From: "Reinis Danne" <rei4dan@gmail.com>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/
Date: Sat, 3 Mar 2012 21:06:52 +0000 (UTC) [thread overview]
Message-ID: <1330808084.8ce9886cd5e61b892ee7e1087c09013e310a15ea.rei4dan@gentoo> (raw)
commit: 8ce9886cd5e61b892ee7e1087c09013e310a15ea
Author: Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Sat Mar 3 20:54:44 2012 +0000
Commit: Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Sat Mar 3 20:54:44 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8ce9886c
sci-chemistry/ambertools: Add bugfixes 22-27
---
sci-chemistry/ambertools/ChangeLog | 8 +-
sci-chemistry/ambertools/ambertools-1.5-r3.ebuild | 157 +
.../files/ambertools-1.5-bugfix_22-27.patch | 3343 ++++++++++++++++++++
3 files changed, 3507 insertions(+), 1 deletions(-)
diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog
index 50f0545..0945272 100644
--- a/sci-chemistry/ambertools/ChangeLog
+++ b/sci-chemistry/ambertools/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-chemistry/ambertools
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $
+*ambertools-1.5-r3 (03 Mar 2012)
+
+ 03 Mar 2012; Reinis Danne <rei4dan@gmail.com> +ambertools-1.5-r3.ebuild,
+ +files/ambertools-1.5-bugfix_22-27.patch:
+ Add bugfixes 22-27.
+
26 Oct 2011; Reinis Danne <rei4dan@gmail.com>
files/ambertools-1.5-gentoo2.patch:
Fix possible buffer overflow.
diff --git a/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild
new file mode 100644
index 0000000..bebf36c
--- /dev/null
+++ b/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild
@@ -0,0 +1,157 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.2 2011/08/02 14:42:37 alexxy Exp $
+
+EAPI=4
+
+inherit eutils fortran-2 toolchain-funcs
+
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations"
+HOMEPAGE="http://ambermd.org/#AmberTools"
+SRC_URI="
+ AmberTools-${PV}.tar.bz2"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="openmp X"
+
+RESTRICT="fetch"
+
+RDEPEND="
+ virtual/cblas
+ virtual/lapack
+ sci-libs/clapack
+ sci-libs/arpack
+ sci-libs/cifparse-obj
+ sci-chemistry/mopac7
+ sci-libs/netcdf
+ sci-libs/fftw:2.1
+ sci-chemistry/reduce
+ virtual/fortran"
+DEPEND="${RDEPEND}
+ dev-util/byacc
+ dev-libs/libf2c
+ sys-devel/ucpp"
+S="${WORKDIR}/amber11"
+
+pkg_nofetch() {
+ einfo "Go to ${HOMEPAGE} and get ${A}"
+ einfo "Place it in ${DISTDIR}"
+}
+
+pkg_setup() {
+ fortran-2_pkg_setup
+ if use openmp; then
+ tc-has-openmp || \
+ die "Please select an openmp capable compiler like gcc[openmp]"
+ fi
+ AMBERHOME="${S}"
+}
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}/${P}-bugfix_1-21.patch" \
+ "${FILESDIR}/${P}-bugfix_22-27.patch" \
+ "${FILESDIR}/${P}-gentoo2.patch"
+ cd "${S}"/AmberTools/src
+ rm -r \
+ arpack \
+ blas \
+ byacc \
+ lapack \
+ fftw-2.1.5 \
+ fftw-3.2.2 \
+ c9x-complex \
+ cifparse \
+ netcdf \
+ pnetcdf \
+ reduce \
+ ucpp-1.3 \
+ || die
+}
+
+src_configure() {
+ cd "${S}"/AmberTools/src
+ sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \
+ -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \
+ -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \
+ -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+ -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \
+ -e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \
+ -e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \
+ -e "s:GENTOO_FFLAGS:${FFLAGS}:g" \
+ -e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \
+ -e "s:fc=g77:fc=$(tc-getFC):g" \
+ -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \
+ -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \
+ -i configure || die
+ sed -e "s:arsecond_:arscnd_:g" \
+ -i sff/time.c \
+ -i sff/sff.h \
+ -i sff/sff.c || die
+ sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \
+ -i nss/Makefile || die
+
+ local myconf
+
+ use X || myconf="${myconf} -noX11"
+
+ use openmp && myconf="${myconf} -openmp"
+
+ ./configure \
+ ${myconf} \
+ -nobintraj \
+ -nomdgx \
+ -nomtkpp \
+ -nopython \
+ -nosleap \
+ gnu
+}
+
+src_compile() {
+ cd "${S}"/AmberTools/src
+ emake || die
+}
+
+src_test() {
+ cd "${S}"/AmberTools/test
+ make test || die
+}
+
+src_install() {
+ rm -r bin/chemistry bin/MMPBSA_mods
+ rm bin/ante-MMPBSA.py bin/extractFrcmod.py
+
+ for x in bin/*
+ do dobin ${x} || die
+ done
+
+ dobin AmberTools/src/antechamber/mopac.sh
+ sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \
+ -i "${ED}/usr/bin/mopac.sh" || die
+
+ # Make symlinks untill binpath for amber will be fixed
+ dodir /usr/share/${PN}/bin
+ cd "${ED}/usr/bin"
+ for x in *
+ do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x}
+ done
+ cd "${S}"
+
+ dodoc doc/AmberTools.pdf doc/leap_pg.pdf
+ dolib.a lib/*
+ insinto /usr/include/${PN}
+ doins include/*
+ insinto /usr/share/${PN}
+ doins -r dat
+ cd AmberTools
+ doins -r benchmarks
+ doins -r examples
+ doins -r test
+
+ cat >> "${T}"/99ambertools <<- EOF
+ AMBERHOME="${EPREFIX}/usr/share/ambertools"
+ EOF
+ doenvd "${T}"/99ambertools
+}
diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_22-27.patch b/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_22-27.patch
new file mode 100644
index 0000000..6df705c
--- /dev/null
+++ b/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_22-27.patch
@@ -0,0 +1,3343 @@
+diff -urN amber11.orig/AmberTools/examples/mtkpp/MCPB/run.MCPB.csh amber11/AmberTools/examples/mtkpp/MCPB/run.MCPB.csh
+--- amber11.orig/AmberTools/examples/mtkpp/MCPB/run.MCPB.csh 2011-04-14 15:30:12.000000000 +0300
++++ amber11/AmberTools/examples/mtkpp/MCPB/run.MCPB.csh 2012-03-03 20:03:01.387032575 +0200
+@@ -2,111 +2,10 @@
+ echo " "
+ echo " MTK++ MCPB example "
+ echo " "
+-
+-# Clean up
+-rm -rf 1AMP_OH.README
+-rm -rf *.bcl
+-rm -rf createLibraries.sh createRespAdditions.sh getCharges.sh
+-rm -rf *.pdb
+-rm -rf *.log
+-
+-cp data/*.pdb .
+-cp data/*.bcl .
+-cp data/*.log .
+-cp data/*.fchk .
+-
+-echo "Generating scripts "
+-sh genMetalFF.sh -n 1AMP_OH
+-
+-cp data/1AMP.pdb .
+-cp data/1AMP_OH_fixed.pdb .
+-cp data/1AMP_OH_sidechain.bcl .
+-cp data/1AMP_OH_addStdMol.bcl .
+-cp data/1AMP_OH_large.bcl .
+-cp data/1AMP_OH_large_mk.log .
+-
+-cp data/1AMP_OH_sidechain_fc_md.log .
+-cp data/1AMP_OH_sidechain_opt_md.fchk .
+-cp data/1AMP_OH_sidechain_opt_md.log .
+-
+-echo "Adding Hydrogens to pdb file "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_addHs.bcl \
+- -l 1AMP_OH_addHs.bcl.log || goto error
+-
+-echo "Creating Model 1"
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_sidechain.bcl \
+- -l 1AMP_OH_sidechain.bcl.log || goto error
+-
+-echo "Adding standard molecule to library "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_addStdMol.bcl \
+- -l 1AMP_OH_addStdMol.bcl.log || goto error
+-
+-echo "Creating Model 2 "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large.bcl \
+- -l 1AMP_OH_large.bcl.log || goto error
+-
+-echo "Creating RESP files 0 "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_mk0.bcl \
+- -l 1AMP_OH_large_mk0.bcl.log || goto error
+-mv 1AMP_OH_large_respAdds 1AMP_OH_large_respAdds0 || goto error
+-
+-echo "Creating RESP files 1 "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_mk1.bcl \
+- -l 1AMP_OH_large_mk1.bcl.log || goto error
+-mv 1AMP_OH_large_respAdds 1AMP_OH_large_respAdds1 || goto error
+-
+-echo "Creating RESP files 2 "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_mk2.bcl \
+- -l 1AMP_OH_large_mk2.bcl.log || goto error
+-mv 1AMP_OH_large_respAdds 1AMP_OH_large_respAdds2 || goto error
+-
+-echo "Creating RESP files 3 "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_mk3.bcl \
+- -l 1AMP_OH_large_mk3.bcl.log || goto error
+-mv 1AMP_OH_large_respAdds 1AMP_OH_large_respAdds3 || goto error
+-
+-echo "Determining charges "
+-sh ./getCharges.sh 0 || goto error
+-sh ./getCharges.sh 1 || goto error
+-sh ./getCharges.sh 2 || goto error
+-sh ./getCharges.sh 3 || goto error
+-
+-echo "Creating library files "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_chg0.bcl \
+- -l 1AMP_OH_large_chg0.bcl.log || goto error
+-
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_chg1.bcl \
+- -l 1AMP_OH_large_chg1.bcl.log || goto error
+-
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_chg2.bcl \
+- -l 1AMP_OH_large_chg2.bcl.log || goto error
+-
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_chg3.bcl \
+- -l 1AMP_OH_large_chg3.bcl.log || goto error
+-
+-echo "Determining Seminario force constants "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_sidechain_fc_sem.bcl \
+- -l 1AMP_OH_sidechain_fc_sem.bcl.log || goto error
+-
+-echo "Determining Traditional force constants "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_sidechain_fc_md.bcl \
+- -l 1AMP_OH_sidechain_fc_md.bcl.log || goto error
+-
+-echo "Exporting Seminario library to AMBER format "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_toAmberFormats_sem.bcl \
+- -l 1AMP_OH_toAmberFormats_sem.bcl.log || goto error
+-
+-echo "Exporting Traditional library to AMBER format "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_toAmberFormats_md.bcl \
+- -l 1AMP_OH_toAmberFormats_md.bcl.log || goto error
+-
+-echo "Reading protonated file and updating residue names "
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_resNames.bcl \
+- -l 1AMP_OH_resNames.bcl.log || goto error
+-
+-echo No errors detected
++echo " "
++echo " This example has been removed due to incompatibility with"
++echo " the current minor revision of MTK++. An updated MCPB example"
++echo " is planned for a future release."
++echo " "
+ exit(0)
+
+-error:
+-echo Problem: check log files and try again
+-exit(1)
+diff -urN amber11.orig/AmberTools/examples/mtkpp/stats/pca1/run.stats.csh amber11/AmberTools/examples/mtkpp/stats/pca1/run.stats.csh
+--- amber11.orig/AmberTools/examples/mtkpp/stats/pca1/run.stats.csh 2011-04-14 15:30:12.000000000 +0300
++++ amber11/AmberTools/examples/mtkpp/stats/pca1/run.stats.csh 2012-03-03 20:03:01.387032575 +0200
+@@ -3,12 +3,12 @@
+ echo " MTK++ stats example"
+ echo " "
+
+-../$AMBERHOME/bin/stats -i pca.stats \
+- -l pca.stats.log || goto error
++$AMBERHOME/bin/stats -i pca.stats \
++ -l pca.stats.log || goto error
+
+ echo No errors detected
+ exit(0)
+
+ error:
+ echo Problem: check .out and try again
+-exit(1)
+\ Nav jaunu rindu faila beigās
++exit(1)
+diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure
+--- amber11.orig/AmberTools/src/configure 2012-03-03 22:42:38.558776473 +0200
++++ amber11/AmberTools/src/configure 2012-03-03 20:02:57.727033628 +0200
+@@ -61,6 +61,9 @@
+ -debug Compile with debug symbols
+ -noopt Disable all compiler optimisations (sometimes needed if
+ debug symbols are requested)
++ -nopatch Do NOT run \$AMBERHOME/AT15_Amber11.py after configure writes
++ the config.h file, even if Amber11 is found in the directory.
++ This flag has no effect if Amber11 is not present.
+
+ Rarely used/tested NAB options:
+ -scalapack Use ScaLAPACK for linear algebra. Do not use in
+@@ -165,6 +168,7 @@
+ debug='no'
+ optimise='yes'
+ is_mac='no'
++nopatch='no'
+
+ #------------------------------------------------------------------------------
+ # Architecture specific:
+@@ -216,6 +220,7 @@
+ -nomtkpp) mtkpp='';;
+ -debug) debug='yes';;
+ -noopt) optimise='no';;
++ -nopatch) nopatch='yes';;
+ -help) usage;;
+ --help) usage;;
+ -h) usage;;
+@@ -2144,7 +2149,7 @@
+ fi
+
+ # For AmberTools 1.5 + Amber 11, print a message about running AT15_Amber11.py
+-if [ -d ../../src/sander ]; then
++if [ -d ../../src/sander -a "$nopatch" = 'yes' ]; then
+ echo ""
+ echo " NOTE: after installing AmberTools, if you want to compile"
+ echo " Amber11 using AmberTools 1.5, you must run the "
+@@ -2155,5 +2160,14 @@
+ echo " script will modify your Amber11 files.)"
+ fi
+
++if [ -d ../../src/sander -a "$nopatch" = 'no' ]; then
++ echo ""
++ echo " Running \$AMBERHOME/AT15_Amber11.py to patch config.h for building Amber 11."
++ echo " Check Amber11_Conversion.log for details of what was done. Running this script"
++ echo " a second time has no effect (positive or negative)"
++ echo ""
++ ../../AT15_Amber11.py > Amber11_Conversion.log 2>&1
++fi
++
+ exit
+
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/AmberRestart.cpp amber11/AmberTools/src/cpptraj/src/AmberRestart.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/AmberRestart.cpp 2012-03-03 22:42:00.557775196 +0200
++++ amber11/AmberTools/src/cpptraj/src/AmberRestart.cpp 2012-03-03 20:03:06.928030979 +0200
+@@ -53,7 +53,7 @@
+ mprintf("Error: AmberRestart::open(): Reading restart atoms/time.\n");
+ return 1;
+ }
+- nread=sscanf(buffer,"%5i%15lE%15lE",&restartAtoms,&restartTime,&restartTemp);
++ nread=sscanf(buffer,"%i %lE %lE",&restartAtoms,&restartTime,&restartTemp);
+ if (nread<1) {
+ mprintf("Error: AmberRestart::open(): Getting restart atoms/time.\n");
+ return 1;
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/main.cpp amber11/AmberTools/src/cpptraj/src/main.cpp
+--- amber11.orig/AmberTools/src/cpptraj/src/main.cpp 2012-03-03 22:42:47.132776753 +0200
++++ amber11/AmberTools/src/cpptraj/src/main.cpp 2012-03-03 20:03:06.928030979 +0200
+@@ -6,7 +6,7 @@
+ #include "PtrajMpi.h"
+ #include "CpptrajStdio.h"
+ #ifndef CPPTRAJ_VERSION_STRING
+-#define CPPTRAJ_VERSION_STRING "V1.1.1"
++#define CPPTRAJ_VERSION_STRING "V1.1.2"
+ #endif
+
+ void Usage(char *programName) {
+diff -urN amber11.orig/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py
+--- amber11.orig/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py 2011-04-14 15:30:17.000000000 +0300
++++ amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py 2012-03-03 20:03:11.481029669 +0200
+@@ -2315,7 +2315,7 @@
+ return math.sqrt(abs(_stdev(self.com_data[0]) ** 2 + _stdev(self.rec_data[0]) ** 2 + _stdev(self.lig_data[0]) ** 2))
+
+ sum = sum2 = 0
+- for i in range(len(self.com_data)):
++ for i in range(len(self.com_data[0])):
+ sum += self.com_data[0][i] - self.rec_data[0][i] - self.lig_data[0][i]
+ sum2 += (self.com_data[0][i] - self.rec_data[0][i] - self.lig_data[0][i]) ** 2
+
+diff -urN amber11.orig/AmberTools/src/mtkpp/configure amber11/AmberTools/src/mtkpp/configure
+--- amber11.orig/AmberTools/src/mtkpp/configure 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/configure 2012-03-03 20:03:01.397032571 +0200
+@@ -788,7 +788,6 @@
+ with_gnu_ld
+ with_sysroot
+ enable_libtool_lock
+-with_gnu_ld
+ with_mkl_dir
+ with_mkl_libs
+ with_boost
+@@ -811,22 +810,9 @@
+ CCC
+ CC
+ CFLAGS
+-LDFLAGS
+-LIBS
+-CPPFLAGS
+ CPP
+-CPPFLAGS
+ CXXCPP
+-CPPFLAGS
+-XMKMF
+-CXX
+-LDFLAGS
+-LIBS
+-CPPFLAGS
+-CCC
+-CC
+-LDFLAGS
+-LIBS'
++XMKMF'
+
+
+ # Initialize some variables set by options.
+@@ -16665,7 +16651,7 @@
+ *) platform=UNKNOWN
+ is_unknown=yes
+ echo 'ERROR: this platform is not supported at this time!'
+- exit 1 ;;
++ exit ;;
+ esac
+ if test "$is_darwin" = "yes"; then
+ IS_DARWIN_TRUE=
+@@ -17838,8 +17824,8 @@
+ $as_echo "#define HAVE_ZLIB 1" >>confdefs.h
+
+ CFLAGS=$CFLAGS" -DHAVE_ZLIB"
+- CXXFLAGS=$CXXFLAGS" -DHAVE_ZLIB -DHAVE_ZLIB"
+- defines_string=$defines_string" -DHAVE_ZLIB -DHAVE_ZLIB"
++ CXXFLAGS=$CXXFLAGS" -DHAVE_ZLIB"
++ defines_string=$defines_string" -DHAVE_ZLIB"
+ FLIBS=$FLIBS" -lz"
+ else
+
+diff -urN amber11.orig/AmberTools/src/mtkpp/configure.in amber11/AmberTools/src/mtkpp/configure.in
+--- amber11.orig/AmberTools/src/mtkpp/configure.in 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/configure.in 2012-03-03 20:03:01.400032571 +0200
+@@ -383,7 +383,7 @@
+ *) platform=UNKNOWN
+ is_unknown=yes
+ echo 'ERROR: this platform is not supported at this time!'
+- exit 1 ;;
++ exit ;;
+ esac
+ AM_CONDITIONAL(IS_DARWIN, test "$is_darwin" = "yes")
+ AM_CONDITIONAL(IS_LINUX, test "$is_linux" = "yes")
+@@ -457,8 +457,8 @@
+ if test $ac_have_zlibh = yes; then
+ AC_DEFINE(HAVE_ZLIB, 1, [Define to 1 if ZLIB is available.])
