Commit 578030a7 authored by sruizcarmona's avatar sruizcarmona

updated all files for correct compilation in gcc 4

parent 5a410bc8
......@@ -19,7 +19,7 @@ use lib "$ENV{'RBT_ROOT'}/lib";
use SDRecord;
# Default field names and headings for RiboDock v4.00 scores
# Default field names and headings for rDock v4.00 scores
my @defaultFields = ('SCORE','SCORE.INTER','SCORE.INTRA','SCORE.RESTR','SCORE.INTER.VDW');
my @defaultHeadings = ('TOTAL','INTER','INTRA','RESTR','VDW');
......@@ -27,7 +27,7 @@ my @defaultHeadings = ('TOTAL','INTER','INTRA','RESTR','VDW');
my @defaultNormFields = ('SCORE.norm','SCORE.INTER.norm','SCORE.INTRA.norm','SCORE.RESTR.norm','SCORE.heavy');
my @defaultNormHeadings = ('TOTALn','INTERn','INTRAn','RESTRn','#heavy');
# Default field names and headings for RiboDock v3.00 scores
# Default field names and headings for rDock v3.00 scores
my @defaultOldFields = ('Rbt.Score.Corrected','Rbt.Score.Inter','Rbt.Score.Intra','Rbt.Score.IntraMin','Rbt.Score.Restraint');
my @defaultOldHeadings = ('TOTAL','INTER','INTRA','INTRAMIN','RESTR');
......@@ -42,6 +42,9 @@ my $headings = 1;#DM 21 Nov 2000, If false, don't output headings
my @outputFields;
my @outputHeadings;
#Print help if no command line arguments
printHelpAndExit() if (scalar(@ARGV) == 0);
#Parse command line arguments
my $nArgs = scalar(@ARGV);
......@@ -426,7 +429,7 @@ sub printHelpAndExit {
print "\t-norm use normalised score field names as default columns in -t and -c formats (normalised = score / #ligand heavy atoms)\n";
print "\nNote:\tIf -l, -t or -c are combined with -s, the listing/table is output within each ligand summary\n";
print "\t-sup should not be combined with other options\n";
print "\tDefault field names for -t and -c are RiboDock score field names\n";
print "\tDefault field names for -t and -c are rDock score field names\n";
print "\tDefault ID field name is Name\n";
print "\n\tIf sdFiles not given, reads from standard input\n";
print "\tOutput is to standard output\n\n";
......
......@@ -4,6 +4,12 @@
# it will add a TETHERED ATOM property field to the output SDF that is correctly understood by rDock
# rDock will restrain the matching atom positions to the reference molecule coordinates.
#
# Initially implemented with a conformational search algorithm to better match target coordinates.
# But had problems with OBabel FF generating non-sense conformers. So in this version the conformer search is commented out.
# Now if the input molecule do not have a good conformation, might not align well with the target. This effect will be
# dimished or even vanish if the SMARTS string is defined for a rigid region (like a ring).
# I'm still trying to incorporate somehow this conformational search.
#
# Script distributed under GNU LGPL 3.0 along rDock software.
#
# Author: Daniel Alvarez-Garcia
......@@ -101,10 +107,11 @@ def mapToCrystal(xtal, pose):
return mappingpose[0]
def takeCoords(obmol):
"""Take coordinates of an OBMol as a npy array"""
return npy.array([atom.coords for atom in obmol])
def updateCoords(obmol, newcoords):
"newcoords as numpy array"
"Update OBMol coordinates. newcoords is a numpy array"
for i,atom in enumerate(obmol):
atom.OBAtom.SetVector(*newcoords[i])
......@@ -130,21 +137,20 @@ if __name__ == "__main__":
outsdf = sys.argv[3]
smarts = pybel.Smarts(sys.argv[4])
# Logging
sys.stdout = open(outsdf.replace('sdf','log'), 'w', 0)
sys.stderr = open(outsdf.replace('sdf','err'), 'w', 0)
# Read reference pose and get atom list matching smarts query
# if more than 1 match, take the first one
ref = next(pybel.readfile("sdf", refsdf))
refMatchIds = smarts.findall(ref)
if len(refMatchIds) > 1: refMatchIds = refMatchIds[0]
else: refMatchIds = refMatchIds[0]
refMatchIndx = npy.array(refMatchIds) - 1
numRefMatchs = len(refMatchIds)
if numRefMatchs > 1:
print "More than one match in the reference molecule for the SMARTS string given. Will tether each input molecule all possible ways."
