diff --git a/.github/workflows/merge-gate.yml b/.github/workflows/merge-gate.yml index 2cf3514bec..fa24a95404 100644 --- a/.github/workflows/merge-gate.yml +++ b/.github/workflows/merge-gate.yml @@ -149,7 +149,7 @@ jobs: - name: Install conda packages run: | which conda - conda install conda=23.11.0 python=3.10 + conda install conda=24.11.0 python=3.10 conda --version conda env update --file devtools/ci/environment.yml --name base - name: Install cpptraj diff --git a/Makefile b/Makefile index 55e0de5497..095b150091 100644 --- a/Makefile +++ b/Makefile @@ -33,8 +33,8 @@ unittest: config.h # Clean up clean: config.h cd src && $(MAKE) clean - cd test && $(MAKE) clean - cd unitTests && $(MAKE) clean +# cd test && $(MAKE) clean +# cd unitTests && $(MAKE) clean docs: src/cpptraj.Doxyfile cd doc && make docs diff --git a/configure b/configure index 5b30d9c218..89a6bb859e 100755 --- a/configure +++ b/configure @@ -318,9 +318,9 @@ LIB_D_ON[$LFFTW3]='-DFFTW_FFT' LIB_DOFF[$LFFTW3]='' LIB_TYPE[$LFFTW3]='cpp' -LIB_STAT[$LREADLINE]='bundled' +LIB_STAT[$LREADLINE]='enabled' LIB_CKEY[$LREADLINE]='readline' -LIB_HOME[$LREADLINE]='readline' +LIB_HOME[$LREADLINE]='' LIB_FLAG[$LREADLINE]='-lreadline' LIB_STTC[$LREADLINE]='libreadline.a' LIB_D_ON[$LREADLINE]='' @@ -1073,13 +1073,42 @@ EOF TestReadline() { cat > testp.cpp < -#include +#include static char *line_read = (char *)NULL; // Do not want to actually run this so leave outside main void Unused() { line_read = readline(""); } int main() { return 0; } EOF - TestProgram " Checking Readline" "$CXX" "$CXXFLAGS ${LIB_INCL[$LREADLINE]}" testp.cpp "${LIB_FLAG[$LREADLINE]}" + + if [ "${LIB_STAT[$LREADLINE]}" = 'specified' ] ; then + TestProgram " Checking Readline" "$CXX" "$CXXFLAGS ${LIB_INCL[$LREADLINE]}" testp.cpp "${LIB_FLAG[$LREADLINE]}" + else + # Test with just -lreadline + TestProgram silent " Checking Readline" "$CXX" "$CXXFLAGS ${LIB_INCL[$LREADLINE]}" testp.cpp "${LIB_FLAG[$LREADLINE]}" + lreadline_err=$? + if [ $lreadline_err -ne 0 ] ; then + # Try -ltermcap + TestProgram silent " Checking Readline with termcap" "$CXX" "$CXXFLAGS ${LIB_INCL[$LREADLINE]}" testp.cpp "${LIB_FLAG[$LREADLINE]} -ltermcap" + lreadline_err=$? + if [ $lreadline_err -eq 0 ] ; then + LIB_FLAG[$LREADLINE]="${LIB_FLAG[$LREADLINE]} -ltermcap" + fi + fi + if [ $lreadline_err -ne 0 ] ; then + # Try -lncurses + TestProgram silent " Checking Readline with ncurses" "$CXX" "$CXXFLAGS ${LIB_INCL[$LREADLINE]}" testp.cpp "${LIB_FLAG[$LREADLINE]} -lncurses" + lreadline_err=$? + if [ $lreadline_err -eq 0 ] ; then + LIB_FLAG[$LREADLINE]="${LIB_FLAG[$LREADLINE]} -lncurses" + fi + fi + if [ $lreadline_err -ne 0 ] ; then + echo "No readline available; using bundled readline." + LIB_STAT[$LREADLINE]='bundled' + LIB_FLAG[$LREADLINE]='readline/libreadline.a' + LIB_INCL[$LREADLINE]='-I.' + fi + fi } TestXdrfile() { @@ -1503,22 +1532,22 @@ SetupLibraries() { lflag="-L$lhdir ${LIB_FLAG[$i]}" fi # Library-specific CPPTRAJ_INC fixes when home specified. - if [ $i -eq $LREADLINE ] ; then - linc="$linc/readline" - fi + #if [ $i -eq $LREADLINE ] ; then + # linc="$linc/readline" + #fi if [ $i -eq $LXDRFILE ] ; then linc="$linc/xdrfile" fi fi # Library-specific flag fixes - if [ $i -eq $LREADLINE ] ; then +# if [ $i -eq $LREADLINE ] ; then # For external readline, we need to link libtermcap for windows # and libncurses for Linux - #if [ $USE_WINDOWS -eq 1 ]; then + if [ $USE_WINDOWS -eq 1 ]; then lflag="$lflag -ltermcap" - #else - # lflag="$lflag -lncurses" - #fi + else + lflag="$lflag -lncurses" + fi elif [ $i -eq $LSANDER ] ; then # Always specify libsander location to prevent pulling in # other amber libraries. @@ -1662,7 +1691,7 @@ SetupCompilers() { if [ -z "$FC" ]; then FC=gfortran; fi hostflags='' optflags='-O3' - ompflag='-fopenmp' + ompflag='-Xclang -fopenmp' freefmtflag='-ffree-form' foptflags='-O3' FLINK='-lgfortran' @@ -1671,8 +1700,8 @@ SetupCompilers() { # Check the GNU compiler version CheckCompilerVersion gcc # Set version-specific flags - if [ $cc_version_major -ge 14 ] ; then - # Needed for readline with gcc >= 14 + if [ $cc_version_major -ge 13 ] ; then + # Needed for readline with gcc >= 13 CFLAGS="$CFLAGS -D_DEFAULT_SOURCE -D_XOPEN_SOURCE" fi ;; @@ -2565,6 +2594,12 @@ if [ -z "`which grep`" ] ; then Err "CPPTRAJ configure requires 'grep'." fi +# Check for the 'install/ binary +INSTALL=`which install` +if [ -z "$INSTALL" ] ; then + Err "CPPTRAJ configure requires 'install'." +fi + #echo "Path to configure: $WORKDIR" #echo "Current dir : $CURRENTDIR" @@ -2953,6 +2988,10 @@ CPPTRAJDAT="$CPPTRAJDAT" INSTALL_TARGETS=$INSTALL_TARGETS +INSTALL=$INSTALL +INSTALL_PROGRAM=$INSTALL +INSTALL_DATA=$INSTALL -m 644 + EOF if [ ! -z "$DBGFLAGS" ] ; then echo "DBGFLAGS=$DBGFLAGS" >> config.h diff --git a/devtools/GetHeaders.sh b/devtools/GetHeaders.sh new file mode 100755 index 0000000000..a86cdd7052 --- /dev/null +++ b/devtools/GetHeaders.sh @@ -0,0 +1,23 @@ +#!/bin/bash + +# Get all header files + +WORKDIR=`pwd` +BASEDIR=`basename $WORKDIR` +if [ "$BASEDIR" != 'src' ] ; then + echo "Should be executed from the CPPTRAJ src directory." + exit 1 +fi + +OUTFILE='cpptrajheaders' +echo "# All cpptraj headers that should be installed for the cpptraj library." > $OUTFILE +echo "CPPTRAJ_HEADERS = \\" >> $OUTFILE + +for DIR in . Cluster Structure Energy ; do + for FILE in `ls $DIR/*.h` ; do + echo " $FILE \\" >> $OUTFILE + done +done +echo "" >> $OUTFILE + +exit 0 diff --git a/doc/CpptrajManual.lyx b/doc/CpptrajManual.lyx index 2a329d8673..e7772f53e3 100644 --- a/doc/CpptrajManual.lyx +++ b/doc/CpptrajManual.lyx @@ -1,16 +1,16 @@ #LyX 2.4 created this file. For more info see https://www.lyx.org/ -\lyxformat 620 +\lyxformat 544 \begin_document \begin_header \save_transient_properties true \origin unavailable \textclass article \use_default_options true -\maintain_unincluded_children no +\maintain_unincluded_children false \language english \language_package default -\inputencoding auto-legacy -\fontencoding auto +\inputencoding auto +\fontencoding global \font_roman "default" "default" \font_sans "default" "default" \font_typewriter "default" "default" @@ -18,9 +18,7 @@ \font_default_family default \use_non_tex_fonts false \font_sc false -\font_roman_osf false -\font_sans_osf false -\font_typewriter_osf false +\font_osf false \font_sf_scale 100 100 \font_tt_scale 100 100 \use_microtype false @@ -64,9 +62,7 @@ \suppress_date false \justification true \use_refstyle 1 -\use_formatted_ref 0 \use_minted 0 -\use_lineno 0 \index Index \shortcut idx \color #008000 @@ -82,16 +78,11 @@ \papercolumns 1 \papersides 1 \paperpagestyle default -\tablestyle default \tracking_changes false \output_changes false -\change_bars false -\postpone_fragile_content false \html_math_output 0 \html_css_as_file 0 \html_be_strict false -\docbook_table_output 0 -\docbook_mathml_prefix 1 \end_header \begin_body @@ -133,7 +124,6 @@ LatexCommand tableofcontents \begin_inset CommandInset include LatexCommand input filename "cpptraj.lyx" -literal "true" \end_inset diff --git a/doc/CpptrajManual.pdf