+ CFLAGS=$CFLAGS" -DHAVE_ZLIB"
+- CXXFLAGS=$CXXFLAGS" -DHAVE_ZLIB -DHAVE_ZLIB"
+- defines_string=$defines_string" -DHAVE_ZLIB -DHAVE_ZLIB"
++ CXXFLAGS=$CXXFLAGS" -DHAVE_ZLIB"
++ defines_string=$defines_string" -DHAVE_ZLIB"
+ FLIBS=$FLIBS" -lz"
+ else
+ AC_DEFINE(HAVE_ZLIB, 0, [Define to 0 if ZLIB is unavailable.])
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Minimizers/Makefile.am amber11/AmberTools/src/mtkpp/src/Minimizers/Makefile.am
+--- amber11.orig/AmberTools/src/mtkpp/src/Minimizers/Makefile.am 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Minimizers/Makefile.am 2012-03-03 20:03:01.400032571 +0200
+@@ -1,4 +1,4 @@
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics/$(SRCDIR)
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR)
+ DIAGNOSTICS_LIB=-lDiagnostics
+ INCLUDES = -I$(srcdir)/..
+
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Minimizers/Makefile.in amber11/AmberTools/src/mtkpp/src/Minimizers/Makefile.in
+--- amber11.orig/AmberTools/src/mtkpp/src/Minimizers/Makefile.in 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Minimizers/Makefile.in 2012-03-03 20:03:01.401032571 +0200
+@@ -239,7 +239,7 @@
+ top_builddir = @top_builddir@
+ top_srcdir = @top_srcdir@
+ xerces_path = @xerces_path@
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics/$(SRCDIR)
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR)
+ DIAGNOSTICS_LIB = -lDiagnostics
+ INCLUDES = -I$(srcdir)/..
+ lib_LTLIBRARIES = libMinimizers.la
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/MM/Makefile.am amber11/AmberTools/src/mtkpp/src/MM/Makefile.am
+--- amber11.orig/AmberTools/src/mtkpp/src/MM/Makefile.am 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/MM/Makefile.am 2012-03-03 20:03:01.400032571 +0200
+@@ -1,6 +1,6 @@
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics/$(SRCDIR)
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR)
+ DIAGNOSTICS_LIB=-lDiagnostics
+-LOG_LD=-L$(top_builddir)/src/Log/$(SRCDIR)
++LOG_LD=-L$(abs_top_builddir)/src/Log/$(SRCDIR)
+ LOG_LIB=-lLog
+
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/..
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/MM/Makefile.in amber11/AmberTools/src/mtkpp/src/MM/Makefile.in
+--- amber11.orig/AmberTools/src/mtkpp/src/MM/Makefile.in 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/MM/Makefile.in 2012-03-03 20:03:01.400032571 +0200
+@@ -241,9 +241,9 @@
+ top_builddir = @top_builddir@
+ top_srcdir = @top_srcdir@
+ xerces_path = @xerces_path@
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics/$(SRCDIR)
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR)
+ DIAGNOSTICS_LIB = -lDiagnostics
+-LOG_LD = -L$(top_builddir)/src/Log/$(SRCDIR)
++LOG_LD = -L$(abs_top_builddir)/src/Log/$(SRCDIR)
+ LOG_LIB = -lLog
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/..
+ lib_LTLIBRARIES = libMM.la
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/atomType.h amber11/AmberTools/src/mtkpp/src/Molecule/atomType.h
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/atomType.h 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Molecule/atomType.h 2012-03-03 20:03:01.402032570 +0200
+@@ -74,6 +74,9 @@
+
+ //!
+ double evalue;
++
++ //! Atomic polarizability in A**3
++ double atomPolarizability;
+ };
+
+ // ============================================================
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/collection.cpp amber11/AmberTools/src/mtkpp/src/Molecule/collection.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/collection.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Molecule/collection.cpp 2012-03-03 20:03:01.403032569 +0200
+@@ -484,6 +484,11 @@
+ for (moleculeIterator m = this->itsMoleculeList.begin();
+ m != this->itsMoleculeList.end(); m++) {
+ pMolecule = *m;
++
++ if (pMolecule->getName() == "Reference") {
++ continue;
++ }
++
+ std::vector<submolecule*> subMolList = pMolecule->getSubMoleculeList();
+ for (sMolIterator c = subMolList.begin(); c != subMolList.end(); c++) {
+ pSubMolecule = *c;
+@@ -3408,7 +3413,10 @@
+ }
+ errMessage += metalAtom->getParent()->getName() + "@|"
+ + metalAtom->getName() + "|-"
+- + primShellAtoms[e]->getParent()->getName() + "@|"
++ + primShellAtoms[e]->getParent()->getName()
++ + i2s(primShellAtoms[e]->getParent()->getSubMolId())
++ + primShellAtoms[e]->getParent()->getiCode()
++ + "@|"
+ + primShellAtoms[e]->getName() + "| dist = " + d2s(localBond->size) +"\n";
+
+ // Angles
+@@ -3488,7 +3496,8 @@
+ std::vector<stdGroup*> stdGrpList = this->pStdLibrary->getStdGroupList();
+
+ for (unsigned int i = 0; i < stdGrpList.size(); i++) {
+-//std::cout << i << " " << stdGrpList.size() << " " << stdGrpList[i]->getName() << " " << stdGrpList[i]->hasStdMolecule() << std::endl;
++//std::cout << "\n\ncollection::assignMetalParameters " << i << " " << stdGrpList.size() << " " << stdGrpList[i]->getName() << " "
++// << stdGrpList[i]->hasStdMolecule() << std::endl;
+ if (stdGrpList[i]->hasStdMolecule()) {
+ //std::cout << "stdgroup name: " << stdGrpList[i]->getName() << std::endl;
+ //stdGroup* pStdGroup = stdGrpList[i];
+@@ -3515,6 +3524,7 @@
+
+ // create new molecule
+ molecule* pNewMolecule = this->addMolecule();
++ std::vector<atom*> atomList;
+
+ // copy residues
+ std::vector<metalCenter*> metCens = itsMetalGroups[j]->getMetalCenters();
+@@ -3536,6 +3546,10 @@
+ addedResidues.push_back(primShellAtoms[l]->getParent());
+ submolecule* pNewSubmolecule = pNewMolecule->addSubMolecule();
+ pNewSubmolecule->copy(primShellAtoms[l]->getParent());
++ std::vector<atom*> atomListTmp = primShellAtoms[l]->getParent()->getAtomList();
++ for (unsigned int i = 0 ; i < atomListTmp.size(); i++) {
++ atomList.push_back(atomListTmp[i]);
++ }
+ /*
+ std::cout << "Primary Shell " << primShellAtoms[l]->getParent()->getName() << " "
+ << primShellAtoms[l]->getParent()->getSubMolId() << " "
+@@ -3556,6 +3570,11 @@
+ addedResidues.push_back(secShellAtoms[l]->getParent());
+ submolecule* pNewSubmolecule = pNewMolecule->addSubMolecule();
+ pNewSubmolecule->copy(secShellAtoms[l]->getParent());
++
++ std::vector<atom*> atomListTmp = secShellAtoms[l]->getParent()->getAtomList();
++ for (unsigned int i = 0 ; i < atomListTmp.size(); i++) {
++ atomList.push_back(atomListTmp[i]);
++ }
+ /*
+ std::cout << "Secondary Shell " << secShellAtoms[l]->getParent()->getName() << " "
+ << secShellAtoms[l]->getParent()->getSubMolId()
+@@ -3573,6 +3592,12 @@
+ addedResidues.push_back(metalAtom->getParent());
+ submolecule* pNewSubmolecule = pNewMolecule->addSubMolecule();
+ pNewSubmolecule->copy(metalAtom->getParent());
++
++ std::vector<atom*> atomListTmp = metalAtom->getParent()->getAtomList();
++ for (unsigned int i = 0 ; i < atomListTmp.size(); i++) {
++ atomList.push_back(atomListTmp[i]);
++ }
++
+ /*
+ std::cout << "Metal Atom " << metalAtom->getParent()->getName() << " "
+ << metalAtom->getParent()->getSubMolId()
+@@ -3582,7 +3607,7 @@
+ }
+ }
+
+-//std::cout << " \n\n NEW MOLECULE \n";
++//std::cout << "NEW MOLECULE \n";
+
+ // Copy bonds
+ if (pNewMolecule) {
+@@ -3646,16 +3671,26 @@
+ }
+ }
+ }
++
++//std::cout << " After copy " << std::endl;
++
+ int nAtomsA = pStdMolecule->getNumAtoms();
+ int nAtomsB = pNewMolecule->getNumAtoms();
++
++ int nBondsA = pStdMolecule->getNumBonds();
++ int nBondsB = pNewMolecule->getNumBonds();
++
+ int nHeavyAtomsA = pStdMolecule->getNumHeavyAtoms();
+ int nHeavyAtomsB = pNewMolecule->getNumHeavyAtoms();
+
++//std::cout << "CHECK " << nAtomsA << " " << nAtomsB << " " << nBondsA << " " << nBondsB << "\n";
+ int w = 0;
+ if (nAtomsA != nAtomsB) w++;
+ int h = 0;
+ if (nHeavyAtomsA != nHeavyAtomsB) h++;
+
++//std::cout << " w = " << w << " h = " << h << std::endl;
++
+ if (w or h) {
+ std::string eMes = " " + stdGrpList[i]->getName() + " is not a match \n";
+ eMes += " std mol nAtoms: " + i2s(nAtomsA) +
+@@ -3671,8 +3706,17 @@
+ // Determine corresponences between two molecules
+ std::vector<std::vector<int> > correspondenceMatrices;
+ //int cor = 0;
++//std::cout << " superimpose " << std::endl;
+ superimpose* pSuperImpose = new superimpose();
+- int f = pSuperImpose->initializeCorrespondences(pStdMolecule, pNewMolecule, 3, correspondenceMatrices);
++ int f = 0;
++ try {
++ f = pSuperImpose->initializeCorrespondences(pStdMolecule, pNewMolecule, 3, correspondenceMatrices);
++ }
++ catch (...) {
++ f = 1;
++ }
++
++//std::cout << " after superimpose " << std::endl;
+
+ if (f != 0) {
+ std::string eMes = " Error initializing correspondences\n " + stdGrpList[i]->getName() + " is not a match \n";
+@@ -3689,6 +3733,8 @@
+ pNewMolecule->getCoordinates(CoordsB);
+ int cor = 0;
+
++//std::cout << " f = 0 " << std::endl;
++
+ double dRMSD = pSuperImpose->rmsd(pStdMolecule, CoordsB, correspondenceMatrices, cor);
+ std::string eMes = " " + stdGrpList[i]->getName() + " is a match with rmsd of " + d2s(dRMSD) + "\n";
+ MTKpp::errorLogger.throwError("collection::assignMetalParameters", eMes, INFO);
+@@ -3703,38 +3749,52 @@
+ for (int t = 0; t < nHeavyAtoms; t++) {
+ for (int t2 = 0; t2 < nHeavyAtoms; t2++) {
+ if (correspondenceMatrices[cor][t*nHeavyAtoms+t2]) {
+-//std::cout << t+1 << ":" << t2+1 << "; |";
+-
+ atom* pA1 = molHeavyAtoms1[t];
+ atom* pA2 = molHeavyAtoms2[t2];
+
+ if (pA1 and pA2) {
+-//atom* collection::getAtom(int number, bool atomIndex, bool fileId, bool atomColIndex)
+-
++ // getAtom(int number, bool atomIndex, bool fileId, bool atomColIndex)
+ atom* pOrgAtom = this->getAtom(pA2->getFileID(), 0, 1, 0);
+-/*
+-std::cout << pA1->getName() << "|" << pA2->getName() << "|" << pOrgAtom->getName() << " "
+- << pA1->getParent()->getName() << "|" << pA2->getParent()->getName() << "|" << pOrgAtom->getParent()->getName() << " |"
+- << pA1->getFileID() << "|" << pA2->getFileID() << "|" << pOrgAtom->getFileID() << "|"
+- << pA1->getColIndex() << "|" << pA2->getColIndex() << "|" << pOrgAtom->getColIndex()
+- << " |\n";
+-*/
+- pOrgAtom->getParent()->setName(pA1->getParent()->getName());
++ // atom* pOrgAtom = this->getAtom(pA2->getColIndex(), 0, 0, 1);
++
++
++//std::cout << pA1->getName() << "|" << pA2->getName() << "|" << pOrgAtom->getName() << " "
++// << pA1->getParent()->getName() << "|" << pA2->getParent()->getName() << "|" << pOrgAtom->getParent()->getName() << " |"
++// << pA1->getFileID() << "|" << pA2->getFileID() << "|" << pOrgAtom->getFileID() << "|"
++// << pA1->getColIndex() << "|" << pA2->getColIndex() << "|" << pOrgAtom->getColIndex()
++// << " |\n";
++
++ //pOrgAtom->getParent()->setName(pA1->getParent()->getName());
++
++ for (unsigned int i = 0 ; i < atomList.size(); i++) {
++ if (atomList[i]->getFileID() == pA2->getFileID()) {
++ //std::cout << "setting " << atomList[i]->getParent()->getName() << " to "
++ // << pA1->getParent()->getName() << "\n";
++ atomList[i]->getParent()->setName(pA1->getParent()->getName());
++ }
+ }
++//std::cout << pOrgAtom->getParent() << " " << pOrgAtom->getParent()->getName() << " "
++//<< pA2->getFileID()
++// << " " << pOrgAtom->getParent()->getColIndex() << "\n";
+ }
+ }
+ }
+ }
++
++ }
+ }
+ }
+ }
++
+ // delete new molecule
++ if (pNewMolecule) {
+ this->delMolecule(pNewMolecule);
+ }
+ }
+ }
+ }
+ }
++ }
+
+ ///////////////////////////////////////////////////////////////////////////////
+ ///////////////////////////////////////////////////////////////////////////////
+@@ -4377,6 +4437,7 @@
+ }
+ std::cout << " TOTAL CHARGE = " << localTotalCharge << std::endl;
+ */
++
+ }
+
+ // ============================================================
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/hydrophobize.cpp amber11/AmberTools/src/mtkpp/src/Molecule/hydrophobize.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/hydrophobize.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Molecule/hydrophobize.cpp 2012-03-03 20:03:01.404032569 +0200
+@@ -315,7 +315,7 @@
+ if (!vertices[i]->isVisited()) {
+ graph* subGraph = new graph();
+
+- std::cout << "\n " << vertices[i]->getIndex() << " ";
++// std::cout << "\n " << vertices[i]->getIndex() << " ";
+ molGraph->dfs(vertices[i]);
+
+ for (unsigned int j = 0; j < vertices.size(); j++) {
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/Makefile.am amber11/AmberTools/src/mtkpp/src/Molecule/Makefile.am
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/Makefile.am 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Molecule/Makefile.am 2012-03-03 20:03:01.401032571 +0200
+@@ -1,8 +1,8 @@
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics/$(SRCDIR)
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR)
+ DIAGNOSTICS_LIB=-lDiagnostics
+-GRAPH_LD=-L$(top_builddir)/src/Graph/$(SRCDIR)
++GRAPH_LD=-L$(abs_top_builddir)/src/Graph/$(SRCDIR)
+ GRAPH_LIB=-lGraph
+-LOG_LD=-L$(top_builddir)/src/Log/$(SRCDIR)
++LOG_LD=-L$(abs_top_builddir)/src/Log/$(SRCDIR)
+ LOG_LIB=-lLog
+
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/.. -I$(top_srcdir)/src/eigen3b2
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/Makefile.in amber11/AmberTools/src/mtkpp/src/Molecule/Makefile.in
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/Makefile.in 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Molecule/Makefile.in 2012-03-03 20:03:01.401032571 +0200
+@@ -248,11 +248,11 @@
+ top_builddir = @top_builddir@
+ top_srcdir = @top_srcdir@
+ xerces_path = @xerces_path@
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics/$(SRCDIR)
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR)
+ DIAGNOSTICS_LIB = -lDiagnostics
+-GRAPH_LD = -L$(top_builddir)/src/Graph/$(SRCDIR)
++GRAPH_LD = -L$(abs_top_builddir)/src/Graph/$(SRCDIR)
+ GRAPH_LIB = -lGraph
+-LOG_LD = -L$(top_builddir)/src/Log/$(SRCDIR)
++LOG_LD = -L$(abs_top_builddir)/src/Log/$(SRCDIR)
+ LOG_LIB = -lLog
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/.. -I$(top_srcdir)/src/eigen3b2
+ lib_LTLIBRARIES = libMolecule.la
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/parameters.cpp amber11/AmberTools/src/mtkpp/src/Molecule/parameters.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/parameters.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Molecule/parameters.cpp 2012-03-03 20:03:01.404032569 +0200
+@@ -145,6 +145,7 @@
+ pAtomType->description = "";
+ pAtomType->rvalue = 0.0;
+ pAtomType->evalue = 0.0;
++ pAtomType->atomPolarizability = 0.0;
+ pAtomType->groupName = "";
+ pAtomType->optimize = false;
+ this->itsTypeList.push_back(pAtomType);
+@@ -184,6 +185,7 @@
+ pAtomType->description = a->description;
+ pAtomType->rvalue = a->rvalue;
+ pAtomType->evalue = a->evalue;
++ pAtomType->atomPolarizability = a->atomPolarizability;
+ pAtomType->groupName = g;
+ pAtomType->optimize = a->optimize;
+
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/parameters.h amber11/AmberTools/src/mtkpp/src/Molecule/parameters.h
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/parameters.h 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Molecule/parameters.h 2012-03-03 20:03:01.405032569 +0200
+@@ -76,6 +76,9 @@
+ //! Well Depth
+ double evalue;
+
++ //! Atomic polarizability in A**3
++ double atomPolarizability;
++
+ //! group name
+ std::string groupName;
+
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdFrag.cpp amber11/AmberTools/src/mtkpp/src/Molecule/stdFrag.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdFrag.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Molecule/stdFrag.cpp 2012-03-03 20:03:01.405032569 +0200
+@@ -305,7 +305,8 @@
+ this->itsSymbol = symbol;
+ }
+ else {
+- std::cout << " Length of Fragment Symbol = " << symbol.size()
++ std::cout << " Length of Fragment Symbol (" << symbol
++ << ") = " << symbol.size()
+ << " --> Must be 3." << std::endl;
+ }
+ }
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdGroup.cpp amber11/AmberTools/src/mtkpp/src/Molecule/stdGroup.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdGroup.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Molecule/stdGroup.cpp 2012-03-03 20:03:01.406032569 +0200
+@@ -35,6 +35,7 @@
+ #include "stdLibrary.h"
+
+ #include "molecule.h"
++#include "submolecule.h"
+
+ namespace MTKpp
+ {
+@@ -258,5 +259,24 @@
+ }
+ }
+
++// ============================================================
++// Function : getCharge()
++// ------------------------------------------------------------
++//
++// ============================================================
++double stdGroup::getCharge()
++{
++ double d = 0.0;
++ if (pMolecule) {
++ std::vector<submolecule*> sList = this->pMolecule->getSubMoleculeList();
++ for (unsigned int p = 0; p < sList.size(); p++) {
++ this->pStdFrag = this->getStdFrag(sList[p]->getName());
++ d += this->pStdFrag->getCharge();
++ //std::cout << this->pStdFrag->getSymbol() << " " << this->pStdFrag->getCharge() << std::endl;
++ }
++ }
++ return d;
++}
++
+ } // MTKpp namespace
+
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdGroup.h amber11/AmberTools/src/mtkpp/src/Molecule/stdGroup.h
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdGroup.h 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Molecule/stdGroup.h 2012-03-03 20:03:01.406032569 +0200
+@@ -160,6 +160,12 @@
+ */
+ molecule* getStdMolecule();
+
++ /*!