refIndxPerMatch = [npy.array(rmi) - 1 for rmi in refMatchIds]
# Take coordinates for the reference matched atoms
refCoords = takeCoords(ref)
refMatchCoords = npy.take(refCoords, refMatchIndx, axis=0)
refMatchCoords = [npy.take(refCoords, refIndx, axis=0) for refIndx in refIndxPerMatch]
# Do the same for molecule in molsdf
out=pybel.Outputfile('sdf', outsdf, overwrite=True)
......@@ -154,76 +160,98 @@ if __name__ == "__main__":
print "## Molecule %i"%(i+1)
mol.OBMol.DeleteNonPolarHydrogens()
molMatchAllIds = smarts.findall(mol)
numMatchs = len(molMatchAllIds)
if numMatchs == 0:
print "No match"
continue
elif numMatchs ==1:
print "Match"
elif numMatchs > 1:
print "Multiple SMART Matches for this molecule (%d)"%numMatchs
# If more than one match, write an output of the same molecule for each match
# Start a default bestcoord and rmsd for later looping for each pose
bestCoordPerMatch = [[0 for i in range(numMatchs)] for i in range(numRefMatchs)]
bestRMSPerMatch = [[999 for i in range(numMatchs)] for i in range(numRefMatchs)]
# Will do a randomrotorsearch to find conformer with the lower rmsd when superposing
# At least 20 when possible
ff.Setup(mol.OBMol)
numats = mol.OBMol.NumAtoms()
numrot = mol.OBMol.NumRotors()
print "Atoms: %i, Rotors: %i"%(numats, numrot)
bestCoord = 0
bestrms = 100
geomopt = 300
genconf = 100
if numats > 40 and numrot > 5:
geomopt = 300
genconf = 150
if numats > 55 and numrot > 7:
genconf = 100
geomopt = 500
print "\tDoing conformational search with WeightedRotorSearch (%i, %i)..."%(genconf, geomopt),
ff.SteepestDescent(500, 1.0e-4)
ff.WeightedRotorSearch(genconf,geomopt)
ff.ConjugateGradients(500, 1.0e-6)
ff.GetConformers(mol.OBMol)
numconf = mol.OBMol.NumConformers()
print "%i conformers generated"%numconf
#ff.Setup(mol.OBMol)
#numats = mol.OBMol.NumAtoms()
#numrot = mol.OBMol.NumRotors()
#print "Atoms: %i, Rotors: %i"%(numats, numrot)
#geomopt = 300
#genconf = 100
# increase iterations if bigger molecule or bigger number of rotatable bonds
# for allowing better sampling
#if numats > 40 and numrot > 5:
# geomopt = 300
# genconf = 150
#if numats > 55 and numrot > 7:
# genconf = 100
# geomopt = 500
#print "\tDoing conformational search with WeightedRotorSearch (%i, %i)..."%(genconf, geomopt),
#ff.SteepestDescent(500, 1.0e-4)
#ff.WeightedRotorSearch(genconf,geomopt)
#ff.ConjugateGradients(500, 1.0e-6)
#ff.GetConformers(mol.OBMol)
#numconf = mol.OBMol.NumConformers()
numconf = 1
#print "%i conformers generated"%numconf
if numconf > 1:
# Doing conf search
for i in range(numconf):
mol.OBMol.SetConformer(i)
confCoords = takeCoords(mol)
print 'coord:',confCoords[0,:]
for molMatchIds in molMatchAllIds:
molMatchIndx = npy.array(molMatchIds) - 1
confMatchCoords = npy.take(confCoords, molMatchIndx, axis=0)
# Align: Get rotation matrix between the two sets of coords
# Apply rotation to the whole target molecule
# change molecule coordinates, set TETHERED ATOMS property and save
rotMat, targetCentroid, refCentroid, rmsd = superpose3D(confMatchCoords, refMatchCoords, returnRotMat=True)
