1 |
commit: 8ce9886cd5e61b892ee7e1087c09013e310a15ea |
2 |
Author: Reinis Danne <rei4dan <AT> gmail <DOT> com> |
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AuthorDate: Sat Mar 3 20:54:44 2012 +0000 |
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Commit: Reinis Danne <rei4dan <AT> gmail <DOT> com> |
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CommitDate: Sat Mar 3 20:54:44 2012 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8ce9886c |
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|
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sci-chemistry/ambertools: Add bugfixes 22-27 |
9 |
|
10 |
--- |
11 |
sci-chemistry/ambertools/ChangeLog | 8 +- |
12 |
sci-chemistry/ambertools/ambertools-1.5-r3.ebuild | 157 + |
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.../files/ambertools-1.5-bugfix_22-27.patch | 3343 ++++++++++++++++++++ |
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3 files changed, 3507 insertions(+), 1 deletions(-) |
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|
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diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog |
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index 50f0545..0945272 100644 |
18 |
--- a/sci-chemistry/ambertools/ChangeLog |
19 |
+++ b/sci-chemistry/ambertools/ChangeLog |
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@@ -1,7 +1,13 @@ |
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# ChangeLog for sci-chemistry/ambertools |
22 |
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 |
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+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 |
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# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $ |
25 |
|
26 |
+*ambertools-1.5-r3 (03 Mar 2012) |
27 |
+ |
28 |
+ 03 Mar 2012; Reinis Danne <rei4dan@×××××.com> +ambertools-1.5-r3.ebuild, |
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+ +files/ambertools-1.5-bugfix_22-27.patch: |
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+ Add bugfixes 22-27. |
31 |
+ |
32 |
26 Oct 2011; Reinis Danne <rei4dan@×××××.com> |
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files/ambertools-1.5-gentoo2.patch: |
34 |
Fix possible buffer overflow. |
35 |
|
36 |
diff --git a/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild b/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild |
37 |
new file mode 100644 |
38 |
index 0000000..bebf36c |
39 |
--- /dev/null |
40 |
+++ b/sci-chemistry/ambertools/ambertools-1.5-r3.ebuild |
41 |
@@ -0,0 +1,157 @@ |
42 |
+# Copyright 1999-2012 Gentoo Foundation |
43 |
+# Distributed under the terms of the GNU General Public License v2 |
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+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ambertools-1.5-r1.ebuild,v 1.2 2011/08/02 14:42:37 alexxy Exp $ |
45 |
+ |
46 |
+EAPI=4 |
47 |
+ |
48 |
+inherit eutils fortran-2 toolchain-funcs |
49 |
+ |
50 |
+DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" |
51 |
+HOMEPAGE="http://ambermd.org/#AmberTools" |
52 |
+SRC_URI=" |
53 |
+ AmberTools-${PV}.tar.bz2" |
54 |
+ |
55 |
+LICENSE="GPL-2" |
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+SLOT="0" |
57 |
+KEYWORDS="~amd64 ~x86 ~amd64-linux" |
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+IUSE="openmp X" |
59 |
+ |
60 |
+RESTRICT="fetch" |
61 |
+ |
62 |
+RDEPEND=" |
63 |
+ virtual/cblas |
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+ virtual/lapack |
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+ sci-libs/clapack |
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+ sci-libs/arpack |
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+ sci-libs/cifparse-obj |
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+ sci-chemistry/mopac7 |
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+ sci-libs/netcdf |
70 |
+ sci-libs/fftw:2.1 |
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+ sci-chemistry/reduce |
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+ virtual/fortran" |
73 |
+DEPEND="${RDEPEND} |
74 |
+ dev-util/byacc |
75 |
+ dev-libs/libf2c |
76 |
+ sys-devel/ucpp" |
77 |
+S="${WORKDIR}/amber11" |
78 |
+ |
79 |
+pkg_nofetch() { |
80 |
+ einfo "Go to ${HOMEPAGE} and get ${A}" |
81 |
+ einfo "Place it in ${DISTDIR}" |
82 |
+} |
83 |
+ |
84 |
+pkg_setup() { |
85 |
+ fortran-2_pkg_setup |
86 |
+ if use openmp; then |
87 |
+ tc-has-openmp || \ |
88 |
+ die "Please select an openmp capable compiler like gcc[openmp]" |
89 |
+ fi |
90 |
+ AMBERHOME="${S}" |
91 |
+} |
92 |
+ |
93 |
+src_prepare() { |
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+ epatch \ |
95 |
+ "${FILESDIR}/${P}-bugfix_1-21.patch" \ |
96 |
+ "${FILESDIR}/${P}-bugfix_22-27.patch" \ |
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+ "${FILESDIR}/${P}-gentoo2.patch" |
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+ cd "${S}"/AmberTools/src |
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+ rm -r \ |
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+ arpack \ |
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+ blas \ |
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+ byacc \ |
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+ lapack \ |
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+ fftw-2.1.5 \ |
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+ fftw-3.2.2 \ |
106 |
+ c9x-complex \ |
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+ cifparse \ |
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+ netcdf \ |
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+ pnetcdf \ |
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+ reduce \ |
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+ ucpp-1.3 \ |
112 |
+ || die |
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+} |
114 |
+ |
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+src_configure() { |
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+ cd "${S}"/AmberTools/src |
117 |
+ sed -e "s:\\\\\$(LIBDIR)/arpack.a:-larpack:g" \ |
118 |
+ -e "s:\\\\\$(LIBDIR)/lapack.a:$(pkg-config lapack --libs) -lclapack:g" \ |
119 |
+ -e "s:\\\\\$(LIBDIR)/blas.a:$(pkg-config blas cblas --libs):g" \ |
120 |
+ -e "s:\\\\\$(LIBDIR)/libdrfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ |
121 |
+ -e "s:\\\\\$(LIBDIR)/libdfftw.a:${EPREFIX}/usr/$(get_libdir)/libdrfftw.a:g" \ |
122 |
+ -e "s:GENTOO_CFLAGS:${CFLAGS} -DBINTRAJ :g" \ |
123 |
+ -e "s:GENTOO_CXXFLAGS:${CXXFLAGS}:g" \ |