++ \brief Get getCharge
++ \return molecule charge
++ */
++ double getCharge();
++
+ protected:
+ //! stdLibrary pointer
+ stdLibrary* pParent;
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/frcmodParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/frcmodParser.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/frcmodParser.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Parsers/frcmodParser.cpp 2012-03-03 20:03:01.407032569 +0200
+@@ -98,6 +98,7 @@
+ while (ifrcmod) {
+ std::string buffer(80,'*');
+ getline(ifrcmod,fileline);
++//std::cout << "|" << fileline << "|" << std::endl;
+ bMASS = false;
+ bBOND = false;
+ bANGLE = false;
+@@ -105,118 +106,311 @@
+ bIMPROPER = false;
+ bNONBON = false;
+
++ if ( (fileline.size() > 0) and (stripString(fileline, " ") != "") ) {
++ std::vector<std::string> splitstring;
++ splitString(fileline, " ", splitstring, 0);
++
++ if (splitstring[0] == "MASS") bMASS = true;
++ if (splitstring[0] == "BOND") bBOND = true;
++ if (splitstring[0] == "ANGL" or splitstring[0] == "ANGLE") bANGLE = true;
++ if (splitstring[0] == "DIHE" or splitstring[0] == "DIHEDRAL") bDIHE = true;
++ if (splitstring[0] == "IMPROP" or splitstring[0] == "IMPROPER") bIMPROPER = true;
++ if (splitstring[0] == "NONB" or splitstring[0] == "NONBON") bNONBON = true;
++ }
++/*
++ try {
+ if (fileline.substr(0,4) == "MASS") bMASS = true;
++ }
++ catch (std::out_of_range) {
++ std::cout << " out_of_range MAS " << std::endl;
++ }
++
++ try {
+ if (fileline.substr(0,4) == "BOND") bBOND = true;
++ }
++ catch (std::out_of_range) {
++ std::cout << " out_of_range BOND " << std::endl;
++ }
++
++ try {
+ if (fileline.substr(0,5) == "ANGLE") bANGLE = true;
++ }
++ catch (std::out_of_range) {
++ std::cout << " out_of_range ANG" << std::endl;
++ }
++
++ try {
+ if (fileline.substr(0,4) == "DIHE") bDIHE = true;
++ }
++ catch (std::out_of_range) {
++ std::cout << " out_of_range DIHE " << std::endl;
++ }
++
++ try {
+ if (fileline.substr(0,8) == "IMPROPER") bIMPROPER = true;
++ }
++ catch (std::out_of_range) {
++ std::cout << " out_of_range IMP " << std::endl;
++ }
++
++ try {
+ if (fileline.substr(0,6) == "NONBON") bNONBON = true;
++ }
++ catch (std::out_of_range) {
++ std::cout << " out_of_range NONB" << std::endl;
++ }
++*/
+
+ if (bMASS) {
+ getline(ifrcmod,fileline);
+- while (fileline != "") {
++ while (stripString(fileline, " ") != "") {
++ //while (GetAlphaChar(fileline, 0) != "0") {
++ std::vector<std::string> splitLine;
++ splitString(fileline, " ", splitLine, 0);
++ if (splitLine.size() >= 2) {
++ for (unsigned int i = 0; i < 2; i++) {
++ splitLine[i] = stripString(splitLine[i], " ");
++ }
+ pAtomType = pParameters->addAtomType();
++ pAtomType->name = splitLine[0];
+ pAtomType->groupName = this->groupName;
+- pAtomType->mass = strtod(fileline.substr(3,5).c_str(), 0);
++ pAtomType->mass = string2Double(splitLine[1]); //strtod(fileline.substr(3,5).c_str(), 0);
++
++ if (splitLine.size() > 2) {
++ char *end;
++ double ret_double = strtod(splitLine[2].c_str(), &end);
++ if (!*end) {
++ pAtomType->atomPolarizability = ret_double;
++ }
++//std::cout << splitLine[2] << " " << ret_double << std::endl;
++ }
++
+ getline(ifrcmod,fileline);
+ }
+ }
++ }
+
+ if (bBOND) {
+ getline(ifrcmod,fileline);
+- while (fileline != "") {
+- std::string atomNames = fileline.substr(0,5);
++ //while (fileline != "") {
++ while (stripString(fileline, " ") != "") {
++ //std::string atomNames = fileline.substr(0,5);
+ std::vector<std::string> splitLine;
+- splitString(atomNames, "-", splitLine, 0);
+- if (splitLine.size() == 2) {
+- for (unsigned int i = 0; i < 2; i++) {
+- splitLine[i] = stripString(splitLine[i]," ");
+- }
++ splitString(fileline, "-", splitLine, 0);
++
++ std::vector<std::string> splitLine2;
++ splitString(splitLine[1], " ", splitLine2, 0);
++
++ //if (splitLine.size() == 2) {
++ //for (unsigned int i = 0; i < 2; i++) {
++ // splitLine[i] = stripString(splitLine[i]," ");
++ //}
+ pBondParam = pParameters->addBondParam();
+ pBondParam->groupName = this->groupName;
+- pBondParam->atomType1 = std::string(splitLine[0]);
+- pBondParam->atomType2 = std::string(splitLine[1]);
+- pBondParam->keq = strtod(fileline.substr(7,5).c_str(), 0);
+- pBondParam->req = strtod(fileline.substr(16,5).c_str(), 0);
++ pBondParam->atomType1 = stripString(splitLine[0], " ");
++ pBondParam->atomType2 = stripString(splitLine2[0], " ");
++//std::cout << "|" << pBondParam->atomType1 << "|" << pBondParam->atomType2 << "|" << std::endl;
++ pBondParam->keq = string2Double(splitLine2[1]);
++ pBondParam->req = string2Double(splitLine2[2]);
++
++// pBondParam->keq = strtod(fileline.substr(7,5).c_str(), 0);
++// pBondParam->req = strtod(fileline.substr(16,5).c_str(), 0);
++
++//std::cout << "\n " << fileline << std::endl;
++//std::cout << " BOND " << pBondParam->atomType1 << " " << pBondParam->atomType2 << " " << pBondParam->keq << " " << pBondParam->req << std::endl;
++//std::cout << " BOND " << fileline.substr(7,5) << " " << fileline.substr(16,5) <<std::endl;
++
+ getline(ifrcmod,fileline);
+- }
++ //}
+ }
+ }
+
+ if (bANGLE) {
+ getline(ifrcmod,fileline);
+- while (fileline != "") {
+- std::string atomNames = fileline.substr(0,8);
++ //while (fileline != "") {
++ while (stripString(fileline, " ") != "") {
++// std::string atomNames = fileline.substr(0,8);
++
+ std::vector<std::string> splitLine;
+- splitString(atomNames, "-", splitLine, 0);
+- if (splitLine.size() == 3) {
+- for (unsigned int i = 0; i < 3; i++) {
+- splitLine[i] = stripString(splitLine[i]," ");
+- }
++ splitString(fileline, "-", splitLine, 0);
++
++ std::vector<std::string> splitLine2;
++ splitString(splitLine[2], " ", splitLine2, 0);
++
++ //std::vector<std::string> splitLine;
++ //splitString(atomNames, "-", splitLine, 0);
++
++ //std::vector<std::string> splitLine2;
++ //splitString(fileline, " ", splitLine2, 0);
++
++ //if (splitLine.size() == 3) {
++ //for (unsigned int i = 0; i < 3; i++) {
++ // splitLine[i] = stripString(splitLine[i]," ");
++ //}
+ pAngleParam = pParameters->addAngleParam();
+ pAngleParam->groupName = this->groupName;
+- pAngleParam->atomType1 = std::string(splitLine[0]);
+- pAngleParam->atomType2 = std::string(splitLine[1]);
+- pAngleParam->atomType3 = std::string(splitLine[2]);
+- pAngleParam->keq = strtod(fileline.substr(11,7).c_str(), 0);
+- pAngleParam->req = strtod(fileline.substr(20,8).c_str(), 0) * DEG2RAD;
++ pAngleParam->atomType1 = stripString(splitLine[0], " ");
++ pAngleParam->atomType2 = stripString(splitLine[1], " ");
++ pAngleParam->atomType3 = stripString(splitLine2[0], " ");
++//std::cout << "|" << pAngleParam->atomType1 << "|" << pAngleParam->atomType2 << "|" << pAngleParam->atomType3 << "|" << std::endl;
++
++ pAngleParam->keq = string2Double(splitLine2[1]);
++ pAngleParam->req = string2Double(splitLine2[2]) * DEG2RAD;
++
++ //pAngleParam->keq = strtod(fileline.substr(11,7).c_str(), 0);
++ //pAngleParam->req = strtod(fileline.substr(20,8).c_str(), 0) * DEG2RAD;
++
++//std::cout << "\n " << fileline << std::endl;
++//std::cout << " ANGLE " << pAngleParam->atomType1 << " " << pAngleParam->atomType2 << " " << pAngleParam->atomType3 << " " << pAngleParam->keq << " " << string2Double(splitLine2[2]) << std::endl;
++
+ getline(ifrcmod,fileline);
+- }
++ //}
+ }
+ }
+
+ if (bDIHE) {
+ getline(ifrcmod,fileline);
+- while (fileline != "") {
+- std::string atomNames = fileline.substr(0,11);
++ //while (fileline != "") {
++ while (stripString(fileline, " ") != "") {
++
++//std::cout << "\n " << fileline << std::endl;
++
++//std::cout << fileline.substr(0,12) << std::endl;
++
++// snip = str.substr(0,12);
++//(3) erase the substring of 0..where str.erase(0,where);
++
++ std::string atTypes = fileline.substr(0,12);
+ std::vector<std::string> splitLine;
+- splitString(atomNames, "-", splitLine, 0);
+- if (splitLine.size() == 4) {
+- for (unsigned int i = 0; i < 4; i++) {
+- splitLine[i] = stripString(splitLine[i]," ");
+- }
++ splitString(atTypes, "-", splitLine, 0);
++
++/*for (unsigned int i = 0; i < splitLine.size(); i++) {
++ std::cout << splitLine[i] << std::endl;
++}*/
++
++ fileline.erase(0,12);
++
++ std::vector<std::string> splitLine2;
++ splitString(fileline, " ", splitLine2, 0);
++/*
++for (unsigned int i = 0; i < splitLine2.size(); i++) {
++ std::cout << splitLine2[i] << std::endl;
++}*/
++
++ //std::string atomNames = fileline.substr(0,11);
++ //std::vector<std::string> splitLine;
++ //splitString(atomNames, "-", splitLine, 0);
++
++ //if (splitLine.size() == 4) {
++ //for (unsigned int i = 0; i < 4; i++) {
++ //splitLine[i] = stripString(splitLine[i], " ");
++ //}
+ pTorsionParam = pParameters->addTorsionParam();
+ pTorsionParam->groupName = this->groupName;
+- pTorsionParam->atomType1 = std::string(splitLine[0]);
+- pTorsionParam->atomType2 = std::string(splitLine[1]);
+- pTorsionParam->atomType3 = std::string(splitLine[2]);
+- pTorsionParam->atomType4 = std::string(splitLine[3]);
+- pTorsionParam->npth = atoi(fileline.substr(11,4).c_str());
+- pTorsionParam->Vn = strtod(fileline.substr(18,8).c_str(), 0);
+- pTorsionParam->gamma = strtod(fileline.substr(31,8).c_str(), 0) * DEG2RAD;
+- pTorsionParam->Nt = strtod(fileline.substr(42,12).c_str(), 0);
++ pTorsionParam->atomType1 = stripString(splitLine[0], " ");
++ pTorsionParam->atomType2 = stripString(splitLine[1], " ");
++ pTorsionParam->atomType3 = stripString(splitLine[2], " ");
++ pTorsionParam->atomType4 = stripString(splitLine[3], " ");
++
++ pTorsionParam->npth = string2Int(splitLine2[0]);
++ pTorsionParam->Vn = string2Double(splitLine2[1]);
++ pTorsionParam->gamma = string2Double(splitLine2[2]) * DEG2RAD;
++ pTorsionParam->Nt = string2Double(splitLine2[3]);
++
++ //pTorsionParam->npth = atoi(fileline.substr(11,4).c_str());
++ //pTorsionParam->Vn = strtod(fileline.substr(18,8).c_str(), 0);
++ //pTorsionParam->gamma = strtod(fileline.substr(31,8).c_str(), 0) * DEG2RAD;
++ //pTorsionParam->Nt = strtod(fileline.substr(42,12).c_str(), 0);
++
++//std::cout << " DIHE " << pTorsionParam->atomType1 << " " << pTorsionParam->atomType2 << " " << pTorsionParam->atomType3 << " " << pTorsionParam->atomType4 << " " << pTorsionParam->npth << " " << pTorsionParam->Vn << " " << string2Double(splitLine2[2]) << " " << pTorsionParam->Nt << std::endl;
++
+ getline(ifrcmod,fileline);
+- }
++//std::cout << " DIHE LINE: " << fileline << std::endl;
++ //}
+ }
+ }
+
+ if (bIMPROPER) {
+ getline(ifrcmod,fileline);
+- while (fileline != "") {
+- std::string atomNames = fileline.substr(0,11);
++ //while (fileline != "") {
++ while (stripString(fileline, " ") != "") {
++
++ std::string atTypes = fileline.substr(0,12);
+ std::vector<std::string> splitLine;
+- splitString(atomNames, "-", splitLine, 0);
+- if (splitLine.size() == 4) {
+- for (unsigned int i = 0; i < 4; i++) {
+- splitLine[i] = stripString(splitLine[i]," ");
+- }
++ splitString(atTypes, "-", splitLine, 0);
++
++ fileline.erase(0,12);
++
++ std::vector<std::string> splitLine2;
++ splitString(fileline, " ", splitLine2, 0);
++
++// std::vector<std::string> splitLine;
++// splitString(fileline, "-", splitLine, 0);
++
++// std::vector<std::string> splitLine2;
++// splitString(splitLine[3], " ", splitLine2, 0);
++
++ //std::string atomNames = fileline.substr(0,11);
++ //std::vector<std::string> splitLine;
++ //splitString(atomNames, "-", splitLine, 0);
++ //if (splitLine.size() == 4) {
++ //for (unsigned int i = 0; i < 4; i++) {
++ //splitLine[i] = stripString(splitLine[i]," ");
++ //}
+ pImproperParam = pParameters->addImproperParam();
+ pImproperParam->groupName = this->groupName;
+- pImproperParam->atomType1 = std::string(splitLine[0]);
+- pImproperParam->atomType2 = std::string(splitLine[1]);
+- pImproperParam->atomType3 = std::string(splitLine[2]);
+- pImproperParam->atomType4 = std::string(splitLine[3]);
+- pImproperParam->Vn = strtod(fileline.substr(18,8).c_str(), 0);
+- pImproperParam->gamma = strtod(fileline.substr(31,8).c_str(), 0) * DEG2RAD;
+- pImproperParam->Nt = strtod(fileline.substr(42,12).c_str(), 0);
++ pImproperParam->atomType1 = stripString(splitLine[0], " ");
++ pImproperParam->atomType2 = stripString(splitLine[1], " ");
++ pImproperParam->atomType3 = stripString(splitLine[2], " ");
++ pImproperParam->atomType4 = stripString(splitLine[3], " ");
++
++ pImproperParam->Vn = string2Double(splitLine2[0]);
++ pImproperParam->gamma = string2Double(splitLine2[1]) * DEG2RAD;
++ pImproperParam->Nt = string2Double(splitLine2[2]);
++
++ //pImproperParam->Vn = strtod(fileline.substr(18,8).c_str(), 0);
++ //pImproperParam->gamma = strtod(fileline.substr(31,8).c_str(), 0) * DEG2RAD;
++ //pImproperParam->Nt = strtod(fileline.substr(42,12).c_str(), 0);
++
++//std::cout << "\n " << fileline << std::endl;
++//std::cout << " IMPR " << pImproperParam->atomType1 << " " << pImproperParam->atomType2 << " " << pImproperParam->atomType3 << " " << pImproperParam->atomType4 << " " << pImproperParam->Vn << " " << string2Double(splitLine2[1]) << " " << pImproperParam->Nt << std::endl;
++
+ getline(ifrcmod,fileline);
+- }
++ //}
+ }
+ }
+ if (bNONBON) {
++ getline(ifrcmod,fileline);
++//std::cout << fileline << std::endl;
++ //while (fileline != "") {
++ while (stripString(fileline, " ") != "") {
++ std::vector<std::string> splitLine;
++ splitString(fileline, " ", splitLine, 0);
++ if (splitLine.size() >= 3) {
++ for (unsigned int i = 0; i < 3; i++) {
++ splitLine[i] = stripString(splitLine[i], " ");
++ }
++//std::cout << " |" << splitLine[0] << "|" << std::endl;
++
++//std::cout << "\n " << fileline << std::endl;
++
++ pAtomType = pParameters->getAtomType(stripString(splitLine[0], " "));
++ if (pAtomType) {
++ pAtomType->rvalue = string2Double(splitLine[1]);
++ pAtomType->evalue = string2Double(splitLine[2]);
+
++//std::cout << pAtomType->name << " " << pAtomType->rvalue << " " << pAtomType->evalue << std::endl;
++
++ }
++ else {
++ std::cout << " Can't find atom type " << std::endl;
++ }
++ getline(ifrcmod,fileline);
++ }
++ }
+ }
+ }
++
+ ifrcmod.close();
+ }
+
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/gaussianParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/gaussianParser.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/gaussianParser.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Parsers/gaussianParser.cpp 2012-03-03 20:03:01.408032569 +0200
+@@ -84,7 +84,7 @@
+
+ this->bMem = 0;
+
+- this->bnProc = 0;
++ this->bNProc = 0;
+
+ this->bWriteInternalCoords = true;
+ this->bWriteCartCoords = false;
+@@ -168,7 +168,7 @@
+ while (igau) {
+ getline(igau,fileline);
+
+- if (containsSubStr(fileline, "modredundant")) {
++ if (containsSubStr(fileline, "ModRedundant")) {
+ bModRedundant = true;
+ }
+ if (fileline.substr(0,59) == " Redundant internal coordinates taken from checkpoint file:") {
+@@ -626,6 +626,7 @@
+ void gaussianParser::Write(const std::string &gaussfile, molecule* pMolecule,
+ std::vector< vector3d > &coordinates)
+ {
++ std::string routecard;
+ std::ofstream ogauss;
+ ogauss.open(gaussfile.c_str());
+
+@@ -643,52 +644,64 @@
+ return;
+ }
+
+- ogauss << "$rungauss" << std::endl;
++ ogauss << "$RunGauss" << std::endl;
+
+ if (bChkPt) {
+- ogauss << "%chk=" << this->itsChkPtFile << std::endl;
++ ogauss << "%Chk=" << this->itsChkPtFile << std::endl;
+ }
+ if (bMem) {
+- ogauss << "%mem=" << this->itsMem << std::endl;
++ ogauss << "%Mem=" << this->itsMem << std::endl;
+ }
+- if (bnProc) {
+- ogauss << "%nproc=" << this->itsnProc << std::endl;
++ if (bNProc) {
++ ogauss << "%NProcShared=" << this->itsNProc << std::endl;
+ }
+
+- ogauss << "#" << this->itsVerbosity << " " << this->itsTheory << "/" << this->itsBasisSet << " ";
++ routecard = "#" + this->itsVerbosity + " " + this->itsTheory + "/" + this->itsBasisSet;
+
+ if (!itsCommandOptions.empty()) {
+ for (mapIterator p = itsCommandOptions.begin(); p != itsCommandOptions.end(); p++) {
+ std::string c = p->first;
+ std::vector<std::string> o = p->second;
++ std::string opts = "";
+ if (o.size() == 1) {
+- if ( p->second[0] == "NONE") {
+- ogauss << p->first << " ";
+- }
+- else {
+- ogauss << p->first << "=" << p->second[0] << " ";
++ if ( p->second[0] != "NONE") {
++ opts = "=" + p->second[0];
+ }
+ }
+ else {
+- ogauss << p->first << "(";
++ opts = "(";
+ for (unsigned int i = 0; i < o.size(); i++) {
+- if (i == o.size()-1) {
+- ogauss << o[i];
++ opts = opts + o[i];
++ if (i != o.size()-1) {
++ opts = opts + ",";
+ }
+- else {
+- ogauss << o[i] << ",";
+ }
++ opts = opts + ")";
+ }
+- ogauss << ")" << " ";
++
++ if (routecard.length() + c.length() + opts.length() < 72) {
++ routecard = routecard + " " + c + opts;
++ } else {
++ if (routecard.length() != 0) {
++ ogauss << routecard << std::endl;
++ }
++ routecard = c + opts;
+ }
+ }
+ }
+ for (unsigned int i = 0; i < this->iops.size(); i++) {
+- ogauss << this->iops[i] << " ";
++ if (routecard.length() + this->iops[i].length() < 72) {
++ routecard = routecard + " " + this->iops[i];
++ } else {
++ if (routecard.length() != 0) {
++ ogauss << routecard << std::endl;
++ }
++ routecard = this->iops[i];
++ }
+ }
+
+ // Flush command block and follow with a blank line
+- ogauss << "\n" << std::endl;
++ ogauss << routecard << "\n" << std::endl;
+
+ // Write name (if required) and follow with a blank line
+ if (bWriteMoleculeName) {
+@@ -740,11 +753,11 @@
+ ogauss << std::endl;
+ }
+
+- std::vector<std::string> optOptions = this->getCommandOption("opt");
++ std::vector<std::string> optOptions = this->getCommandOption("Opt");
+ if (optOptions.size() > 0) {
+ bool bMD = 0;
+ for (unsigned int x = 0; x < optOptions.size(); x++) {
+- if (optOptions[x] == "modredundant") {
++ if (optOptions[x] == "ModRedundant") {
+ bMD = 1;
+ }
+ }
+@@ -766,13 +779,13 @@
+ }
+ }
+
+- if (this->itsBasisSet.substr(0,3) == "GEN") {
++ if (this->itsBasisSet.substr(0,3) == "Gen") {
+ std::ifstream iBSFile;
+ iBSFile.open(this->itsBasisSetFile.c_str());
+
+ if (!iBSFile) {
+ std::cout << "\nERROR!"
