===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
apbs-3.0.0+dfsg1/.github/workflows/action.yml-113- #export LD_LIBRARY_PATH=${HOME}/local/lib:$LD_LIBRARY_PATH
apbs-3.0.0+dfsg1/.github/workflows/action.yml:114: for name in `echo $TEST_LIST`
apbs-3.0.0+dfsg1/.github/workflows/action.yml-115- do
##############################################
apbs-3.0.0+dfsg1/.travis.yml-223- fi
apbs-3.0.0+dfsg1/.travis.yml:224: for name in `echo $TEST_LIST`
apbs-3.0.0+dfsg1/.travis.yml-225- do
##############################################
apbs-3.0.0+dfsg1/apbs/.build.sh-38-#ldd ${INSTALL_DIR}/bin/apbs
apbs-3.0.0+dfsg1/apbs/.build.sh:39:#for testname in `echo $TESTNAMES`
apbs-3.0.0+dfsg1/apbs/.build.sh-40-#do
##############################################
apbs-3.0.0+dfsg1/apbs/README.md-31-If you would like to use the FEM, you will need to be on OS X or Linux. To enable, when invoking CMake, set ENABLE_FETK to ON, e.g., `-DENABLE_FETK=ON`.
apbs-3.0.0+dfsg1/apbs/README.md:32:On Linux the FETK shared libraries need to be locatable by the shared library loader. One way to do this is to update LD_LIBRARY_PATH to point at `<build-dir>/fetk/lib`, e.g., `export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<build-dir>/fetk/lib`.
apbs-3.0.0+dfsg1/apbs/README.md-33-
##############################################
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/Amber/patches/amber10_mm_pbsa.patch-60-+ my $lncommand = "ln -s " . $pqrfname . " ./pqr";
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/Amber/patches/amber10_mm_pbsa.patch:61:+ system($lncommand) && die ("Linking pqr file $pqrfname failed!\n");
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/Amber/patches/amber10_mm_pbsa.patch:62:+ system($command) && die(" $command not successful\n");
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/Amber/patches/amber10_mm_pbsa.patch-63-+ system("rm -f ./pqr");
##############################################
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/Amber/patches/amber9_mm_pbsa.patch-63-+ my $lncommand = "ln -s " . $pqrfname . " ./pqr";
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/Amber/patches/amber9_mm_pbsa.patch:64:+ system($lncommand) && die ("Linking pqr file $pqrfname failed!\n");
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/Amber/patches/amber9_mm_pbsa.patch:65:+ system($command) && die(" $command not successful\n");
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/Amber/patches/amber9_mm_pbsa.patch-66-+ system("rm -f ./pqr");
##############################################
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/NAMD/test/dipeptide/test.sh-29-do
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/NAMD/test/dipeptide/test.sh:30: base=`basename $i .conf`
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/NAMD/test/dipeptide/test.sh-31- echo "Working on $base ..."
##############################################
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/NAMD/test/ubq/ubq.conf-90-#############################################################
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/NAMD/test/ubq/ubq.conf:91:## EXECUTION SCRIPT ##
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/modules/NAMD/test/ubq/ubq.conf-92-#############################################################
##############################################
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/test/mem.sh-23-while [ -e $status_file ] ; do
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/test/mem.sh:24: VM_SIZE=`awk '/VmSize/ {print $2}' < $status_file`
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/test/mem.sh:25: VM_RSS=`awk '/VmRSS/ {print $2}' < $status_file`
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/test/mem.sh-26- echo "$counter $VM_SIZE $VM_RSS" >> $LOG
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/test/mem.sh-27- sleep $PERIOD
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/test/mem.sh:28: counter=`echo $counter + $PERIOD|bc`
apbs-3.0.0+dfsg1/apbs/contrib/iapbs/test/mem.sh-29- VM_SIZE=""
##############################################
apbs-3.0.0+dfsg1/apbs/doc/release_procedure.md-86- protein-rna"
apbs-3.0.0+dfsg1/apbs/doc/release_procedure.md:87: for testname in `echo $TESTNAMES`
apbs-3.0.0+dfsg1/apbs/doc/release_procedure.md-88- do
##############################################
apbs-3.0.0+dfsg1/apbs/examples/alkanes/Makefile.in-239-distdir: $(DISTFILES)