if rmsd < bestrms:
newcoords = npy.dot((confCoords - targetCentroid), rotMat) + refCentroid
bestrms = rmsd
bestCoord = newcoords
if bestrms < 0.1: break
#for i in range(numconf):
# mol.OBMol.SetConformer(i)
# confCoords = takeCoords(mol)
# print 'coord:',confCoords[0,:]
#
# for imatch, molMatchIds in enumerate(molMatchAllIds):
# molMatchIndx = npy.array(molMatchIds) - 1
# confMatchCoords = npy.take(confCoords, molMatchIndx, axis=0)
#
# # Align: Get rotation matrix between the two sets of coords
# # Apply rotation to the whole target molecule
# rotMat, targetCentroid, refCentroid, rmsd = superpose3D(confMatchCoords, refMatchCoords, returnRotMat=True)
# if rmsd < bestRMSPerMatch[imatch]:
# newcoords = npy.dot((confCoords - targetCentroid), rotMat) + refCentroid
# bestRMSPerMatch[imatch] = rmsd
# bestCoordPerMatch[imatch] = newcoords
# #if bestrms < 0.01: break
pass
else:
molCoords = takeCoords(mol)
for molMatchIds in molMatchAllIds:
for imatch, molMatchIds in enumerate(molMatchAllIds):
# loop in each matching way for the input molecule
molMatchIndx = npy.array(molMatchIds) - 1
molMatchCoords = npy.take(molCoords, molMatchIndx, axis=0)
# Loop over the reference matches
# Align: Get rotation matrix between the two sets of coords
# Apply rotation to the whole target molecule
# change molecule coordinates, set TETHERED ATOMS property and save
rotMat, targetCentroid, refCentroid, rmsd = superpose3D(molMatchCoords, refMatchCoords, returnRotMat=True)
if rmsd < bestrms:
newcoords = npy.dot((molCoords - targetCentroid), rotMat) + refCentroid
bestrms = rmsd
bestCoord = newcoords
for ir, refMatchCoord in enumerate(refMatchCoords):
rotMat, targetCentroid, refCentroid, rmsd = superpose3D(molMatchCoords, refMatchCoord, returnRotMat=True)
if rmsd < bestRMSPerMatch[ir][imatch]:
newcoords = npy.dot((molCoords - targetCentroid), rotMat) + refCentroid
bestRMSPerMatch[ir][imatch] = rmsd
bestCoordPerMatch[ir][imatch] = newcoords
# Finally update molecule coordinates with the best matching coordinates found
print "\tBest RMSD reached: %.2f"%bestrms
updateCoords(mol, bestCoord)
# Add TETHERED ATOM property field to SDF
newData = pybel.ob.OBPairData()
newData.SetAttribute("TETHERED ATOMS")
newData.SetValue(prepareAtomString(molMatchIds))
mol.OBMol.CloneData(newData)
out.write(mol)
# change molecule coordinates, set TETHERED ATOMS property and save
for imatch in range(numMatchs):
for irefmatch in range(numRefMatchs):
bestCoord = bestCoordPerMatch[irefmatch][imatch]
bestRMS = bestRMSPerMatch[irefmatch][imatch]
print "\tBest RMSD reached (match %d, refmatch %d): %s"%(imatch, irefmatch, bestRMS)
molMatchID = molMatchAllIds[imatch]
updateCoords(mol, bestCoord)
newData = pybel.ob.OBPairData()
newData.SetAttribute("TETHERED ATOMS")
newData.SetValue(prepareAtomString(molMatchID))
mol.OBMol.DeleteData("TETHERED ATOMS") # Remove Previous DATA
mol.OBMol.CloneData(newData) # Add new data
out.write(mol)
out.close()
......