124 |
+ -e "s:GENTOO_FFLAGS:${FFLAGS}:g" \ |
125 |
+ -e "s:GENTOO_LDFLAGS:${LDFLAGS}:g" \ |
126 |
+ -e "s:fc=g77:fc=$(tc-getFC):g" \ |
127 |
+ -e "s:\$netcdflib:$(pkg-config netcdf --libs):g" \ |
128 |
+ -e "s:NETCDF=\$netcdf:NETCDF=netcdf.mod:g" \ |
129 |
+ -i configure || die |
130 |
+ sed -e "s:arsecond_:arscnd_:g" \ |
131 |
+ -i sff/time.c \ |
132 |
+ -i sff/sff.h \ |
133 |
+ -i sff/sff.c || die |
134 |
+ sed -e "s:\$(NAB):\$(NAB) -lrfftw:g" \ |
135 |
+ -i nss/Makefile || die |
136 |
+ |
137 |
+ local myconf |
138 |
+ |
139 |
+ use X || myconf="${myconf} -noX11" |
140 |
+ |
141 |
+ use openmp && myconf="${myconf} -openmp" |
142 |
+ |
143 |
+ ./configure \ |
144 |
+ ${myconf} \ |
145 |
+ -nobintraj \ |
146 |
+ -nomdgx \ |
147 |
+ -nomtkpp \ |
148 |
+ -nopython \ |
149 |
+ -nosleap \ |
150 |
+ gnu |
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+} |
152 |
+ |
153 |
+src_compile() { |
154 |
+ cd "${S}"/AmberTools/src |
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+ emake || die |
156 |
+} |
157 |
+ |
158 |
+src_test() { |
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+ cd "${S}"/AmberTools/test |
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+ make test || die |
161 |
+} |
162 |
+ |
163 |
+src_install() { |
164 |
+ rm -r bin/chemistry bin/MMPBSA_mods |
165 |
+ rm bin/ante-MMPBSA.py bin/extractFrcmod.py |
166 |
+ |
167 |
+ for x in bin/* |
168 |
+ do dobin ${x} || die |
169 |
+ done |
170 |
+ |
171 |
+ dobin AmberTools/src/antechamber/mopac.sh |
172 |
+ sed -e "s:\$AMBERHOME/bin/mopac:mopac7:g" \ |
173 |
+ -i "${ED}/usr/bin/mopac.sh" || die |
174 |
+ |
175 |
+ # Make symlinks untill binpath for amber will be fixed |
176 |
+ dodir /usr/share/${PN}/bin |
177 |
+ cd "${ED}/usr/bin" |
178 |
+ for x in * |
179 |
+ do dosym /usr/bin/${x} /usr/share/${PN}/bin/${x} |
180 |
+ done |
181 |
+ cd "${S}" |
182 |
+ |
183 |
+ dodoc doc/AmberTools.pdf doc/leap_pg.pdf |
184 |
+ dolib.a lib/* |
185 |
+ insinto /usr/include/${PN} |
186 |
+ doins include/* |
187 |
+ insinto /usr/share/${PN} |
188 |
+ doins -r dat |
189 |
+ cd AmberTools |
190 |
+ doins -r benchmarks |
191 |
+ doins -r examples |
192 |
+ doins -r test |
193 |
+ |
194 |
+ cat >> "${T}"/99ambertools <<- EOF |
195 |
+ AMBERHOME="${EPREFIX}/usr/share/ambertools" |
196 |
+ EOF |
197 |
+ doenvd "${T}"/99ambertools |
198 |
+} |
199 |
|
200 |
diff --git a/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_22-27.patch b/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_22-27.patch |
201 |
new file mode 100644 |
202 |
index 0000000..6df705c |
203 |
--- /dev/null |
204 |
+++ b/sci-chemistry/ambertools/files/ambertools-1.5-bugfix_22-27.patch |
205 |
@@ -0,0 +1,3343 @@ |
206 |
+diff -urN amber11.orig/AmberTools/examples/mtkpp/MCPB/run.MCPB.csh amber11/AmberTools/examples/mtkpp/MCPB/run.MCPB.csh |
207 |
+--- amber11.orig/AmberTools/examples/mtkpp/MCPB/run.MCPB.csh 2011-04-14 15:30:12.000000000 +0300 |
208 |
++++ amber11/AmberTools/examples/mtkpp/MCPB/run.MCPB.csh 2012-03-03 20:03:01.387032575 +0200 |
209 |
+@@ -2,111 +2,10 @@ |
210 |
+ echo " " |
211 |
+ echo " MTK++ MCPB example " |
212 |
+ echo " " |
213 |
+- |
214 |
+-# Clean up |
215 |
+-rm -rf 1AMP_OH.README |
216 |
+-rm -rf *.bcl |
217 |
+-rm -rf createLibraries.sh createRespAdditions.sh getCharges.sh |
218 |
+-rm -rf *.pdb |
219 |
+-rm -rf *.log |
220 |
+- |
221 |
+-cp data/*.pdb . |
222 |
+-cp data/*.bcl . |
223 |
+-cp data/*.log . |
224 |
+-cp data/*.fchk . |
225 |
+- |
226 |
+-echo "Generating scripts " |
227 |
+-sh genMetalFF.sh -n 1AMP_OH |
228 |
+- |
229 |
+-cp data/1AMP.pdb . |
230 |
+-cp data/1AMP_OH_fixed.pdb . |
231 |
+-cp data/1AMP_OH_sidechain.bcl . |
232 |
+-cp data/1AMP_OH_addStdMol.bcl . |
233 |
+-cp data/1AMP_OH_large.bcl . |
234 |
+-cp data/1AMP_OH_large_mk.log . |
235 |
+- |
236 |
+-cp data/1AMP_OH_sidechain_fc_md.log . |
237 |
+-cp data/1AMP_OH_sidechain_opt_md.fchk . |
238 |
+-cp data/1AMP_OH_sidechain_opt_md.log . |
239 |
+- |
240 |
+-echo "Adding Hydrogens to pdb file " |
241 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_addHs.bcl \ |
242 |
+- -l 1AMP_OH_addHs.bcl.log || goto error |
243 |
+- |
244 |
+-echo "Creating Model 1" |
245 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_sidechain.bcl \ |
246 |
+- -l 1AMP_OH_sidechain.bcl.log || goto error |
247 |
+- |
248 |
+-echo "Adding standard molecule to library " |
249 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_addStdMol.bcl \ |
250 |
+- -l 1AMP_OH_addStdMol.bcl.log || goto error |
251 |
+- |
252 |
+-echo "Creating Model 2 " |
253 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large.bcl \ |
254 |
+- -l 1AMP_OH_large.bcl.log || goto error |
255 |
+- |
256 |
+-echo "Creating RESP files 0 " |
257 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_mk0.bcl \ |
258 |
+- -l 1AMP_OH_large_mk0.bcl.log || goto error |
259 |
+-mv 1AMP_OH_large_respAdds 1AMP_OH_large_respAdds0 || goto error |
260 |
+- |
261 |
+-echo "Creating RESP files 1 " |
262 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_mk1.bcl \ |
263 |
+- -l 1AMP_OH_large_mk1.bcl.log || goto error |
264 |
+-mv 1AMP_OH_large_respAdds 1AMP_OH_large_respAdds1 || goto error |
265 |
+- |
266 |
+-echo "Creating RESP files 2 " |
267 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_mk2.bcl \ |
268 |
+- -l 1AMP_OH_large_mk2.bcl.log || goto error |
269 |
+-mv 1AMP_OH_large_respAdds 1AMP_OH_large_respAdds2 || goto error |
270 |
+- |
271 |
+-echo "Creating RESP files 3 " |
272 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_mk3.bcl \ |
273 |
+- -l 1AMP_OH_large_mk3.bcl.log || goto error |
274 |
+-mv 1AMP_OH_large_respAdds 1AMP_OH_large_respAdds3 || goto error |
275 |
+- |
276 |
+-echo "Determining charges " |
277 |
+-sh ./getCharges.sh 0 || goto error |
278 |
+-sh ./getCharges.sh 1 || goto error |
279 |
+-sh ./getCharges.sh 2 || goto error |
280 |
+-sh ./getCharges.sh 3 || goto error |
281 |
+- |
282 |
+-echo "Creating library files " |
283 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_chg0.bcl \ |
284 |
+- -l 1AMP_OH_large_chg0.bcl.log || goto error |
285 |
+- |
286 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_chg1.bcl \ |
287 |
+- -l 1AMP_OH_large_chg1.bcl.log || goto error |
288 |
+- |
289 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_chg2.bcl \ |
290 |
+- -l 1AMP_OH_large_chg2.bcl.log || goto error |
291 |
+- |
292 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_large_chg3.bcl \ |
293 |
+- -l 1AMP_OH_large_chg3.bcl.log || goto error |
294 |
+- |
295 |