+- << "\nBasis set \"GEN\" requires a custom file."
++ << "\nBasis set \"Gen\" requires a custom file."
+ << "\nFile \"" << this->itsBasisSetFile << "\" is missing or unreadable."
+ << "\nPlease choose another file. For instructions, consult your program's"
+ << "\ndocumentation."
+@@ -789,13 +802,13 @@
+ }
+
+ // +BPR
+- if (this->getCommandOption("pseudo").size() > 0) {
++ if (this->getCommandOption("Pseudo").size() > 0) {
+ std::ifstream iPseudoFile;
+ iPseudoFile.open(this->itsPseudoPotentialFile.c_str());
+
+ if (!iPseudoFile) {
+ std::cout << "\nERROR!"
+- << "\npseudo=read or pseudo=cards requires a custom file."
++ << "\nPseudo=Read or Pseudo=Cards requires a custom file."
+ << "\nFile \"" << this->itsPseudoPotentialFile << "\" is missing or unreadable."
+ << "\nPlease choose another file. For instructions, consult your program's"
+ << "\ndocumentation."
+@@ -812,7 +825,7 @@
+ }
+ // -BPR
+
+- if (this->getCommandOption("pop").size() > 0) {
++ if (this->getCommandOption("Pop").size() > 0) {
+ if (!itsMKRadii.empty()) {
+ for (dMapIterator p = itsMKRadii.begin(); p != itsMKRadii.end(); p++) {
+ ogauss << p->first << "=" << p->second << "\n";
+@@ -1037,14 +1050,14 @@
+ }
+
+ // ============================================================
+-// Function : setnProc
++ // Function : setNProc
+ // ------------------------------------------------------------
+ //
+ // ============================================================
+-void gaussianParser::setnProc(const std::string &n)
++ void gaussianParser::setNProc(const std::string &n)
+ {
+- this->bnProc = 1;
+- this->itsnProc = n;
++ this->bNProc = 1;
++ this->itsNProc = n;
+ }
+
+ // ============================================================
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/gaussianParser.h amber11/AmberTools/src/mtkpp/src/Parsers/gaussianParser.h
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/gaussianParser.h 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Parsers/gaussianParser.h 2012-03-03 20:03:01.408032569 +0200
+@@ -196,9 +196,9 @@
+
+ /*!
+ \brief Set number of processors to use
+- \param n nprocs
++ \param n number of processors
+ */
+- void setnProc(const std::string &n);
++ void setNProc(const std::string &n);
+
+ /*!
+ \brief Set level of theory
+@@ -354,10 +354,10 @@
+ bool bMem;
+
+ //! number of processors
+- std::string itsnProc;
++ std::string itsNProc;
+
+- //! Turn on mem
+- bool bnProc;
++ //! Turn on number of processors
++ bool bNProc;
+
+ //! Use internal or cartesian coordinates
+ bool bWriteInternalCoords;
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/Makefile.am amber11/AmberTools/src/mtkpp/src/Parsers/Makefile.am
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/Makefile.am 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Parsers/Makefile.am 2012-03-03 20:03:01.406032569 +0200
+@@ -1,15 +1,15 @@
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics/$(SRCDIR)
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR)
+ DIAGNOSTICS_LIB=-lDiagnostics
+-MOLECULE_LD=-L$(top_builddir)/src/Molecule/$(SRCDIR)
++MOLECULE_LD=-L$(abs_top_builddir)/src/Molecule/$(SRCDIR)
+ MOLECULE_LIB=-lMolecule
+-GA_LD=-L$(top_builddir)/src/GA/$(SRCDIR)
++GA_LD=-L$(abs_top_builddir)/src/GA/$(SRCDIR)
+ GA_LIB=-lGA
+-LOG_LD=-L$(top_builddir)/src/Log/$(SRCDIR)
++LOG_LD=-L$(abs_top_builddir)/src/Log/$(SRCDIR)
+ LOG_LIB=-lLog
+-STATS_LD=-L$(top_builddir)/src/Statistics/$(SRCDIR)
++STATS_LD=-L$(abs_top_builddir)/src/Statistics/$(SRCDIR)
+ STATS_LIB=-lStatistics
+
+-TINYXML_LD=-L$(top_builddir)/src/tinyxml/$(SRCDIR)
++TINYXML_LD=-L$(abs_top_builddir)/src/tinyxml/$(SRCDIR)
+ TINYXML_LIB=-ltinyxml
+
+ if USE_XERCES
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/Makefile.in amber11/AmberTools/src/mtkpp/src/Parsers/Makefile.in
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/Makefile.in 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Parsers/Makefile.in 2012-03-03 20:03:01.407032569 +0200
+@@ -267,17 +267,17 @@
+ top_builddir = @top_builddir@
+ top_srcdir = @top_srcdir@
+ xerces_path = @xerces_path@
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics/$(SRCDIR)
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR)
+ DIAGNOSTICS_LIB = -lDiagnostics
+-MOLECULE_LD = -L$(top_builddir)/src/Molecule/$(SRCDIR)
++MOLECULE_LD = -L$(abs_top_builddir)/src/Molecule/$(SRCDIR)
+ MOLECULE_LIB = -lMolecule
+-GA_LD = -L$(top_builddir)/src/GA/$(SRCDIR)
++GA_LD = -L$(abs_top_builddir)/src/GA/$(SRCDIR)
+ GA_LIB = -lGA
+-LOG_LD = -L$(top_builddir)/src/Log/$(SRCDIR)
++LOG_LD = -L$(abs_top_builddir)/src/Log/$(SRCDIR)
+ LOG_LIB = -lLog
+-STATS_LD = -L$(top_builddir)/src/Statistics/$(SRCDIR)
++STATS_LD = -L$(abs_top_builddir)/src/Statistics/$(SRCDIR)
+ STATS_LIB = -lStatistics
+-TINYXML_LD = -L$(top_builddir)/src/tinyxml/$(SRCDIR)
++TINYXML_LD = -L$(abs_top_builddir)/src/tinyxml/$(SRCDIR)
+ TINYXML_LIB = -ltinyxml
+ @USE_XERCES_TRUE@XERCES_LD = -L@xerces_path@/lib/
+ @USE_XERCES_TRUE@XERCES_LIB = -lxerces-c
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/mtkppParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/mtkppParser.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/mtkppParser.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Parsers/mtkppParser.cpp 2012-03-03 20:03:01.409032568 +0200
+@@ -1769,6 +1769,15 @@
+ atomElem->SetAttribute("type", int2String(pAtom->getType()));
+ atomElem->SetAttribute("formalCharge", int2String(pAtom->getFormalCharge()));
+
++ // Coordinates
++ TiXmlElement* coordElem = new TiXmlElement("coord");
++ atomElem->LinkEndChild(coordElem);
++
++ coordElem->SetAttribute("x", double2String(pAtom->getX()));
++ coordElem->SetAttribute("y", double2String(pAtom->getY()));
++ coordElem->SetAttribute("z", double2String(pAtom->getZ()));
++
++ // Properties
+ std::map<std::string, double> atomDMap = pAtom->getPropertyMap();
+ std::map<std::string, int> atomIMap = pAtom->getIntPropertyMap();
+
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/paramParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/paramParser.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/paramParser.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Parsers/paramParser.cpp 2012-03-03 20:03:01.410032567 +0200
+@@ -144,6 +144,10 @@
+ pAtomType->evalue = string2Double(element->Attribute("potentialWellDepth"));
+ }
+
++ if (element->Attribute("atomPolarizability")) {
++ pAtomType->atomPolarizability = string2Double(element->Attribute("atomPolarizability"));
++ }
++
+ if (element->Attribute("element")) {
+ pAtomType->element = element->Attribute("element");
+ }
+@@ -1808,6 +1812,7 @@
+ entry->SetAttribute("mass" , double2String(pAtomType->mass).c_str());
+ entry->SetAttribute("vdwRadius" , double2String(pAtomType->rvalue).c_str());
+ entry->SetAttribute("potentialWellDepth" , double2String(pAtomType->evalue).c_str());
++ entry->SetAttribute("atomPolarizability" , double2String(pAtomType->atomPolarizability).c_str());
+ entry->SetAttribute("element" , pAtomType->element);
+ entry->SetAttribute("hybridization" , pAtomType->hybridization);
+ entry->SetAttribute("groupName" , pAtomType->groupName);
+@@ -2035,6 +2040,7 @@
+ typeElem->setAttribute(X("mass"), X(double2String(pAtomType->mass).c_str()));
+ typeElem->setAttribute(X("vdwRadius"), X(double2String(pAtomType->rvalue).c_str()));
+ typeElem->setAttribute(X("potentialWellDepth"), X(double2String(pAtomType->evalue).c_str()));
++ typeElem->setAttribute(X("atomPolarizability"), X(double2String(pAtomType->atomPolarizability).c_str()));
+ typeElem->setAttribute(X("element"), X(pAtomType->element.c_str()));
+ typeElem->setAttribute(X("hybridization"), X(pAtomType->hybridization.c_str()));
+ typeElem->setAttribute(X("groupName"), X(pAtomType->groupName.c_str()));
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/pdbParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/pdbParser.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/pdbParser.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Parsers/pdbParser.cpp 2012-03-03 20:03:01.410032567 +0200
+@@ -840,6 +840,7 @@
+ for (atomIterator a = atomList.begin(); a != atomList.end(); a++) {
+ pAtom = *a;
+ pSubMolecule = pAtom->getParent();
++ //std::cout << pSubMolecule->getColIndex() << std::endl;
+ char temp[100];
+
+ char tmp_element[3];
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/prepParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/prepParser.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/prepParser.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Parsers/prepParser.cpp 2012-03-03 20:03:01.411032567 +0200
+@@ -66,71 +66,106 @@
+ prepParser::~prepParser() {}
+
+ // =========================================================
+-// Function : Read
+-// ---------------------------------------------------------
+-// parsers a prep file
+-// ---------------------------------------------------------
+-// Format :
+-// =========================================================
+-void prepParser::Read(const std::string &prepfile, stdGroup* pStdGroup)
+-{
+- std::string errorMessage = " Reading " + prepfile + " " +
+- pStdGroup->getName() + " ... implement ";
+- errorLogger.throwError("prepParser", errorMessage, 1);
+-}
+-
+-// =========================================================
+-// Function : Read
++// Function : openFile
+ // ---------------------------------------------------------
+-// parsers a prep file
++// open a prep file
+ // ---------------------------------------------------------
+ // Format :
+ // =========================================================
+-void prepParser::Read(const std::string &prepfile, stdFrag* pStdFrag)
++int prepParser::openFile(const std::string &prepfile)
+ {
+- errorLogger.throwError("prepParser", "Read", INFO);
+-
+- std::ifstream iprep;
+ iprep.open(prepfile.c_str());
+
++ //std::cout << "\n\n prepParser::openFile " << prepfile << std::endl;
+ if (!iprep) {
+ setError(1);
+ std::string errorMessage = " Error, Can't Find " + prepfile;
+ setErrorMessage(errorMessage);
+ errorLogger.throwError("prepParser::Read", errorMessage, 1);
+- return;
++ return 1;
+ }
+
+ std::string fileline;
+- std::string title;
+- std::string atom;
+- std::string buffer(80,'*');
+
+ // SKIP FIRST TWO LINES
+ getline(iprep,fileline);
+ getline(iprep,fileline);
++
++ return 0;
++}
++
++// =========================================================
++// Function : read fragment header section
++// ---------------------------------------------------------
++//
++// ---------------------------------------------------------
++// Format :
++// =========================================================
++int prepParser::readHeader(std::string &name, std::string &symbol, double &charge)
++{
++ std::string fileline;
++
+ getline(iprep,fileline);
+- //std::string name = stripString(fileline," ");
+- //pStdFrag->setName(fileline);
++ if (stripString(fileline, " ") == "STOP") return 1;
++
++ name = stripString(fileline," ");
++
++ // blank line
+ getline(iprep,fileline);
++
++ // symbol
+ getline(iprep,fileline);
+ std::vector<std::string> splitLine;
+ splitString(fileline, " ", splitLine, 0);
+- pStdFrag->setSymbol(splitLine[0]);
++ symbol = splitLine[0];
++
++ //
+ getline(iprep,fileline);
++
++ // charge
+ getline(iprep,fileline);
+- //pStdFrag->setCharge(splitLine[0]);
++ charge = string2Double(stripString(fileline, " "));
++
++ return 0;
++}
++
++// =========================================================
++// Function : read fragment main section
++// ---------------------------------------------------------
++//
++// ---------------------------------------------------------
++// Format :
++// =========================================================
++void prepParser::readFragment(stdFrag* pStdFrag)
++{
++ std::string fileline;
++
++ std::vector<stdBond*> todos;
+
+ while (iprep) {
+ getline(iprep,fileline);
+- if (fileline == "") break;
++
++ std::string filelineTest = stripString(fileline, " ");
++ if (filelineTest == "") break;
++
++//std::cout << "|" << fileline << "|" << std::endl;
+
+ std::vector<std::string> splitstring;
+ splitString(fileline, " ", splitstring, 0);
+ if (atoi(splitstring[0].c_str()) > 3) {
+ stdAtom* pStdAtom = pStdFrag->addStdAtom();
+ int atIndex = atoi(splitstring[0].c_str()) - 3;
+- std::string atomName = fileline.substr(6,4);
++
++////////
++ //std::string atomName = fileline.substr(6,4);
++ std::string atomName = splitstring[1];
++ if (atomName.size() == 1) atomName = " " + atomName + " ";
++ else if (atomName.size() == 2) atomName = " " + atomName + " ";
++ else if (atomName.size() == 3) atomName = " " + atomName;
++
++//std::cout << "|" << atomName << "|" << std::endl;
++/////////
++
+ std::string atomType = splitstring[2];
+ std::string atomChain = splitstring[3];
+
+@@ -170,32 +205,54 @@
+ pStdBond->atom1 = pStdAtom->index;
+ pStdBond->atom2 = pStdAtom->bond12;
+ pStdBond->type = 1;
++
+ if (pStdAtom->atSymbol == "H") {
+ if (pStdAtom->bond12 > 0) {
+ stdAtom* pStdBondedAtom = pStdFrag->getStdAtom(pStdAtom->bond12);
++
++ if (pStdBondedAtom) {
+ std::string bondedAtomSymbol = pStdBondedAtom->atSymbol;
+ if (bondedAtomSymbol == "N" or bondedAtomSymbol == "O" or bondedAtomSymbol == "S") {
+ pStdBond->kind = 1;
+ }
+ }
++ else {
++ todos.push_back(pStdBond);
++ }
++ }
+ }
+ else {
+ pStdBond->kind = 0;
+ }
++
+ pStdBond->topology = 2;
+ pStdBond->stereo = 0;
+ pStdBond->length = pStdAtom->bondLength;
+ }
+ }
+
++ for (unsigned int x = 0; x < todos.size(); x++) {
++ stdAtom* pStdBondedAtom1 = pStdFrag->getStdAtom(todos[x]->atom1);
++ stdAtom* pStdBondedAtom2 = pStdFrag->getStdAtom(todos[x]->atom2);
++ if (pStdBondedAtom1 and pStdBondedAtom2) {
++ std::string bondedAtomSymbol = pStdBondedAtom2->atSymbol;
++ if (bondedAtomSymbol == "N" or bondedAtomSymbol == "O" or bondedAtomSymbol == "S") {
++ todos[x]->kind = 1;
++ }
++ }
++ }
++
+ // Read charge, alias, loop, and improper data
+ while (iprep) {
+ getline(iprep,fileline);
++//std::cout << "!" << fileline << "!" << std::endl;
+ if (fileline != "") {
+ if (fileline.substr(0,6) == "CHARGE") {
+ while (iprep) {
+ getline(iprep,fileline);
+- if (fileline == "") break;
++
++ std::string filelineTest = stripString(fileline, " ");
++ if (filelineTest == "") break;
+ }
+ }
+ else if (fileline.substr(0,5) == "ALIAS") {
+@@ -252,7 +309,7 @@
+ else {
+ std::string errorMessage = " ALIAS Tag Error ... exiting ";
+ errorLogger.throwError("prepParser::Read", errorMessage, 1);
+- //exit(0);
++
+ std::stringstream ss;
+ ss << "prepParser::Read"<< errorMessage;
+ throw MTKException(ss.str());
+@@ -263,11 +320,20 @@
+ else if (fileline.substr(0,4) == "LOOP") {
+ while (iprep) {
+ getline(iprep,fileline);
+- if (fileline == "") break;
++
++ std::string filelineTest = stripString(fileline, " ");
++ if (filelineTest == "") break;
++
++ //if (fileline == "") break;
+
+ std::vector<std::string> atomNames;
+ splitString(fileline, " ", atomNames, 0);
+-
++/*
++for (unsigned int x = 0; x <atomNames.size();x++){
++ std::cout << atomNames[x] <<std::endl;
++}
++pStdFrag->print();
++*/
+ std::vector< std::vector<std::string> > possibleNames;
+ for (int d = 0; d < 2; d++) {
+ int atNameSize = atomNames[d].size();
+@@ -315,17 +381,22 @@
+ else {
+ std::string errorMessage = " LOOP Tag Error ... exiting ";
+ errorLogger.throwError("prepParser::Read", errorMessage, 1);
+- //exit(0);
+-
+ std::stringstream ss;
+ ss << "prepParser::Read"<< errorMessage;
+ throw MTKException(ss.str());
+ }
+ }
+ }
++ else if (fileline.substr(0,4) == "DONE") {
++ break;
++ }
+ else if (fileline.substr(0,8) == "IMPROPER") {
+ while (iprep) {
+ getline(iprep,fileline);
++
++ std::string filelineTest = stripString(fileline, " ");
++ if (filelineTest == "") break;
++
+ if (fileline == "") break;
+
+ std::vector<std::string> atomNames;
+@@ -424,7 +495,6 @@
+ else {
+ std::string errorMessage = " IMPROPER Tag Error ... exiting ";
+ errorLogger.throwError("prepParser::Read", errorMessage, 1);
+- //exit(0);
+
+ std::stringstream ss;
+ ss << "prepParser::Read" << errorMessage;
+@@ -642,8 +712,112 @@
+ }
+ // QBio end
+ }
+-
+ errorLogger.throwError("prepParser::Read", eMessage, INFO);
++}
++
++// =========================================================
++// Function : Read
++// ---------------------------------------------------------
++// parsers a prep file
++// ---------------------------------------------------------
++// Format :
++// =========================================================
++void prepParser::Read(const std::string &prepfile, stdGroup* pStdGroup)