......@@ -29,7 +29,7 @@ PROJECT = libRbt.pro # tmake project file to create
BINDIR = ../bin # Install location for exes
LIBDIR = ../lib # Install location for libs
CP = cp -df
PARALLEL = 2 # Uses make -j to build across 2 processors
PARALLEL = 4 # Uses make -j to build across 2 processors
# Configurations
RELEASE = release
......@@ -40,7 +40,7 @@ DEBUG_DEFINES = _DEBUG
# Default platform, configuration, and version
# PLATFORM must define a valid tmake configuration
# i.e. ./tmakelib/$(PLATFORM)/tmake.conf must exist.
PLATFORM = linux-g++
PLATFORM = linux-g++-64
CONFIG = $(RELEASE)
VERSION = enspiral_dev
......
......@@ -29,8 +29,8 @@ Step 1) BUILD
Either:
$ make linux-g++ for 32-bit INTEL build with g++ compiler
$ make linux-g++-64 for 64-bit AMD Opteron build with g++ compiler
$ make linux-g++ for 32-bit build with g++ compiler
$ make linux-g++-64 for 64-bit build with g++ compiler
or
$ make linux-pathCC-64 for 64-bit AMD Opteron build with PathScale compiler
......
......@@ -326,7 +326,7 @@ SOURCES = ../import/simplex/src/NMSearch.cxx \
../src/lib/RbtVdwIntraSF.cxx \
../src/lib/RbtVdwSF.cxx \
../src/lib/RbtWorkSpace.cxx
VERSION = rDock_2013_SRC.0
VERSION = rDock_2013.1
INCLUDEPATH = ../include;../include/GP;../import/simplex/include;../import/tnt/include
DEPENDPATH = $INCLUDEPATH
DEFINES += _NDEBUG
......
This diff is collapsed.
......@@ -2,8 +2,8 @@
#
# Compilation build targets
#
# make linux-g++ g++, 32-bit (INTEL)
# make linux-g++-64 g++, 64-bit (AMD Opteron x86_64)
# make linux-g++ g++, 32-bit
# make linux-g++-64 g++, 64-bit
# make linux-pathCC-64 Pathscale 64-bit (AMD Opteron x86_64)
#
# The above targets are also available with a -dt suffix to build the
......@@ -30,8 +30,10 @@
# the most compact source-only distribution
################################################################
#
PRODUCT := $(shell ./p4utils.pl PRODUCT)
CODELINE := $(shell ./p4utils.pl CODELINE)
#PRODUCT := $(shell ./p4utils.pl PRODUCT)
#CODELINE := $(shell ./p4utils.pl CODELINE)
PRODUCT := ..
CODELINE :=
VERSION := $(shell ./p4utils.pl VERSION)
TAR = tar -cvzf
......@@ -53,6 +55,9 @@ DIST_SRC = $(PRODUCT)/$(CODELINE)/include/ \
$(PRODUCT)/$(CODELINE)/import/simplex/ \
$(PRODUCT)/$(CODELINE)/import/tnt/
# Environment for running rDock unit tests
export RBT_ROOT = ../
export RBT_HOME = ./test/RBT_HOME
......@@ -97,28 +102,45 @@ linux-pathCC-64-dt:
# Requires unit_test executable (should be built by the above) and active site (.as) files
# for 1koc and 1YET, generated by rbcavity (cavity mapping)
.PHONY: test
test: ./test/RBT_HOME/1YET.as
test: ./test/unit_test ./test/RBT_HOME/1koc.as ./test/RBT_HOME/1YET.as ./test/RBT_HOME/1YET_test.as
@echo ""
@echo "Running rDock unit tests..."