+-echo "Determining Seminario force constants " |
296 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_sidechain_fc_sem.bcl \ |
297 |
+- -l 1AMP_OH_sidechain_fc_sem.bcl.log || goto error |
298 |
+- |
299 |
+-echo "Determining Traditional force constants " |
300 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_sidechain_fc_md.bcl \ |
301 |
+- -l 1AMP_OH_sidechain_fc_md.bcl.log || goto error |
302 |
+- |
303 |
+-echo "Exporting Seminario library to AMBER format " |
304 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_toAmberFormats_sem.bcl \ |
305 |
+- -l 1AMP_OH_toAmberFormats_sem.bcl.log || goto error |
306 |
+- |
307 |
+-echo "Exporting Traditional library to AMBER format " |
308 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_toAmberFormats_md.bcl \ |
309 |
+- -l 1AMP_OH_toAmberFormats_md.bcl.log || goto error |
310 |
+- |
311 |
+-echo "Reading protonated file and updating residue names " |
312 |
+-$AMBERHOME/bin/MCPB -i 1AMP_OH_resNames.bcl \ |
313 |
+- -l 1AMP_OH_resNames.bcl.log || goto error |
314 |
+- |
315 |
+-echo No errors detected |
316 |
++echo " " |
317 |
++echo " This example has been removed due to incompatibility with" |
318 |
++echo " the current minor revision of MTK++. An updated MCPB example" |
319 |
++echo " is planned for a future release." |
320 |
++echo " " |
321 |
+ exit(0) |
322 |
+ |
323 |
+-error: |
324 |
+-echo Problem: check log files and try again |
325 |
+-exit(1) |
326 |
+diff -urN amber11.orig/AmberTools/examples/mtkpp/stats/pca1/run.stats.csh amber11/AmberTools/examples/mtkpp/stats/pca1/run.stats.csh |
327 |
+--- amber11.orig/AmberTools/examples/mtkpp/stats/pca1/run.stats.csh 2011-04-14 15:30:12.000000000 +0300 |
328 |
++++ amber11/AmberTools/examples/mtkpp/stats/pca1/run.stats.csh 2012-03-03 20:03:01.387032575 +0200 |
329 |
+@@ -3,12 +3,12 @@ |
330 |
+ echo " MTK++ stats example" |
331 |
+ echo " " |
332 |
+ |
333 |
+-../$AMBERHOME/bin/stats -i pca.stats \ |
334 |
+- -l pca.stats.log || goto error |
335 |
++$AMBERHOME/bin/stats -i pca.stats \ |
336 |
++ -l pca.stats.log || goto error |
337 |
+ |
338 |
+ echo No errors detected |
339 |
+ exit(0) |
340 |
+ |
341 |
+ error: |
342 |
+ echo Problem: check .out and try again |
343 |
+-exit(1) |
344 |
+\ Nav jaunu rindu faila beigās |
345 |
++exit(1) |
346 |
+diff -urN amber11.orig/AmberTools/src/configure amber11/AmberTools/src/configure |
347 |
+--- amber11.orig/AmberTools/src/configure 2012-03-03 22:42:38.558776473 +0200 |
348 |
++++ amber11/AmberTools/src/configure 2012-03-03 20:02:57.727033628 +0200 |
349 |
+@@ -61,6 +61,9 @@ |
350 |
+ -debug Compile with debug symbols |
351 |
+ -noopt Disable all compiler optimisations (sometimes needed if |
352 |
+ debug symbols are requested) |
353 |
++ -nopatch Do NOT run \$AMBERHOME/AT15_Amber11.py after configure writes |
354 |
++ the config.h file, even if Amber11 is found in the directory. |
355 |
++ This flag has no effect if Amber11 is not present. |
356 |
+ |
357 |
+ Rarely used/tested NAB options: |
358 |
+ -scalapack Use ScaLAPACK for linear algebra. Do not use in |
359 |
+@@ -165,6 +168,7 @@ |
360 |
+ debug='no' |
361 |
+ optimise='yes' |
362 |
+ is_mac='no' |
363 |
++nopatch='no' |
364 |
+ |
365 |
+ #------------------------------------------------------------------------------ |
366 |
+ # Architecture specific: |
367 |
+@@ -216,6 +220,7 @@ |
368 |
+ -nomtkpp) mtkpp='';; |
369 |
+ -debug) debug='yes';; |
370 |
+ -noopt) optimise='no';; |
371 |
++ -nopatch) nopatch='yes';; |
372 |
+ -help) usage;; |
373 |
+ --help) usage;; |
374 |
+ -h) usage;; |
375 |
+@@ -2144,7 +2149,7 @@ |
376 |
+ fi |
377 |
+ |
378 |
+ # For AmberTools 1.5 + Amber 11, print a message about running AT15_Amber11.py |
379 |
+-if [ -d ../../src/sander ]; then |
380 |
++if [ -d ../../src/sander -a "$nopatch" = 'yes' ]; then |
381 |
+ echo "" |
382 |
+ echo " NOTE: after installing AmberTools, if you want to compile" |
383 |
+ echo " Amber11 using AmberTools 1.5, you must run the " |
384 |
+@@ -2155,5 +2160,14 @@ |
385 |
+ echo " script will modify your Amber11 files.)" |
386 |
+ fi |
387 |
+ |
388 |
++if [ -d ../../src/sander -a "$nopatch" = 'no' ]; then |
389 |
++ echo "" |
390 |
++ echo " Running \$AMBERHOME/AT15_Amber11.py to patch config.h for building Amber 11." |
391 |
++ echo " Check Amber11_Conversion.log for details of what was done. Running this script" |
392 |
++ echo " a second time has no effect (positive or negative)" |
393 |
++ echo "" |
394 |
++ ../../AT15_Amber11.py > Amber11_Conversion.log 2>&1 |
395 |
++fi |
396 |
++ |
397 |
+ exit |
398 |
+ |
399 |
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/AmberRestart.cpp amber11/AmberTools/src/cpptraj/src/AmberRestart.cpp |
400 |
+--- amber11.orig/AmberTools/src/cpptraj/src/AmberRestart.cpp 2012-03-03 22:42:00.557775196 +0200 |
401 |
++++ amber11/AmberTools/src/cpptraj/src/AmberRestart.cpp 2012-03-03 20:03:06.928030979 +0200 |
402 |
+@@ -53,7 +53,7 @@ |
403 |
+ mprintf("Error: AmberRestart::open(): Reading restart atoms/time.\n"); |
404 |
+ return 1; |
405 |
+ } |
406 |
+- nread=sscanf(buffer,"%5i%15lE%15lE",&restartAtoms,&restartTime,&restartTemp); |
407 |
++ nread=sscanf(buffer,"%i %lE %lE",&restartAtoms,&restartTime,&restartTemp); |
408 |
+ if (nread<1) { |
409 |
+ mprintf("Error: AmberRestart::open(): Getting restart atoms/time.\n"); |
410 |
+ return 1; |
411 |
+diff -urN amber11.orig/AmberTools/src/cpptraj/src/main.cpp amber11/AmberTools/src/cpptraj/src/main.cpp |
412 |
+--- amber11.orig/AmberTools/src/cpptraj/src/main.cpp 2012-03-03 22:42:47.132776753 +0200 |
413 |
++++ amber11/AmberTools/src/cpptraj/src/main.cpp 2012-03-03 20:03:06.928030979 +0200 |
414 |
+@@ -6,7 +6,7 @@ |
415 |
+ #include "PtrajMpi.h" |
416 |
+ #include "CpptrajStdio.h" |
417 |
+ #ifndef CPPTRAJ_VERSION_STRING |
418 |
+-#define CPPTRAJ_VERSION_STRING "V1.1.1" |
419 |
++#define CPPTRAJ_VERSION_STRING "V1.1.2" |
420 |
+ #endif |
421 |
+ |
422 |
+ void Usage(char *programName) { |
423 |
+diff -urN amber11.orig/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py |
424 |
+--- amber11.orig/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py 2011-04-14 15:30:17.000000000 +0300 |
425 |
++++ amber11/AmberTools/src/mmpbsa_py/MMPBSA_mods/amberoutputs.py 2012-03-03 20:03:11.481029669 +0200 |
426 |
+@@ -2315,7 +2315,7 @@ |
427 |
+ return math.sqrt(abs(_stdev(self.com_data[0]) ** 2 + _stdev(self.rec_data[0]) ** 2 + _stdev(self.lig_data[0]) ** 2)) |
428 |
+ |
429 |
+ sum = sum2 = 0 |
430 |
+- for i in range(len(self.com_data)): |
431 |
++ for i in range(len(self.com_data[0])): |
