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[#4769] subdir for cprodrg is Prodrg

removed CCP4pipeline22.py, CCP4pipeline.py should work with Python2.2 now

Removed mafft as it will now go into the third party directory

Added mafft source code build

add r500ccp4

use -I$(incdir) rather than -I$(incdir)/mmdb -I$(incdir)/ccp4
this hopefully fixes building broken by headers change yesterday

add edstats subdir

add nautilus_pipeline

remove makecif from build

update for 5.7.0015

reintroduce r500

corrections for refmac 5.7 build

update includes and modules for refmac 5.7

add gesamt

pass MAKEFLAGS to ccp4_build

znd_subs added to FTARGETS

src/zanuda_source/zanuda -> src/zanuda.py ; src/zanuda_source/znd_subs.f -> src/znd_subs.f; Makefile.in changed accordingly

a bit of protection for when the Makefile does not exist in a subdir

set up recursive targets

better build fsplit

merge to branch-30_07_11

remove references to lib/src

add fsplit to src

binsort.h now in src

change incdir to reflect include/ccp4

add aimless

first make of zanuda added

[#4435] add prosmart in src

copy jligand to CBIN

upper case for JLigand

jligand Makefile does not have install target

remove stray backslash

missed ncs_rest.mod

first stab at updating refmac to 5.6.0098

add jligand.jar to binary files

remove get_heavy and add_heavy

update balbes_progs

remove information for programs in spin out crank software sub configure

first stab at spinning out crank software

update for refmac 5.6.0091

clean target for cprodrg missed

add cprodrg

update for refmac5 and libcheck after testing with intel compilers

add removal of .mod files to clean

update for refmac 5.6.0081, first attempt at getting this working

[#4141] add align.mod to build

reinstate refmac5.6 build

remove multicomb for now

update for deficiencies in merge

send CCP4pipeline scripts to share.python

update for buccaneer pipelines

remove the 6_2 stuff from this series

bug 4125, include CVs fix

merge in series-6_1 to release-6_1_3

Updated Makefile to include new chef src files. Bugzilla #4081

bug 4022, remove r500 from 6.1.3

change for refmac 5.6

merge in 6.1.1 changes

use MAKE variable instead of make, and  set for pdb_extract call

remove control character irritating emacs

bug 3243, leave libatomic_ops makefile lying around

do not quote the phaseropts as this confuses the parser in ccp4_build

bug 3242, remove calls to clipper_progs pisa rapper and pointless Makefiles from realclean target

bug 3242, add libcheck.a libbp3.a to the realclean targent

bug 3242, switch the rspslib.dir object files to the clean target

bug 3235, do not require heavy.o for refmac 5.5.0047

Sfcheck 7.3 needs F90

Sfcheck 7.3 needs F90

bug 3041, need to pass CCC to get compilation under irix 6.5

remove -v option hardwired into refmac5 build

bug 3123, consolidate shared object files into libcheck.a

bug 3112, correction of minor errors in last commit, still need to rationalise objects list to stop spurious messages

bugs 3112 and 3115, remove tlsgroups build, and update dependencies for refmac5.5

bug 3112, build refmac5.5 series files, but tlsgroups still broken and object dependencies need rationalising and updating

bug 3002, add crank helper routines

make BALBESTARGETS part of REFMACTARGETS - only built if you have fortran90

balbes utilities

Added the correct dependencies for chef_model.

Renamed file from model.f to chef_model.f to prevent clash with bp3 file.
Updated Makefile.in accordingly - should mend the auto-build

Updated source files for latest version of chef (this one appears to work
ok...) and included additional file in Makefile.in

Bug #2958: part of Claus Flensburg fix for pdb_extract build - pass on
C compiler explicitly at compile time.

Remove .py extension from ccp4_pipeline_simple when copying to $CBIN (Bug 2856).

Move  doser mat2symop symop2mat to OTHERS so don't have duplicate targets.
Add echo to solomon so can see what it is doing.

Added in rules to build the XIA2 programs in the xia2_apps_ subdirectory
(chef, doser, symop2mat and mat2symop).

Add wave2f2prime to Refmac

mtzcat, generate_xml_datasetinfo_from_mtz no longer exist

crank_app removed in crank 1.2.0

bug 2814, add ccp4_pipeline_simple.py to the installation step

make pointless lines consistent with others

bug 2751, add pointless to Makefile.in

roll out clipper_progs, pisa, rapper to targets other than install

make install step not working for clipper_progs, so fix it

add rapper and pisa to make

Added r500 to list of programs for compilation

putting inout_routines into reflibobjs3 to prevent useless warnings

Bug #2737: reverse earlier changes where areaimol was split out to a
separate subdirectory along with the newuoa library - newuoa has been
removed and areaimol.f restored to $CPROG.