++{
++ int r = openFile(prepfile);
++ if (r == 1) return;
++
++ while(iprep) {
++ std::string name = "";
++ std::string symbol = "";
++ double charge = 0.0;
++ int h = readHeader(name, symbol, charge);
++ if (h == 1) break;
++
++ stdFrag* pStdFrag = pStdGroup->addStdFrag();
++ if (!pStdFrag) {
++ setError(1);
++ std::string errorMessage = " Error creating fragment ";
++ setErrorMessage(errorMessage);
++ errorLogger.throwError("prepParser::Read", errorMessage, 1);
++ return;
++ }
++
++ if (symbol.size() == 1) symbol = symbol + " ";
++ if (symbol.size() == 2) symbol = symbol + " ";
++ if (symbol.size() > 3) symbol = symbol.substr(1,3);
++
++ pStdFrag->setSymbol(symbol); // 3L code
++ //pStdFrag->setCode("P2XML"+name); // 8L code
++ pStdFrag->setName(name); // long name
++ pStdFrag->setType("m"); // fragment type
++
++ //std::cout << " prepParser::Read " << name << " charge " << charge << " symbol " << symbol << std::endl;
++ readFragment(pStdFrag);
++ }
++
++ iprep.close();
++
++ return;
++}
++
++// =========================================================
++// Function : Read
++// ---------------------------------------------------------
++// parsers a prep file
++// ---------------------------------------------------------
++// Format :
++// =========================================================
++void prepParser::Read(const std::string &prepfile, stdFrag* pStdFrag)
++{
++ errorLogger.throwError("prepParser", "Read", INFO);
++/*
++ std::ifstream iprep;
++ iprep.open(prepfile.c_str());
++
++ if (!iprep) {
++ setError(1);
++ std::string errorMessage = " Error, Can't Find " + prepfile;
++ setErrorMessage(errorMessage);
++ errorLogger.throwError("prepParser::Read", errorMessage, 1);
++ return;
++ }
++*/
++
++ int r = openFile(prepfile);
++ if (r == 1) return;
++
++ std::string fileline;
++ std::string title;
++ std::string atom;
++ //std::string buffer(80,'*');
++
++ // SKIP FIRST TWO LINES
++ //getline(iprep,fileline);
++ //getline(iprep,fileline);
++
++/*
++ getline(iprep,fileline);
++ //std::string name = stripString(fileline," ");
++ //pStdFrag->setName(fileline);
++ getline(iprep,fileline);
++ getline(iprep,fileline);
++ std::vector<std::string> splitLine;
++ splitString(fileline, " ", splitLine, 0);
++ pStdFrag->setSymbol(splitLine[0]);
++ getline(iprep,fileline);
++ getline(iprep,fileline);
++ //pStdFrag->setCharge(splitLine[0]);
++*/
++
++ std::string name = "";
++ std::string symbol = "";
++ double charge = 0.0;
++ readHeader(name, symbol, charge);
++
++ pStdFrag->setSymbol(symbol);
++
++ readFragment(pStdFrag);
+
+ iprep.close();
+ }
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/prepParser.h amber11/AmberTools/src/mtkpp/src/Parsers/prepParser.h
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/prepParser.h 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Parsers/prepParser.h 2012-03-03 20:03:01.411032567 +0200
+@@ -89,6 +89,25 @@
+ ~prepParser();
+
+ /*!
++ \brief open prep file
++ \param i input file
++ */
++ int openFile(const std::string &i);
++
++ /*!
++ \brief read fragment header section
++ \param name fragment name
++ \param symbol fragment symbol
++ \param charge fragment charge
++ */
++ int readHeader(std::string &name, std::string &symbol, double &charge);
++
++ /*!
++ \brief read fragment main section
++ */
++ void readFragment(stdFrag* pStdFrag);
++
++ /*!
+ \brief Read prep file
+ \param i input file
+ \param g stdGroup pointer
+@@ -127,6 +146,9 @@
+
+ //! atom pointer
+ atom* pAtom;
++
++ //! file handler
++ std::ifstream iprep;
+ };
+
+ } // MTKpp namespace
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/stdLibParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/stdLibParser.cpp
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/stdLibParser.cpp 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Parsers/stdLibParser.cpp 2012-03-03 20:03:01.412032567 +0200
+@@ -3280,7 +3280,7 @@
+ // ------------------------------------------------------------
+ // Write xml files using tinyxml
+ // ------------------------------------------------------------
+-void stdLibParser::Write(std::string fileName)
++void stdLibParser::Write(std::string fileName) // TinyXML
+ {
+ std::string errMessage = " Writing " + fileName;
+ errorLogger.throwError("stdLibParser", errMessage, INFO);
+@@ -3512,6 +3512,7 @@
+ TiXmlElement* impElem = new TiXmlElement("improper");
+ frag->LinkEndChild(impElem);
+
++ /*
+ if (improperList[k]->atom1 == -1) {
+ impElem->SetAttribute("Atom1", "p1");
+ }
+@@ -3520,7 +3521,8 @@
+ }
+ else {
+ impElem->SetAttribute("Atom1", int2String(improperList[k]->atom1));
+- }
++ }*/
++ impElem->SetAttribute("Atom1", int2String(improperList[k]->atom1));
+ impElem->SetAttribute("Atom2", int2String(improperList[k]->atom2));
+ impElem->SetAttribute("Atom3", int2String(improperList[k]->atom3));
+ impElem->SetAttribute("Atom4", int2String(improperList[k]->atom4));
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Statistics/Makefile.am amber11/AmberTools/src/mtkpp/src/Statistics/Makefile.am
+--- amber11.orig/AmberTools/src/mtkpp/src/Statistics/Makefile.am 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Statistics/Makefile.am 2012-03-03 20:03:01.413032567 +0200
+@@ -1,4 +1,4 @@
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics/$(SRCDIR)
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR)
+ DIAGNOSTICS_LIB=-lDiagnostics
+
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/.. -I$(top_srcdir)/src/eigen3b2
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Statistics/Makefile.in amber11/AmberTools/src/mtkpp/src/Statistics/Makefile.in
+--- amber11.orig/AmberTools/src/mtkpp/src/Statistics/Makefile.in 2011-04-14 15:30:18.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/src/Statistics/Makefile.in 2012-03-03 20:03:01.413032567 +0200
+@@ -241,7 +241,7 @@
+ top_builddir = @top_builddir@
+ top_srcdir = @top_srcdir@
+ xerces_path = @xerces_path@
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics/$(SRCDIR)
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR)
+ DIAGNOSTICS_LIB = -lDiagnostics
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/.. -I$(top_srcdir)/src/eigen3b2
+ lib_LTLIBRARIES = libStatistics.la
+diff -urN amber11.orig/AmberTools/src/mtkpp/tests/Makefile.am amber11/AmberTools/src/mtkpp/tests/Makefile.am
+--- amber11.orig/AmberTools/src/mtkpp/tests/Makefile.am 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/tests/Makefile.am 2012-03-03 20:03:01.414032567 +0200
+@@ -42,25 +42,25 @@
+ LAPACK_LIB=-llapack -lblas -lg2c
+ endif
+
+-MOLECULE_LD=-L$(top_builddir)/src/Molecule
++MOLECULE_LD=-L$(abs_top_builddir)/src/Molecule
+ MOLECULE_LIB=-lMolecule
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics
+ DIAGNOSTICS_LIB=-lDiagnostics
+-LOG_LD=-L$(top_builddir)/src/Log
++LOG_LD=-L$(abs_top_builddir)/src/Log
+ LOG_LIB=-lLog
+-GRAPH_LD=-L$(top_builddir)/src/Graph
++GRAPH_LD=-L$(abs_top_builddir)/src/Graph
+ GRAPH_LIB=-lGraph
+-GA_LD=-L$(top_builddir)/src/GA
++GA_LD=-L$(abs_top_builddir)/src/GA
+ GA_LIB=-lGA
+-MM_LD=-L$(top_builddir)/src/MM
++MM_LD=-L$(abs_top_builddir)/src/MM
+ MM_LIB=-lMM
+-MINIMIZERS_LD=-L$(top_builddir)/src/Minimizers
++MINIMIZERS_LD=-L$(abs_top_builddir)/src/Minimizers
+ MINIMIZERS_LIB=-lMinimizers
+-PARSERS_LD=-L$(top_builddir)/src/Parsers
++PARSERS_LD=-L$(abs_top_builddir)/src/Parsers
+ PARSERS_LIB=-lParsers
+-STATS_LD=-L$(top_builddir)/src/Statistics
++STATS_LD=-L$(abs_top_builddir)/src/Statistics
+ STATS_LIB=-lStatistics
+-TINYXML_LD=-L$(top_builddir)/src/tinyxml
++TINYXML_LD=-L$(abs_top_builddir)/src/tinyxml
+ TINYXML_LIB=-ltinyxml
+
+ # INCLUDES = -I@boost_inc@ -I@xerces_path@/include -I$(top_srcdir)/src -I$(top_srcdir)/include -I$(top_srcdir)/src/tinyxml -I$(top_srcdir)/src/Parsers -I$(top_srcdir)/src/Molecule -I$(top_srcdir)/src/Statistics -I$(top_srcdir)/src/Utils $(tmpQT_INCPATH)
+diff -urN amber11.orig/AmberTools/src/mtkpp/tests/Makefile.in amber11/AmberTools/src/mtkpp/tests/Makefile.in
+--- amber11.orig/AmberTools/src/mtkpp/tests/Makefile.in 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/tests/Makefile.in 2012-03-03 20:03:01.414032567 +0200
+@@ -303,25 +303,25 @@
+ @USE_QT_TRUE@tmpQT_LIBS = $(QT_LIBS)
+ @IS_LINUX_TRUE@LAPACK_LD = -L/usr/lib64
+ @IS_LINUX_TRUE@LAPACK_LIB = -llapack -lblas -lg2c
+-MOLECULE_LD = -L$(top_builddir)/src/Molecule
++MOLECULE_LD = -L$(abs_top_builddir)/src/Molecule
+ MOLECULE_LIB = -lMolecule
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics
+ DIAGNOSTICS_LIB = -lDiagnostics
+-LOG_LD = -L$(top_builddir)/src/Log
++LOG_LD = -L$(abs_top_builddir)/src/Log
+ LOG_LIB = -lLog
+-GRAPH_LD = -L$(top_builddir)/src/Graph
++GRAPH_LD = -L$(abs_top_builddir)/src/Graph
+ GRAPH_LIB = -lGraph
+-GA_LD = -L$(top_builddir)/src/GA
++GA_LD = -L$(abs_top_builddir)/src/GA
+ GA_LIB = -lGA
+-MM_LD = -L$(top_builddir)/src/MM
++MM_LD = -L$(abs_top_builddir)/src/MM
+ MM_LIB = -lMM
+-MINIMIZERS_LD = -L$(top_builddir)/src/Minimizers
++MINIMIZERS_LD = -L$(abs_top_builddir)/src/Minimizers
+ MINIMIZERS_LIB = -lMinimizers
+-PARSERS_LD = -L$(top_builddir)/src/Parsers
++PARSERS_LD = -L$(abs_top_builddir)/src/Parsers
+ PARSERS_LIB = -lParsers
+-STATS_LD = -L$(top_builddir)/src/Statistics
++STATS_LD = -L$(abs_top_builddir)/src/Statistics
+ STATS_LIB = -lStatistics
+-TINYXML_LD = -L$(top_builddir)/src/tinyxml
++TINYXML_LD = -L$(abs_top_builddir)/src/tinyxml
+ TINYXML_LIB = -ltinyxml
+
+ # INCLUDES = -I@boost_inc@ -I@xerces_path@/include -I$(top_srcdir)/src -I$(top_srcdir)/include -I$(top_srcdir)/src/tinyxml -I$(top_srcdir)/src/Parsers -I$(top_srcdir)/src/Molecule -I$(top_srcdir)/src/Statistics -I$(top_srcdir)/src/Utils $(tmpQT_INCPATH)
+diff -urN amber11.orig/AmberTools/src/mtkpp/tools/Makefile.am amber11/AmberTools/src/mtkpp/tools/Makefile.am
+--- amber11.orig/AmberTools/src/mtkpp/tools/Makefile.am 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/tools/Makefile.am 2012-03-03 20:03:01.417032565 +0200
+@@ -25,7 +25,7 @@
+ tmpQT_LIBS = $(QT_LIBS)
+ endif
+
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics
+ DIAGNOSTICS_LIB = -lDiagnostics
+ MOLECULE_LD = -L$(top_builddir)/src/Molecule
+ MOLECULE_LIB = -lMolecule
+diff -urN amber11.orig/AmberTools/src/mtkpp/tools/Makefile.in amber11/AmberTools/src/mtkpp/tools/Makefile.in
+--- amber11.orig/AmberTools/src/mtkpp/tools/Makefile.in 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/tools/Makefile.in 2012-03-03 20:03:01.417032565 +0200
+@@ -392,7 +392,7 @@
+ @USE_XERCES_TRUE@XERCES_LIB = -lxerces-c
+ @USE_QT_TRUE@tmpQT_INCPATH = $(QT_INCPATH)
+ @USE_QT_TRUE@tmpQT_LIBS = $(QT_LIBS)
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics
+ DIAGNOSTICS_LIB = -lDiagnostics
+ MOLECULE_LD = -L$(top_builddir)/src/Molecule
+ MOLECULE_LIB = -lMolecule
+diff -urN amber11.orig/AmberTools/src/mtkpp/tools/MCPB.cpp amber11/AmberTools/src/mtkpp/tools/MCPB.cpp
+--- amber11.orig/AmberTools/src/mtkpp/tools/MCPB.cpp 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/tools/MCPB.cpp 2012-03-03 20:03:01.416032566 +0200
+@@ -67,6 +67,7 @@
+ #include "Parsers/mtkppParser.h"
+ #include "Parsers/dMParser.h"
+ #include "Parsers/commLineOptions.h"
++#include "Parsers/StringManip.h"
+
+ // - Log
+ #include "Log/errorHandler.h"
+@@ -84,6 +85,12 @@
+
+ using namespace MTKpp;
+
++std::string getEnvVar(std::string const& key)
++{
++ char const* val = getenv(key.c_str());
++ return val == NULL ? std::string() : std::string(val);
++}
++
+ void printFunctionList()
+ {
+ std::string functionList = "\n MCPB Functions:\n";
+@@ -181,32 +188,32 @@
+ functionList += " Find all metal centers in the collection\n";
+ functionList += " syntax: findMetalCenters\n";
+ functionList += "\n";
+- functionList += " g03Charges\n";
++ functionList += " gaussianCharges\n";
+ functionList += " Generate a Gaussian input file for partial-charge computation\n";
+ functionList += " Optional: set the Gaussian job file name\n";
+- functionList += " syntax: g03Charges //cuCYM4 cuCYM4.com\n";
++ functionList += " syntax: gaussianCharges //cuCYM4 cuCYM4.com\n";
+ functionList += "\n";
+- functionList += " g03Mem\n";
+- functionList += " Set amount of memory requested for g03\n";
+- functionList += " syntax: g03Mem 3600MB\n";
++ functionList += " gaussianMem\n";
++ functionList += " Set amount of memory requested for Gaussian\n";
++ functionList += " syntax: gaussianMem 3600MB\n";
+ functionList += "\n";
+- functionList += " g03MoldenFormat\n";
++ functionList += " gaussianMoldenFormat\n";
+ functionList += " Request Gaussian log files formatted for viewing in Molden\n";
+- functionList += " (adds the GFINPUT and IOP(6/7=3) keywords)\n";
+- functionList += " syntax: g03MoldenFormat\n";
++ functionList += " (adds the GFInput and IOp(6/7=3) keywords)\n";
++ functionList += " syntax: gaussianMoldenFormat\n";
+ functionList += "\n";
+- functionList += " g03nProc\n";
+- functionList += " Set number of processors requested for g03\n";
+- functionList += " syntax: g03nProc 2\n";
++ functionList += " gaussianNProc\n";
++ functionList += " Set number of processors requested for Gaussian\n";
++ functionList += " syntax: gaussianNProc 2\n";
+ functionList += "\n";
+- functionList += " g03OptAndFC\n";
++ functionList += " gaussianOptAndFC\n";
+ functionList += " Generate Gaussian input files for optimisation and force constants\n";
+ functionList += " Optional: set the Gaussian job file name\n";
+- functionList += " syntax: g03OptAndFC //cuCYM4 cuCYM4.com\n";
++ functionList += " syntax: gaussianOptAndFC //cuCYM4 cuCYM4.com\n";
+ functionList += "\n";
+- functionList += " g03Verbosity\n";
++ functionList += " gaussianVerbosity\n";
+ functionList += " Set the verbosity of Gaussian output ([T]erse, [N]ormal, [P]rolix)\n";
+- functionList += " syntax: g03Verbosity [T|N|P]\n";
++ functionList += " syntax: gaussianVerbosity [T|N|P]\n";
+ functionList += "\n";
+ functionList += " levelOfTheory\n";
+ functionList += " Set Gaussian Theory Level\n";
+@@ -256,9 +263,9 @@
+ functionList += " Read Formatted Checkpoint file\n";
+ functionList += " syntax: readFormattedChkPtFile file.fchk\n";
+ functionList += "\n";
+- functionList += " readG03Output\n";
+- functionList += " Read G03 Output\n";
+- functionList += " syntax: readG03Output cuCYM4.log\n";
++ functionList += " readGaussianOutput\n";
++ functionList += " Read Gaussian Output\n";
++ functionList += " syntax: readGaussianOutput cuCYM4.log\n";
+ functionList += "\n";
+ functionList += " readMolZmatMapping\n";
+ functionList += " Read Molecule <--> Z-Matrix mapping file\n";
+@@ -470,7 +477,7 @@
+ else {
+ printHeader(std::cout, prog_name, authors);
+ clo->printUsage();
+- std::cout << " Please provide a MCPB file " << std::endl;
++ std::cout << " Please provide an MCPB file " << std::endl;
+ return 0;
+ }
+
+@@ -515,7 +522,9 @@
+ std::string errorMessage = "";
+
+ std::vector<std::vector<std::string> > inputFileContents;
++
+ int failure = readInputFile(inputFile, inputFileContents);
++
+ if (failure) {
+ printHeader(std::cout, prog_name, authors);
+ clo->printUsage();
+@@ -660,7 +669,7 @@
+ std::vector<std::vector<std::string> > sourceInputFileContents;
+ failure = readInputFile(cur[1], sourceInputFileContents);
+ if (failure) {
+- errorMessage = " Error Reading File " + cur[1];
++ errorMessage = " Error reading file " + cur[1];
+ MTKpp::errorLogger.throwError("MCPB::source", errorMessage, 1);
+ exit(1);
+ }
+@@ -668,7 +677,7 @@
+ sourceInputFileContents.end());
+ }
+ else {
+- errorMessage = " Error Reading File " + cur[1];
++ errorMessage = " Error reading file " + cur[1];
+ MTKpp::errorLogger.throwError("MCPB::source", errorMessage, 1);
+ exit(1);
+ }
+@@ -742,6 +751,20 @@
+ \endcode
+ */
+ if ((inputFileContents[i].size() == 3)) {
++ //std::cout << "SET COMMAND " << inputFileContents[i][2] << std::endl;
++ if (inputFileContents[i][2].compare(0,1,"$") == 0) {
++ std::string envVariable = "";
++ std::string tVar = inputFileContents[i][2];
++ envVariable = getEnvVar(tVar.substr(1,tVar.size()-1));
++ if (envVariable == "") {
++ std::cout << " Environment variable " << tVar.substr(1,tVar.size()-1)
++ << " is unset " << std::endl;
++ exit(1);
++ }
++ //std::cout << "Environment variable = " << envVariable << std::endl;
++ inputFileContents[i][2] = envVariable;
++ }
++
+ variableMap[inputFileContents[i][1]] = inputFileContents[i][2];
+ for (unsigned int j = i+1; j < inputFileContents.size(); j++) {
+ bool bReplaced = false;
+@@ -813,6 +836,115 @@
+ }
+ }
+
++ else if (inputFileContents[i][0] == "printGroupCharge") {
++ /*!