432 |
+ sum += self.com_data[0][i] - self.rec_data[0][i] - self.lig_data[0][i] |
433 |
+ sum2 += (self.com_data[0][i] - self.rec_data[0][i] - self.lig_data[0][i]) ** 2 |
434 |
+ |
435 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/configure amber11/AmberTools/src/mtkpp/configure |
436 |
+--- amber11.orig/AmberTools/src/mtkpp/configure 2011-04-14 15:30:18.000000000 +0300 |
437 |
++++ amber11/AmberTools/src/mtkpp/configure 2012-03-03 20:03:01.397032571 +0200 |
438 |
+@@ -788,7 +788,6 @@ |
439 |
+ with_gnu_ld |
440 |
+ with_sysroot |
441 |
+ enable_libtool_lock |
442 |
+-with_gnu_ld |
443 |
+ with_mkl_dir |
444 |
+ with_mkl_libs |
445 |
+ with_boost |
446 |
+@@ -811,22 +810,9 @@ |
447 |
+ CCC |
448 |
+ CC |
449 |
+ CFLAGS |
450 |
+-LDFLAGS |
451 |
+-LIBS |
452 |
+-CPPFLAGS |
453 |
+ CPP |
454 |
+-CPPFLAGS |
455 |
+ CXXCPP |
456 |
+-CPPFLAGS |
457 |
+-XMKMF |
458 |
+-CXX |
459 |
+-LDFLAGS |
460 |
+-LIBS |
461 |
+-CPPFLAGS |
462 |
+-CCC |
463 |
+-CC |
464 |
+-LDFLAGS |
465 |
+-LIBS' |
466 |
++XMKMF' |
467 |
+ |
468 |
+ |
469 |
+ # Initialize some variables set by options. |
470 |
+@@ -16665,7 +16651,7 @@ |
471 |
+ *) platform=UNKNOWN |
472 |
+ is_unknown=yes |
473 |
+ echo 'ERROR: this platform is not supported at this time!' |
474 |
+- exit 1 ;; |
475 |
++ exit ;; |
476 |
+ esac |
477 |
+ if test "$is_darwin" = "yes"; then |
478 |
+ IS_DARWIN_TRUE= |
479 |
+@@ -17838,8 +17824,8 @@ |
480 |
+ $as_echo "#define HAVE_ZLIB 1" >>confdefs.h |
481 |
+ |
482 |
+ CFLAGS=$CFLAGS" -DHAVE_ZLIB" |
483 |
+- CXXFLAGS=$CXXFLAGS" -DHAVE_ZLIB -DHAVE_ZLIB" |
484 |
+- defines_string=$defines_string" -DHAVE_ZLIB -DHAVE_ZLIB" |
485 |
++ CXXFLAGS=$CXXFLAGS" -DHAVE_ZLIB" |
486 |
++ defines_string=$defines_string" -DHAVE_ZLIB" |
487 |
+ FLIBS=$FLIBS" -lz" |
488 |
+ else |
489 |
+ |
490 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/configure.in amber11/AmberTools/src/mtkpp/configure.in |
491 |
+--- amber11.orig/AmberTools/src/mtkpp/configure.in 2011-04-14 15:30:18.000000000 +0300 |
492 |
++++ amber11/AmberTools/src/mtkpp/configure.in 2012-03-03 20:03:01.400032571 +0200 |
493 |
+@@ -383,7 +383,7 @@ |
494 |
+ *) platform=UNKNOWN |
495 |
+ is_unknown=yes |
496 |
+ echo 'ERROR: this platform is not supported at this time!' |
497 |
+- exit 1 ;; |
498 |
++ exit ;; |
499 |
+ esac |
500 |
+ AM_CONDITIONAL(IS_DARWIN, test "$is_darwin" = "yes") |
501 |
+ AM_CONDITIONAL(IS_LINUX, test "$is_linux" = "yes") |
502 |
+@@ -457,8 +457,8 @@ |
503 |
+ if test $ac_have_zlibh = yes; then |
504 |
+ AC_DEFINE(HAVE_ZLIB, 1, [Define to 1 if ZLIB is available.]) |
505 |
+ CFLAGS=$CFLAGS" -DHAVE_ZLIB" |
506 |
+- CXXFLAGS=$CXXFLAGS" -DHAVE_ZLIB -DHAVE_ZLIB" |
507 |
+- defines_string=$defines_string" -DHAVE_ZLIB -DHAVE_ZLIB" |
508 |
++ CXXFLAGS=$CXXFLAGS" -DHAVE_ZLIB" |
509 |
++ defines_string=$defines_string" -DHAVE_ZLIB" |
510 |
+ FLIBS=$FLIBS" -lz" |
511 |
+ else |
512 |
+ AC_DEFINE(HAVE_ZLIB, 0, [Define to 0 if ZLIB is unavailable.]) |
513 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Minimizers/Makefile.am amber11/AmberTools/src/mtkpp/src/Minimizers/Makefile.am |
514 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Minimizers/Makefile.am 2011-04-14 15:30:18.000000000 +0300 |
515 |
++++ amber11/AmberTools/src/mtkpp/src/Minimizers/Makefile.am 2012-03-03 20:03:01.400032571 +0200 |
516 |
+@@ -1,4 +1,4 @@ |
517 |
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics/$(SRCDIR) |
518 |
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR) |
519 |
+ DIAGNOSTICS_LIB=-lDiagnostics |
520 |
+ INCLUDES = -I$(srcdir)/.. |
521 |
+ |
522 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Minimizers/Makefile.in amber11/AmberTools/src/mtkpp/src/Minimizers/Makefile.in |
523 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Minimizers/Makefile.in 2011-04-14 15:30:18.000000000 +0300 |
524 |
++++ amber11/AmberTools/src/mtkpp/src/Minimizers/Makefile.in 2012-03-03 20:03:01.401032571 +0200 |
525 |
+@@ -239,7 +239,7 @@ |
526 |
+ top_builddir = @top_builddir@ |
527 |
+ top_srcdir = @top_srcdir@ |
528 |
+ xerces_path = @xerces_path@ |
529 |
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics/$(SRCDIR) |
530 |
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR) |
531 |
+ DIAGNOSTICS_LIB = -lDiagnostics |
532 |
+ INCLUDES = -I$(srcdir)/.. |
533 |
+ lib_LTLIBRARIES = libMinimizers.la |
534 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/MM/Makefile.am amber11/AmberTools/src/mtkpp/src/MM/Makefile.am |
535 |
+--- amber11.orig/AmberTools/src/mtkpp/src/MM/Makefile.am 2011-04-14 15:30:18.000000000 +0300 |
536 |
++++ amber11/AmberTools/src/mtkpp/src/MM/Makefile.am 2012-03-03 20:03:01.400032571 +0200 |
537 |
+@@ -1,6 +1,6 @@ |
538 |
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics/$(SRCDIR) |
539 |
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR) |
540 |
+ DIAGNOSTICS_LIB=-lDiagnostics |
541 |
+-LOG_LD=-L$(top_builddir)/src/Log/$(SRCDIR) |
542 |
++LOG_LD=-L$(abs_top_builddir)/src/Log/$(SRCDIR) |
543 |
+ LOG_LIB=-lLog |
544 |
+ |
545 |
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/.. |
546 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/MM/Makefile.in amber11/AmberTools/src/mtkpp/src/MM/Makefile.in |
547 |
+--- amber11.orig/AmberTools/src/mtkpp/src/MM/Makefile.in 2011-04-14 15:30:18.000000000 +0300 |
548 |
++++ amber11/AmberTools/src/mtkpp/src/MM/Makefile.in 2012-03-03 20:03:01.400032571 +0200 |
549 |
+@@ -241,9 +241,9 @@ |
550 |
+ top_builddir = @top_builddir@ |
551 |
+ top_srcdir = @top_srcdir@ |
552 |
+ xerces_path = @xerces_path@ |
553 |
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics/$(SRCDIR) |
554 |
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR) |
555 |
+ DIAGNOSTICS_LIB = -lDiagnostics |
556 |
+-LOG_LD = -L$(top_builddir)/src/Log/$(SRCDIR) |
557 |
++LOG_LD = -L$(abs_top_builddir)/src/Log/$(SRCDIR) |
558 |
+ LOG_LIB = -lLog |
559 |
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/.. |
560 |
+ lib_LTLIBRARIES = libMM.la |
561 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/atomType.h amber11/AmberTools/src/mtkpp/src/Molecule/atomType.h |
562 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/atomType.h 2011-04-14 15:30:18.000000000 +0300 |
563 |
++++ amber11/AmberTools/src/mtkpp/src/Molecule/atomType.h 2012-03-03 20:03:01.402032570 +0200 |
564 |
+@@ -74,6 +74,9 @@ |
565 |
+ |
566 |
+ //! |
567 |
+ double evalue; |
568 |
++ |
569 |
++ //! Atomic polarizability in A**3 |
570 |
++ double atomPolarizability; |
571 |
+ }; |
572 |
+ |
573 |