apbs-3.0.0+dfsg1/apbs/examples/alkanes/Makefile.in:240: @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/examples/alkanes/Makefile.in:241: topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/examples/alkanes/Makefile.in-242- list='$(DISTFILES)'; \
##############################################
apbs-3.0.0+dfsg1/apbs/examples/alkanes/Makefile.in-253- if test -d $$d/$$file; then \
apbs-3.0.0+dfsg1/apbs/examples/alkanes/Makefile.in:254: dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
apbs-3.0.0+dfsg1/apbs/examples/alkanes/Makefile.in-255- if test -d "$(distdir)/$$file"; then \
##############################################
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/Makefile.in-239-distdir: $(DISTFILES)
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/Makefile.in:240: @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/Makefile.in:241: topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/Makefile.in-242- list='$(DISTFILES)'; \
##############################################
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/Makefile.in-253- if test -d $$d/$$file; then \
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/Makefile.in:254: dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/Makefile.in-255- if test -d "$(distdir)/$$file"; then \
##############################################
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/test.sh-39- $1 ${input[i]}.in > ${input[i]}.out
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/test.sh:40: answer=( `grep "Global net ELEC" ${input[i]}.out | awk '{print $6}'` )
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/test.sh-41-
##############################################
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/postprocess.sh-9- ionstr=${stem#apbs-}
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/postprocess.sh:10: energy_kJ=`cat ${outfile} | grep Global | awk '{print $6}'`
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/postprocess.sh-11- echo ${ionstr} ${energy_kJ} >> conc-energykJ.dat
##############################################
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/postprocess.sh-16-cat lnconc-energyRT.dat | python3 fit.py > lnconc-energyRT.fit
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/postprocess.sh:17:n=`grep "slope:" lnconc-energyRT.fit | awk '{print $2}'`
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/postprocess.sh:18:dn=`grep "slope error:" lnconc-energyRT.fit | awk '{print $3}'`
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/postprocess.sh-19-echo "n = -(${n} +/- ${dn})"
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/postprocess.sh-20-cat log10conc-energykcal.dat | python3 fit.py > log10conc-energykcal.fit
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/postprocess.sh:21:dGdl=`grep "slope:" log10conc-energykcal.fit | awk '{print $2}'`
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/postprocess.sh:22:ddGdl=`grep "slope error:" log10conc-energykcal.fit | awk '{print $3}'`
apbs-3.0.0+dfsg1/apbs/examples/protein-rna/postprocess.sh-23-echo "dG/d(log10 [KCl]) = ${dGdl} +/- (${ddGdl})"
##############################################
apbs-3.0.0+dfsg1/apbs/examples/solv/Makefile.in-238-distdir: $(DISTFILES)
apbs-3.0.0+dfsg1/apbs/examples/solv/Makefile.in:239: @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/examples/solv/Makefile.in:240: topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/examples/solv/Makefile.in-241- list='$(DISTFILES)'; \
##############################################
apbs-3.0.0+dfsg1/apbs/examples/solv/Makefile.in-252- if test -d $$d/$$file; then \
apbs-3.0.0+dfsg1/apbs/examples/solv/Makefile.in:253: dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
apbs-3.0.0+dfsg1/apbs/examples/solv/Makefile.in-254- if test -d "$(distdir)/$$file"; then \
##############################################
apbs-3.0.0+dfsg1/apbs/include/Eigen/src/Core/arch/NEON/PacketMath.h-52-#ifndef __pld
apbs-3.0.0+dfsg1/apbs/include/Eigen/src/Core/arch/NEON/PacketMath.h:53:#define __pld(x) asm volatile ( " pld [%[addr]]\n" :: [addr] "r" (x) : "cc" );
apbs-3.0.0+dfsg1/apbs/include/Eigen/src/Core/arch/NEON/PacketMath.h-54-#endif
##############################################
apbs-3.0.0+dfsg1/apbs/include/Eigen/src/Eigen2Support/LeastSquares.h-112- * \f[ r_0 x_0 + \cdots + r_{n-1}x_{n-1} + r_n = 0, \f]
apbs-3.0.0+dfsg1/apbs/include/Eigen/src/Eigen2Support/LeastSquares.h:113: * where \f$n=Size\f$, \f$r_i=retCoefficients[i]\f$, and we denote by
apbs-3.0.0+dfsg1/apbs/include/Eigen/src/Eigen2Support/LeastSquares.h-114- * \f$x_0,\ldots,x_{n-1}\f$ the n coordinates in the n-dimensional space.