Correcting refmac /libcheck/tlsgroup/makecif files to be compiled

bug 2725, add  calls for clipper_progs

removed bplot polypose rsearch arp_waters prepform prepshel t_shift rdent restrain

Bug #2676: updated targets for building areaimol, to accommodate the fact
that the program now depends on the NEWUOA package.

bug 2664, break out .o files for bp3, etc

Added a target to make the JLogGraph "jar" file.

Updated refmac5 and related targets for changes in Refmac5.3.0040.

Added missing dependency for seqwt program.

Updated to build new program SEQWT.

molrep (version 10.1) now included in REFMACTARGETS

Explicitly specify the source and target Java versions for JLogGraph and
JLogCanvas as 1.2 on compilation, to try and maintain backwards
compatibility with older JVMs.

Removed beast

Added targets to build SYMCONV.

reinstate crunch2 and pmf targets

Update bp3, and add in afro and gcx

Make Refmac targets configurable

updated for Refmac 5.3

Add rules for building new MTZ2CIF program.

Fix for clean, realclean and distclean targets for ccp4mapwish (bug #1552)
- same as r1.175 in main trunk).

Fix for clean, realclean and distclean targets for ccp4mapwish (bug #1552).

Added chainsaw

crunch2 pmf multimerge temporarily removed from suite

bug 1178, use -fno-move-all-moveables for stereo shared build

bug 1172, seperate out CXX and C builds, also add F_LIBS, C_LIBS, CXX_LIBS

pass phaseropts from configure to phaser build

include pdb_merge

add in multimerge

add a PMF dependency

trigger SETFLAGS for more cases, I need it for C++ code under icc

tidy sapi make

resolve conflict introduced by last step

replace fft by fftbig

added PMF

make sure we find ccp4_build

sapi gives problems under linux ppc

add crank jiffies: generate_xml_datasetinfo_from_mtz mtzcat

add phaser to build

Added new file "subnumrec.f" which is required by Refmac5.

oops, correction to last change for crunch2

adding in crunch2

add in bp3 build

extra files for DM

extra include file dependencies for molrep

Added new dependency for scala.

PP: call 'make compile' instead of 'make' for pdb_extract: this checks compiler in case linux_intel_compilers are used

adding in tlsextract

new jiffy coord_format in mmdb_app_

Added --disable-pdb_extract option - this option does not build pdb_extract suite

split off libcheckobjs compilation to use libcheck_FLAGS

Change to makefile for pdb-extract version 1.4

requires semi colon

beast_FLAGS added

Refmac5 objects: extra_eigen.o and subcf_scale1.o now also depend on
gaussian.fh.

Forgot bulk dependencies - required for certain makes

Remove ml3mat.o from dtrek2scala objects

Add BULK programs

Refmac5: vdw_symmetry.f now also depends on vitals.fh.

Solomon not longer needs Fortran libs, just those for C.

missing dependency

remove solomon FORTRAN dependencies

Updated for latest version of Refmac5/Libcheck.

Added rules to build developers utility programs (mtzdiff, mapdiff, pdbdiff).

Edited makefile to build PDB_EXTRACT suite in harvest_apps/pdb_extract

revert back to 1.129

switched CXXFLAGS to CXXOPTIM for C++ compilation as -DG2C
causes problems for gnu compilers.  Note: -DPROTOTYPE is irrelevant
for C++

C++ programs now use LDCFLAGS

Tidy up attempt of the Javatargets. Now by default they will not (or attempted)
be built. If people have problems with JLogGraph.class they can make JLogGraph.class

its still a mess. but less likely to break.

Rename C++ variables to CXX
Add cif2xml cross_validate targets (harvest progs)

OSF1 at least doesn't like spurious backslash

adding dtrek2scala from GwyndafE

Link ncont and pdbcur with CCPP as FC on OSF1 gets confused

Add in CPPTARGETS comprising pdbcur and ncont

remove absurd and undupl

Added pls_incl.fh to dependencies for ncs_const.o (Refmac5 component).

Clemens Vonrhein: added removal of ccp4mapwish objects to realclean.