+ // ============================================================ |
574 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/collection.cpp amber11/AmberTools/src/mtkpp/src/Molecule/collection.cpp |
575 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/collection.cpp 2011-04-14 15:30:18.000000000 +0300 |
576 |
++++ amber11/AmberTools/src/mtkpp/src/Molecule/collection.cpp 2012-03-03 20:03:01.403032569 +0200 |
577 |
+@@ -484,6 +484,11 @@ |
578 |
+ for (moleculeIterator m = this->itsMoleculeList.begin(); |
579 |
+ m != this->itsMoleculeList.end(); m++) { |
580 |
+ pMolecule = *m; |
581 |
++ |
582 |
++ if (pMolecule->getName() == "Reference") { |
583 |
++ continue; |
584 |
++ } |
585 |
++ |
586 |
+ std::vector<submolecule*> subMolList = pMolecule->getSubMoleculeList(); |
587 |
+ for (sMolIterator c = subMolList.begin(); c != subMolList.end(); c++) { |
588 |
+ pSubMolecule = *c; |
589 |
+@@ -3408,7 +3413,10 @@ |
590 |
+ } |
591 |
+ errMessage += metalAtom->getParent()->getName() + "@|" |
592 |
+ + metalAtom->getName() + "|-" |
593 |
+- + primShellAtoms[e]->getParent()->getName() + "@|" |
594 |
++ + primShellAtoms[e]->getParent()->getName() |
595 |
++ + i2s(primShellAtoms[e]->getParent()->getSubMolId()) |
596 |
++ + primShellAtoms[e]->getParent()->getiCode() |
597 |
++ + "@|" |
598 |
+ + primShellAtoms[e]->getName() + "| dist = " + d2s(localBond->size) +"\n"; |
599 |
+ |
600 |
+ // Angles |
601 |
+@@ -3488,7 +3496,8 @@ |
602 |
+ std::vector<stdGroup*> stdGrpList = this->pStdLibrary->getStdGroupList(); |
603 |
+ |
604 |
+ for (unsigned int i = 0; i < stdGrpList.size(); i++) { |
605 |
+-//std::cout << i << " " << stdGrpList.size() << " " << stdGrpList[i]->getName() << " " << stdGrpList[i]->hasStdMolecule() << std::endl; |
606 |
++//std::cout << "\n\ncollection::assignMetalParameters " << i << " " << stdGrpList.size() << " " << stdGrpList[i]->getName() << " " |
607 |
++// << stdGrpList[i]->hasStdMolecule() << std::endl; |
608 |
+ if (stdGrpList[i]->hasStdMolecule()) { |
609 |
+ //std::cout << "stdgroup name: " << stdGrpList[i]->getName() << std::endl; |
610 |
+ //stdGroup* pStdGroup = stdGrpList[i]; |
611 |
+@@ -3515,6 +3524,7 @@ |
612 |
+ |
613 |
+ // create new molecule |
614 |
+ molecule* pNewMolecule = this->addMolecule(); |
615 |
++ std::vector<atom*> atomList; |
616 |
+ |
617 |
+ // copy residues |
618 |
+ std::vector<metalCenter*> metCens = itsMetalGroups[j]->getMetalCenters(); |
619 |
+@@ -3536,6 +3546,10 @@ |
620 |
+ addedResidues.push_back(primShellAtoms[l]->getParent()); |
621 |
+ submolecule* pNewSubmolecule = pNewMolecule->addSubMolecule(); |
622 |
+ pNewSubmolecule->copy(primShellAtoms[l]->getParent()); |
623 |
++ std::vector<atom*> atomListTmp = primShellAtoms[l]->getParent()->getAtomList(); |
624 |
++ for (unsigned int i = 0 ; i < atomListTmp.size(); i++) { |
625 |
++ atomList.push_back(atomListTmp[i]); |
626 |
++ } |
627 |
+ /* |
628 |
+ std::cout << "Primary Shell " << primShellAtoms[l]->getParent()->getName() << " " |
629 |
+ << primShellAtoms[l]->getParent()->getSubMolId() << " " |
630 |
+@@ -3556,6 +3570,11 @@ |
631 |
+ addedResidues.push_back(secShellAtoms[l]->getParent()); |
632 |
+ submolecule* pNewSubmolecule = pNewMolecule->addSubMolecule(); |
633 |
+ pNewSubmolecule->copy(secShellAtoms[l]->getParent()); |
634 |
++ |
635 |
++ std::vector<atom*> atomListTmp = secShellAtoms[l]->getParent()->getAtomList(); |
636 |
++ for (unsigned int i = 0 ; i < atomListTmp.size(); i++) { |
637 |
++ atomList.push_back(atomListTmp[i]); |
638 |
++ } |
639 |
+ /* |
640 |
+ std::cout << "Secondary Shell " << secShellAtoms[l]->getParent()->getName() << " " |
641 |
+ << secShellAtoms[l]->getParent()->getSubMolId() |
642 |
+@@ -3573,6 +3592,12 @@ |
643 |
+ addedResidues.push_back(metalAtom->getParent()); |
644 |
+ submolecule* pNewSubmolecule = pNewMolecule->addSubMolecule(); |
645 |
+ pNewSubmolecule->copy(metalAtom->getParent()); |
646 |
++ |
647 |
++ std::vector<atom*> atomListTmp = metalAtom->getParent()->getAtomList(); |
648 |
++ for (unsigned int i = 0 ; i < atomListTmp.size(); i++) { |
649 |
++ atomList.push_back(atomListTmp[i]); |
650 |
++ } |
651 |
++ |
652 |
+ /* |
653 |
+ std::cout << "Metal Atom " << metalAtom->getParent()->getName() << " " |
654 |
+ << metalAtom->getParent()->getSubMolId() |
655 |
+@@ -3582,7 +3607,7 @@ |
656 |
+ } |
657 |
+ } |
658 |
+ |
659 |
+-//std::cout << " \n\n NEW MOLECULE \n"; |
660 |
++//std::cout << "NEW MOLECULE \n"; |
661 |
+ |
662 |
+ // Copy bonds |
663 |
+ if (pNewMolecule) { |
664 |
+@@ -3646,16 +3671,26 @@ |
665 |
+ } |
666 |
+ } |
667 |
+ } |
668 |
++ |
669 |
++//std::cout << " After copy " << std::endl; |
670 |
++ |
671 |
+ int nAtomsA = pStdMolecule->getNumAtoms(); |
672 |
+ int nAtomsB = pNewMolecule->getNumAtoms(); |
673 |
++ |
674 |
++ int nBondsA = pStdMolecule->getNumBonds(); |
675 |
++ int nBondsB = pNewMolecule->getNumBonds(); |
676 |
++ |
677 |
+ int nHeavyAtomsA = pStdMolecule->getNumHeavyAtoms(); |
678 |
+ int nHeavyAtomsB = pNewMolecule->getNumHeavyAtoms(); |
679 |
+ |
680 |
++//std::cout << "CHECK " << nAtomsA << " " << nAtomsB << " " << nBondsA << " " << nBondsB << "\n"; |
681 |
+ int w = 0; |
682 |
+ if (nAtomsA != nAtomsB) w++; |
683 |
+ int h = 0; |
684 |
+ if (nHeavyAtomsA != nHeavyAtomsB) h++; |
685 |
+ |
686 |
++//std::cout << " w = " << w << " h = " << h << std::endl; |
687 |
++ |
688 |
+ if (w or h) { |
689 |
+ std::string eMes = " " + stdGrpList[i]->getName() + " is not a match \n"; |
690 |
+ eMes += " std mol nAtoms: " + i2s(nAtomsA) + |
691 |
+@@ -3671,8 +3706,17 @@ |
692 |
+ // Determine corresponences between two molecules |
693 |
+ std::vector<std::vector<int> > correspondenceMatrices; |
694 |
+ //int cor = 0; |
695 |
++//std::cout << " superimpose " << std::endl; |
696 |
+ superimpose* pSuperImpose = new superimpose(); |
697 |
+- int f = pSuperImpose->initializeCorrespondences(pStdMolecule, pNewMolecule, 3, correspondenceMatrices); |
698 |
++ int f = 0; |
699 |
++ try { |
700 |
++ f = pSuperImpose->initializeCorrespondences(pStdMolecule, pNewMolecule, 3, correspondenceMatrices); |
701 |
++ } |
702 |
++ catch (...) { |
703 |
++ f = 1; |
704 |
++ } |
705 |
++ |
706 |
++//std::cout << " after superimpose " << std::endl; |
707 |
+ |
708 |
+ if (f != 0) { |
709 |
+ std::string eMes = " Error initializing correspondences\n " + stdGrpList[i]->getName() + " is not a match \n"; |
710 |
+@@ -3689,6 +3733,8 @@ |
711 |
+ pNewMolecule->getCoordinates(CoordsB); |
712 |
+ int cor = 0; |
713 |
+ |
714 |
++//std::cout << " f = 0 " << std::endl; |