##############################################
apbs-3.0.0+dfsg1/apbs/include/Eigen/src/Eigenvalues/Tridiagonalization.h-336- * \f$ H_i = (I - h_i v_i v_i^T) \f$
apbs-3.0.0+dfsg1/apbs/include/Eigen/src/Eigenvalues/Tridiagonalization.h:337: * where \f$ h_i = hCoeffs[i]\f$ is the \f$ i \f$th Householder coefficient and
apbs-3.0.0+dfsg1/apbs/include/Eigen/src/Eigenvalues/Tridiagonalization.h-338- * \f$ v_i \f$ is the Householder vector defined by
##############################################
apbs-3.0.0+dfsg1/apbs/src/fem/vfetk.c-658- /* Get the data from the Bvec */
apbs-3.0.0+dfsg1/apbs/src/fem/vfetk.c:659: solution = Bvec_addr(am->w0);
apbs-3.0.0+dfsg1/apbs/src/fem/vfetk.c-660- /* Get the length of the data from the Bvec */
##############################################
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER.tex-40-
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER.tex:41:where $u\left(\mathbf{r}\right)=e_{c}\Phi\left(\mathbf{r}\right)/K_{B}T$
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER.tex-42-and $magic=4\pi e_{c}^{2}/K_{B}T.$ For a diagonal dielectric tensor,
##############################################
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_5/MATLAB_PB_SOLVER_5.tex-53-
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_5/MATLAB_PB_SOLVER_5.tex:54:where $u\left(\mathbf{r}\right)=e_{c}\Phi\left(\mathbf{r}\right)/K_{B}T$
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_5/MATLAB_PB_SOLVER_5.tex-55-and $magic=4\pi e_{c}^{2}/K_{B}T.$ For a diagonal dielectric tensor,
##############################################
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_6/MATLAB_PB_SOLVER_6.tex-55-
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_6/MATLAB_PB_SOLVER_6.tex:56:where $u\left(\mathbf{r}\right)=e_{c}\Phi\left(\mathbf{r}\right)/K_{B}T$
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_6/MATLAB_PB_SOLVER_6.tex-57-and $magic=4\pi e_{c}^{2}/K_{B}T.$ For a diagonal dielectric tensor,
##############################################
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_6/MATLAB_PB_SOLVER_6.tex-479-
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_6/MATLAB_PB_SOLVER_6.tex:480:where \textbf{I} is the ionic strength defined by $I=0.5\sum_{i}c_{i}z_{i}^{2}$
apbs-3.0.0+dfsg1/apbs/tools/matlab/solver/MATLAB_PB_SOLVER_6/MATLAB_PB_SOLVER_6.tex-481-where the dummy sum is over all different ionic species, $z_{i}$
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/CMakeLists.txt-6-FIND_PACKAGE(SWIG REQUIRED)
apbs-3.0.0+dfsg1/apbs/tools/python/CMakeLists.txt:7:INCLUDE(${SWIG_USE_FILE})
apbs-3.0.0+dfsg1/apbs/tools/python/CMakeLists.txt-8-
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-95- while test -n "$$dir1"; do \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:96: first=`echo "$$dir1" | sed -e "$$sed_first"`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-97- if test "$$first" != "."; then \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-98- if test "$$first" = ".."; then \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:99: dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:100: dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-101- else \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:102: first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-103- if test "$$first2" = "$$first"; then \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:104: dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-105- else \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-110- fi; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:111: dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-112- done; \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-321- test -n "$(EXEEXT)" || exit 0; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:322: list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-323- echo " rm -f" $$list; \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-338-.c.obj:
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:339: $(COMPILE) -c `$(CYGPATH_W) '$<'`
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-340-
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-364- dot_seen=no; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:365: target=`echo $@ | sed s/-recursive//`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-366- list='$(SUBDIRS)'; for subdir in $$list; do \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-399- rev="$$rev ."; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:400: target=`echo $@ | sed s/-recursive//`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-401- for subdir in $$rev; do \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-477-GTAGS:
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:478: here=`$(am__cd) $(top_builddir) && pwd` \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-479- && $(am__cd) $(top_srcdir) \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-485-distdir: $(DISTFILES)
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:486: @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:487: topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-488- list='$(DISTFILES)'; \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-499- if test -d $$d/$$file; then \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile:500: dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile-501- if test -d "$(distdir)/$$file"; then \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-95- while test -n "$$dir1"; do \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:96: first=`echo "$$dir1" | sed -e "$$sed_first"`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-97- if test "$$first" != "."; then \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-98- if test "$$first" = ".."; then \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:99: dir2=`echo "$$dir0" | sed -e "$$sed_last"`/"$$dir2"; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:100: dir0=`echo "$$dir0" | sed -e "$$sed_butlast"`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-101- else \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:102: first2=`echo "$$dir2" | sed -e "$$sed_first"`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-103- if test "$$first2" = "$$first"; then \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:104: dir2=`echo "$$dir2" | sed -e "$$sed_rest"`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-105- else \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-110- fi; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:111: dir1=`echo "$$dir1" | sed -e "$$sed_rest"`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-112- done; \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-321- test -n "$(EXEEXT)" || exit 0; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:322: list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-323- echo " rm -f" $$list; \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-338-.c.obj:
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:339: $(COMPILE) -c `$(CYGPATH_W) '$<'`
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-340-
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-364- dot_seen=no; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:365: target=`echo $@ | sed s/-recursive//`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-366- list='$(SUBDIRS)'; for subdir in $$list; do \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-399- rev="$$rev ."; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:400: target=`echo $@ | sed s/-recursive//`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-401- for subdir in $$rev; do \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-477-GTAGS:
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:478: here=`$(am__cd) $(top_builddir) && pwd` \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-479- && $(am__cd) $(top_srcdir) \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-485-distdir: $(DISTFILES)
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:486: @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:487: topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-488- list='$(DISTFILES)'; \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-499- if test -d $$d/$$file; then \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in:500: dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/Makefile.in-501- if test -d "$(distdir)/$$file"; then \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile-281- test -n "$(EXEEXT)" || exit 0; \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile:282: list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile-283- echo " rm -f" $$list; \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile-298-.c.obj:
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile:299: $(COMPILE) -c `$(CYGPATH_W) '$<'`
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile-300-
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile-354-GTAGS:
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile:355: here=`$(am__cd) $(top_builddir) && pwd` \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile-356- && $(am__cd) $(top_srcdir) \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile-362-distdir: $(DISTFILES)
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile:363: @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile:364: topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile-365- list='$(DISTFILES)'; \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile-376- if test -d $$d/$$file; then \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile:377: dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile-378- if test -d "$(distdir)/$$file"; then \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in-281- test -n "$(EXEEXT)" || exit 0; \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in:282: list=`for p in $$list; do echo "$$p"; done | sed 's/$(EXEEXT)$$//'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in-283- echo " rm -f" $$list; \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in-298-.c.obj:
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in:299: $(COMPILE) -c `$(CYGPATH_W) '$<'`
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in-300-
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in-354-GTAGS:
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in:355: here=`$(am__cd) $(top_builddir) && pwd` \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in-356- && $(am__cd) $(top_srcdir) \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in-362-distdir: $(DISTFILES)
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in:363: @srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in:364: topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in-365- list='$(DISTFILES)'; \
##############################################
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in-376- if test -d $$d/$$file; then \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in:377: dir=`echo "/$$file" | sed -e 's,/[^/]*$$,,'`; \
apbs-3.0.0+dfsg1/apbs/tools/python/vgrid/Makefile.in-378- if test -d "$(distdir)/$$file"; then \
##############################################
apbs-3.0.0+dfsg1/apbs/CMakeLists.txt-487- list(APPEND CMAKE_MODULE_PATH ${EXTERNALS_PATH}/pb_s_am/cmake/modules)
apbs-3.0.0+dfsg1/apbs/CMakeLists.txt:488: include(${EXTERNALS_PATH}/pb_s_am/cmake/Utils.cmake)
apbs-3.0.0+dfsg1/apbs/CMakeLists.txt:489: include(${EXTERNALS_PATH}/pb_s_am/cmake/Dependencies.cmake)
apbs-3.0.0+dfsg1/apbs/CMakeLists.txt:490: include(${EXTERNALS_PATH}/pb_s_am/cmake/Summary.cmake)
apbs-3.0.0+dfsg1/apbs/CMakeLists.txt-491-
##############################################
apbs-3.0.0+dfsg1/doc/_build/html/_sources/apbs/invoking.rst.txt-5-
apbs-3.0.0+dfsg1/doc/_build/html/_sources/apbs/invoking.rst.txt:6:As mentioned in the installation and availability section, the main APBS binary is installed in ``${APBS_PREFIX}/bin`` where ``${APBS_PREFIX}`` is the top-level directory you chose for the installation.
apbs-3.0.0+dfsg1/doc/_build/html/_sources/apbs/invoking.rst.txt-7-You can move the binary to any directory you choose.