++ @ingroup MCPB_commands
++ \code
++ Function: printFrag
++
++ Description: Print fragment details
++
++ syntax: printGroupCharge Zn-CCCC
++
++ \endcode
++ */
++ if ((inputFileContents[i].size() != 2) or (!pCollection)) {
++ MTKpp::errorLogger.throwError("MCPB::printGroupCharge", " Incorrect use of printGroupCharge ... exiting", MTK_ERROR);
++ exit(1);
++ }
++ else {
++ stdLibrary* pStdLibrary = pCollection->getStdLibrary();
++ if (pStdLibrary) {
++ stdGroup* pStdGroup = pStdLibrary->getStdGroup(inputFileContents[i][1]);
++ std::cout << " Group " << pStdGroup->getName() << "\n";
++ if (pStdGroup) {
++ molecule* pM = pStdGroup->getStdMolecule();
++ if (pM) {
++ double groupCharge = 0.0;
++ std::vector<submolecule*> pSM = pM->getSubMoleculeList();
++ //std::cout << " Number of submolecules = " << pSM.size() << "\n";
++ for (unsigned int x = 0; x < pSM.size(); x++) {
++ stdFrag* pSF = pStdGroup->getStdFrag(pSM[x]->getName());
++ if (pSF) {
++ std::cout << " " << pSF->getSymbol() << "\n";
++ double fCharge = 0.0;
++ std::vector<atom*> pA = pSM[x]->getAtomList();
++ for (unsigned int y = 0; y < pA.size(); y++) {
++ stdAtom* pSA = pA[y]->getStdAtom();
++ if (pSA) {
++ fCharge += pSA->atmCharge;
++ std::cout << " |" << pSA->identity << "| " << pSA->atmCharge << "\n";
++ }
++ else {
++ std::cout << " Error find std atom " << std::endl;
++ exit(1);
++ }
++ }
++ groupCharge += fCharge;
++ std::cout << " Total Fragment Charge " << pSF->getCharge() << "\n";
++ }
++ }
++ /*std::vector<stdFrag*> pL = pStdGroup->getStdFragList();
++ for (unsigned int x = 0; x < pL.size(); x++) {
++ std::cout << " Fragment " << pL[x]->getSymbol() << "\n";
++ std::vector<stdAtom*> pL2 = pL[x]->getStdAtomList();
++ double fCharge = 0.0;
++ for (unsigned int y = 0; y < pL2.size(); y++) {
++ fCharge += pL2[y]->atmCharge;
++ std::cout << " Atom " << pL2[y]->identity << " " << pL2[y]->atmCharge << "\n";
++ }
++ groupCharge += fCharge;
++ //groupCharge += pL[x]->getCharge();
++ std::cout << " Fragment Charge " << pL[x]->getCharge() << "\n";
++ }
++ */
++
++ std::cout << " Total Charge = " << groupCharge << "\n" << std::endl;
++ }
++ }
++ }
++ }
++ }
++
++ else if (inputFileContents[i][0] == "printFrag") {
++ /*!
++ @ingroup MCPB_commands
++ \code
++ Function: printFrag
++
++ Description: Print fragment details
++
++ syntax: printFrag Zn-CCCC CY1
++
++ \endcode
++ */
++ if ((inputFileContents[i].size() != 3) or (!pCollection)) {
++ MTKpp::errorLogger.throwError("MCPB::printFrag", " Incorrect use of printFrag ... exiting", MTK_ERROR);
++ exit(1);
++ }
++ else {
++ stdLibrary* pStdLibrary = pCollection->getStdLibrary();
++ if (pStdLibrary) {
++ stdGroup* pStdGroup = pStdLibrary->getStdGroup(inputFileContents[i][1]);
++
++ double groupCharge = 0.0;
++ std::vector<stdFrag*> pL = pStdGroup->getStdFragList();
++ for (unsigned int x = 0; x < pL.size(); x++) {
++ groupCharge += pL[x]->getCharge();
++
++ }
++ std::cout << " Group " << inputFileContents[i][1] << " charge = "
++ << groupCharge << std::endl;
++
++ stdFrag* pStdFrag = pStdGroup->getStdFrag(inputFileContents[i][2]);
++ if (pStdFrag) {
++ std::cout << " Fragment " << inputFileContents[i][2] << " charge = "
++ << pStdFrag->getCharge() << std::endl;
++ }
++ }
++ }
++ }
++
+ else if (inputFileContents[i][0] == "readPdb") {
+ /*!
+ @ingroup MCPB_commands
+@@ -2227,7 +2359,8 @@
+ double resCharge = 0.0;
+ for (unsigned int y = 0; y < residueAtoms.size(); y++) {
+ stdAtom* pLStdAtom = residueAtoms[y]->getStdAtom();
+- std::cout << " " << residueAtoms[y]->getName() << " " << residueAtoms[y]->getFileID()
++ std::cout << " "
++ << residueAtoms[y]->getName() << " " << residueAtoms[y]->getFileID()
+ << " " << residueAtoms[y]->getType() << " " << residueAtoms[y]->getValence()
+ << " " << residueAtoms[y]->getHybridization() << " ";
+ if (pLStdAtom) {
+@@ -2437,6 +2570,11 @@
+ molecule* selMol = pSel->getMol();
+ pPdbParser->Write(inputFileContents[i][2], selMol);
+ }
++ else {
++ MTKpp::errorLogger.throwError("MCPB::writePdb",
++ " Error molecule was not selected ... exiting ", MTK_ERROR);
++ exit(1);
++ }
+ }
+ }
+
+@@ -2674,7 +2812,6 @@
+
+ syntax: basisSet GEN bs.txt
+ syntax: basisSet GEN.6D.7F bs.txt
+- syntax: basisSet GENECP bs.txt pseudo.txt
+ \endcode
+ */
+ if (inputFileContents[i].size() == 2) {
+@@ -2685,6 +2822,11 @@
+ pGParser->setBasisSet(inputFileContents[i][1]);
+ pGParser->setBasisSetFile(inputFileContents[i][2]);
+ }
++ else {
++ MTKpp::errorLogger.throwError("MCPB::basisSet",
++ " Incorrect use ... exiting ", MTK_ERROR);
++ exit(1);
++ }
+ }
+
+ else if (inputFileContents[i][0] == "pseudoPotentials") {
+@@ -2698,8 +2840,15 @@
+ syntax: pseudoPotential pseudo.txt
+ \endcode
+ */
+- pGParser->addCommandOption("pseudo","read");
++ if (inputFileContents[i].size() == 2) {
++ pGParser->addCommandOption("Pseudo","Read");
+ pGParser->setPseudoPotentialFile(inputFileContents[i][1]);
++ } else {
++ MTKpp::errorLogger.throwError("MCPB::pseudoPotentials",
++ " Incorrect use ... exiting ", MTK_ERROR);
++ exit(1);
++ }
++
+ }
+
+ else if (inputFileContents[i][0] == "modRedundant") {
+@@ -2713,8 +2862,14 @@
+ syntax: modRedundant modred.txt
+ \endcode
+ */
+- pGParser->addCommandOption("opt","modredundant");
++ if (inputFileContents[i].size() == 2) {
++ pGParser->addCommandOption("Opt","ModRedundant");
+ pGParser->setModRedundantFile(inputFileContents[i][1]);
++ } else {
++ MTKpp::errorLogger.throwError("MCPB::modRedundant",
++ " Incorrect use ... exiting ", MTK_ERROR);
++ exit(1);
++ }
+ }
+
+ else if (inputFileContents[i][0] == "clusterCharge") {
+@@ -2728,7 +2883,13 @@
+ syntax: clusterCharge cuCYM4 -3
+ \endcode
+ */
++ if (inputFileContents[i].size() == 3) {
+ pGParser->setCharge(atoi(inputFileContents[i][2].c_str()));
++ } else {
++ MTKpp::errorLogger.throwError("MCPB::clusterCharge",
++ " Incorrect use ... exiting ", MTK_ERROR);
++ exit(1);
++ }
+ }
+
+ else if (inputFileContents[i][0] == "clusterSpin") {
+@@ -2742,76 +2903,94 @@
+ syntax: clusterSpin 0
+ \endcode
+ */
++ if (inputFileContents[i].size() == 2) {
+ pGParser->setMultiplicity(atoi(inputFileContents[i][1].c_str()));
++ } else {
++ MTKpp::errorLogger.throwError("MCPB::clusterSpin",
++ " Incorrect use ... exiting ", MTK_ERROR);
++ exit(1);
++ }
+ }
+
+- else if (inputFileContents[i][0] == "g03MoldenFormat") {
++ else if (inputFileContents[i][0] == "gaussianMoldenFormat") {
+ /*!
+ @ingroup MCPB_commands
+ \code
+- Function: g03MoldenFormat
++ Function: gaussianMoldenFormat
+
+ Description: Use Molden formatted output in log file. Print out
+ details of the basis set and the molecular orbitals.
+
+- syntax: g03MoldenFormat (bare word)
++ syntax: gaussianMoldenFormat (bare word)
+ \endcode
+ */
+- pGParser->addCommandOption("gfinput");
+- pGParser->addIop("iop(6/7=3)");
++ pGParser->addCommandOption("GFInput");
++ pGParser->addIop("IOp(6/7=3)");
+ }
+
+- else if (inputFileContents[i][0] == "g03Verbosity") {
++ else if (inputFileContents[i][0] == "gaussianVerbosity") {
+ if (inputFileContents[i].size() == 2) {
+ pGParser->setVerbosity(inputFileContents[i][1]);
++ } else {
++ MTKpp::errorLogger.throwError("MCPB::gaussianVerbosity",
++ " Incorrect use ... exiting ", MTK_ERROR);
++ exit(1);
+ }
+ }
+
+- else if (inputFileContents[i][0] == "g03Mem") {
++ else if (inputFileContents[i][0] == "gaussianMem") {
+ /*!
+ @ingroup MCPB_commands
+ \code
+- Function: g03Mem
++ Function: gaussianMem
+
+- Description: Set amount of memory requested for g03
++ Description: Set amount of memory requested for Gaussian
+
+- syntax: g03Mem 3600MB
++ syntax: gaussianMem 3600MB
+ \endcode
+ */
+ if (inputFileContents[i].size() == 2) {
+ pGParser->setMem(inputFileContents[i][1]);
++ } else {
++ MTKpp::errorLogger.throwError("MCPB::gaussianMem",
++ " Incorrect use ... exiting ", MTK_ERROR);
++ exit(1);
+ }
+ }
+
+- else if (inputFileContents[i][0] == "g03nProc") {
++ else if (inputFileContents[i][0] == "gaussianNProc") {
+ /*!
+ @ingroup MCPB_commands
+ \code
+- Function: g03nProc
++ Function: gaussianNProc
+
+- Description: Set number of processors requested for g03
++ Description: Set number of processors requested for Gaussian
+
+- syntax: g03nProc 2
++ syntax: gaussianNProc 2
+ \endcode
+ */
+ if (inputFileContents[i].size() == 2) {
+- pGParser->setnProc(inputFileContents[i][1]);
++ pGParser->setNProc(inputFileContents[i][1]);
++ } else {
++ MTKpp::errorLogger.throwError("MCPB::gaussianNProc",
++ " Incorrect use ... exiting ", MTK_ERROR);
++ exit(1);
+ }
+ }
+
+- else if (inputFileContents[i][0] == "g03OptAndFC") {
++ else if (inputFileContents[i][0] == "gaussianOptAndFC") {
+ /*!
+ @ingroup MCPB_commands
+ \code
+- Function: g03OptAndFC
++ Function: gaussianOptAndFC
+
+ Description: Set Gaussian input name
+
+- syntax: g03OptAndFC //cuCYM4 cuCYM4.com
++ syntax: gaussianOptAndFC //cuCYM4 cuCYM4.com
+ \endcode
+ */
+ if ((inputFileContents[i].size() != 3) or (!pCollection)) {
+- MTKpp::errorLogger.throwError("MCPB::g03OptAndFC",
++ MTKpp::errorLogger.throwError("MCPB::gaussianOptAndFC",
+ " Incorrect use ... exiting ", MTK_ERROR);
+ exit(1);
+ }
+@@ -2819,7 +2998,7 @@
+ selection* pSel = new selection(pCollection);
+ failure = pSel->parse(inputFileContents[i][1]);
+ if (failure) {
+- MTKpp::errorLogger.throwError("MCPB::g03OptAndFC",
++ MTKpp::errorLogger.throwError("MCPB::gaussianOptAndFC",
+ " Error in selection parsing ... exiting ", MTK_ERROR);
+ exit(1);
+ }
+@@ -2833,17 +3012,17 @@
+ pGParser->setCartesian(1);
+ pGParser->setWriteMoleculeName(1);
+ pGParser->setWriteChargeAndMult(1);
+- pGParser->addCommandOption("integral(Grid=UltraFine)");
++ pGParser->addCommandOption("Integral", "(Grid=UltraFine)");
+
+- std::vector<std::string> optOptions = pGParser->getCommandOption("opt");
++ std::vector<std::string> optOptions = pGParser->getCommandOption("Opt");
+ if (optOptions.size() == 0) {
+- pGParser->addCommandOption("opt");
++ pGParser->addCommandOption("Opt");
+ }
+
+- pGParser->addCommandOption("scf", "xqc");
+- pGParser->addCommandOption("geom", "PrintInputOrient");
++ pGParser->addCommandOption("SCF", "XQC");
++ pGParser->addCommandOption("Geom", "PrintInputOrient");
+ pGParser->Write(fileNameBase+"_opt.com", pSelMol);
+- pGParser->removeCommandOption("opt");
++ pGParser->removeCommandOption("Opt");
+
+ // k's
+ // Do not write coordinates, name, charge or multiplicity,
+@@ -2851,40 +3030,40 @@
+ pGParser->setNoCoords();
+ pGParser->setWriteMoleculeName(0);
+ pGParser->setWriteChargeAndMult(0);
+- pGParser->addCommandOption("freq", "noraman");
+- pGParser->addCommandOption("geom", "allcheckpoint");
+- pGParser->addCommandOption("guess", "read");
+- pGParser->addIop("iop(7/33=1)");
++ pGParser->addCommandOption("Freq", "NoRaman");
++ pGParser->addCommandOption("Geom", "AllCheckpoint");
++ pGParser->addCommandOption("Guess", "Read");
++ pGParser->addIop("IOp(7/33=1)");
+ pGParser->Write(fileNameBase+"_fc.com", pSelMol);
+ pGParser->clearIop();
+
+ /*
+ // optimization
+- pGParser->addCommandOption("opt", "z-matrix");
++ pGParser->addCommandOption("Opt", "Z-Matrix");
+ pGParser->generateZMatrix(pSelMol);
+ // [molecule index] = zmatrix index;
+ pGParser->writeMappingFile(fileNameBase+"_zmat.map");
+- pGParser->addCommandOption("geom", "PrintInputOrient");
++ pGParser->addCommandOption("Geom", "PrintInputOrient");
+ pGParser->Write(fileNameBase+"_opt.com", pSelMol);
+- pGParser->removeCommandOption("opt");
++ pGParser->removeCommandOption("Opt");
+ */
+ }
+ }
+ }
+
+- else if (inputFileContents[i][0] == "g03Charges") {
++ else if (inputFileContents[i][0] == "gaussianCharges") {
+ /*!