715 |
++ |
716 |
+ double dRMSD = pSuperImpose->rmsd(pStdMolecule, CoordsB, correspondenceMatrices, cor); |
717 |
+ std::string eMes = " " + stdGrpList[i]->getName() + " is a match with rmsd of " + d2s(dRMSD) + "\n"; |
718 |
+ MTKpp::errorLogger.throwError("collection::assignMetalParameters", eMes, INFO); |
719 |
+@@ -3703,38 +3749,52 @@ |
720 |
+ for (int t = 0; t < nHeavyAtoms; t++) { |
721 |
+ for (int t2 = 0; t2 < nHeavyAtoms; t2++) { |
722 |
+ if (correspondenceMatrices[cor][t*nHeavyAtoms+t2]) { |
723 |
+-//std::cout << t+1 << ":" << t2+1 << "; |"; |
724 |
+- |
725 |
+ atom* pA1 = molHeavyAtoms1[t]; |
726 |
+ atom* pA2 = molHeavyAtoms2[t2]; |
727 |
+ |
728 |
+ if (pA1 and pA2) { |
729 |
+-//atom* collection::getAtom(int number, bool atomIndex, bool fileId, bool atomColIndex) |
730 |
+- |
731 |
++ // getAtom(int number, bool atomIndex, bool fileId, bool atomColIndex) |
732 |
+ atom* pOrgAtom = this->getAtom(pA2->getFileID(), 0, 1, 0); |
733 |
+-/* |
734 |
+-std::cout << pA1->getName() << "|" << pA2->getName() << "|" << pOrgAtom->getName() << " " |
735 |
+- << pA1->getParent()->getName() << "|" << pA2->getParent()->getName() << "|" << pOrgAtom->getParent()->getName() << " |" |
736 |
+- << pA1->getFileID() << "|" << pA2->getFileID() << "|" << pOrgAtom->getFileID() << "|" |
737 |
+- << pA1->getColIndex() << "|" << pA2->getColIndex() << "|" << pOrgAtom->getColIndex() |
738 |
+- << " |\n"; |
739 |
+-*/ |
740 |
+- pOrgAtom->getParent()->setName(pA1->getParent()->getName()); |
741 |
++ // atom* pOrgAtom = this->getAtom(pA2->getColIndex(), 0, 0, 1); |
742 |
++ |
743 |
++ |
744 |
++//std::cout << pA1->getName() << "|" << pA2->getName() << "|" << pOrgAtom->getName() << " " |
745 |
++// << pA1->getParent()->getName() << "|" << pA2->getParent()->getName() << "|" << pOrgAtom->getParent()->getName() << " |" |
746 |
++// << pA1->getFileID() << "|" << pA2->getFileID() << "|" << pOrgAtom->getFileID() << "|" |
747 |
++// << pA1->getColIndex() << "|" << pA2->getColIndex() << "|" << pOrgAtom->getColIndex() |
748 |
++// << " |\n"; |
749 |
++ |
750 |
++ //pOrgAtom->getParent()->setName(pA1->getParent()->getName()); |
751 |
++ |
752 |
++ for (unsigned int i = 0 ; i < atomList.size(); i++) { |
753 |
++ if (atomList[i]->getFileID() == pA2->getFileID()) { |
754 |
++ //std::cout << "setting " << atomList[i]->getParent()->getName() << " to " |
755 |
++ // << pA1->getParent()->getName() << "\n"; |
756 |
++ atomList[i]->getParent()->setName(pA1->getParent()->getName()); |
757 |
++ } |
758 |
+ } |
759 |
++//std::cout << pOrgAtom->getParent() << " " << pOrgAtom->getParent()->getName() << " " |
760 |
++//<< pA2->getFileID() |
761 |
++// << " " << pOrgAtom->getParent()->getColIndex() << "\n"; |
762 |
+ } |
763 |
+ } |
764 |
+ } |
765 |
+ } |
766 |
++ |
767 |
++ } |
768 |
+ } |
769 |
+ } |
770 |
+ } |
771 |
++ |
772 |
+ // delete new molecule |
773 |
++ if (pNewMolecule) { |
774 |
+ this->delMolecule(pNewMolecule); |
775 |
+ } |
776 |
+ } |
777 |
+ } |
778 |
+ } |
779 |
+ } |
780 |
++ } |
781 |
+ |
782 |
+ /////////////////////////////////////////////////////////////////////////////// |
783 |
+ /////////////////////////////////////////////////////////////////////////////// |
784 |
+@@ -4377,6 +4437,7 @@ |
785 |
+ } |
786 |
+ std::cout << " TOTAL CHARGE = " << localTotalCharge << std::endl; |
787 |
+ */ |
788 |
++ |
789 |
+ } |
790 |
+ |
791 |
+ // ============================================================ |
792 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/hydrophobize.cpp amber11/AmberTools/src/mtkpp/src/Molecule/hydrophobize.cpp |
793 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/hydrophobize.cpp 2011-04-14 15:30:18.000000000 +0300 |
794 |
++++ amber11/AmberTools/src/mtkpp/src/Molecule/hydrophobize.cpp 2012-03-03 20:03:01.404032569 +0200 |
795 |
+@@ -315,7 +315,7 @@ |
796 |
+ if (!vertices[i]->isVisited()) { |
797 |
+ graph* subGraph = new graph(); |
798 |
+ |
799 |
+- std::cout << "\n " << vertices[i]->getIndex() << " "; |
800 |
++// std::cout << "\n " << vertices[i]->getIndex() << " "; |
801 |
+ molGraph->dfs(vertices[i]); |
802 |
+ |
803 |
+ for (unsigned int j = 0; j < vertices.size(); j++) { |
804 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/Makefile.am amber11/AmberTools/src/mtkpp/src/Molecule/Makefile.am |
805 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/Makefile.am 2011-04-14 15:30:18.000000000 +0300 |
806 |
++++ amber11/AmberTools/src/mtkpp/src/Molecule/Makefile.am 2012-03-03 20:03:01.401032571 +0200 |
807 |
+@@ -1,8 +1,8 @@ |
808 |
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics/$(SRCDIR) |
809 |
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR) |
810 |
+ DIAGNOSTICS_LIB=-lDiagnostics |
811 |
+-GRAPH_LD=-L$(top_builddir)/src/Graph/$(SRCDIR) |
812 |
++GRAPH_LD=-L$(abs_top_builddir)/src/Graph/$(SRCDIR) |
813 |
+ GRAPH_LIB=-lGraph |
814 |
+-LOG_LD=-L$(top_builddir)/src/Log/$(SRCDIR) |
815 |
++LOG_LD=-L$(abs_top_builddir)/src/Log/$(SRCDIR) |
816 |
+ LOG_LIB=-lLog |
817 |
+ |
818 |
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/.. -I$(top_srcdir)/src/eigen3b2 |
819 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/Makefile.in amber11/AmberTools/src/mtkpp/src/Molecule/Makefile.in |
820 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/Makefile.in 2011-04-14 15:30:18.000000000 +0300 |
821 |
++++ amber11/AmberTools/src/mtkpp/src/Molecule/Makefile.in 2012-03-03 20:03:01.401032571 +0200 |
822 |
+@@ -248,11 +248,11 @@ |
823 |
+ top_builddir = @top_builddir@ |
824 |
+ top_srcdir = @top_srcdir@ |
825 |
+ xerces_path = @xerces_path@ |
826 |
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics/$(SRCDIR) |
827 |
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR) |
828 |
+ DIAGNOSTICS_LIB = -lDiagnostics |
829 |
+-GRAPH_LD = -L$(top_builddir)/src/Graph/$(SRCDIR) |
830 |
++GRAPH_LD = -L$(abs_top_builddir)/src/Graph/$(SRCDIR) |
831 |
+ GRAPH_LIB = -lGraph |
832 |
+-LOG_LD = -L$(top_builddir)/src/Log/$(SRCDIR) |
833 |
++LOG_LD = -L$(abs_top_builddir)/src/Log/$(SRCDIR) |
834 |
+ LOG_LIB = -lLog |
835 |
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/.. -I$(top_srcdir)/src/eigen3b2 |
836 |
+ lib_LTLIBRARIES = libMolecule.la |
837 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/parameters.cpp amber11/AmberTools/src/mtkpp/src/Molecule/parameters.cpp |
838 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/parameters.cpp 2011-04-14 15:30:18.000000000 +0300 |
839 |
++++ amber11/AmberTools/src/mtkpp/src/Molecule/parameters.cpp 2012-03-03 20:03:01.404032569 +0200 |