@echo ""
@$(RBT_ROOT)/bin/rbdock -r1YET.prm -i ./test/RBT_HOME/1YET_c.sd -p dock.prm -n 1 -s 48151623 -o 1YET_test_out > 1YET_test_out.log
@./test/unit_test
@$(RBT_ROOT)/bin/rbdock -r1YET_test.prm -i ./test/RBT_HOME/1YET_c.sd -p dock.prm -n 1 -s 48151623 -o 1YET_test_out > 1YET_test_out.log
@mv 1YET_test_out.log 1YET_test_out.sd ./test/RBT_HOME/
@python ./test/RBT_HOME/check_test.py ./test/RBT_HOME/1YET_test_out.sd ./test/RBT_HOME/1YET_reference_out.sd
@python ./test/RBT_HOME/check_test.py ./test/RBT_HOME/1YET_reference_out.sd ./test/RBT_HOME/1YET_test_out.sd
./test/unit_test:
$(warning [email protected] executable not found)
$(warning Use 'make <PLATFORM>' first)
$(warning e.g. 'make linux-g++-64')
$(warning e.g. 'make linux-g++')
$(error Unit tests failed)
# Generate the .as file for 1koc
./test/RBT_HOME/1koc.as: ./test/RBT_HOME/1koc.prm
@echo ""
@echo "Cavity mapping of 1koc.prm"
@echo ""
@$(RBT_ROOT)/bin/rbcavity -r1koc.prm -was
@mv 1koc.as ./test/RBT_HOME/
# Generate the .as file for 1YET
./test/RBT_HOME/1YET.as: ./test/RBT_HOME/1YET.prm
@echo ""
@echo "Cavity mapping of 1YET.prm"
@echo ""
@$(RBT_ROOT)/bin/rbcavity -r1YET.prm -was
@$(RBT_ROOT)/bin/rbcavity -r1YET.prm -was
@mv 1YET.as ./test/RBT_HOME/
# Generate the .as file for 1koc
./test/RBT_HOME/1YET_test.as: ./test/RBT_HOME/1YET_test.prm
@echo ""
@echo "Cavity mapping of 1YET_test.prm"
@echo ""
@$(RBT_ROOT)/bin/rbcavity -r1YET_test.prm -was
@mv 1YET_test.as ./test/RBT_HOME/
##################################################
# Create distributions (.tgz files)
#
......@@ -150,7 +172,7 @@ clean:
-rm -f ./test/*.o
-rm -f ./test/RBT_HOME/*.as
-rm -f ./test/unit_test
-rm -f ./test/RBT_HOME/1YET_test*
-rm -f ./test/RBT_HOME/1YET_test_out*
-rm -f ./restart.sd
# Also removes the installed libraries and exes
......
......@@ -23,7 +23,9 @@ UNITTEST_CXXFLAGS = $(CXXFLAGS) -I$(UNITTESTDIR)
UNITTEST_LINKLIBS = -lRbt -ldl -lcppunit
#
# Build targets
all: exe dt_exe unit_test
#all: exe dt_exe unit_test
# XB Build targets except the ones requiring daylight toolkits
all: exe unit_test
# Standalone rDock executables
exe: $(DESTDIR)/rbdock \
......@@ -62,12 +64,12 @@ $(DESTDIR)/rbrms: $(SRCDIR)/rbrms.cxx $(DEPLIBS)
$(CXX) $(CXXFLAGS) $(SRCDIR)/rbrms.cxx $(LINKLIBS) -o [email protected]
# These exes depend on the Daylight SMARTS/SMILES toolkit libraries
# XB comment following lines as daylight is not needed in 2013
#$(OBJECTS_DIR)/RbtSmarts.o : ../src/daylight/RbtSmarts.cxx
# $(CXX) $(DT_CXXFLAGS) ../src/daylight/RbtSmarts.cxx -c -o [email protected]
$(OBJECTS_DIR)/RbtSmarts.o : ../src/daylight/RbtSmarts.cxx