b/doc/CpptrajManual.pdf index 432281bdc6..9538085a43 100644 Binary files a/doc/CpptrajManual.pdf and b/doc/CpptrajManual.pdf differ diff --git a/doc/DocumentChecksums.txt b/doc/DocumentChecksums.txt index 7cd22a8665..9bf71d8580 100644 --- a/doc/DocumentChecksums.txt +++ b/doc/DocumentChecksums.txt @@ -1,3 +1,3 @@ b37726e7a841f6fc695ecd7fb040ffbf CpptrajDevelopmentGuide.lyx -786c4aec62d60a3f9265dec52b767e02 cpptraj.lyx -07c4039e732fc2eb1df0c1e0863cb949 CpptrajManual.lyx +1f4d9c647b6717314560290a4d3f9f06 cpptraj.lyx +5d9b5b5ed47a3ded57b6464df99b3585 CpptrajManual.lyx diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx index bf4ff459c8..ef80cacef0 100644 --- a/doc/cpptraj.lyx +++ b/doc/cpptraj.lyx @@ -1,16 +1,25 @@ #LyX 2.4 created this file. For more info see https://www.lyx.org/ -\lyxformat 620 +\lyxformat 544 \begin_document \begin_header \save_transient_properties true \origin unavailable \textclass article +\begin_preamble +% Added by lyx2lyx +%% Variable width box for table cells +\newenvironment{cellvarwidth}[1][t] + {\begin{varwidth}[#1]{\linewidth}} + {\@finalstrut\@arstrutbox\end{varwidth}} +% Added by lyx2lyx +\usepackage{varwidth} +\end_preamble \use_default_options true -\maintain_unincluded_children no +\maintain_unincluded_children false \language english \language_package default -\inputencoding auto-legacy -\fontencoding auto +\inputencoding auto +\fontencoding global \font_roman "default" "default" \font_sans "default" "default" \font_typewriter "default" "default" @@ -18,9 +27,7 @@ \font_default_family default \use_non_tex_fonts false \font_sc false -\font_roman_osf false -\font_sans_osf false -\font_typewriter_osf false +\font_osf false \font_sf_scale 100 100 \font_tt_scale 100 100 \use_microtype false @@ -64,9 +71,7 @@ \suppress_date false \justification true \use_refstyle 1 -\use_formatted_ref 0 \use_minted 0 -\use_lineno 0 \index Index \shortcut idx \color #008000 @@ -82,16 +87,11 @@ \papercolumns 1 \papersides 1 \paperpagestyle default -\tablestyle default \tracking_changes false \output_changes false -\change_bars false -\postpone_fragile_content false \html_math_output 0 \html_css_as_file 0 \html_be_strict false -\docbook_table_output 0 -\docbook_mathml_prefix 1 \end_header \begin_body @@ -157,7 +157,6 @@ cpptraj \begin_inset CommandInset ref LatexCommand ref reference "subsec:CpptrajOpenMP" -nolink "false" \end_inset @@ -262,7 +261,6 @@ Users can manipulate data sets using mathematical expressions (with some limitat \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-Data-Set-Math" -nolink "false" \end_inset @@ -723,7 +721,6 @@ loadcrd \begin_inset CommandInset ref LatexCommand vref reference "sec:Coordinates-as-a" -nolink "false" \end_inset @@ -751,7 +748,6 @@ Coords (Immediate) These commands are used to manipulate COORDS data sets; \begin_inset CommandInset ref LatexCommand vref reference "sec:Coordinates-as-a" -nolink "false" \end_inset @@ -793,7 +789,6 @@ cpptraj \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-Data-Set-Math" -nolink "false" \end_inset @@ -1189,7 +1184,6 @@ reference "subsec:cpptraj-calcdiffusion" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -1712,7 +1706,6 @@ number} e.g. \begin_inset CommandInset ref LatexCommand vref reference "subsec:parmed_addPDB" -nolink "false" \end_inset @@ -3013,7 +3006,6 @@ readdata \begin_inset CommandInset ref LatexCommand ref reference "tab:cpptraj-DataFile-formats" -nolink "false" \end_inset @@ -3044,7 +3036,6 @@ ptraj \begin_inset CommandInset ref LatexCommand vref reference "sec:Datafile-Commands" -nolink "false" \end_inset @@ -3112,8 +3103,6 @@ Note that when reading the Amber Prep and Amber OFF Library formats, \begin_layout Standard \begin_inset Float table -placement document -alignment document wide false sideways false status open @@ -5177,7 +5166,6 @@ writedata \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_writedata" -nolink "false" \end_inset @@ -5191,7 +5179,6 @@ create \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_create" -nolink "false" \end_inset @@ -5206,7 +5193,6 @@ readdata \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_readdata" -nolink "false" \end_inset @@ -5249,7 +5235,6 @@ cpptraj \begin_inset CommandInset ref LatexCommand ref reference "tab:cpptraj-DataFile-formats" -nolink "false" \end_inset @@ -5265,7 +5250,6 @@ datafile \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_datafile_command" -nolink "false" \end_inset @@ -6061,7 +6045,6 @@ readdata \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-remlog" -nolink "false" \end_inset @@ -6182,7 +6165,6 @@ This can be used to write out a representation of a vector data set which can th \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-vector" -nolink "false" \end_inset @@ -6212,7 +6194,6 @@ trajfmt \begin_inset CommandInset ref LatexCommand vref reference "tab:cpptraj-trajformats" -nolink "false" \end_inset @@ -6387,7 +6368,6 @@ Note that when reading in constant pH data the data set aspect will be set to th \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_sortensembledata" -nolink "false" \end_inset @@ -7257,7 +7237,6 @@ This command is actually an Action that can be used to create COORDS data sets d \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_createcrd" -nolink "false" \end_inset @@ -8045,7 +8024,6 @@ reference "subsec:cpptraj_trajin" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -9060,7 +9038,6 @@ Reference coordinates can now be used and manipulated like COORDS data sets. \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_reference" -nolink "false" \end_inset @@ -9309,7 +9286,6 @@ reference "subsec:cpptraj-datasetcmd" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -10287,8 +10263,6 @@ activeref \begin_layout LyX-Code activeref \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -10327,7 +10301,6 @@ calc \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-Data-Set-Math" -nolink "false" \end_inset @@ -10389,8 +10362,6 @@ name "subsec:cpptraj_create" \begin_layout LyX-Code create \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -10419,7 +10390,6 @@ Add specified data sets to the data file named ; \begin_inset CommandInset ref LatexCommand vref reference "sec:Datafile-Commands" -nolink "false" \end_inset @@ -10486,8 +10456,6 @@ name "subsec:cpptraj_datafile_command" \begin_layout LyX-Code datafile \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -10505,7 +10473,6 @@ Pass to data file . \begin_inset CommandInset ref LatexCommand vref reference "sec:Datafile-Commands" -nolink "false" \end_inset @@ -10740,7 +10707,6 @@ filter \begin_inset CommandInset ref LatexCommand pageref reference "subsec:cpptraj-filter" -nolink "false" \end_inset @@ -11089,7 +11055,6 @@ reference "subsec:cpptraj-sequence" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -12373,8 +12338,6 @@ debug | prnlev \begin_layout LyX-Code debug \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -12610,8 +12573,6 @@ help \begin_layout LyX-Code help \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -12723,8 +12684,6 @@ noexitonerror \begin_layout LyX-Code noexitonerror \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -12764,8 +12723,6 @@ noprogress \begin_layout LyX-Code noprogress \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -12807,7 +12764,6 @@ reference "subsec:cpptraj_hausdorff" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -12993,8 +12949,6 @@ precision \begin_layout LyX-Code precision \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -13187,8 +13141,6 @@ name "subsec:cpptraj_readdata" \begin_layout LyX-Code readdata \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -13233,7 +13185,6 @@ Read data from file and store as data sets. \begin_inset CommandInset ref LatexCommand vref reference "tab:cpptraj-DataFile-formats" -nolink "false" \end_inset @@ -13242,7 +13193,6 @@ nolink "false" \begin_inset CommandInset ref LatexCommand ref reference "sec:Datafile-Commands" -nolink "false" \end_inset @@ -13348,7 +13298,6 @@ If one filename is given, \begin_inset CommandInset ref LatexCommand vref reference "sec:Datafile-Commands" -nolink "false" \end_inset @@ -13391,8 +13340,6 @@ readinput \begin_layout LyX-Code readinput \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -13638,8 +13585,6 @@ select \begin_layout LyX-Code select \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -13788,7 +13733,6 @@ With no arguments, \begin_inset CommandInset ref LatexCommand vref reference "sec:Datafile-Commands" -nolink "false" \end_inset @@ -16207,8 +16151,6 @@ parm \begin_layout LyX-Code parm \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -16255,7 +16197,6 @@ parm \begin_inset CommandInset ref LatexCommand vref reference "subsec:Parameter/Reference-Tagging" -nolink "false" \end_inset @@ -16337,7 +16278,6 @@ Read in parameter file. \begin_inset CommandInset ref LatexCommand vpageref reference "tab:cpptraj-Topology-formats" -nolink "false" \end_inset @@ -16466,7 +16406,6 @@ reference "subsec:cpptraj-trajin-pdb" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -16511,8 +16450,6 @@ parmbox \begin_layout LyX-Code parmbox \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -16657,8 +16594,6 @@ parminfo \begin_layout LyX-Code parminfo \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -16681,8 +16616,6 @@ parmstrip \begin_layout LyX-Code parmstrip \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -16749,8 +16682,6 @@ parmwrite \begin_layout LyX-Code parmwrite \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -16949,8 +16880,6 @@ resinfo \begin_layout LyX-Code resinfo \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -18652,8 +18581,6 @@ name "subsec:cpptraj_reference" \begin_layout LyX-Code reference \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -18736,7 +18663,6 @@ Use specified trajectory as reference coordinates. \begin_inset CommandInset ref LatexCommand vref reference "subsec:Parameter/Reference-Tagging" -nolink "false" \end_inset @@ -18804,8 +18730,6 @@ name "subsec:cpptraj_trajin" \begin_layout LyX-Code trajin \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -19003,7 +18927,6 @@ Read in trajectory specified by filename. \begin_inset CommandInset ref LatexCommand pageref reference "tab:cpptraj-trajformats" -nolink "false" \end_inset @@ -19284,7 +19207,6 @@ reference "subsec:cpptraj-parm-pdb" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -19305,8 +19227,6 @@ name "subsec:cpptraj-trajout" \begin_layout LyX-Code trajout \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -19352,7 +19272,6 @@ trajout \begin_inset CommandInset ref LatexCommand vpageref reference "tab:cpptraj-trajformats" -nolink "false" \end_inset @@ -19460,7 +19379,6 @@ During a run, \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_outtraj" -nolink "false" \end_inset @@ -19469,7 +19387,6 @@ nolink "false" \begin_inset CommandInset ref LatexCommand pageref reference "tab:cpptraj-trajformats" -nolink "false" \end_inset @@ -19868,7 +19785,6 @@ reference "subsec:cpptraj_atomicfluct" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -20122,7 +20038,6 @@ reference "subsec:cpptraj-Options-for-CHARMM" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -20379,7 +20294,6 @@ crdaction \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_crdaction" -nolink "false" \end_inset @@ -21233,11 +21147,33 @@ Calculate the dihedral angle using four points. \begin_inset Text \begin_layout Plain Layout +\begin_inset ERT +status collapsed + +\begin_layout Plain Layout + + +\backslash +begin{cellvarwidth} +\end_layout + +\end_inset dihrms \end_layout \begin_layout Plain Layout dihedralrms +\begin_inset ERT +status collapsed + +\begin_layout Plain Layout + + +\backslash +end{cellvarwidth} +\end_layout + +\end_inset \end_layout \end_inset @@ -23595,8 +23531,6 @@ angle \begin_layout LyX-Code angle \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -23845,8 +23779,6 @@ name "subsec:cpptraj_atomicfluct" \begin_layout LyX-Code atomicfluct \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -24155,8 +24087,6 @@ atommap \begin_layout LyX-Code atommap \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -24528,8 +24458,6 @@ name "subsec:cpptraj-average" \begin_layout LyX-Code average \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -24640,7 +24568,6 @@ rms \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-rmsd" -nolink "false" \end_inset @@ -24658,7 +24585,6 @@ trajout \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-trajout" -nolink "false" \end_inset @@ -24760,7 +24686,6 @@ reference "subsec:cpptraj_unwrap" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -24940,7 +24865,6 @@ grid \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_grid" -nolink "false" \end_inset @@ -25134,8 +25058,6 @@ center \begin_layout LyX-Code center \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -25234,8 +25156,6 @@ check | checkoverlap | checkstructure \begin_layout LyX-Code check \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -25538,8 +25458,6 @@ closest | closestwaters \begin_layout LyX-Code closest \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -25730,7 +25648,6 @@ solvent \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_solvent" -nolink "false" \end_inset @@ -25800,7 +25717,6 @@ Although the \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-cluster-analysis" -nolink "false" \end_inset @@ -25814,8 +25730,6 @@ clusterdihedral \begin_layout LyX-Code clusterdihedral \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -25975,7 +25889,6 @@ nativecontacts \begin_inset CommandInset ref LatexCommand vpageref reference "subsec:cpptraj-nativecontacts" -nolink "false" \end_inset @@ -26742,7 +26655,6 @@ reference "subsec:cpptraj_avgbox" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -26762,7 +26674,6 @@ reference "subsec:cpptraj_unwrap" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -26944,7 +26855,6 @@ reference "subsec:cpptraj-calcdiffusion" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -26967,8 +26877,6 @@ dihedral \begin_layout LyX-Code dihedral \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -27053,7 +26961,6 @@ reference "subsec:cpptraj_multidihedral" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -27168,7 +27075,6 @@ reference "subsec:cpptraj_multidihedral" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -27191,7 +27097,6 @@ permutedihedrals \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_permutedihedrals" -nolink "false" \end_inset @@ -27453,7 +27358,6 @@ grid \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_grid" -nolink "false" \end_inset @@ -27472,8 +27376,6 @@ distance \begin_layout LyX-Code distance \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -27673,7 +27575,6 @@ type noe \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_statistics" -nolink "false" \end_inset @@ -27687,8 +27588,6 @@ drms | drmsd (distance RMSD) \begin_layout LyX-Code drmsd \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -27899,7 +27798,6 @@ See \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-secstruct" -nolink "false" \end_inset @@ -28138,7 +28036,6 @@ reference "subsec:cpptraj-emin" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -28662,7 +28559,6 @@ ntc \begin_inset CommandInset ref LatexCommand vref reference "chap:sander" -nolink "false" \end_inset @@ -28968,7 +28864,6 @@ datafilter \begin_inset CommandInset ref LatexCommand pageref reference "subsec:cpptraj-datafilter" -nolink "false" \end_inset @@ -29150,8 +29045,6 @@ gist (Grid Inhomogeneous Solvation Theory) \begin_layout LyX-Code gist \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -29849,7 +29742,6 @@ literal "true" \begin_inset CommandInset ref LatexCommand ref reference "gist-1-1" -nolink "false" \end_inset @@ -29881,8 +29773,6 @@ In order to carry out a GIST calculation, \begin_layout Standard \begin_inset Float figure -placement document -alignment document wide false sideways false status open @@ -30939,8 +30829,6 @@ Inhomogeneous fluid solvation theory, \begin_layout Standard \begin_inset Float table -placement document -alignment document wide false sideways false status open @@ -31891,7 +31779,6 @@ bounds \begin_inset CommandInset ref LatexCommand vpageref reference "subsec:cpptraj-bounds" -nolink "false" \end_inset @@ -32073,8 +31960,6 @@ name "subsec:cpptraj-hbond" \begin_layout LyX-Code hbond \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -32599,7 +32484,6 @@ reference "subsec:cpptraj-keep" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -32621,7 +32505,6 @@ lifetime \begin_inset CommandInset ref LatexCommand vpageref reference "subsec:cpptraj-lifetime" -nolink "false" \end_inset @@ -32888,8 +32771,6 @@ image \begin_layout LyX-Code image \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -33048,8 +32929,6 @@ jcoupling \begin_layout LyX-Code jcoupling \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -33327,7 +33206,6 @@ reference "subsec:cpptraj-hbond" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -33604,8 +33482,6 @@ lie \begin_layout LyX-Code lie \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -34831,8 +34707,6 @@ mask \begin_layout LyX-Code mask \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -35328,7 +35202,6 @@ ired \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-vector" -nolink "false" \end_inset @@ -35455,7 +35328,6 @@ vector \begin_inset CommandInset ref LatexCommand vpageref reference "subsec:cpptraj-vector" -nolink "false" \end_inset @@ -35513,7 +35385,6 @@ reference "sec:Datafile-Commands" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -35758,8 +35629,6 @@ molsurf \begin_layout LyX-Code molsurf \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -35877,7 +35746,6 @@ surf \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_surf" -nolink "false" \end_inset @@ -36365,8 +36233,6 @@ nastruct \begin_layout LyX-Code nastruct \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -37865,7 +37731,6 @@ hbond \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-lifetime" -nolink "false" \end_inset @@ -37955,8 +37820,6 @@ name "subsec:cpptraj_outtraj" \begin_layout LyX-Code outtraj \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -37990,7 +37853,6 @@ args] Output trajectory arguments (see \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-trajout" -nolink "false" \end_inset @@ -38742,7 +38604,6 @@ matrix \begin_inset CommandInset ref LatexCommand vref reference "sec:cpptraj-Matrix-Vector-Analysis-Examples" -nolink "false" \end_inset @@ -38768,7 +38629,6 @@ reference "subsec:cpptraj-projectdata" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -38782,8 +38642,6 @@ pucker \begin_layout LyX-Code pucker \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -38995,8 +38853,6 @@ radgyr | rog \begin_layout LyX-Code radgyr \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -39086,8 +38942,6 @@ radial | rdf \begin_layout LyX-Code radial \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -39756,8 +39610,6 @@ name "subsec:cpptraj-rmsd" \begin_layout LyX-Code rmsd \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -40213,7 +40065,6 @@ Although the \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-rms2d" -nolink "false" \end_inset @@ -40237,7 +40088,6 @@ Although the \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-rmsavgcorr" -nolink "false" \end_inset @@ -40253,7 +40103,6 @@ See \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_atomicfluct" -nolink "false" \end_inset @@ -40540,7 +40389,6 @@ The \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-rotdif" -nolink "false" \end_inset @@ -40590,8 +40438,6 @@ runavg | runningaverage \begin_layout LyX-Code runavg \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -40672,8 +40518,6 @@ name "subsec:cpptraj-secstruct" \begin_layout LyX-Code secstruct \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -41895,7 +41739,6 @@ peakfile \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_volmap" -nolink "false" \end_inset @@ -42027,8 +41870,6 @@ strip \begin_layout LyX-Code strip \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -42196,8 +42037,6 @@ name "subsec:cpptraj_surf" \begin_layout LyX-Code surf \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -42839,7 +42678,6 @@ reference "subsec:cpptraj-diffusion" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -42856,7 +42694,6 @@ reference "subsec:cpptraj_unwrap" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -42879,7 +42716,6 @@ reference "subsec:cpptraj-diffusion" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -42998,8 +42834,6 @@ unstrip \begin_layout LyX-Code unstrip \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -43290,7 +43124,6 @@ reference "subsec:cpptraj_avgbox" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -43713,7 +43546,6 @@ Cpptraj supports writing out vector data in a pseudo-trajectory format for easy \begin_inset CommandInset ref LatexCommand vref reference "sec:Datafile-Commands" -nolink "false" \end_inset @@ -44516,7 +44348,6 @@ readdata \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_readdata" -nolink "false" \end_inset @@ -44577,7 +44408,6 @@ runanalysis \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_runanalysis" -nolink "false" \end_inset @@ -46483,7 +46313,6 @@ reference "subsec:cpptraj-diffusion" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -46504,7 +46333,6 @@ reference "subsec:cpptraj_unwrap" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -46523,7 +46351,6 @@ reference "subsec:cpptraj-diffusion" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -46542,7 +46369,6 @@ reference "subsec:cpptraj-loadtraj" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -47010,7 +46836,6 @@ Lifetime curves (see \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-lifetime" -nolink "false" \end_inset @@ -47137,8 +46962,6 @@ cluster \begin_layout LyX-Code cluster \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -47721,7 +47544,6 @@ srmsd \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_symmrmsd" -nolink "false" \end_inset @@ -48390,7 +48212,6 @@ reference "subsec:cpptraj-lifetime" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -49193,7 +49014,6 @@ readdata \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_cphdatafile" -nolink "false" \end_inset @@ -49245,7 +49065,6 @@ cphstats \begin_inset CommandInset ref LatexCommand vref reference "sec:cphstats" -nolink "false" \end_inset @@ -49270,7 +49089,6 @@ readensembledata \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_readensembledata" -nolink "false" \end_inset @@ -49284,7 +49102,6 @@ sortensembledata \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_sortensembledata" -nolink "false" \end_inset @@ -49316,8 +49133,6 @@ corr | correlationcoe \begin_layout LyX-Code corr \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -49643,7 +49458,6 @@ curvefit { | \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-Data-Set-Math" -nolink "false" \end_inset @@ -49787,7 +49601,6 @@ Perform non-linear curve fitting for the specified data set using the Levenberg- \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-Data-Set-Math" -nolink "false" \end_inset @@ -50818,8 +50631,6 @@ hist | histogram \begin_layout LyX-Code hist \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -52915,7 +52726,6 @@ set \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-Data-Set-Math" -nolink "false" \end_inset @@ -53051,7 +52861,6 @@ curvefit \begin_inset CommandInset ref LatexCommand vpageref reference "subsec:cpptraj_curvefit" -nolink "false" \end_inset @@ -53359,7 +53168,6 @@ reference "subsec:cpptraj-projection" plural "false" caps "false" noprefix "false" -nolink "false" \end_inset @@ -53699,8 +53507,6 @@ name "subsec:cpptraj-rms2d" \begin_layout LyX-Code rms2d \begin_inset Index idx -range none -pageformat default status collapsed \begin_layout Plain Layout @@ -53769,7 +53575,6 @@ set>] Name of previously generated COORDS DataSet. \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_symmrmsd" -nolink "false" \end_inset @@ -53963,8 +53768,6 @@ name "subsec:cpptraj-rmsavgcorr" \begin_layout LyX-Code rmsavgcorr \begin_inset Index idx -range none -pageformat default status open \begin_layout Plain Layout @@ -54525,7 +54328,6 @@ Rotation matrices are generated via an RMS fit to a reference structure (see \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-rmsd" -nolink "false" \end_inset @@ -54534,7 +54336,6 @@ nolink "false" \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-average" -nolink "false" \end_inset @@ -56544,7 +56345,6 @@ epsilon \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj_dbscan_Hints" -nolink "false" \end_inset diff --git a/mkrelease b/mkrelease new file mode 100755 index 0000000000..4882fa36bc --- /dev/null +++ b/mkrelease @@ -0,0 +1,14 @@ +#!/bin/sh + +version=$1 + +tar cvf ../cpptraj-$version.tar configure dat get_library.sh \ + LICENSE Makefile src test doc README.md +cd .. +gzip cpptraj-$version.tar + +rsync -av cpptraj-$version.tar.gz \ + amber@194.195.210.182:ambermd-website.rcsb.rutgers.edu/downloads + +curl -sL https://ambermd.org/downloads/cpptraj-$version.tar.gz | openssl sha256 + diff --git a/recipe/activate.sh b/recipe/activate.sh new file mode 100644 index 0000000000..e263648114 --- /dev/null +++ b/recipe/activate.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +export CPPTRAJHOME=${CONDA_PREFIX} +export CPPTRAJ_HEADERDIR=${CONDA_PREFIX}/include/cpptraj + diff --git a/recipe/build.sh b/recipe/build.sh new file mode 100755 index 0000000000..01eb4546d8 --- /dev/null +++ b/recipe/build.sh @@ -0,0 +1,46 @@ +#!/bin/sh + +export NVCC=nvcc +# export SHADER_MODEL=sm_89 + +arch=`uname` + +if [ "$arch" == "Darwin" ]; then + + ./configure -openmp -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack clang + make install + make clean + ./configure -mpi -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack clang + make install + make clean + ./configure -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack clang + make install + +else + + ./configure -cuda -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack gnu + make install + make clean + ./configure -mpi -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack gnu + make install + make clean + ./configure -openmp -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack gnu + make install + make clean + ./configure -readline -openmm -openblas -fftw3 -zlib -bzlib -shared -arpack gnu + make install + +fi + + +rsync -a README.md config.h LICENSE dat bin lib test $PREFIX + +mkdir -p $PREFIX/doc +rsync -a doc/CpptrajManual.pdf $PREFIX/doc +mkdir -p $PREFIX/include/cpptraj +rsync src/*.h $PREFIX/include/cpptraj/ + +# Export CPPTRAJHOME automatically +mkdir -p ${PREFIX}/etc/conda/{activate,deactivate}.d +cp ${RECIPE_DIR}/activate.sh ${PREFIX}/etc/conda/activate.d/cpptraj.sh +cp ${RECIPE_DIR}/deactivate.sh ${PREFIX}/etc/conda/deactivate.d/cpptraj.sh diff --git a/recipe/conda_build_config.yaml b/recipe/conda_build_config.yaml new file mode 100644 index 0000000000..e486028c6d --- /dev/null +++ b/recipe/conda_build_config.yaml @@ -0,0 +1,8 @@ +c_compiler_version: + - 11.4.0 # [linux] + +cxx_compiler_version: + - 11.4.0 # [linux] + +fortran_compiler_version: + - 11.4.0 # [linux] diff --git a/recipe/deactivate.sh b/recipe/deactivate.sh new file mode 100644 index 0000000000..3ff15053c5 --- /dev/null +++ b/recipe/deactivate.