840 |
+@@ -145,6 +145,7 @@ |
841 |
+ pAtomType->description = ""; |
842 |
+ pAtomType->rvalue = 0.0; |
843 |
+ pAtomType->evalue = 0.0; |
844 |
++ pAtomType->atomPolarizability = 0.0; |
845 |
+ pAtomType->groupName = ""; |
846 |
+ pAtomType->optimize = false; |
847 |
+ this->itsTypeList.push_back(pAtomType); |
848 |
+@@ -184,6 +185,7 @@ |
849 |
+ pAtomType->description = a->description; |
850 |
+ pAtomType->rvalue = a->rvalue; |
851 |
+ pAtomType->evalue = a->evalue; |
852 |
++ pAtomType->atomPolarizability = a->atomPolarizability; |
853 |
+ pAtomType->groupName = g; |
854 |
+ pAtomType->optimize = a->optimize; |
855 |
+ |
856 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/parameters.h amber11/AmberTools/src/mtkpp/src/Molecule/parameters.h |
857 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/parameters.h 2011-04-14 15:30:18.000000000 +0300 |
858 |
++++ amber11/AmberTools/src/mtkpp/src/Molecule/parameters.h 2012-03-03 20:03:01.405032569 +0200 |
859 |
+@@ -76,6 +76,9 @@ |
860 |
+ //! Well Depth |
861 |
+ double evalue; |
862 |
+ |
863 |
++ //! Atomic polarizability in A**3 |
864 |
++ double atomPolarizability; |
865 |
++ |
866 |
+ //! group name |
867 |
+ std::string groupName; |
868 |
+ |
869 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdFrag.cpp amber11/AmberTools/src/mtkpp/src/Molecule/stdFrag.cpp |
870 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdFrag.cpp 2011-04-14 15:30:18.000000000 +0300 |
871 |
++++ amber11/AmberTools/src/mtkpp/src/Molecule/stdFrag.cpp 2012-03-03 20:03:01.405032569 +0200 |
872 |
+@@ -305,7 +305,8 @@ |
873 |
+ this->itsSymbol = symbol; |
874 |
+ } |
875 |
+ else { |
876 |
+- std::cout << " Length of Fragment Symbol = " << symbol.size() |
877 |
++ std::cout << " Length of Fragment Symbol (" << symbol |
878 |
++ << ") = " << symbol.size() |
879 |
+ << " --> Must be 3." << std::endl; |
880 |
+ } |
881 |
+ } |
882 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdGroup.cpp amber11/AmberTools/src/mtkpp/src/Molecule/stdGroup.cpp |
883 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdGroup.cpp 2011-04-14 15:30:18.000000000 +0300 |
884 |
++++ amber11/AmberTools/src/mtkpp/src/Molecule/stdGroup.cpp 2012-03-03 20:03:01.406032569 +0200 |
885 |
+@@ -35,6 +35,7 @@ |
886 |
+ #include "stdLibrary.h" |
887 |
+ |
888 |
+ #include "molecule.h" |
889 |
++#include "submolecule.h" |
890 |
+ |
891 |
+ namespace MTKpp |
892 |
+ { |
893 |
+@@ -258,5 +259,24 @@ |
894 |
+ } |
895 |
+ } |
896 |
+ |
897 |
++// ============================================================ |
898 |
++// Function : getCharge() |
899 |
++// ------------------------------------------------------------ |
900 |
++// |
901 |
++// ============================================================ |
902 |
++double stdGroup::getCharge() |
903 |
++{ |
904 |
++ double d = 0.0; |
905 |
++ if (pMolecule) { |
906 |
++ std::vector<submolecule*> sList = this->pMolecule->getSubMoleculeList(); |
907 |
++ for (unsigned int p = 0; p < sList.size(); p++) { |
908 |
++ this->pStdFrag = this->getStdFrag(sList[p]->getName()); |
909 |
++ d += this->pStdFrag->getCharge(); |
910 |
++ //std::cout << this->pStdFrag->getSymbol() << " " << this->pStdFrag->getCharge() << std::endl; |
911 |
++ } |
912 |
++ } |
913 |
++ return d; |
914 |
++} |
915 |
++ |
916 |
+ } // MTKpp namespace |
917 |
+ |
918 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdGroup.h amber11/AmberTools/src/mtkpp/src/Molecule/stdGroup.h |
919 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Molecule/stdGroup.h 2011-04-14 15:30:18.000000000 +0300 |
920 |
++++ amber11/AmberTools/src/mtkpp/src/Molecule/stdGroup.h 2012-03-03 20:03:01.406032569 +0200 |
921 |
+@@ -160,6 +160,12 @@ |
922 |
+ */ |
923 |
+ molecule* getStdMolecule(); |
924 |
+ |
925 |
++ /*! |
926 |
++ \brief Get getCharge |
927 |
++ \return molecule charge |
928 |
++ */ |
929 |
++ double getCharge(); |
930 |
++ |
931 |
+ protected: |
932 |
+ //! stdLibrary pointer |
933 |
+ stdLibrary* pParent; |
934 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/frcmodParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/frcmodParser.cpp |
935 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/frcmodParser.cpp 2011-04-14 15:30:18.000000000 +0300 |
936 |
++++ amber11/AmberTools/src/mtkpp/src/Parsers/frcmodParser.cpp 2012-03-03 20:03:01.407032569 +0200 |
937 |
+@@ -98,6 +98,7 @@ |
938 |
+ while (ifrcmod) { |
939 |
+ std::string buffer(80,'*'); |
940 |
+ getline(ifrcmod,fileline); |
941 |
++//std::cout << "|" << fileline << "|" << std::endl; |
942 |
+ bMASS = false; |
943 |
+ bBOND = false; |
944 |
+ bANGLE = false; |
945 |
+@@ -105,118 +106,311 @@ |
946 |
+ bIMPROPER = false; |
947 |
+ bNONBON = false; |
948 |
+ |
949 |
++ if ( (fileline.size() > 0) and (stripString(fileline, " ") != "") ) { |
950 |
++ std::vector<std::string> splitstring; |
951 |
++ splitString(fileline, " ", splitstring, 0); |
952 |
++ |
953 |
++ if (splitstring[0] == "MASS") bMASS = true; |
954 |
++ if (splitstring[0] == "BOND") bBOND = true; |
955 |
++ if (splitstring[0] == "ANGL" or splitstring[0] == "ANGLE") bANGLE = true; |
956 |
++ if (splitstring[0] == "DIHE" or splitstring[0] == "DIHEDRAL") bDIHE = true; |
957 |
++ if (splitstring[0] == "IMPROP" or splitstring[0] == "IMPROPER") bIMPROPER = true; |
958 |
++ if (splitstring[0] == "NONB" or splitstring[0] == "NONBON") bNONBON = true; |
959 |
++ } |
960 |
++/* |
961 |
++ try { |
962 |
+ if (fileline.substr(0,4) == "MASS") bMASS = true; |
963 |
++ } |
964 |
++ catch (std::out_of_range) { |
965 |
++ std::cout << " out_of_range MAS " << std::endl; |
966 |
++ } |
967 |
++ |
968 |
++ try { |
969 |
+ if (fileline.substr(0,4) == "BOND") bBOND = true; |
970 |
++ } |
971 |
++ catch (std::out_of_range) { |
972 |
++ std::cout << " out_of_range BOND " << std::endl; |
973 |
++ } |
974 |
++ |
975 |
++ try { |
976 |
+ if (fileline.substr(0,5) == "ANGLE") bANGLE = true; |
977 |
++ } |
978 |
++ catch (std::out_of_range) { |
979 |
++ std::cout << " out_of_range ANG" << std::endl; |
980 |
++ } |
981 |
++ |
982 |
++ try { |
983 |
+ if (fileline.substr(0,4) == "DIHE") bDIHE = true; |
984 |
++ } |
985 |
++ catch (std::out_of_range) { |
986 |
++ std::cout << " out_of_range DIHE " << std::endl; |
987 |
++ } |
988 |
++ |
989 |
++ try { |
990 |
+ if (fileline.substr(0,8) == "IMPROPER") bIMPROPER = true; |
991 |
++ } |
992 |
++ catch (std::out_of_range) { |
993 |
++ std::cout << " out_of_range IMP " << std::endl; |
994 |
++ } |
995 |
++ |
996 |
++ try { |
997 |