+ @ingroup MCPB_commands
+ \code
+- Function: g03Charges
++ Function: gaussianCharges
+
+ Description: Set Gaussian input name
+
+- syntax: g03Charges //cuCYM4 cuCYM4.com
++ syntax: gaussianCharges //cuCYM4 cuCYM4.com
+ \endcode
+ */
+ if ((inputFileContents[i].size() != 3) or (!pCollection)) {
+- MTKpp::errorLogger.throwError("MCPB::g03Charges",
++ MTKpp::errorLogger.throwError("MCPB::gaussianCharges",
+ " Incorrect use ... exiting ", MTK_ERROR);
+ exit(1);
+ }
+@@ -2892,7 +3071,7 @@
+ selection* pSel = new selection(pCollection);
+ failure = pSel->parse(inputFileContents[i][1]);
+ if (failure) {
+- MTKpp::errorLogger.throwError("MCPB::g03Charges",
++ MTKpp::errorLogger.throwError("MCPB::gaussianCharges",
+ " Error in selection parsing ... exiting ", MTK_ERROR);
+ exit(1);
+ }
+@@ -2907,14 +3086,14 @@
+
+ // q's
+ std::vector<std::string> popOptions;
+- popOptions.push_back("mk");
+- popOptions.push_back("readradii");
+- pGParser->addCommandOption("pop", popOptions);
+- pGParser->removeCommandOption("freq");
+- pGParser->addIop("iop(6/33=2)");
++ popOptions.push_back("MK");
++ popOptions.push_back("ReadRadii");
++ pGParser->addCommandOption("Pop", popOptions);
++ pGParser->removeCommandOption("Freq");
++ pGParser->addIop("IOp(6/33=2)");
+
+- pGParser->addCommandOption("integral(Grid=UltraFine)");
+- pGParser->addCommandOption("scf", "xqc");
++ pGParser->addCommandOption("Integral", "(Grid=UltraFine)");
++ pGParser->addCommandOption("SCF", "XQC");
+
+ pGParser->Write(fileNameBase+"_mk.com", pSelMol);
+
+@@ -3053,7 +3232,8 @@
+ result = find(bbb.begin(), bbb.end(), dd);
+
+ if (result != bbb.end()) {
+- freezingAtoms += "\n BBB " + submols[s]->getName() + " " + int2String(submols[s]->getSubMolId()) + " " + dd;
++ freezingAtoms += "\n BBB " + submols[s]->getName() + " "
++ + int2String(submols[s]->getSubMolId()) + " " + dd;
+ sprintf(temp,"%5d%10.5f", 1, pStdAtom_a->atmCharge);
+ orespAdd << temp << std::endl;
+ sprintf(temp,"%5d%5d", 1, subAtoms[a]->getIndex());
+@@ -3071,7 +3251,6 @@
+ MTKpp::errorLogger.throwError("MCPB::respgenAdditions",
+ freezingAtoms, INFO);
+ }
+-
+ orespAdd << "\n" << std::endl;
+ orespAdd.close();
+ }
+@@ -3099,22 +3278,22 @@
+ }
+ }
+
+- else if (inputFileContents[i][0] == "readG03Output") {
++ else if (inputFileContents[i][0] == "readGaussianOutput") {
+ /*!
+ @ingroup MCPB_commands
+ \code
+- Function: readG03Output
++ Function: readGaussianOutput
+
+- Description: Read G03 Output
++ Description: Read Gaussian Output
+
+- syntax: readG03Output cuCYM4.log
++ syntax: readGaussianOutput cuCYM4.log
+ \endcode
+ */
+ if ((inputFileContents[i].size() == 2) or (pGParser)) {
+ pGParser->Read(inputFileContents[i][1], pSheet);
+ }
+ else {
+- MTKpp::errorLogger.throwError("MCPB::readG03Output",
++ MTKpp::errorLogger.throwError("MCPB::readGaussianOutput",
+ " Incorrect use ... exiting ", MTK_ERROR);
+ exit(1);
+ }
+@@ -3481,8 +3660,8 @@
+ pGParser->setCartesian(0);
+ pGParser->setWriteMoleculeName(1);
+ pGParser->setWriteChargeAndMult(1);
+- pGParser->addCommandOption("freq", "noraman");
+- pGParser->addIop("iop(7/33=1)");
++ pGParser->addCommandOption("Freq", "NoRaman");
++ pGParser->addIop("IOp(7/33=1)");
+ pGParser->Write(inputFileContents[i][2], pSelMol);
+ pGParser->writeMappingFile(inputFileContents[i][2]+".map");
+ }
+@@ -3826,6 +4005,7 @@
+ if (pStdFrag) {
+ bool doIt = pStdGroup->hasStdFrag(pStdFrag->getSymbol());
+ if (doIt) {
++ //std::cout << " " << pStdFrag->getSymbol() << "\n";
+ //submolecule* pStdSubmol = pStdMolecule->addSubMolecule();
+ //pStdSubmol->copy(submolList[t]);
+ std::vector<atom*> lAtomList = submolList[t]->getAtomList();
+@@ -3834,7 +4014,8 @@
+ if (pStdAtom) {
+ //std::cout << " |" << lAtomList[r]->getName() << "| " << lAtomList[r]->getZcharge() << "\n";
+ pStdAtom->atmCharge = lAtomList[r]->getZcharge();
+- groupCharge += lAtomList[r]->getZcharge();
++ //groupCharge += lAtomList[r]->getZcharge();
++ groupCharge += pStdAtom->atmCharge;
+ }
+ }
+ }
+@@ -3861,11 +4042,398 @@
+ */
+ }
+ updateRespChargesMessage += " Charge: " + double2String(groupCharge, 2);
++ //std::cout << " Group charge = " << double2String(groupCharge, 2) << "\n";
+ MTKpp::errorLogger.throwError("MCPB::updateRespCharges",
+ updateRespChargesMessage, INFO);
+ }
+ }
+
++ else if (inputFileContents[i][0] == "respgen") {
++ /*!
++ @ingroup MCPB_commands
++ \code
++ Function: respgen
++
++ Description: Create resp1 and resp2 files (recreates functionality of respgen)
++
++ syntax: respgen /COL/MOL Group fileName
++ \endcode
++ */
++
++ if ((inputFileContents[i].size() != 4) or (!pCollection)) {
++ MTKpp::errorLogger.throwError("MCPB::respgen",
++ " Incorrect use ... exiting ", MTK_ERROR);
++ exit(1);
++ }
++ else {
++ selection* pSel = new selection(pCollection);
++ failure = pSel->parse(inputFileContents[i][1]);
++ if (failure) {
++ MTKpp::errorLogger.throwError("MCPB::respgen",
++ " Error in selection parsing ... exiting ", MTK_ERROR);
++ exit(1);
++ }
++
++ stdLibrary* pStdLibrary = pCollection->getStdLibrary();
++ stdGroup* pStdGroup = 0;
++ if (pStdLibrary) {
++ pStdGroup = pStdLibrary->getStdGroup(inputFileContents[i][2]);
++ if (!pStdGroup) {
++ MTKpp::errorLogger.throwError("MCPB::respgen",
++ " Can't find stdGroup ... exiting ", MTK_ERROR);
++ exit(1);
++ }
++ }
++ else {
++ MTKpp::errorLogger.throwError("MCPB::respgen",
++ " Error in selection parsing ... exiting ", MTK_ERROR);
++ }
++
++ if (pSel->getSelectionType() == 1) {
++ molecule* pSelMol = pSel->getMol();
++ if (!pSelMol) {
++ std::cout << " Error in respgen selection \n";
++ exit(1);
++ }
++
++ std::vector<std::string>::iterator result;
++
++ acParser* pAcParser = new acParser();
++ pAcParser->Write(inputFileContents[i][3]+".ac", pCollection);
++ delete pAcParser;
++
++ std::string bb0FileResp1 = inputFileContents[i][3] + "_bb0.resp1";
++ std::string bb0FileResp2 = inputFileContents[i][3] + "_bb0.resp2";
++ std::ofstream obb0FileResp1;
++ std::ofstream obb0FileResp2;
++ obb0FileResp1.open(bb0FileResp1.c_str());
++ obb0FileResp2.open(bb0FileResp2.c_str());
++
++ std::string bb1FileResp1 = inputFileContents[i][3] + "_bb1.resp1";
++ std::string bb1FileResp2 = inputFileContents[i][3] + "_bb1.resp2";
++ std::ofstream obb1FileResp1;
++ std::ofstream obb1FileResp2;
++ obb1FileResp1.open(bb1FileResp1.c_str());
++ obb1FileResp2.open(bb1FileResp2.c_str());
++
++ std::string bb2FileResp1 = inputFileContents[i][3] + "_bb2.resp1";
++ std::string bb2FileResp2 = inputFileContents[i][3] + "_bb2.resp2";
++ std::ofstream obb2FileResp1;
++ std::ofstream obb2FileResp2;
++ obb2FileResp1.open(bb2FileResp1.c_str());
++ obb2FileResp2.open(bb2FileResp2.c_str());
++
++ std::string bb3FileResp1 = inputFileContents[i][3] + "_bb3.resp1";
++ std::string bb3FileResp2 = inputFileContents[i][3] + "_bb3.resp2";
++ std::ofstream obb3FileResp1;
++ std::ofstream obb3FileResp2;
++ obb3FileResp1.open(bb3FileResp1.c_str());
++ obb3FileResp2.open(bb3FileResp2.c_str());
++
++ if (!obb0FileResp1 or !obb0FileResp2 or !obb1FileResp1 or !obb1FileResp2 or
++ !obb2FileResp1 or !obb2FileResp2 or !obb3FileResp1 or !obb3FileResp2) {
++ MTKpp::errorLogger.throwError("MCPB::respgen",
++ " Unable to open RESP files ... exiting ", MTK_ERROR);
++ exit(1);
++ }
++
++ std::vector<molecule*> molList = pCollection->getMoleculeList();
++
++ std::string terminalFrags = "";
++ char temp[100];
++ bool bFirst = true;
++ for (unsigned int m = 0; m < molList.size(); m++) {
++ molecule* pMol = molList[m];
++ std::vector<submolecule*> submols = pMol->getSubMoleculeList();
++ for (unsigned int s = 0; s < submols.size(); s++) {
++ if (submols[s]->hasStdFrag()) {
++ stdFrag* pStdFrag = submols[s]->getStdFrag();
++ if (pStdFrag->getParent()->getName() != inputFileContents[i][2]) {
++ if (bFirst) {
++ sprintf(temp,"%5d%10.5f\n", pStdFrag->numStdAtoms(), 0.0);
++ bFirst = false;
++ }
++ else {
++ sprintf(temp,"\n%5d%10.5f\n", pStdFrag->numStdAtoms(), 0.0);
++ }
++
++ terminalFrags += std::string(temp);
++ std::vector<atom*> atomList = submols[s]->getAtomList();
++ char temp2[80];
++ int counter = 0;
++ for (unsigned int a = 0; a < atomList.size(); a++) {
++ if (counter > 7) { // was 6
++ terminalFrags += "\n";
++ counter = 0;
++ }
++ sprintf(temp2,"%5d%5d", 1, atomList[a]->getIndex());
++ terminalFrags += std::string(temp2);
++ counter++;
++ }
++ //terminalFrags += "\n";
++ }
++ }
++ }
++ }
++ //std::cout << terminalFrags << std::endl;
++
++ std::string bb0 = terminalFrags + "\n";
++ std::string bb1 = terminalFrags + "\n";
++ std::string bb2 = terminalFrags + "\n";
++ std::string bb3 = terminalFrags + "\n";
++
++ int lInd = 0;
++ for (unsigned int m = 0; m < molList.size(); m++) {
++ molecule* pMol = molList[m];
++
++ if (pMol->getName() == "Reference") continue;
++
++ std::vector<submolecule*> submols = pMol->getSubMoleculeList();
++ for (unsigned int s = 0; s < submols.size(); s++) {
++ if (submols[s]->hasStdFrag()) {
++ stdFrag* pStdFrag = submols[s]->getStdFrag();
++ //std::cout << " respgen " << pStdFrag->getParent()->getName() << " " << inputFileContents[i][2] << " \n ";
++ if (pStdFrag->getParent()->getName() != inputFileContents[i][2]) continue;
++ std::vector<atom*> subAtoms = submols[s]->getAtomList();
++ for (unsigned int a = 0; a < subAtoms.size(); a++) {
++ stdAtom* pStdAtom_a = subAtoms[a]->getStdAtom();
++ lInd++;
++ // iBB == 1
++ if (pStdAtom_a) {
++ std::string dd = pStdAtom_a->identity + ":" + pStdAtom_a->type;
++
++ //result = find(bb_heavy.begin(), bb_heavy.end(), subAtoms[a]->getName());
++ //result = find(bb_heavy.begin(), bb_heavy.end(), pStdAtom_a->identity);
++ result = find(bb_heavy.begin(), bb_heavy.end(), dd);
++
++ if (result != bb_heavy.end()) {
++ sprintf(temp,"%5d%10.5f\n", 1, pStdAtom_a->atmCharge);
++ //freezingAtoms += "\n BB Heavy " + submols[s]->getName() + " " + int2String(submols[s]->getSubMolId()) + " " + dd;
++ //std::cout << "\n BB Heavy " + submols[s]->getName() + " " + int2String(submols[s]->getSubMolId()) + " " + dd;
++ //std::cout << dd << " " << subAtoms[a]->getName() << " ---> " << subAtoms[a]->getStdAtom()->type << std::endl;
++ //orespAdd << temp << std::endl;
++ bb1 += std::string(temp);
++ sprintf(temp,"%5d%5d\n", 1, subAtoms[a]->getIndex());
++ //orespAdd << temp << std::endl;
++ bb1 += std::string(temp);
++ }
++
++ // iBB == 2
++ dd = pStdAtom_a->identity + ":" + pStdAtom_a->type;
++
++ //result = find(bb.begin(), bb.end(), subAtoms[a]->getName());
++ result = find(bb.begin(), bb.end(), dd);
++
++ if (result != bb.end()) {
++ //freezingAtoms += "\n BB " + submols[s]->getName() + " " + int2String(submols[s]->getSubMolId()) + " " + dd;
++ sprintf(temp,"%5d%10.5f\n", 1, pStdAtom_a->atmCharge);
++ //orespAdd << temp << std::endl;
++ bb2 += std::string(temp);
++ sprintf(temp,"%5d%5d\n", 1, subAtoms[a]->getIndex());
++ //orespAdd << temp << std::endl;
++ bb2 += std::string(temp);
++ }
++ // iBB == 3
++ dd = pStdAtom_a->identity + ":" + pStdAtom_a->type;
++
++ //result = find(bbb.begin(), bbb.end(), subAtoms[a]->getName());
++ result = find(bbb.begin(), bbb.end(), dd);
++
++ if (result != bbb.end()) {
++ //freezingAtoms += "\n BBB " + submols[s]->getName() + " "
++ // + int2String(submols[s]->getSubMolId()) + " " + dd;
++ sprintf(temp,"%5d%10.5f\n", 1, pStdAtom_a->atmCharge);
++ bb3 += std::string(temp);
++ //orespAdd << temp << std::endl;
++ sprintf(temp,"%5d%5d\n", 1, subAtoms[a]->getIndex());
++ bb3 += std::string(temp);
++ //orespAdd << temp << std::endl;
++ }
++ }
++ else {
++ MTKpp::errorLogger.throwError("MCPB::respgen",
++ " Unknown option ... exiting ", MTK_ERROR);
++ }
++ }
++ }
++ }
++ }
++
++ std::string resp1 = "";
++ resp1 += "Resp charges for organic molecule\n";
++ resp1 += "\n";
++ resp1 += " &cntrl\n";
++ resp1 += "\n";
++ resp1 += " nmol = 1,\n";
++ resp1 += " ihfree = 1,\n";
++ resp1 += " ioutopt = 1,\n";
++ resp1 += "\n";
++ resp1 += " &end\n";
++ resp1 += " 1.0\n";
++ resp1 += "Resp charges for organic molecule\n";
++
++ //std::cout << pStdGroup->getCharge() << " " << pSelMol->getNumAtoms() << std::endl;
++ sprintf(temp,"%5d%5d\n", int(pStdGroup->getCharge()), pSelMol->getNumAtoms());
++ resp1 += std::string(temp);
++
++ std::vector<submolecule*> sList = pSelMol->getSubMoleculeList();
++ typedef std::map<std::string, int>::iterator mapIterator;
++
++ std::map<std::string, int> lMap;
++ int ind = 0;
++ for (unsigned int p = 0; p < sList.size(); p++) {
++ std::vector<atom*> aList = sList[p]->getAtomList();
++ for (unsigned int a = 0; a < aList.size(); a++) {
++ if (!aList[a]->getStdAtom()) {
++ std::cout << " Error ... exiting()\n";
++ exit(1);
++ }
++ int elNum = aList[a]->getAtomicNum();
++ std::string key = "";
++ if (elNum == 1) {
++ std::vector<atom*> hBondedAtoms = aList[a]->getBondedAtoms();
++ if (hBondedAtoms.size() == 1) {
++ key = aList[a]->getParent()->getName() + ":" + hBondedAtoms[0]->getName() + ":" + aList[a]->getStdAtom()->type;
++ }
++ else {
++ key = aList[a]->getParent()->getName() + ":" + aList[a]->getStdAtom()->type;
++ }
++ }
++ else {
++ key = aList[a]->getParent()->getName() + ":" + aList[a]->getName();
++ }
++
++ mapIterator mi = lMap.find(key);
++
++ int fg = 0;
++ if (mi != lMap.end()){
++ fg = lMap[key]+1;
++ }
++ else {
++ lMap[key] = ind;
++ }
++ //sprintf(temp,"%4d %-11s%5d%5d\n", ind+1, key.c_str(), aList[a]->getAtomicNum(), fg);
++ sprintf(temp,"%5d%5d\n", aList[a]->getAtomicNum(), fg);
++ resp1 += std::string(temp);
++ ind++;
++ }
++ }
++
++ std::string resp2 = "";
++
++ resp2 += "Resp charges for organic molecule\n";
++ resp2 += "\n";
++ resp2 += " &cntrl\n";
++ resp2 += "\n";
++ resp2 += " nmol = 1,\n";
++ resp2 += " ihfree = 1,\n";
++ resp2 += " ioutopt = 1,\n";
++ resp2 += " iqopt = 2,\n";
++ resp2 += " qwt = 0.001,\n";
++ resp2 += "\n";
++ resp2 += " &end\n";
++ resp2 += " 1.0\n";
++ resp2 += "Resp charges for organic molecule\n";
++
++ sprintf(temp,"%5d%5d\n", int(pStdGroup->getCharge()), pSelMol->getNumAtoms());
++ resp2 += std::string(temp);
++
++ ind = 0;
++ std::map<std::string, int> lMap2;
++
++ for (unsigned int p = 0; p < sList.size(); p++) {
++ std::vector<atom*> aList = sList[p]->getAtomList();
++ for (unsigned int a = 0; a < aList.size(); a++) {
++
++ if (!aList[a]->getStdAtom()) {
++ std::cout << " Error ... exiting()\n";
++ exit(1);
++ }
++ int elNum = aList[a]->getAtomicNum();
++ std::string key = "";
++ if (elNum == 1) {
++ std::vector<atom*> hBondedAtoms = aList[a]->getBondedAtoms();
++ if (hBondedAtoms.size() == 1) {
++ key = aList[a]->getParent()->getName() + ":" + hBondedAtoms[0]->getName() + ":" +
++ aList[a]->getStdAtom()->type;
++ }
++ else {
++ key = aList[a]->getParent()->getName() + ":" + aList[a]->getStdAtom()->type;
++ }
++ }
++ else {
++ key = aList[a]->getParent()->getName() + ":" + aList[a]->getName();
++ }
++
++ mapIterator mi = lMap2.find(key);
++
++ int fg = 0;
++ if (mi != lMap2.end()){
++ fg = lMap2[key]+1;
++ }
++ else {
++ lMap2[key] = ind;
++ }
++ std::string atName = aList[a]->getName();
++ std::string atType = aList[a]->getStdAtom()->type;
++ int atNum = aList[a]->getAtomicNum();
++
++ if (atName == " CH3" or atName == " CB " or containsSubStr(key, " CB :H1") or
++ containsSubStr(key, " CB :HC") or
++ containsSubStr(key, " CH3:HC") or containsSubStr(key, " CH3:H1") or
++ containsSubStr(key, "GLY: CA ")) {// or (atNum > 16)) {
++ //if (atName == " CH3" or atName == " CB " or atType == "H1" or atType == "HC") {
++ //sprintf(temp,"%4d %-11s%5d%5d\n", ind+1, key.c_str(), aList[a]->getAtomicNum(), fg);
++ sprintf(temp,"%5d%5d\n", aList[a]->getAtomicNum(), fg);
++ }
++ else {
++ //sprintf(temp,"%4d %-11s%5d%5d\n", ind+1, key.c_str(), aList[a]->getAtomicNum(), -99);
++ sprintf(temp,"%5d%5d\n", aList[a]->getAtomicNum(), -99);
++ }
++ resp2 += std::string(temp);
++
++ ind++;
++ }
++ }
++
++ std::string twoBlankLine = "\n\n";
++ bb0 += twoBlankLine;
++ bb1 += twoBlankLine;
++ bb2 += twoBlankLine;
++ bb3 += twoBlankLine;
++
++ obb0FileResp1 << resp1;
++ obb0FileResp1 << bb0;
++ obb0FileResp2 << resp2;
++ obb0FileResp2 << bb0;
++
++ obb1FileResp1 << resp1;
++ obb1FileResp1 << bb1;
++ obb1FileResp2 << resp2;
++ obb1FileResp2 << bb1;
++
++ obb2FileResp1 << resp1;
++ obb2FileResp1 << bb2;
++ obb2FileResp2 << resp2;
++ obb2FileResp2 << bb2;
++
++ obb3FileResp1 << resp1;
++ obb3FileResp1 << bb3;
++ obb3FileResp2 << resp2;
++ obb3FileResp2 << bb3;
++
++ obb0FileResp1.close();
++ obb0FileResp2.close();
++ obb1FileResp1.close();
++ obb1FileResp2.close();
++ obb2FileResp1.close();
++ obb2FileResp2.close();
++ obb3FileResp1.close();
++ obb3FileResp2.close();
++ }
++ }
++ }
++
+ else if (inputFileContents[i][0] == "addStdMol") {
+ /*!
