Molby - 分子モデリングソフトウェア

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新機能
・GAMESS を子プロセスとして実行できるようになった。
・X線データについて、結合距離・結合角を標準偏差つきで計算する機能を実装。
・GAMESS で F, G 型の軌道を含むログをインポートできるようになった（cube の計算は未実装）
・GAMESS エキスポートのダイアログで、基底関数系をファイルから読み込めるようになった。
・Particle mesh Ewald 計算を実装（試験的に）。
・"Pi アンカー" 原子を実装（試験的に）。シクロペンタジエニルと金属の結合などに使う。
・Ruby コンソールにヒストリ機能を実装。

バグ修正
・古い TeXsan で生成した CIF ファイルが読めなかったのを修正。
・CIF ファイルデータの対称操作による拡大の不具合改善（まだ不十分かも）。
・結合を削除するとバスエラーが発生していたのを修正。
・異なる２つの原子を別々にドラッグするとアンドゥが機能していなかったのを修正。
・分子の追加・削除機能を大幅書き直し。アンドゥの不具合が改善した。
・その他多くの不具合修正。

Document is updated for local execution of GAMESS and invocation of Antechamber.
Antechamber command is made more visible (e.g. when MM/MD parameters are not complete, user is asked whether to invoke antechamber).
Local execution of GAMESS is implemented.
Kernel#show_console_window, Kernel#hide_console_window, Kernel#filecopy are implemented.
Kernel#call_subprocess can now accept a callback procedure.
Importing PM3/GAMESS log is improved. (The atomic information was not recognized correctly)
On creating PM3 input for GAMESS, NGAUSS=3 is also specified
Calculation of bonds and angles with standard deviations (for X-ray data) is implemented.
CIF files from old TeXsan software cannot be loaded. Fixed.
Symmetry expansion was incomplete in CIF import. Improved, but may not be complete yet.
GAMESS log containing F and G type orbitals can now be imported. (MO calculation is not yet implemented.)
export_gamess is modified so that arbitrary keyword/value pairs can be given.
Bond creation is updated so that duplicate bond/angle/dihedrals are not generated.
Molecule#neutralize was not working. Fixed.
Copyright statement was updated to include FFTW.
Deleting bonds was causing bus error. Fixed.
MSW: when the console frame gets focus, all text was selected instead of the previous insertion point getting restored. Fixed.
Handling of GAMESS basis set is modified. The 'external' basis set files are now collected in Scripts/basis_sets. Also implemented is a button in the 'GAMESS export' dialog to load other basis set files.
Calculation of reciprocal cell parameter was incorrect. Fixed.
Some wrong behavior of PME calculation is fixed.
An error in PME energy calculation is corrected. MDArean#ewald_order is implemented.
Error message in Molecule#atoms[] was not working. Fixed.
Particle Mesh Ewald calculation is implemented (experimental). MDArena#use_ewald, ewald_beta, ewald_grid, ewald_freq are implemented.
Molecule#expand_by_symmetry was not working correctly when no symmetry operations are defined (and expansion with only translation is specified). Fixed.
Change in Antechamber/Resp dialog: molecular charge can be always assigned, and 'optimize' checkbox is no longer visible in the Resp dialog
In calling a subprocess, a wait of 10 msec is inserted between termination check (may be or not useful for more stable handling of subprocesses...?
Suppress output of pi-anchors when generating GAMESS or Gaussian input files.
Utility methods Enumerable#sum and Enumerable#average are implemented.
When new bonds are created, angles of type X-##-## (## is pi-anchor) should not be automatically added.
Parameter lookup was not working correctly when neither local or global search is specified and 'missing' is turned on. Fixed.
'==' operator is defined for Parameter, ParameterRef, AtomRef, ParEnumerable, MolEnumerable, and Molecule classes.
Create Pi Anchor menu command is implemented.
Parameter#lookup (and related methods) can now look up parameters from the atom indices, even when the parameter is described in atom types.
History functionality is available in the Ruby console. Handling of fonts in Windows version is improved.
Parameter methods angle, angles, bond, bonds, etc. can now be used as singleton methods (i.e. Parameter.element(1) is now allowed)
Flashing of the table while pressing the shift key (and other modifier keys) is reduced.
Symmetry expanded atoms now can be selected by mouse drag.
Expanding by symmetry (and loading cif file) was not working correctly. Hopefully fixed.
Attribute table was not updated correctly after revert. Fixed.
Revert command is implemented.
Atom renumbering was not working for pi anchor table. Fixed.
Two subsequent dragging of different atoms were causing undo failure. Fixed.
Remove previous pi-anchor codes.
"Pi anchor" atoms are implemented.
The load/save codes are rewritten, so that the error/warning messages are shown in the console.
Merging/unmerging molecules are extensively revised. Hopefully undo works more consistently than before.
The third argument to Molecule#get_coord_from_frame() is now obsolete, but causes warning instead of ArgumentError
Molecule#get_coord_from_frame now always tries to copy the cell information.
Kernel#exit is now untouched in the command line version. The command line version now displays version message on startup.
Molecule#cell_flexibility, set_cell_flexibility are obsolete, and the unit cell is always flexible (i.e. different frames can have different cells). Molecule#cell_periodicity and set_cell_periodicity are implemented.