##############################################
apbs-3.0.0+dfsg1/doc/_build/html/_sources/formats/pdb2pqr-xml-names.rst.txt-46-There are a few other additional notes when using the :file:`.names` file.
apbs-3.0.0+dfsg1/doc/_build/html/_sources/formats/pdb2pqr-xml-names.rst.txt:47:First, the ``$group`` variable is used to denote the matching group of a regular expression, for instance:
apbs-3.0.0+dfsg1/doc/_build/html/_sources/formats/pdb2pqr-xml-names.rst.txt-48-
##############################################
apbs-3.0.0+dfsg1/doc/_build/html/apbs/invoking.html-45-<p>Unless invoked by <a class="reference internal" href="../pdb2pqr/index.html"><span class="doc">PDB2PQR</span></a> or another software package (see <a class="reference internal" href="../other-software.html"><span class="doc">Other software</span></a>), most APBS calculations are performed from the command line by running an APBS input file through the APBS program.</p>
apbs-3.0.0+dfsg1/doc/_build/html/apbs/invoking.html:46:<p>As mentioned in the installation and availability section, the main APBS binary is installed in <code class="docutils literal"><span class="pre">${APBS_PREFIX}/bin</span></code> where <code class="docutils literal"><span class="pre">${APBS_PREFIX}</span></code> is the top-level directory you chose for the installation.
apbs-3.0.0+dfsg1/doc/_build/html/apbs/invoking.html-47-You can move the binary to any directory you choose.</p>
##############################################
apbs-3.0.0+dfsg1/doc/apbs/invoking.rst-5-
apbs-3.0.0+dfsg1/doc/apbs/invoking.rst:6:As mentioned in the installation and availability section, the main APBS binary is installed in ``${APBS_PREFIX}/bin`` where ``${APBS_PREFIX}`` is the top-level directory you chose for the installation.
apbs-3.0.0+dfsg1/doc/apbs/invoking.rst-7-You can move the binary to any directory you choose.
##############################################
apbs-3.0.0+dfsg1/doc/formats/pdb2pqr-xml-names.rst-46-There are a few other additional notes when using the :file:`.names` file.
apbs-3.0.0+dfsg1/doc/formats/pdb2pqr-xml-names.rst:47:First, the ``$group`` variable is used to denote the matching group of a regular expression, for instance:
apbs-3.0.0+dfsg1/doc/formats/pdb2pqr-xml-names.rst-48-
##############################################
apbs-3.0.0+dfsg1/debian/patches/python3.patch-23-+cat lnconc-energyRT.dat | python3 fit.py > lnconc-energyRT.fit
apbs-3.0.0+dfsg1/debian/patches/python3.patch:24: n=`grep "slope:" lnconc-energyRT.fit | awk '{print $2}'`
apbs-3.0.0+dfsg1/debian/patches/python3.patch:25: dn=`grep "slope error:" lnconc-energyRT.fit | awk '{print $3}'`
apbs-3.0.0+dfsg1/debian/patches/python3.patch-26- echo "n = -(${n} +/- ${dn})"
##############################################
apbs-3.0.0+dfsg1/debian/patches/python3.patch-28-+cat log10conc-energykcal.dat | python3 fit.py > log10conc-energykcal.fit
apbs-3.0.0+dfsg1/debian/patches/python3.patch:29: dGdl=`grep "slope:" log10conc-energykcal.fit | awk '{print $2}'`
apbs-3.0.0+dfsg1/debian/patches/python3.patch:30: ddGdl=`grep "slope error:" log10conc-energykcal.fit | awk '{print $3}'`
apbs-3.0.0+dfsg1/debian/patches/python3.patch-31- echo "dG/d(log10 [KCl]) = ${dGdl} +/- (${ddGdl})"
##############################################
apbs-3.0.0+dfsg1/.pc/debian_testfiles.patch/apbs/CMakeLists.txt-493- list(APPEND CMAKE_MODULE_PATH ${EXTERNALS_PATH}/pb_s_am/cmake/modules)
