Have configure and cmake install headers for libcpptraj (Amber-MD#1129)

* Use the install binary

* Script to get all headers that should be installed for libcpptraj

* Contains all headers that should be installed for libcpptraj

* Add target for installing headers

* Make header install less verbose. Have libcpptraj install depend on
install_headers

* Cmake install headers for inside/outside amber

* Convert back down to lyx 2.3 for Amber

* Update the PDF

configure

@@ -2595,6 +2595,12 @@ 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"
 
@@ -2983,6 +2989,10 @@ 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

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

doc/CpptrajManual.lyx

@@ -1,26 +1,24 @@
 #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"
 \font_math "auto" "auto"
 \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
 

doc/DocumentChecksums.txt

@@ -1,3 +1,3 @@
 b37726e7a841f6fc695ecd7fb040ffbf  CpptrajDevelopmentGuide.lyx
-786c4aec62d60a3f9265dec52b767e02  cpptraj.lyx
-07c4039e732fc2eb1df0c1e0863cb949  CpptrajManual.lyx
+1f4d9c647b6717314560290a4d3f9f06  cpptraj.lyx
+5d9b5b5ed47a3ded57b6464df99b3585  CpptrajManual.lyx