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +unset CPPTRAJHOME +unset CPPTRAJ_HEADERDIR + diff --git a/recipe/meta.yaml b/recipe/meta.yaml new file mode 100644 index 0000000000..507a947678 --- /dev/null +++ b/recipe/meta.yaml @@ -0,0 +1,85 @@ +{% set version = "0.5" %} +{% set mpi = "mpich" %} + +package: + name: cpptraj +# version 0.1 trying to adapt recipe from AmberClassic +# version 0.2 small tweaks get allow osx-64 build +# version 0.3 add mpi and pnetcdf support +# version 0.4 build from url; add cuda +# version 0.5 try to get all exectuables; add headers for pytraj + version: {{ version }} + +source: + path: ../ +# url: https://ambermd.org/downloads/cpptraj-{{ version }}.tar.gz +# sha256: 6be4dda3f6f59610d97b2cdb8f6745ca05cff60705ba95dbcfc07c10fd083d95 + +build: + number: 0 + skip: True # [win or ppc65le] + +mpi: + - {{ mpi }} + +requirements: + build: + - make + - {{ compiler('fortran') }} + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{ mpi }} # [ mpi == "mpich" ] + - libpnetcdf + - {{ compiler('nvcc') }} # [ linux ] + - coreutils # [ linux ] + - nvcc_linux-64 # [ linux ] + - llvm-openmp # [osx] + - libgomp # [linux] + - fftw + - readline + - libnetcdf + - netcdf-fortran + + host: + - openblas + - arpack + - openmm + - libnetcdf + - netcdf-fortran + - llvm-openmp # [osx] + - libgomp # [linux and not aarch64] + - {{ mpi }} # [ mpi == "mpich" ] + - libpnetcdf + - fftw + - readline + + run: + - llvm-openmp # [osx] + - libgomp # [linux and not aarch64] + - openblas + - arpack + - openmm + - libnetcdf + - netcdf-fortran + - {{ mpi }} # [ mpi == "mpich" ] + - libpnetcdf + - fftw + - readline + +test: + commands: + - cpptraj --help + +about: + home: https://github.com/Amber-MD/cpptraj.git + license: GPL-3.0-or-later + license_file: + - LICENSE + summary: 'Performs analysis of MD trajectories, especially for biomolecules' + description: | + CPPTRAJ is a program designed to process and analyze molecular + dynamics trajectories and relevant data sets derived from their + analysis. CPPTRAJ supports many popular MD software packages including + Amber, CHARMM, Gromacs, and NAMD. + + diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 70c8e644c7..9d5582c206 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -179,16 +179,30 @@ endif() #------------------------------------------------------------------------------------------ # Header installation -if(INSTALL_HEADERS) +#if(INSTALL_HEADERS) # grab all .h files from the main directory. file(GLOB CPPTRAJ_HEADERS "*.h") list(REMOVE_ITEM CPPTRAJ_HEADERS "SymbolExporting.h") # also grab xdrfile headers since some of them are used by cpptraj headers - file(GLOB XDRFILE_HEADERS "xdrfile/*.h") - - install(FILES ${CPPTRAJ_HEADERS} DESTINATION ${INCDIR}/cpptraj) - install(FILES ${XDRFILE_HEADERS} DESTINATION ${INCDIR}/cpptraj/xdrfile) + #file(GLOB XDRFILE_HEADERS "xdrfile/*.h") + file(GLOB CLUSTER_HEADERS "Cluster/*.h") + file(GLOB STRUCTURE_HEADERS "Structure/*.h") + file(GLOB ENERGY_HEADERS "Energy/*.h") + + if(INSIDE_AMBER) + install(FILES ${CPPTRAJ_HEADERS} DESTINATION ${INCDIR}/cpptraj) + #install(FILES ${XDRFILE_HEADERS} DESTINATION ${INCDIR}/cpptraj/xdrfile) + install(FILES ${CLUSTER_HEADERS} DESTINATION ${INCDIR}/cpptraj/Cluster) + install(FILES ${STRUCTURE_HEADERS} DESTINATION ${INCDIR}/cpptraj/Structure) + install(FILES ${ENERGY_HEADERS} DESTINATION ${INCDIR}/cpptraj/Energy) + else() + install(FILES ${CPPTRAJ_HEADERS} DESTINATION ${INCDIR}) + #install(FILES ${XDRFILE_HEADERS} DESTINATION ${INCDIR}/xdrfile) + install(FILES ${CLUSTER_HEADERS} DESTINATION ${INCDIR}/Cluster) + install(FILES ${STRUCTURE_HEADERS} DESTINATION ${INCDIR}/Structure) + install(FILES ${ENERGY_HEADERS} DESTINATION ${INCDIR}/Energy) + endif() # configure SymbolExporting.h specially for the current install type if(SHARED) @@ -200,7 +214,7 @@ if(INSTALL_HEADERS) install(FILES ${CMAKE_CURRENT_BINARY_DIR}/SymbolExporting-installversion.h DESTINATION ${INCDIR}/cpptraj RENAME SymbolExporting.h) -endif() +#endif() # Check for C++11 support set(HAS_C11_SUPPORT FALSE) diff --git a/src/Makefile b/src/Makefile index 4c7d82db76..3c6b8e5990 100644 --- a/src/Makefile +++ b/src/Makefile @@ -3,6 +3,8 @@ include ../config.h include cpptrajfiles +include cpptrajheaders + # Object files from subdirectories go here include Cluster/clusterfiles CLUSTER_SOURCEFILES=$(CLUSTER_SOURCES:%.cpp=Cluster/%.cpp) @@ -43,7 +45,7 @@ install: $(INSTALL_TARGETS) # Cpptraj ------------------------------ install_cpptraj: cpptraj$(SFX)$(EXE) $(VB)echo Install cpptraj$(SFX)$(EXE) to $(CPPTRAJBIN) - $(VB)mv cpptraj$(SFX)$(EXE) $(CPPTRAJBIN) + $(VB)$(INSTALL_PROGRAM) cpptraj$(SFX)$(EXE) $(CPPTRAJBIN) cpptraj$(SFX)$(EXE): $(OBJECTS) $(FFT_TARGET) $(READLINE_TARGET) $(CUDA_TARGET) $(XDRFILE_TARGET) $(ARPACK_TARGET) $(TNGFILE_TARGET) $(VB)echo Link cpptraj$(SFX)$(EXE) @@ -57,18 +59,28 @@ cpptraj$(SFX)$(EXE): $(OBJECTS) $(FFT_TARGET) $(READLINE_TARGET) $(CUDA_TARGET) libcpptraj: $(LIBCPPTRAJ_TARGET) -$(CPPTRAJLIB)/libcpptraj$(SHARED_SUFFIX): $(LIBCPPTRAJ_OBJECTS) $(FFT_TARGET) $(CUDA_TARGET) $(XDRFILE_TARGET) $(ARPACK_TARGET) $(TNGFILE_TARGET) +$(CPPTRAJLIB)/libcpptraj$(SHARED_SUFFIX): $(LIBCPPTRAJ_OBJECTS) $(FFT_TARGET) $(CUDA_TARGET) $(XDRFILE_TARGET) $(ARPACK_TARGET) $(TNGFILE_TARGET) install_headers $(VB)echo Install $(CPPTRAJLIB)/libcpptraj$(SHARED_SUFFIX) $(VB)$(CXX) -shared -o $(CPPTRAJLIB)/libcpptraj$(SHARED_SUFFIX) $(LIBCPPTRAJ_OBJECTS) $(FFT_TARGET) $(CUDA_TARGET) $(CPPTRAJ_LIB) $(LDFLAGS) # Data directory ----------------------- install_dat: - -cp ../dat/ATOMTYPE_CHECK.TAB $(CPPTRAJDAT)/ - -cp ../dat/BONDTYPE_CHECK.TAB $(CPPTRAJDAT)/ - -cp ../dat/Karplus.txt $(CPPTRAJDAT)/ - -cp ../dat/README $(CPPTRAJDAT)/ - -cp ../dat/Carbohydrate_PDB_Glycam_Names.txt $(CPPTRAJDAT)/ - -cp ../dat/PDB_ResidueNames.txt $(CPPTRAJDAT)/ + -$(INSTALL_DATA) ../dat/ATOMTYPE_CHECK.TAB $(CPPTRAJDAT)/ + -$(INSTALL_DATA) ../dat/BONDTYPE_CHECK.TAB $(CPPTRAJDAT)/ + -$(INSTALL_DATA) ../dat/Karplus.txt $(CPPTRAJDAT)/ + -$(INSTALL_DATA) ../dat/README $(CPPTRAJDAT)/ + -$(INSTALL_DATA) ../dat/Carbohydrate_PDB_Glycam_Names.txt $(CPPTRAJDAT)/ + -$(INSTALL_DATA) ../dat/PDB_ResidueNames.txt $(CPPTRAJDAT)/ + +# Headers ------------------------------ +$(CPPTRAJINC): + -mkdir $(CPPTRAJINC) + +install_headers: $(CPPTRAJINC) + $(VB) echo Installing CPPTRAJ headers to $(CPPTRAJINC) + $(VB)-for file in $(CPPTRAJ_HEADERS) ; do \ + $(INSTALL) -D $${file} $(CPPTRAJINC)/$${file} ; \ + done # Static libraries --------------------- #$(CPPTRAJLIB)/libcpptraj.a: $(LIBCPPTRAJ_OBJECTS) $(FFT_TARGET) $(CUDA_TARGET) diff --git a/src/Matrix.h b/src/Matrix.h index 816ec1e916..4a9f5e2bcd 100644 --- a/src/Matrix.h +++ b/src/Matrix.h @@ -2,6 +2,7 @@ #define INC_MATRIX_H #include "ArrayIterator.h" #include // For linear least squares +#include // For copy() /// Two-dimensional matrix template. template class Matrix { // TODO: Type may not be necessary here if in DataSet_2D diff --git a/src/ReadLine.cpp b/src/ReadLine.cpp index 73e11a74e8..04d62a8a44 100644 --- a/src/ReadLine.cpp +++ b/src/ReadLine.cpp @@ -8,8 +8,8 @@ # include #else # define READLINE_LIBRARY -# include -# include +# include +# include #endif #include "ReadLine.h" #include "Command.h" diff --git a/src/cpptrajheaders b/src/cpptrajheaders new file mode 100644 index 0000000000..a41e634b9e --- /dev/null +++ b/src/cpptrajheaders @@ -0,0 +1,608 @@ +# All cpptraj headers that should be installed for the cpptraj library. +CPPTRAJ_HEADERS = \ + ./Action_AddAtom.h \ + ./Action_Align.h \ + ./Action_Angle.h \ + ./Action_AreaPerMol.h \ + ./Action_AtomicCorr.h \ + ./Action_AtomicFluct.h \ + ./Action_AtomMap.h \ + ./Action_AutoImage.h \ + ./Action_Average.h \ + ./Action_AvgBox.h \ + ./Action_Bounds.h \ + ./Action_Box.h \ + ./Action_Center.h \ + ./Action_Channel.h \ + ./Action_CheckChirality.h \ + ./Action_CheckStructure.h \ + ./Action_Closest.h \ + ./Action_ClusterDihedral.h \ + ./Action_Contacts.h \ + ./Action_ConvertToFrac.h \ + ./Action_CreateCrd.h \ + ./Action_CreateReservoir.h \ + ./Action_Density.h \ + ./Action_Diffusion.h \ + ./Action_Dihedral.h \ + ./Action_DihedralRMS.h \ + ./Action_Dipole.h \ + ./Action_Distance.h \ + ./Action_DistRmsd.h \ + ./Action_DNAionTracker.h \ + ./Action_DSSP.h \ + ./Action_EneDecomp.h \ + ./Action_Energy.h \ + ./Action_Esander.h \ + ./Action_FilterByData.h \ + ./Action_FixAtomOrder.h \ + ./Action_FixImagedBonds.h \ + ./ActionFrameCounter.h \ + ./Action_GIST.h \ + ./Action_GridFreeEnergy.h \ + ./Action_Grid.h \ + ./Action.h \ + ./Action_HydrogenBond.h \ + ./Action_Image.h \ + ./Action_InfraredSpectrum.h \ + ./Action_Jcoupling.h \ + ./Action_Keep.h \ + ./Action_LESsplit.h \ + ./Action_LIE.h \ + ./Action_LipidOrder.h \ + ./ActionList.h \ + ./Action_MakeStructure.h \ + ./Action_Mask.h \ + ./Action_Matrix.h \ + ./Action_MinImage.h \ + ./Action_MinMaxDist.h \ + ./Action_Molsurf.h \ + ./Action_MRT.h \ + ./Action_MultiDihedral.h \ + ./Action_MultiPucker.h \ + ./Action_MultiVector.h \ + ./Action_NAstruct.h \ + ./Action_NativeContacts.h \ + ./Action_NMRrst.h \ + ./Action_OrderParameter.h \ + ./Action_Outtraj.h \ + ./Action_PairDist.h \ + ./Action_Pairwise.h \ + ./Action_Principal.h \ + ./Action_Projection.h \ + ./Action_Pucker.h \ + ./Action_Radgyr.h \ + ./Action_Radial.h \ + ./Action_RandomizeIons.h \ + ./Action_Remap.h \ + ./Action_ReplicateCell.h \ + ./Action_Rmsd.h \ + ./Action_Rotate.h \ + ./Action_RunningAvg.h \ + ./Action_Scale.h \ + ./Action_SetVelocity.h \ + ./Action_Spam.h \ + ./ActionState.h \ + ./Action_STFC_Diffusion.h \ + ./Action_Strip.h \ + ./Action_Surf.h \ + ./Action_SymmetricRmsd.h \ + ./Action_Temperature.h \ + ./Action_Test.h \ + ./Action_Time.h \ + ./ActionTopWriter.h \ + ./Action_ToroidalDiffusion.h \ + ./Action_Translate.h \ + ./Action_Unstrip.h \ + ./Action_Unwrap.h \ + ./Action_Vector.h \ + ./Action_VelocityAutoCorr.h \ + ./Action_Volmap.h \ + ./Action_Volume.h \ + ./Action_Watershell.h \ + ./Action_XtalSymm.h \ + ./Analysis_AmdBias.h \ + ./Analysis_AutoCorr.h \ + ./Analysis_Average.h \ + ./Analysis_CalcDiffusion.h \ + ./Analysis_Clustering.h \ + ./Analysis_ConstantPHStats.h \ + ./Analysis_Corr.h \ + ./Analysis_CrankShaft.h \ + ./Analysis_CrdFluct.h \ + ./Analysis_CrossCorr.h \ + ./Analysis_CurveFit.h \ + ./Analysis_Divergence.h \ + ./Analysis_EvalPlateau.h \ + ./Analysis_FFT.h \ + ./Analysis.h \ + ./Analysis_HausdorffDistance.h \ + ./Analysis_Hist.h \ + ./Analysis_Integrate.h \ + ./Analysis_IRED.h \ + ./Analysis_KDE.h \ + ./Analysis_Lifetime.h \ + ./AnalysisList.h \ + ./Analysis_LowestCurve.h \ + ./Analysis_Matrix.h \ + ./Analysis_MeltCurve.h \ + ./Analysis_Modes.h \ + ./Analysis_Multicurve.h \ + ./Analysis_MultiHist.h \ + ./Analysis_Overlap.h \ + ./Analysis_PhiPsi.h \ + ./Analysis_Project.h \ + ./Analysis_Regression.h \ + ./Analysis_RemLog.h \ + ./Analysis_Rms2d.h \ + ./Analysis_RmsAvgCorr.h \ + ./Analysis_Rotdif.h \ + ./Analysis_RunningAvg.h \ + ./Analysis_Slope.h \ + ./Analysis_Spline.h \ + ./Analysis_State.h \ + ./AnalysisState.h \ + ./Analysis_Statistics.h \ + ./Analysis_TICA.h \ + ./Analysis_TI.h \ + ./Analysis_Timecorr.h \ + ./Analysis_VectorMath.h \ + ./Analysis_Wavelet.h \ + ./ArgList.h \ + ./Array1D.h \ + ./ArrayIterator.h \ + ./AssociatedData_Connect.h \ + ./AssociatedData.h \ + ./AssociatedData_NOE.h \ + ./Atom.h \ + ./AtomMap.h \ + ./AtomMask.h \ + ./AtomTopType.h \ + ./AtomType.h \ + ./AxisType.h \ + ./BaseIOtype.h \ + ./BondSearch.h \ + ./BoxArgs.h \ + ./Box.h \ + ./BufferedFrame.h \ + ./BufferedLine.h \ + ./ByteRoutines.h \ + ./CharMask.h \ + ./CharmmParamFile.h \ + ./CIFfile.h \ + ./ClusterMap.h \ + ./Cmd.h \ + ./CmdInput.h \ + ./CmdList.h \ + ./Command.h \ + ./CompactFrameArray.h \ + ./ComplexArray.h \ + ./Constants.h \ + ./Constraints.h \ + ./ControlBlock_For.h \ + ./ControlBlock.h \ + ./CoordCovarMatrix_Full.h \ + ./CoordCovarMatrix.h \ + ./CoordCovarMatrix_Half.h \ + ./CoordinateInfo.h \ + ./Corr.h \ + ./Cph.h \ + ./CpptrajFile.h \ + ./Cpptraj.h \ + ./CpptrajState.h \ + ./CpptrajStdio.h \ + ./CurveFit.h \ + ./DataFile.h \ + ./DataFileList.h \ + ./DataFilter.h \ + ./DataIO_AmberEne.h \ + ./DataIO_AmberLib.h \ + ./DataIO_AmberPrep.h \ + ./DataIO_CCP4.h \ + ./DataIO_CharmmFastRep.h \ + ./DataIO_CharmmOutput.h \ + ./DataIO_CharmmRepLog.h \ + ./DataIO_CharmmRtfPrm.h \ + ./DataIO_Cmatrix_Binary.h \ + ./DataIO_Cmatrix_NC.h \ + ./DataIO_Cpout.h \ + ./DataIO_Evecs.h \ + ./DataIO_Gnuplot.h \ + ./DataIO_Grace.h \ + ./DataIO.h \ + ./DataIO_Mdout.h \ + ./DataIO_NetCDF.h \ + ./DataIO_Numpy.h \ + ./DataIO_OpenDx.h \ + ./DataIO_Peaks.h \ + ./DataIO_RemLog.h \ + ./DataIO_Std.h \ + ./DataIO_VecTraj.h \ + ./DataIO_Xplor.h \ + ./DataIO_XVG.h \ + ./DataSet_1D.h \ + ./DataSet_2D.h \ + ./DataSet_3D.h \ + ./DataSet_Coords_CRD.h \ + ./DataSet_Coords_FRM.h \ + ./DataSet_Coords.h \ + ./DataSet_Coords_REF.h \ + ./DataSet_Coords_TRJ.h \ + ./DataSet_double.h \ + ./DataSet_float.h \ + ./DataSet_GridDbl.h \ + ./DataSet_GridFlt.h \ + ./DataSet.h \ + ./DataSet_integer_disk.h \ + ./DataSet_integer.h \ + ./DataSet_integer_mem.h \ + ./DataSetList.h \ + ./DataSet_Mat3x3.h \ + ./DataSet_MatrixDbl.h \ + ./DataSet_MatrixFlt.h \ + ./DataSet_Mesh.h \ + ./DataSet_Modes.h \ + ./DataSet_PairwiseCache.h \ + ./DataSet_PairwiseCache_MEM.h \ + ./DataSet_PairwiseCache_NC.h \ + ./DataSet_Parameters.h \ + ./DataSet_pH.h \ + ./DataSet_PHREMD_Explicit.h \ + ./DataSet_PHREMD.h \ + ./DataSet_PHREMD_Implicit.h \ + ./DataSet_RemLog.h \ + ./DataSet_string.h \ + ./DataSet_StringVar.h \ + ./DataSet_Tensor.h \ + ./DataSet_Topology.h \ + ./DataSet_unsignedInt.h \ + ./DataSet_Vector.h \ + ./DataSet_Vector_Scalar.h \ + ./DataSet_Zmatrix.h \ + ./Deprecated.h \ + ./DiffusionResults.h \ + ./DihedralSearch.h \ + ./Dimension.h \ + ./DispatchObject.h \ + ./Dist_Imaged.h \ + ./DistRoutines.h \ + ./EnergyArray.h \ + ./Energy.h \ + ./EnergyKernel_NonBond_Simple.h \ + ./Energy_Sander.h \ + ./EnsembleIn.h \ + ./EnsembleIn_Multi.h \ + ./EnsembleIn_Single.h \ + ./EnsembleNavigator.h \ + ./EnsembleOut.h \ + ./EnsembleOutList.h \ + ./EnsembleOut_Multi.h \ + ./EnsembleOut_Single.h \ + ./EwaldOptions.h \ + ./ExclusionArray.h \ + ./Exec_AddMissingRes.h \ + ./Exec_AddMissingRes_Pres.h \ + ./Exec_Analyze.h \ + ./Exec_Calc.h \ + ./Exec_CatCrd.h \ + ./Exec_Change.h \ + ./Exec_ClusterMap.h \ + ./Exec_CombineCoords.h \ + ./Exec_Commands.h \ + ./Exec_CompareClusters.h \ + ./Exec_CompareEnergy.h \ + ./Exec_CompareTop.h \ + ./Exec_CrdAction.h \ + ./Exec_CrdOut.h \ + ./Exec_CrdTransform.h \ + ./Exec_CreateSet.h \ + ./Exec_DataFile.h \ + ./Exec_DataFilter.h \ + ./Exec_DataSetCmd.h \ + ./Exec_Emin.h \ + ./Exec_ExtendedComparison.h \ + ./Exec_Flatten.h \ + ./Exec_GenerateAmberRst.h \ + ./Exec_Graft.h \ + ./Exec.h \ + ./Exec_Help.h \ + ./Exec_HmassRepartition.h \ + ./Exec_LoadCrd.h \ + ./Exec_LoadTraj.h \ + ./Exec_ParallelAnalysis.h \ + ./Exec_ParmBox.h \ + ./Exec_ParmSolvent.h \ + ./Exec_ParmStrip.h \ + ./Exec_ParmWrite.h \ + ./Exec_ParseTiming.h \ + ./Exec_PermuteDihedrals.h \ + ./Exec_Precision.h \ + ./Exec_PrepareForLeap.h \ + ./Exec_PrintData.h \ + ./Exec_Random.h \ + ./Exec_ReadData.h \ + ./Exec_ReadEnsembleData.h \ + ./Exec_ReadInput.h \ + ./Exec_RotateDihedral.h \ + ./Exec_RunAnalysis.h \ + ./Exec_ScaleDihedralK.h \ + ./Exec_SequenceAlign.h \ + ./Exec_Sequence.h \ + ./Exec_Set.h \ + ./Exec_Show.h \ + ./Exec_SortEnsembleData.h \ + ./Exec_SplitCoords.h \ + ./Exec_System.h \ + ./Exec_Top.h \ + ./Exec_Traj.h \ + ./Exec_UpdateParameters.h \ + ./Exec_ViewRst.h \ + ./Exec_Zmatrix.h \ + ./ExtendedSimilarity.h \ + ./ExternalFxn.h \ + ./FileIO_Bzip2.h \ + ./FileIO_Gzip.h \ + ./FileIO.h \ + ./FileIO_Mpi.h \ + ./FileIO_MpiShared.h \ + ./FileIO_Std.h \ + ./FileName.h \ + ./File_TempName.h \ + ./FileType.h \ + ./FileTypes.h \ + ./ForLoop_dataSetBlocks.h \ + ./ForLoop.h \ + ./ForLoop_inData.h \ + ./ForLoop_integer.h \ + ./ForLoop_list.h \ + ./ForLoop_mask.h \ + ./ForLoop_overSets.h \ + ./FrameArray.h \ + ./Frame.h \ + ./FramePtrArray.h \ + ./GistEntropyUtils.h \ + ./GIST_PME.h \ + ./Gpu.h \ + ./GridAction.h \ + ./GridBin.h \ + ./Grid.h \ + ./GridMover.h \ + ./helpme_standalone.h \ + ./HipDefinitions.h \ + ./HistBin.h \ + ./Hungarian.h \ + ./Image_List.h \ + ./Image_List_Mask.h \ + ./Image_List_Pair_CoM.h \ + ./Image_List_Pair_First.h \ + ./Image_List_Pair_Geom.h \ + ./Image_List_Pair.h \ + ./Image_List_Unit_CoM.h \ + ./Image_List_Unit_First.h \ + ./Image_List_Unit_Geom.h \ + ./Image_List_Unit.h \ + ./ImageOption.h \ + ./ImageRoutines.h \ + ./ImageTypes.h \ + ./InputTrajCommon.h \ + ./InteractionData.h \ + ./KDE.h \ + ./LeapInterface.h \ + ./MapAtom.h \ + ./MaskArray.h \ + ./MaskToken.h \ + ./Matrix_3x3.h \ + ./Matrix.h \ + ./MdOpts.h \ + ./MetaData.h \ + ./Minimize_SteepestDescent.h \ + ./Mol2File.h \ + ./Molecule.h \ + ./Mol.h \ + ./molsurf.h \ + ./NameType.h \ + ./NC_Routines.h \ + ./NDiff.h \ + ./NetcdfFile.h \ + ./OMM_helpers.h \ + ./OnlineVarT.h \ + ./OutputTrajCommon.h \ + ./PairListEngine_Ewald_Decomp_LJLR.h \ + ./PairListEngine_Ewald_Decomp_LJPME.h \ + ./PairListEngine_Ewald_LJLR.h \ + ./PairListEngine_Ewald_LJPME.h \ + ./PairList.h \ + ./PairListTemplate.h \ + ./Parallel.h \ + ./ParallelNetcdf.h \ + ./ParallelSetFrameNum.h \ + ./ParameterHolders.h \ + ./ParameterSet.h \ + ./ParameterTypes.h \ + ./Parm_Amber.h \ + ./Parm_CharmmPsf.h \ + ./Parm_CIF.h \ + ./ParmFile.h \ + ./Parm_Gromacs.h \ + ./ParmIO.h \ + ./Parm_Mol2.h \ + ./Parm_PDB.h \ + ./Parm_SDF.h \ + ./Parm_Tinker.h \ + ./PDBfile.h \ + ./PotentialFunction.h \ + ./PotentialTerm_Angle.h \ + ./PotentialTerm_Bond.h \ + ./PotentialTerm_Dihedral.h \ + ./PotentialTerm.h \ + ./PotentialTerm_LJ_Coulomb.h \ + ./PotentialTerm_OpenMM.h \ + ./ProgressBar.h \ + ./ProgressTimer.h \ + ./PubFFT.h \ + ./Pucker.h \ + ./Pucker_PuckerMask.h \ + ./Pucker_PuckerSearch.h \ + ./Pucker_PuckerToken.h \ + ./qcprot.h \ + ./QuaternionRMSD.h \ + ./Random.h \ + ./Range.h \ + ./RangeToken.h \ + ./ReadLine.h \ + ./ReferenceAction.h \ + ./ReferenceFrame.h \ + ./RemdReservoirNC.h \ + ./ReplicaDimArray.h \ + ./ReplicaInfo.h \ + ./Residue.h \ + ./RNG.h \ + ./RNG_Marsaglia.h \ + ./RNG_MersenneTwister.h \ + ./RNG_PCG32.h \ + ./RNG_Stdlib.h \ + ./RNG_Xoshiro128pp.h \ + ./RPNcalc.h \ + ./SDFfile.h \ + ./Segment.h \ + ./SimplexMin.h \ + ./SpaceGroup.h \ + ./SplineFxnTable.h \ + ./Spline.h \ + ./Stats_Reduce.h \ + ./StringRoutines.h \ + ./StructureCheck.h \ + ./StructureMapper.h \ + ./SymbolExporting.h \ + ./SymmetricRmsdCalc.h \ + ./SymmetricTensor.h \ + ./TextBlockBuffer.h \ + ./TextFormat.h \ + ./Timer.h \ + ./TinkerFile.h \ + ./TopInfo.h \ + ./Topology.h \ + ./TorsionRoutines.h \ + ./Traj_AmberCoord.h \ + ./Traj_AmberNetcdf.h \ + ./Traj_AmberRestart.h \ + ./Traj_AmberRestartNC.h \ + ./Traj_Binpos.h \ + ./Traj_CharmmCor.h \ + ./Traj_CharmmDcd.h \ + ./Traj_CharmmRestart.h \ + ./Traj_CIF.h \ + ./Traj_Conflib.h \ + ./Traj_DTR.h \ + ./TrajectoryFile.h \ + ./TrajectoryIO.h \ + ./TrajFrameCounter.h \ + ./TrajFrameIndex.h \ + ./Traj_GmxDump.h \ + ./Traj_GmxTng.h \ + ./Traj_GmxTrX.h \ + ./Traj_GmxXtc.h \ + ./Traj_Gro.h \ + ./Traj_H5.h \ + ./Traj_H5MD.h \ + ./Trajin.h \ + ./TrajinList.h \ + ./Trajin_Multi.h \ + ./Trajin_Single.h \ + ./TrajIOarray.h \ + ./Traj_Mol2File.h \ + ./Traj_NcEnsemble.h \ + ./TrajoutList.h \ + ./Trajout_Single.h \ + ./Traj_PDBfile.h \ + ./Traj_SDF.h \ + ./Traj_SQM.h \ + ./Traj_Tinker.h \ + ./Traj_XYZ.h \ + ./TypeNameHolder.h \ + ./Unit.h \ + ./Units.h \ + ./UpdateParameters.h \ + ./Vec3.h \ + ./Version.h \ + ./ViewRst.h \ + ./xoshiro128plusplus.h \ + Cluster/Algorithm_DBscan.h \ + Cluster/Algorithm_DPeaks.h \ + Cluster/Algorithm.h \ + Cluster/Algorithm_HierAgglo.h \ + Cluster/Algorithm_Kmeans.h \ + Cluster/BestReps.h \ + Cluster/CentroidArray.h \ + Cluster/Centroid_Coord.h \ + Cluster/Centroid.h \ + Cluster/Centroid_Num.h \ + Cluster/Cframes.h \ + Cluster/Cmatrix_Binary.h \ + Cluster/Cmatrix_NC.h \ + Cluster/Control.h \ + Cluster/DBI.h \ + Cluster/DrawGraph.h \ + Cluster/DynamicMatrix.h \ + Cluster/List.h \ + Cluster/MetricArray.h \ + Cluster/Metric_DME.h \ + Cluster/Metric.h \ + Cluster/Metric_Matrix2D.h \ + Cluster/Metric_QuatRMSD.h \ + Cluster/Metric_RMS.h \ + Cluster/Metric_Scalar.h \ + Cluster/Metric_SRMSD.h \ + Cluster/Metric_Torsion.h \ + Cluster/Node.h \ + Cluster/Output.h \ + Cluster/PseudoF.h \ + Cluster/Results_Coords.h \ + Cluster/Results.h \ + Cluster/Sieve.h \ + Cluster/Silhouette.h \ + Structure/BuildAtom.h \ + Structure/Builder.h \ + Structure/Chirality.h \ + Structure/Disulfide.h \ + Structure/FunctionalGroup.h \ + Structure/FxnGroupBuilder.h \ + Structure/HisProt.h \ + Structure/InternalCoords.h \ + Structure/LinkAtom.h \ + Structure/Model.h \ + Structure/ResStatArray.h \ + Structure/StructureEnum.h \ + Structure/StructureRoutines.h \ + Structure/SugarBuilder.h \ + Structure/Sugar.h \ + Structure/SugarLinkAtoms.h \ + Structure/SugarToken.h \ + Structure/Zmatrix.h \ + Energy/Ecalc_Nonbond.h \ + Energy/Ene_Angle.h \ + Energy/Ene_Bond.h \ + Energy/Ene_Decomp_Nonbond.h \ + Energy/Ene_LJ_6_12.h \ + Energy/Ene_LJPME_6_12.h \ + Energy/Ene_Nonbond.h \ + Energy/EnergyDecomposer.h \ + Energy/ErfcFxn.h \ + Energy/EwaldCalc_Decomp.h \ + Energy/EwaldCalc_Decomp_LJPME.h \ + Energy/EwaldCalc_Decomp_PME.h \ + Energy/EwaldCalc.h \ + Energy/EwaldCalc_LJPME.h \ + Energy/EwaldCalc_PME.h \ + Energy/EwaldCalc_Regular.h \ + Energy/EwaldParams.h \ + Energy/EwaldParams_LJPME.h \ + Energy/Ewald_Recip.h \ + Energy/Kernel_EwaldAdjust.h \ + Energy/Kernel_Fourier.h \ + Energy/Kernel_Harmonic.h \ + Energy/Kernel_LJPME_Adjust.h \ + Energy/PME_Recip.h \ + Energy/PME_RecipParams.h \ + Energy/VDW_LongRange_Correction.h \ + diff --git a/src/readline/CMakeLists.txt b/src/readline/CMakeLists.txt index 556e6f6be7..d4de3f58e2 100644 --- a/src/readline/CMakeLists.txt +++ b/src/readline/CMakeLists.txt @@ -44,3 +44,4 @@ add_library(readline STATIC ${CPPTRAJ_READLINE_SOURCES}) target_compile_definitions(readline PRIVATE HAVE_CONFIG_H=1) # make sure the code uses the premade config.h make_pic_if_needed(readline) target_include_directories(readline PUBLIC .) +target_include_directories(readline PUBLIC ../)