apbs-3.0.0+dfsg1/.pc/debian_testfiles.patch/apbs/CMakeLists.txt:494: include(${EXTERNALS_PATH}/pb_s_am/cmake/Utils.cmake)
apbs-3.0.0+dfsg1/.pc/debian_testfiles.patch/apbs/CMakeLists.txt:495: include(${EXTERNALS_PATH}/pb_s_am/cmake/Dependencies.cmake)
apbs-3.0.0+dfsg1/.pc/debian_testfiles.patch/apbs/CMakeLists.txt:496: include(${EXTERNALS_PATH}/pb_s_am/cmake/Summary.cmake)
apbs-3.0.0+dfsg1/.pc/debian_testfiles.patch/apbs/CMakeLists.txt-497-
##############################################
apbs-3.0.0+dfsg1/.pc/debian_make.patch/apbs/CMakeLists.txt-493- list(APPEND CMAKE_MODULE_PATH ${EXTERNALS_PATH}/pb_s_am/cmake/modules)
apbs-3.0.0+dfsg1/.pc/debian_make.patch/apbs/CMakeLists.txt:494: include(${EXTERNALS_PATH}/pb_s_am/cmake/Utils.cmake)
apbs-3.0.0+dfsg1/.pc/debian_make.patch/apbs/CMakeLists.txt:495: include(${EXTERNALS_PATH}/pb_s_am/cmake/Dependencies.cmake)
apbs-3.0.0+dfsg1/.pc/debian_make.patch/apbs/CMakeLists.txt:496: include(${EXTERNALS_PATH}/pb_s_am/cmake/Summary.cmake)
apbs-3.0.0+dfsg1/.pc/debian_make.patch/apbs/CMakeLists.txt-497-
##############################################
apbs-3.0.0+dfsg1/.pc/shared_library_soname.patch/apbs/CMakeLists.txt-486- list(APPEND CMAKE_MODULE_PATH ${EXTERNALS_PATH}/pb_s_am/cmake/modules)
apbs-3.0.0+dfsg1/.pc/shared_library_soname.patch/apbs/CMakeLists.txt:487: include(${EXTERNALS_PATH}/pb_s_am/cmake/Utils.cmake)
apbs-3.0.0+dfsg1/.pc/shared_library_soname.patch/apbs/CMakeLists.txt:488: include(${EXTERNALS_PATH}/pb_s_am/cmake/Dependencies.cmake)
apbs-3.0.0+dfsg1/.pc/shared_library_soname.patch/apbs/CMakeLists.txt:489: include(${EXTERNALS_PATH}/pb_s_am/cmake/Summary.cmake)
apbs-3.0.0+dfsg1/.pc/shared_library_soname.patch/apbs/CMakeLists.txt-490-
##############################################
apbs-3.0.0+dfsg1/.pc/python3.patch/apbs/examples/protein-rna/postprocess.sh-9- ionstr=${stem#apbs-}
apbs-3.0.0+dfsg1/.pc/python3.patch/apbs/examples/protein-rna/postprocess.sh:10: energy_kJ=`cat ${outfile} | grep Global | awk '{print $6}'`
apbs-3.0.0+dfsg1/.pc/python3.patch/apbs/examples/protein-rna/postprocess.sh-11- echo ${ionstr} ${energy_kJ} >> conc-energykJ.dat
##############################################
apbs-3.0.0+dfsg1/.pc/python3.patch/apbs/examples/protein-rna/postprocess.sh-16-cat lnconc-energyRT.dat | python fit.py > lnconc-energyRT.fit
apbs-3.0.0+dfsg1/.pc/python3.patch/apbs/examples/protein-rna/postprocess.sh:17:n=`grep "slope:" lnconc-energyRT.fit | awk '{print $2}'`
apbs-3.0.0+dfsg1/.pc/python3.patch/apbs/examples/protein-rna/postprocess.sh:18:dn=`grep "slope error:" lnconc-energyRT.fit | awk '{print $3}'`
apbs-3.0.0+dfsg1/.pc/python3.patch/apbs/examples/protein-rna/postprocess.sh-19-echo "n = -(${n} +/- ${dn})"
apbs-3.0.0+dfsg1/.pc/python3.patch/apbs/examples/protein-rna/postprocess.sh-20-cat log10conc-energykcal.dat | python fit.py > log10conc-energykcal.fit
apbs-3.0.0+dfsg1/.pc/python3.patch/apbs/examples/protein-rna/postprocess.sh:21:dGdl=`grep "slope:" log10conc-energykcal.fit | awk '{print $2}'`
apbs-3.0.0+dfsg1/.pc/python3.patch/apbs/examples/protein-rna/postprocess.sh:22:ddGdl=`grep "slope error:" log10conc-energykcal.fit | awk '{print $3}'`
apbs-3.0.0+dfsg1/.pc/python3.patch/apbs/examples/protein-rna/postprocess.sh-23-echo "dG/d(log10 [KCl]) = ${dGdl} +/- (${ddGdl})"