Keating:ProcedeLog

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Here the ongoing changes to version d of ProCEDe will be documented. Users are encouranged to read through this and this and ask questions and make suggestions.

Module/Script	Ver	Date	Nature of Change	Affected scripts/modules
ALL	d 2.0	09/07/05	Copied all of the development version into version 2.0 (older version 2.0 was archived and put into /bionet/keating/local/energy/old_versions/).
getStructureEnergy.pl	d	09/06/05	Added the capability to break DelPhi energies (flag --dp) into sci-scj, sci self (self here means sci rf + sci-sci), sci-t and t self (again t rf + t-t). When no --fs is specified or if --fs is 0 (i.e. do a total calculation on the whole structure without breaking terms out), --dp will still calculate the total energy, which has to be equal to the sum of sci-sci, sci self, sci-t, t self (to within calculation error).	It used to be that --dp output only the total energy regardless of the state of --fs. That has changed (see above).
ENERGY.pm	d	09/02/05	Added two routines - ENERGY::writeSelfDDE_min and ENERGY::writePairwiseDDE_min. These are similar to their corresponding "_min"-less versions, except that a short minimization step in the context of the template is performed in CHARMM before evaluating the energies. This makes the routines pretty slow. Additionally, these routines use a constant rdie for self as well as pair interactions. The rdie can be specified as the last argument. The default is specified under "epsilon" in CHARMM.param (currently set to 4). These routines are invoked under two new energy schemes - 1s and vdws (s stands for "smooth"). 1s is the corresponding "smoothed" version of 1 and vdws is that for vdw. When 1s is used and it is desired to eliminate rotamers in stage 1 based on vdW energy, ecut_type should be specified as vdws (since straight vdw is not calculated and specifying it will cause an error). Under energy scheme 1s the following routines are also invoked: ENERGY::writeUnfoldDDE (no too much point in minimizing in the unfolded state, but can be done in the future if proves to be a problem); ENERGY::writeUnfoldDDE_fast; ENERGY::writeSelfEEF_fast; ENERGY::writePairwiseEEF_fast and ENERGY::writePairwiseEEFnoCHARMM. Under energy scheme vdws, the following routines are executed: ENERGY::writeUnfoldDDE; ENERGY::writeSelfDDE_min and ENERGY::writePairwiseDDE_min.	Default behavior did not change, but now energy scheme 1s can be used.
Energy.pl	d	09/02/05	Change the calls to all DDE-calculating routines to include the last parameter ($parm->{rdie}). This parameter can now be specified in the energy.conf file. If not specified, undef values will be passed down to the energy routines and the default behavior will be exhibited.	Since the default behavior did not change, nothing should be effected.
ENERGY.pm	d	09/02/05	Moved ENERGY::writeUnfoldDDE to ENERGY::writeUnfoldDDE_old and writeUnfoldDDE_fast to writeUnfoldDDE. This change was reflected in Energy.pl. Put a deprication statement at the top of the old routine (it no longer supports all the possible parameters). Changed ENERGY::writeUnfoldDDE, writeSelfDDE, writePairwiseDDE, and writePairwiseDDE_fast to have an additional optional parameter - the rdie to use with DDE. If not specified, undef values are sent to CHARMM::setupMulteNonbonded and CHARMM::setupMultePairNonbonded and the default behavior is exhibited (see below).	The default behavior did not change, so nothing should be effected.
CHARMM.pm	d	09/02/05	Changed CHARMM::setupMulteNonbonded and CHARMM::setupMultePairNonbonded such that they can optionally take the rdie constant to use with DDE. By default they use the constants specified in the CHARMM.param file (currently set to 4.0 for self and unfolded and 4/8/16 for pair depending on the amino acid identities). Since this is only useful/applicable for coiled coils, a general way of specifying an rdie is useful.	The default behavior is as before, so nothing should be effected.
CHARMM.pm	d	08/13/05	Communication with CHARMM is now done with a pipe. So when CHARMM dies for some reason, the OS sends a SIGCHLD signal to the perl wrapper and the process is not removed from the process table until the parent examines it with waitpid or ignores the SIGCHLD signal - this is how zombies are made. To avoid zombies I used to set $SIG{CHLD} to "IGNORE" just before printing to CHARMM in CHARMM::send such that if the child process died as a result of the print, the SIGCHLD signal would be ignored and the child process would be removed from the proccess table (and upon the next print or closing of the pipe the fact that the child had died would be discovered). At the end of CHARMM::send $SIG{CHLD} was set to "". This only worked sometime and I think this is because CHARMM would not always die immediately after a bad print statement (it maye take some time for the buffer to be flushed or the command to be processed). So if CHARMM dies when $SIG{CHLD} is "", the signal does not get taken care of and so a zombie is made. Now, I though that if in this condition you set $SIG{CHLD} to ignore, the undelivered signal should now be ignored and the zombie be cleared, but apparently this is not so (if there is no handler at the time of the signal, it does not matter if you make a handler later - the signal will not be processed). To deal with this I simply made a real child reaper (GENERAL::REAPER) according to recipe 16.9 from the Perl Cookbook and set $SIG{CHLD} to its reference in CHARMM::new. Additionally, before doing this I save the previous SIGCHLD handler in $self->{_prev_reaper} (if it is defined) and in CHARMM::DESTROY I restore the handler back to it (again, if it exists).	Anything using CHARMM. This change should not affect anything on the user's side.
naccess	d	08/10/05	I changed the naccess shell script such that error and warning messages are printed to STDERR. It used to be printed to STDOUT and this was an issue since ENERGY::getAtomicSA executed naccess with "> /dev/null" meaning that STDOUT was ignored. So if there was an error, it would never be seen. Printing errors and warnings to STDERR is in general better than having to examine STDOUT after every call.	Anything calling naccess (ENERGY::getAtomicSA)
CHARMM.pm	d	08/10/05	Now that communication with CHARMM is interactive, every write MUST be followed by a proper title ("* something\n*\n"). Otherwise, CHARMM tries to read the title and when it does not find one, it does BACKSPACE on the input stream (really stupid, but that is how it's implemented), which works for regular files, but may fail for pipes. I looked through all occurances of writes in CHARMM.pm and made sure that a proper title follows.	CHARMM.pm and everything depending on it.