+ @ingroup MCPB_commands
+@@ -4496,63 +5064,63 @@
+ table<double>* nmodeEVectors = pSheet->getTable("NMode EigenVectors");
+ ublas::matrix<double> &nmodeEVectorsMatrixT = nmodeEVectors->getMatrix();
+
+- table<double>* g03EValues = pSheet->getTable("Gaussian EigenValues");
+- ublas::matrix<double> &g03EValuesMatrix = g03EValues->getMatrix();
++ table<double>* gaussianEValues = pSheet->getTable("Gaussian EigenValues");
++ ublas::matrix<double> &gaussianEValuesMatrix = gaussianEValues->getMatrix();
+
+- table<double>* g03EVectors = pSheet->getTable("Gaussian EigenVectors");
+- ublas::matrix<double> &g03EVectorsMatrixT = g03EVectors->getMatrix();
++ table<double>* gaussianEVectors = pSheet->getTable("Gaussian EigenVectors");
++ ublas::matrix<double> &gaussianEVectorsMatrixT = gaussianEVectors->getMatrix();
+
+ int nRowsNMode = nmodeEValues->getNumRows();
+- int nRowsG03 = g03EValues->getNumRows();
++ int nRowsGaussian = gaussianEValues->getNumRows();
+
+ int nColsNMode = nmodeEVectors->getNumColumns();
+- int nColsG03 = g03EVectors->getNumColumns();
++ int nColsGaussian = gaussianEVectors->getNumColumns();
+
+- if (nRowsNMode != nRowsG03 and nColsNMode != nColsG03) {
++ if (nRowsNMode != nRowsGaussian and nColsNMode != nColsGaussian) {
+ std::cout << " PROBLEM " << std::endl;
+ }
+ else {
+ std::cout << " EIGENVALUES " << std::endl;
+ for (int z = 0; z < nRowsNMode; z++) {
+- std::cout << nmodeEValuesMatrix(z, 0) << " " << g03EValuesMatrix(z, 0) << std::endl;
++ std::cout << nmodeEValuesMatrix(z, 0) << " " << gaussianEValuesMatrix(z, 0) << std::endl;
+ }
+
+ //std::cout << " NMODE " << std::endl;
+ //nmodeEVectors->printMatrix();
+
+- //std::cout << " G03 " << std::endl;
+- //g03EVectors->printMatrix();
++ //std::cout << " Gaussian " << std::endl;
++ //gaussianEVectors->printMatrix();
+ //std::cout << " \n\n " << std::endl;
+
+ // Normalize Eigenvector matrices
+ for (int zi = 0; zi < nRowsNMode; zi++) {
+ double normNMode = 0.0;
+- double normG03 = 0.0;
++ double normGaussian = 0.0;
+ for (int zk = 0; zk < nColsNMode; zk++) {
+ normNMode += (nmodeEVectorsMatrixT(zi, zk) * nmodeEVectorsMatrixT(zi, zk));
+- normG03 += (g03EVectorsMatrixT(zi, zk) * g03EVectorsMatrixT(zi, zk));
++ normGaussian += (gaussianEVectorsMatrixT(zi, zk) * gaussianEVectorsMatrixT(zi, zk));
+ }
+ normNMode = sqrt(normNMode);
+- normG03 = sqrt(normG03);
++ normGaussian = sqrt(normGaussian);
+ for (int zk = 0; zk < nColsNMode; zk++) {
+- //std::cout << g03EVectorsMatrixT(zi, zk) << " " << normG03 << " "
+- // << g03EVectorsMatrixT(zi, zk) / normG03 << " ";
++ //std::cout << gaussianEVectorsMatrixT(zi, zk) << " " << normGaussian << " "
++ // << gaussianEVectorsMatrixT(zi, zk) / normGaussian << " ";
+ double newValue1 = nmodeEVectorsMatrixT(zi, zk) / normNMode;
+- double newValue2 = g03EVectorsMatrixT(zi, zk) / normG03;
++ double newValue2 = gaussianEVectorsMatrixT(zi, zk) / normGaussian;
+ nmodeEVectors->setCellValue(zi, zk, newValue1);
+- g03EVectors->setCellValue(zi, zk, newValue2);
+- //std::cout << g03EVectors->getCellValue(zi, zk) << std::endl;
++ gaussianEVectors->setCellValue(zi, zk, newValue2);
++ //std::cout << gaussianEVectors->getCellValue(zi, zk) << std::endl;
+ }
+ }
+
+ ublas::matrix<double> &nmodeEVectorsMatrix = nmodeEVectors->getMatrix();
+- ublas::matrix<double> &g03EVectorsMatrix = g03EVectors->getMatrix();
++ ublas::matrix<double> &gaussianEVectorsMatrix = gaussianEVectors->getMatrix();
+
+ //std::cout << " NMODE " << std::endl;
+ //nmodeEVectors->printMatrix();
+
+- //std::cout << " G03 " << std::endl;
+- //g03EVectors->printMatrix();
++ //std::cout << " Gaussian " << std::endl;
++ //gaussianEVectors->printMatrix();
+ //std::cout << " \n\n " << std::endl;
+
+ // dot product
+@@ -4563,12 +5131,12 @@
+ double eN2 = 0.0;
+ double dff = 0.0;
+ for (int zi = 0; zi < nRowsNMode; zi++) { // NMode
+- for (int zj = 0; zj < nRowsNMode; zj++) { // G03
++ for (int zj = 0; zj < nRowsNMode; zj++) { // Gaussian
+ for (int zk = 0; zk < nColsNMode; zk++) { // Loop over coordinates in Eigenvector
+- //std::cout << nmodeEVectorsMatrix(zi, zk) << " " << g03EVectorsMatrix(zj, zk) << " ";
++ //std::cout << nmodeEVectorsMatrix(zi, zk) << " " << gaussianEVectorsMatrix(zj, zk) << " ";
+ eN += (nmodeEVectorsMatrix(zi, zk) * nmodeEVectorsMatrix(zi, zk));
+- eN2 += (g03EVectorsMatrix(zj, zk) * g03EVectorsMatrix(zj, zk));
+- dotProduct += (nmodeEVectorsMatrix(zi, zk) * g03EVectorsMatrix(zj, zk));
++ eN2 += (gaussianEVectorsMatrix(zj, zk) * gaussianEVectorsMatrix(zj, zk));
++ dotProduct += (nmodeEVectorsMatrix(zi, zk) * gaussianEVectorsMatrix(zj, zk));
+ }
+ //std::cout << " eN = " << sqrt(eN) << " eN2 = " << sqrt(eN2) << " ";
+ std::cout << zi << " - " << zj << " " << dotProduct << " " << dotProductMax << std::endl;
+@@ -4582,11 +5150,11 @@
+ }
+ dotProduct = 0.0;
+ }
+- double dffL = nmodeEValuesMatrix(zi, 0) - g03EValuesMatrix(dotProductMaxIndex, 0);
++ double dffL = nmodeEValuesMatrix(zi, 0) - gaussianEValuesMatrix(dotProductMaxIndex, 0);
+ dffL *= dffL;
+ std::cout << " nmode index = " << zi << " BestMatch = " << dotProductMaxIndex
+ << " => dotProduct =" << dotProductMax << " EVALUES: "
+- << " " << nmodeEValuesMatrix(zi, 0) << " " << g03EValuesMatrix(dotProductMaxIndex, 0) << " "
++ << " " << nmodeEValuesMatrix(zi, 0) << " " << gaussianEValuesMatrix(dotProductMaxIndex, 0) << " "
+ << dffL
+ << std::endl;
+
+@@ -4617,7 +5185,7 @@
+ }
+
+ else {
+- std::string unknownCommand = " Unknown command " + inputFileContents[i][0];
++ std::string unknownCommand = " Unknown command: \"" + inputFileContents[i][0] + "\"";
+ MTKpp::errorLogger.throwError("MCPB", unknownCommand, MTK_ERROR);
+ }
+ }
+@@ -4628,4 +5196,3 @@
+ delete pSheet;
+ return 0;
+ }
+-
+diff -urN amber11.orig/AmberTools/src/mtkpp/tools/prep2xml.cpp amber11/AmberTools/src/mtkpp/tools/prep2xml.cpp
+--- amber11.orig/AmberTools/src/mtkpp/tools/prep2xml.cpp 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/tools/prep2xml.cpp 2012-03-03 20:03:01.418032565 +0200
+@@ -86,6 +86,7 @@
+ clo->addUsage( " -a log file " );
+ clo->addUsage( " -l hybridize name \n" );
+ clo->addUsage( " flags: " );
++ clo->addUsage( " -c convert only " );
+ clo->addUsage( " -h help \n" );
+
+ // 4. SET THE OPTION STRINGS/CHARACTERS
+@@ -97,6 +98,7 @@
+ clo->setOption( "hyb", 'l' );
+ clo->setOption( "log", 'a' );
+
++ clo->setFlag ( "convert", 'c' );
+ clo->setFlag ( "help", 'h' );
+
+ // 5. PROVIDE THE COMMANDLINE
+@@ -117,6 +119,11 @@
+ std::string fragName = "";
+ std::string molName = "";
+ std::string logFile = "";
++ bool bConvertOnly = 0;
++
++ if ( clo->getFlag( "convert" ) || clo->getFlag( 'c' ) ) {
++ bConvertOnly = 1;
++ }
+
+ std::string AMBERHOME = getenv("AMBERHOME");
+ std::string parametersFile = AMBERHOME + "/dat/mtkpp/hybridize/labute.txt";
+@@ -166,13 +173,13 @@
+ else if ( clo->getValue( "frag" ) != 0 ) {
+ fragName = clo->getValue( "frag" );
+ }
+- else {
++/* else {
+ printHeader(std::cout, prog_name, authors);
+ clo->printUsage();
+ std::cout << " Please provide a fragment name " << std::endl;
+ return 0;
+ }
+-
++*/
+ if ( clo->getValue( "l" ) != 0 ) {
+ parametersFile = clo->getValue( "l" );
+ }
+@@ -186,13 +193,14 @@
+ else if ( clo->getValue( "mol" ) != 0 ) {
+ molName = clo->getValue( "mol" );
+ }
++/*
+ else {
+ printHeader(std::cout, prog_name, authors);
+ clo->printUsage();
+ std::cout << " Please provide a molecule name " << std::endl;
+ return 0;
+ }
+-
++*/
+ if ( clo->getValue( "a" ) != 0 ) {
+ logFile = clo->getValue( "a" );
+ }
+@@ -307,6 +315,22 @@
+ std::cout << " Incorrect use of prep2xml " << std::endl;
+ exit(1);
+ }
++
++ /////////
++ if (fragName == "") {
++ prepParser* pPrepParser = new prepParser();
++ pPrepParser->Read(prepFile, pStdGroup);
++ delete pPrepParser;
++
++ pStdLibParser->Write(libXmlFile, groupName);
++ delete pStdLibParser;
++
++ // - Clean up - //
++ delete pCollection;
++ return 0;
++ }
++ ///////////
++
+ stdFrag* pStdFrag = pStdGroup->addStdFrag();
+ if (!pStdFrag) {
+ std::cout << " Incorrect use of prep2xml " << std::endl;
+@@ -322,6 +346,15 @@
+ pPrepParser->Read(prepFile, pStdFrag);
+ delete pPrepParser;
+
++ if (bConvertOnly) {
++ pStdLibParser->Write(libXmlFile, groupName);
++ delete pStdLibParser;
++
++ // - Clean up - //
++ delete pCollection;
++ return 0;
++ }
++
+ int f = pStdFrag->generateCoordinates();
+ if (f) {
+ std::cout << " Incorrect use of prep2xml " << std::endl;
+@@ -443,7 +476,7 @@
+ // atoms
+ for (unsigned int i = 0; i < atomList.size(); i++) {
+ stdAtoms[i]->kind = atomList[i]->getType();
+- std::cout << atomList[i]->getIndex() << " " << atomList[i]->getName() << " " << atomList[i]->getType() << std::endl;
++ //std::cout << atomList[i]->getIndex() << " " << atomList[i]->getName() << " " << atomList[i]->getType() << std::endl;
+ }
+
+ // bonds
+diff -urN amber11.orig/AmberTools/src/mtkpp/tools/stdLib2Sdf.cpp amber11/AmberTools/src/mtkpp/tools/stdLib2Sdf.cpp
+--- amber11.orig/AmberTools/src/mtkpp/tools/stdLib2Sdf.cpp 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/mtkpp/tools/stdLib2Sdf.cpp 2012-03-03 20:03:01.418032565 +0200
+@@ -42,6 +42,9 @@
+ // - COMMAND LINE OPTIONS
+ #include "Parsers/commLineOptions.h"
+
++// - Log
++#include "Log/errorHandler.h"
++
+ // temp
+ #include "time.h"
+
+@@ -174,7 +177,7 @@
+ }
+
+ // Set errorLog stream to the log file
+- //MTKpp::errorLogger.setStream(&oLog);
++ MTKpp::errorLogger.setStream(&oLog);
+
+ // Print MTK++ copyright message
+ printHeader(oLog, prog_name, authors);
+diff -urN amber11.orig/AmberTools/src/pbsa/pb_list.f amber11/AmberTools/src/pbsa/pb_list.f
+--- amber11.orig/AmberTools/src/pbsa/pb_list.f 2011-04-14 15:30:19.000000000 +0300
++++ amber11/AmberTools/src/pbsa/pb_list.f 2012-03-03 20:02:55.131034376 +0200
+@@ -949,7 +949,7 @@
+ ymin == ZERO .and. ymax == ZERO .and. &
+ zmin == ZERO .and. zmax == ZERO ) newbox = .true.
+
+- if ( newbox ) then
++ if ( .not. ligand ) then
+ if ( ifcap == 0 .or. ifcap == 5 ) then
+ xmin = 9999.0; ymin = 9999.0; zmin = 9999.0
+ xmax = -9999.0; ymax = -9999.0; zmax = -9999.0
+diff -urN amber11.orig/AmberTools/src/rism/safemem.f amber11/AmberTools/src/rism/safemem.f
+--- amber11.orig/AmberTools/src/rism/safemem.f 2012-03-03 22:43:02.986777264 +0200
++++ amber11/AmberTools/src/rism/safemem.f 2012-03-03 20:02:52.131035237 +0200
+@@ -62,7 +62,7 @@
+ !BYTES_PER_KILOBYTES :: used to convert between bytes and KB
+ integer*8,parameter :: BYTES_PER_KB = 1024**1
+
+- type(memTracker),private :: totalMem
++ type(memTracker),save,private :: totalMem
+
+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
next reply other threads:[~2012-03-03 21:07 UTC|newest]
Thread overview: 18+ messages / expand[flat|nested] mbox.gz Atom feed top
2012-03-03 21:06 Reinis Danne [this message]
-- strict thread matches above, loose matches on Subject: below --
2020-09-26 16:21 [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/ Aisha Tammy
2016-02-19 12:56 Justin Lecher
2016-02-19 12:56 Justin Lecher
2015-10-28 9:07 Justin Lecher
2014-11-11 15:48 Justin Lecher
2012-10-21 12:52 Reinis Danne
2012-10-20 16:41 Reinis Danne
2012-08-28 16:53 Reinis Danne
2012-03-03 22:11 Reinis Danne
2011-10-26 20:06 Reinis Danne
2011-10-25 22:40 Reinis Danne
2011-07-28 13:08 Alexey Shvetsov
2011-06-25 17:21 Justin Lecher
2011-06-05 0:21 Reinis Danne
2011-03-08 13:40 Alexey Shvetsov
2011-03-07 1:49 Alexey Shvetsov
2011-03-06 21:40 Alexey Shvetsov
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