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ChangeLog
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2007-10-29 LI Daobing <[email protected]>
* itcc/tools/tordiff.py: fix a bug.
2007-10-27 LI Daobing <[email protected]>
* itcc/tinker/tinker.py: newton_mol's type from bindmthod to object
* itcc/ccs2/loopclosure.py:
+ remove duplicated code.
+ keep the lowest energy one of the duplicated result.
+ change default eneerror to 0.00015.
+ min_func is dump-able.
* itcc/tools/tordiff.py: add '-F', '-v', '-s'.
* itcc/molecule/rmsd.py: add '-s'.
2007-10-17 LI Daobing <[email protected]>
* itcc/tools/omega2restrain.py: added.
* setup.py: add itcc-omega2restrain.
2007-10-11 LI Daobing <[email protected]>
* itcc/tools/relative.py: add '-n'.
* scripts/itcc-tinker-ene: add '-v'.
* itcc/molecule/chiral.py: add '-v'.
* setup.py: add itcc-tor2omega.
* itcc/tools/tor2omega.py: added.
2007-10-10 LI Daobing <[email protected]>
* scripts/itcc-pro2omega: added.
* itcc/molecule/settype.py: support multi input xyz file.
2007-10-09 LI Daobing <[email protected]>
* itcc/tools/omega.py: added.
* ext/itcc-core-ctools.c: document that torsionangle can also return nan.
* itcc/tools/enestep2countstep.py: add '-b' option.
* setup.py:
add itcc-ranlog2enestep.
add itcc-omega.
* itcc/tools/ranlog2enestep.py: added.
2007-08-30 LI Daobing <[email protected]>
* scripts/itcc-mmlog2enestep: add itcc-mmlog2enestep
* itcc/tools/scanlog2enestep.py: add itcc-scanlog2enestep
* setup.py (entry_points): add itcc-scanlog2enestep
* itcc/tools/enestep2countstep.py (main): support read from
standard input.
* itcc/tools/ccslog2enestep.py: itcc-ccslog2enestep does not work.
2007-08-27 LI Daobing <[email protected]>
* itcc/tools/relative.py: fix a bug when do not use '-b'
2007-08-21 LI Daobing <[email protected]>
* itcc/tools/dlg.py: new class Dlg
* itcc/tools/dlg_stat.py: rename from itcc/tools/dlg.py
* itcc/tools/pdbq_large_charge.py:
- added
- add support to Arg
* setup.py:
- add itcc-pdbq-large-charge
- itcc-dlg -> itcc-dlg-stat
2007-08-20 LI Daobing <[email protected]>
* itcc/tools/relative.py: add '-v' option.
2007-08-18 LI Daobing <[email protected]>
* setup.py (entry_points): add itcc-ccslog2enestep
* itcc/tools/ccslog2enestep.py: added
* itcc/tools/relative.py: handle SIGPIPE correctly.
2007-08-16 LI Daobing <[email protected]>
* itcc/molecule/rmsd.py: support '--mirror'.
* itcc/molecule/utils.py: fix bug in itcc-mirrormol.
2007-08-15 LI Daobing <[email protected]>
* itcc/ccs2/loopclosure.py: fix bug when socket is out of work.
2007-08-11 LI Daobing <[email protected]>
* itcc/ccs2/catordiff.py: improve usage.
2007-08-02 LI Daobing <[email protected]>
* itcc/tools/mtxyz2txyz.py: fix bug.
2007-07-31 LI Daobing <[email protected]>
* itcc/tools/mtxyz2txyz.py: added
2007-07-29 LI Daobing <[email protected]>
* itcc/ccs2/loopclosure.py:
- log the host information.
- log auto-detected check params.
2007-07-19 LI Daobing <[email protected]>
* setup.py: does not build depends on numpy.
2007-07-18 LI Daobing <[email protected]>
* itcc/ccs2/loopclosure.py: fix bug on is_achiral, headtail.
* itcc/ccs2/catordiff.py: use itcc.ccs2.tordiff module.
* itcc/tools/relative.py: added.
* itcc/ccs2/detectloop.py: reduce one pylint warning.
* setup.py:
- does not ship C/C++ source code.
- add itcc-relative.
2007-07-17 LI Daobing <[email protected]>
* itcc/ccs2/tordiff.py: add document that input unit is radian
* itcc/ccs2/loopclosure.py:
- new key `min_method' in config.
- fix a bug about torsion angle unit.
* itcc/tinker/tinker.py: rename minimizamol to minimiza_mol, rename optimizemol
to optimize_mol.
2007-07-15 LI Daobing <[email protected]>
* itcc/molecule/gjf2xyz.py: improve usage
* itcc/tools/xyz2gro.py: improve usage
* itcc/tools/xyz2gjf.py: improve usage
* itcc/ccs2/loopclosure.py:
- update for detectloop
- s/klass/cls/, satisfy pylint.
* itcc/ccs2/findneighbour.py: update for detectloop
* tests/ccs2/test_ccs2_detectloop.py: ditto
* itcc/ccs2/catordiff.py: ditto
* itcc/ccs2/detectloop.py:
- new algorithm support H11C6-C6H11.
- new func `is_simpleloop', `is_allsimpleloop', `pick_largest_simpleloop'.
- clean code.
2007-07-14 LI Daobing <[email protected]>
* tests/ccs2/test_ccs2_detectloop.py: add mol name as comment.
* tests/ccs2/confsearch.py: restore `sys.stdout' and `sys.stderr' after test.
* itcc/itcc_main.py: python2.3 does not have `sorted'.
* itcc/tools/histogram.py: python2.3 does not have `sorted'.
* itcc/molecule/utils.py: python2.3 does not have `sorted'.
* itcc/core/tools.py: add `sorted_'.
* itcc/ccs2/loopclosure.py:
- fix bug on searchrange and keeprange
- fix bug on maxsteps
2007-07-13 LI Daobing <[email protected]>
* itcc/ccs2/loopclosure.py: default loopstep is -1 instead of None
fix maxsteps bug in multicpu.
2007-07-12 LI Daobing <[email protected]>
* itcc/tinker/tinker.py: use communicate to end subprocess as soon as possible
* itcc/ccs2/confsearch.py: rename `testcyc' to `run'.
* itcc/ccs2/loopclosure.py: dont't add 'DEFAULT' section to config file.
add logging code
fix default value of out_mtxyz_fname
2007-07-11 LI Daobing <[email protected]>
* setup.py: add new console_scripts `itcc-moldiff'.
* itcc/tools/moldiff.py: added
* Makefile (install3): add install3
2007-07-10 LI Daobing <[email protected]>
* itcc/ccs2/confsearch.py (testcyc): assign config to correct section.
* tests/ccs2/loopclosure.py: add testcase for typo '__cal__'
* itcc/ccs2/loopclosure.py: improve config handling, now log file will
print full config file.
fix a typo '__cal__'
new config option: out_mtxyz, out_mtxyz_fname, set default out_mtxyz to
true to default output to a mtxyz file.
move 4 keys to tinker section
2007-04-19 LI Daobing <[email protected]>
* itcc/molecule/write.py (writegjf): fix a bug about header was
not used.
* itcc/molecule/gjf2xyz.py: default send to stdout
* itcc/tools/makecyclicalkane.py: cycC3 and cycC4 have different atom
type.
2007-04-16 LI Daobing <[email protected]>
* add itcc-makecyclicalkane:
- itcc/tools/makecyclicalkane.py: added
- setup.py: updated
* delete itcc/scripts
* rename itcc/itcc.py to itcc/itcc_main.py, also update setup.py