$(CXX) $(DT_CXXFLAGS) ../src/daylight/RbtSmarts.cxx -c -o [email protected]
#$(DESTDIR)/rbtether: $(OBJECTS_DIR)/RbtSmarts.o $(SRCDIR)/rbtether.cxx $(DEPLIBS)
# $(CXX) $(DT_CXXFLAGS) $(SRCDIR)/rbtether.cxx $(OBJECTS_DIR)/RbtSmarts.o $(DT_LINKLIBS) -o [email protected]
$(DESTDIR)/rbtether: $(OBJECTS_DIR)/RbtSmarts.o $(SRCDIR)/rbtether.cxx $(DEPLIBS)
$(CXX) $(DT_CXXFLAGS) $(SRCDIR)/rbtether.cxx $(OBJECTS_DIR)/RbtSmarts.o $(DT_LINKLIBS) -o [email protected]
$(DESTDIR)/smart_rms: $(OBJECTS_DIR)/RbtSmarts.o $(SRCDIR)/smart_rms.cxx $(DEPLIBS)
$(CXX) $(DT_CXXFLAGS) $(SRCDIR)/smart_rms.cxx $(OBJECTS_DIR)/RbtSmarts.o $(DT_LINKLIBS) -o [email protected]
#$(DESTDIR)/smart_rms: $(OBJECTS_DIR)/RbtSmarts.o $(SRCDIR)/smart_rms.cxx $(DEPLIBS)
# $(CXX) $(DT_CXXFLAGS) $(SRCDIR)/smart_rms.cxx $(OBJECTS_DIR)/RbtSmarts.o $(DT_LINKLIBS) -o [email protected]
RBT_PARAMETER_FILE_V1.00
TITLE R_1YET
RECEPTOR_FILE R_1YET_protein.mol2
RECEPTOR_TOPOL_FILE 1YET_for_viewer.psf
RECEPTOR_COORD_FILE 1YET_for_viewer.crd
RECEPTOR_FLEX 3.0
RECEPTOR_DIHEDRAL_STEP 10.0
SECTION LIGAND
TRANS_STEP 2.0
ROT_STEP 30.0
TRANS_MODE FREE
ROT_MODE FREE
END_SECTION
SECTION SOLVENT
FILE P_1YET_watx_cav.pdb
TRANS_STEP 0.1
ROT_STEP 10.0
MAX_TRANS 0.5
MAX_ROT 30.0
END_SECTION
##################################################################
### CAVITY DEFINITION: REFERENCE LIGAND METHOD
##################################################################
SECTION MAPPER
SITE_MAPPER RbtLigandSiteMapper
REF_MOL 1YET_c.sd
VOL_INCR 0.0
GRIDSTEP 0.5
RADIUS 6.0
REF_MOL 1YET_c.sd
SMALL_SPHERE 1.0
TRACE 1
MIN_VOLUME 100
MAX_CAVITIES 1
VOL_INCR 0.0
GRIDSTEP 0.5
END_SECTION
#################################
#CAVITY RESTRAINT PENALTY
#################################
SECTION CAVITY
SCORING_FUNCTION RbtCavityGridSF
WEIGHT 1.0
......
RBT_PARAMETER_FILE_V1.00
TITLE R_1YET
RECEPTOR_FILE R_1YET_protein.mol2
RECEPTOR_FLEX 3.0
##################################################################
### CAVITY DEFINITION: REFERENCE LIGAND METHOD
##################################################################
SECTION MAPPER
SITE_MAPPER RbtLigandSiteMapper
REF_MOL 1YET_c.sd
RADIUS 6.0
SMALL_SPHERE 1.0
MIN_VOLUME 100
MAX_CAVITIES 1
VOL_INCR 0.0
GRIDSTEP 0.5
END_SECTION
#################################
#CAVITY RESTRAINT PENALTY
#################################
SECTION CAVITY
SCORING_FUNCTION RbtCavityGridSF
WEIGHT 1.0
END_SECTION
This diff is collapsed.
......@@ -7,7 +7,7 @@ refcoords=ref[4:48]
testcoords=test[4:48]
refscore=float(ref[123][0])
testscore=float(test[125][0])
testscore=float(test[123][0])
checkcoords=[]
for i in range(0,len(refcoords)):
......
