for the vdw cutoff parameter is now made obsolete.
- Vector3D[] and Transform[] are modified to accept an LAMatrix argument. The document is written for LAMatrix.
- Load Script Menu caused crash when no window is open. Fixed.
- Ruby: Kernel#lookup_menu is implemented.
- Document is written for LAMatrix.
- LAMatrix#multiply was not working correctly when on-the-fly size conversion was required. Fixed.
- Execute Script command was broken. Fixed.
- CIF import may fail when _geom_bond_site_symmetry_1 field is missing. Fixed.
- Document was written for the collaboration with other quantum chemistry softwares.
- .log and .out are both accepted as the extension of the Gaussian and GAMESS log files.
- update_version.rb is improved.