Added symmetry.properties (required by AstexViewer) to JAVATARGETS. Really
should be in CDATA though ...

replace cif2mtz by $(CIFTARGETS)

yet another refmac5 file

Added AstexViewer.jar to JAVATARGETS.

sapi and fsearch added

abs added

Added rotamer to build.

Updated for name change of arp_warp to arp_waters.

More fixes for ccp4mapwish build and install.

Add in professs

Added missing make flags etc for ccp4mapwish build.

Added targets to build in the ccp4mapwish_ subdir.

extra file snuk in.... sfch_graph.f

changes to sfcheck

Changes for newest Molrep 7.1

Changes for refmac 5.1

beast added

Updated dependencies for scala.

MDW: new cif2mtz program

changeing the location of split

Changes by Dave Love. fsplit is no longer made into bindir as bindir may not
have write permissions at time of make (but later at make install)

Fix to previous change, needed a tab not spaces.

rule for JAVATARGETS added

included acorn

Added entry for new stgrid program.

Updated dependencies of refmac5 files on their associated .fh headers.

Minor correction for molrep build.

changes for LATEest molrep

Use fsplit from $bindir. Should be built there automatically bu configure.

CSIMPLE target can now use SETFLAGS mechanism (needed for binsort on OSF1
version 5).

Latest Molrep changes

changes to update Molrep 6.2

protin, refmac gone; refmac5 in

takeing out rotaprep - bye see you in unsupported....

Added in anisoanl

Added entries for map2fs.

Added targets for CAVENV (mdw), FFFEAR and FFJOIN.

Compilation of mlphare changed to include mlphare.fh

Changed "rsps[version-no].f" to "rsps.f"

made changes to sc and dyndom entries as well as adding combat

Updated for changes to RSPS (v4.2).

XCIF_LIB now included in LDFLAGS

New files for REFMAC

Extra include file for topp

Changes for arp_warp (was arpp; plus new program t_shift). Added new
program sc. Change for scala.

Added $(XCIF_LIB) for RESTRAIN

Added XCIF_LIB for FTARGETS
Extra include files for SCALA

Added OASIS

Extra file for SFCHECK, and added MOLREP

rwcontents added from unsupported

Added DETWIN

Remove jiffy prog nicelist

Linking pdbhtf to libccp4 caused problems on HPUX; not necessary

Added tabs and corrected dependencies for topp et al

Added pdbhtf for TOPP

Aarrg! Don't want to remove JAVATARGETS, since not built!

Added areaimol (from unsupported), findncs, watncs, topp,
toplist, nicelist

New files for REFMAC

Added mtzMADmod

New file for DM

Added JAVATARGETS target to install java executables JLogGraph.class and
JLogCanvas.class into $CBIN (used by Kevin's libhtml routines).

Adding DYNDOM, and extra dependency for SCALA.

Added sfch_unix.f/o

added gfac2pdb for new procheck

adding SFTOOLS

lost extend,psaver
gained baverage,bplot,mapdump

dmmulti added

New RANTAN and SFCHECK

restrain, tlsanl, rdent were never up-to-date.

.

Entered new progs.

rmsdev wasn't in $OTHER

Removed various progs. that are not in cprog.

MTZMNF, MAPROT and REFMAC added.
New dependency for SOLOMON.

fix rmsdev target

revert dmobjs

solomon changes

Add geomcalc, sortwater, tlsanl, solomon.  Remove watersort.
Various tactical changes and removal of leading spaces.

add freemask for new dm

add hgen, remove lcf2mtz

Add crossec.

use directory stereo_, not stereo

typo

phistats dependency

added in phistats.f

10/4/95

new procheck, mapmask etc.

add stereo

Added polypose.f

add rfcorr

binsort wasn't being compiled/installed

procheck changes

Fix SETFLAGS handling when the variable isn't defined.
Add binsort as a target (moved from lib/src).

change clean, realclean

dm, procheck changes

use $(FC) to compile rsps

scala directory shouldn't have been `scala'

put path in rsps for debugging

.

add rebatch, make emptied targets non-executable

add scala, freerflag; remove heavy

use .f instead of .for

inconsistent naming with SETFLAGS stuff

version pulled straight from york

add gensym, psaver; remove polsig

add gensym

rsps target problems

.

.

emacs mode info

.

.

.

.

.

remove unsupported etc.

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add act.  add actplot dependency.  remove crossec from targets
(real*16 breaks in DECfortran).  fix empty-targets, install on convex.

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fix empty-targets, add dumpreso dependency

remove strip target, fix empty-targets for convex

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add symgen

much hacking

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prior to proper attempt at version control

Initial revision