......@@ -7,17 +7,17 @@
TEMPLATE = app
CONFIG = qt warn_on release
TMAKE_CC = /usr/bin/gcc-3.3
TMAKE_CC = /usr/bin/gcc
TMAKE_CFLAGS = -pipe -m64
TMAKE_CFLAGS_WARN_ON = -Wall -W
TMAKE_CFLAGS_WARN_OFF =
TMAKE_CFLAGS_RELEASE = -O3 -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fomit-frame-pointer -funsafe-math-optimizations -m128bit-long-double
#TMAKE_CFLAGS_RELEASE = -O3 -ffast-math -march=i686 -march=k8
TMAKE_CFLAGS_RELEASE = -O3 -ffast-math
TMAKE_CFLAGS_DEBUG = -g
TMAKE_CFLAGS_SHLIB = -fPIC
TMAKE_CFLAGS_YACC = -Wno-unused -Wno-parentheses
TMAKE_CXX = /usr/bin/g++-3.3
TMAKE_CXX = /usr/bin/g++
TMAKE_CXXFLAGS = $$TMAKE_CFLAGS -fpermissive
TMAKE_CXXFLAGS_WARN_ON = $$TMAKE_CFLAGS_WARN_ON
TMAKE_CXXFLAGS_WARN_OFF = $$TMAKE_CFLAGS_WARN_OFF -Wno-deprecated
......@@ -35,8 +35,8 @@ TMAKE_LIBDIR_QT = $(QTDIR)/lib
TMAKE_INCDIR_OPENGL = /usr/X11R6/include
TMAKE_LIBDIR_OPENGL = /usr/X11R6/lib
TMAKE_LINK = /usr/bin/g++-3.3
TMAKE_LINK_SHLIB = /usr/bin/g++-3.3
TMAKE_LINK = /usr/bin/g++
TMAKE_LINK_SHLIB = /usr/bin/g++
TMAKE_LFLAGS = -m64
TMAKE_LFLAGS_RELEASE =
TMAKE_LFLAGS_DEBUG =
......
......@@ -7,16 +7,16 @@
TEMPLATE = app
CONFIG = qt warn_on release
TMAKE_CC = /usr/bin/gcc-3.3
TMAKE_CC = /usr/bin/gcc
TMAKE_CFLAGS = -pipe -m32
TMAKE_CFLAGS_WARN_ON = -Wall -W
TMAKE_CFLAGS_WARN_OFF =
TMAKE_CFLAGS_RELEASE = -O3 -ffast-math -march=pentium3 -mcpu=pentium3
TMAKE_CFLAGS_RELEASE = -O3 -ffast-math
TMAKE_CFLAGS_DEBUG = -g
TMAKE_CFLAGS_SHLIB = -fPIC
TMAKE_CFLAGS_YACC = -Wno-unused -Wno-parentheses
TMAKE_CXX = /usr/bin/g++-3.3
TMAKE_CXX = /usr/bin/g++
TMAKE_CXXFLAGS = $$TMAKE_CFLAGS -fpermissive
TMAKE_CXXFLAGS_WARN_ON = $$TMAKE_CFLAGS_WARN_ON
TMAKE_CXXFLAGS_WARN_OFF = $$TMAKE_CFLAGS_WARN_OFF -Wno-deprecated
......@@ -34,8 +34,8 @@ TMAKE_LIBDIR_QT = $(QTDIR)/lib
TMAKE_INCDIR_OPENGL = /usr/X11R6/include
TMAKE_LIBDIR_OPENGL = /usr/X11R6/lib
TMAKE_LINK = /usr/bin/g++-3.3
TMAKE_LINK_SHLIB = /usr/bin/g++-3.3
TMAKE_LINK = /usr/bin/g++
TMAKE_LINK_SHLIB = /usr/bin/g++
TMAKE_LFLAGS = -m32
TMAKE_LFLAGS_RELEASE =
TMAKE_LFLAGS_DEBUG =
......
RBT_ELEMENT_FILE_V1.01
TITLE RiboTargets Elemental Data File
VERSION $Id: //depot/dev/client3/rdock/2006.1/data/RbtElements.dat#2 $
VERSION $Id: //depot/dev/client3/rdock/2013.1/data/RbtElements.dat#2 $
####################################################################
#
# Hydrogen-bond donor radius increment
......
......@@ -7,7 +7,7 @@
* These files are a beta release; additional parameter development
* and testing may lead to alteration of the contents.
*
* $Id: //depot/dev/client3/rdock/2006.1/data/cnx.rtf#2 $
* $Id: //depot/dev/client3/rdock/2013.1/data/cnx.rtf#2 $
*
* 30 Apr 1999 (D Morley, RiboTargets)
* Modified for RiboDock:
......
RBT_PARAMETER_FILE_V1.00
TITLE Intermolecular scoring function (without SOLVATION, grid-based VDW)
VERSION $Id: //depot/dev/client3/rdock/2006.1/data/sf/RbtInterGridSF.prm#2 $
VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtInterGridSF.prm#2 $