+ if (fileline.substr(0,6) == "NONBON") bNONBON = true; |
998 |
++ } |
999 |
++ catch (std::out_of_range) { |
1000 |
++ std::cout << " out_of_range NONB" << std::endl; |
1001 |
++ } |
1002 |
++*/ |
1003 |
+ |
1004 |
+ if (bMASS) { |
1005 |
+ getline(ifrcmod,fileline); |
1006 |
+- while (fileline != "") { |
1007 |
++ while (stripString(fileline, " ") != "") { |
1008 |
++ //while (GetAlphaChar(fileline, 0) != "0") { |
1009 |
++ std::vector<std::string> splitLine; |
1010 |
++ splitString(fileline, " ", splitLine, 0); |
1011 |
++ if (splitLine.size() >= 2) { |
1012 |
++ for (unsigned int i = 0; i < 2; i++) { |
1013 |
++ splitLine[i] = stripString(splitLine[i], " "); |
1014 |
++ } |
1015 |
+ pAtomType = pParameters->addAtomType(); |
1016 |
++ pAtomType->name = splitLine[0]; |
1017 |
+ pAtomType->groupName = this->groupName; |
1018 |
+- pAtomType->mass = strtod(fileline.substr(3,5).c_str(), 0); |
1019 |
++ pAtomType->mass = string2Double(splitLine[1]); //strtod(fileline.substr(3,5).c_str(), 0); |
1020 |
++ |
1021 |
++ if (splitLine.size() > 2) { |
1022 |
++ char *end; |
1023 |
++ double ret_double = strtod(splitLine[2].c_str(), &end); |
1024 |
++ if (!*end) { |
1025 |
++ pAtomType->atomPolarizability = ret_double; |
1026 |
++ } |
1027 |
++//std::cout << splitLine[2] << " " << ret_double << std::endl; |
1028 |
++ } |
1029 |
++ |
1030 |
+ getline(ifrcmod,fileline); |
1031 |
+ } |
1032 |
+ } |
1033 |
++ } |
1034 |
+ |
1035 |
+ if (bBOND) { |
1036 |
+ getline(ifrcmod,fileline); |
1037 |
+- while (fileline != "") { |
1038 |
+- std::string atomNames = fileline.substr(0,5); |
1039 |
++ //while (fileline != "") { |
1040 |
++ while (stripString(fileline, " ") != "") { |
1041 |
++ //std::string atomNames = fileline.substr(0,5); |
1042 |
+ std::vector<std::string> splitLine; |
1043 |
+- splitString(atomNames, "-", splitLine, 0); |
1044 |
+- if (splitLine.size() == 2) { |
1045 |
+- for (unsigned int i = 0; i < 2; i++) { |
1046 |
+- splitLine[i] = stripString(splitLine[i]," "); |
1047 |
+- } |
1048 |
++ splitString(fileline, "-", splitLine, 0); |
1049 |
++ |
1050 |
++ std::vector<std::string> splitLine2; |
1051 |
++ splitString(splitLine[1], " ", splitLine2, 0); |
1052 |
++ |
1053 |
++ //if (splitLine.size() == 2) { |
1054 |
++ //for (unsigned int i = 0; i < 2; i++) { |
1055 |
++ // splitLine[i] = stripString(splitLine[i]," "); |
1056 |
++ //} |
1057 |
+ pBondParam = pParameters->addBondParam(); |
1058 |
+ pBondParam->groupName = this->groupName; |
1059 |
+- pBondParam->atomType1 = std::string(splitLine[0]); |
1060 |
+- pBondParam->atomType2 = std::string(splitLine[1]); |
1061 |
+- pBondParam->keq = strtod(fileline.substr(7,5).c_str(), 0); |
1062 |
+- pBondParam->req = strtod(fileline.substr(16,5).c_str(), 0); |
1063 |
++ pBondParam->atomType1 = stripString(splitLine[0], " "); |
1064 |
++ pBondParam->atomType2 = stripString(splitLine2[0], " "); |
1065 |
++//std::cout << "|" << pBondParam->atomType1 << "|" << pBondParam->atomType2 << "|" << std::endl; |
1066 |
++ pBondParam->keq = string2Double(splitLine2[1]); |
1067 |
++ pBondParam->req = string2Double(splitLine2[2]); |
1068 |
++ |
1069 |
++// pBondParam->keq = strtod(fileline.substr(7,5).c_str(), 0); |
1070 |
++// pBondParam->req = strtod(fileline.substr(16,5).c_str(), 0); |
1071 |
++ |
1072 |
++//std::cout << "\n " << fileline << std::endl; |
1073 |
++//std::cout << " BOND " << pBondParam->atomType1 << " " << pBondParam->atomType2 << " " << pBondParam->keq << " " << pBondParam->req << std::endl; |
1074 |
++//std::cout << " BOND " << fileline.substr(7,5) << " " << fileline.substr(16,5) <<std::endl; |
1075 |
++ |
1076 |
+ getline(ifrcmod,fileline); |
1077 |
+- } |
1078 |
++ //} |
1079 |
+ } |
1080 |
+ } |
1081 |
+ |
1082 |
+ if (bANGLE) { |
1083 |
+ getline(ifrcmod,fileline); |
1084 |
+- while (fileline != "") { |
1085 |
+- std::string atomNames = fileline.substr(0,8); |
1086 |
++ //while (fileline != "") { |
1087 |
++ while (stripString(fileline, " ") != "") { |
1088 |
++// std::string atomNames = fileline.substr(0,8); |
1089 |
++ |
1090 |
+ std::vector<std::string> splitLine; |
1091 |
+- splitString(atomNames, "-", splitLine, 0); |
1092 |
+- if (splitLine.size() == 3) { |
1093 |
+- for (unsigned int i = 0; i < 3; i++) { |
1094 |
+- splitLine[i] = stripString(splitLine[i]," "); |
1095 |
+- } |
1096 |
++ splitString(fileline, "-", splitLine, 0); |
1097 |
++ |
1098 |
++ std::vector<std::string> splitLine2; |
1099 |
++ splitString(splitLine[2], " ", splitLine2, 0); |
1100 |
++ |
1101 |
++ //std::vector<std::string> splitLine; |
1102 |
++ //splitString(atomNames, "-", splitLine, 0); |
1103 |
++ |
1104 |
++ //std::vector<std::string> splitLine2; |
1105 |
++ //splitString(fileline, " ", splitLine2, 0); |
1106 |
++ |
1107 |
++ //if (splitLine.size() == 3) { |
1108 |
++ //for (unsigned int i = 0; i < 3; i++) { |
1109 |
++ // splitLine[i] = stripString(splitLine[i]," "); |
1110 |
++ //} |
1111 |
+ pAngleParam = pParameters->addAngleParam(); |
1112 |
+ pAngleParam->groupName = this->groupName; |
1113 |
+- pAngleParam->atomType1 = std::string(splitLine[0]); |
1114 |
+- pAngleParam->atomType2 = std::string(splitLine[1]); |
1115 |
+- pAngleParam->atomType3 = std::string(splitLine[2]); |
1116 |
+- pAngleParam->keq = strtod(fileline.substr(11,7).c_str(), 0); |
1117 |
+- pAngleParam->req = strtod(fileline.substr(20,8).c_str(), 0) * DEG2RAD; |
1118 |
++ pAngleParam->atomType1 = stripString(splitLine[0], " "); |
1119 |
++ pAngleParam->atomType2 = stripString(splitLine[1], " "); |
1120 |
++ pAngleParam->atomType3 = stripString(splitLine2[0], " "); |
1121 |
++//std::cout << "|" << pAngleParam->atomType1 << "|" << pAngleParam->atomType2 << "|" << pAngleParam->atomType3 << "|" << std::endl; |
1122 |
++ |
1123 |
++ pAngleParam->keq = string2Double(splitLine2[1]); |
1124 |
++ pAngleParam->req = string2Double(splitLine2[2]) * DEG2RAD; |
1125 |
++ |
1126 |
++ //pAngleParam->keq = strtod(fileline.substr(11,7).c_str(), 0); |
1127 |
++ //pAngleParam->req = strtod(fileline.substr(20,8).c_str(), 0) * DEG2RAD; |
1128 |
++ |
1129 |
++//std::cout << "\n " << fileline << std::endl; |
1130 |
++//std::cout << " ANGLE " << pAngleParam->atomType1 << " " << pAngleParam->atomType2 << " " << pAngleParam->atomType3 << " " << pAngleParam->keq << " " << string2Double(splitLine2[2]) << std::endl; |
1131 |
++ |
1132 |
+ getline(ifrcmod,fileline); |
1133 |
+- } |
1134 |
++ //} |
1135 |
+ } |
1136 |
+ } |
1137 |
+ |
1138 |
+ if (bDIHE) { |
1139 |
+ getline(ifrcmod,fileline); |
1140 |
+- while (fileline != "") { |
1141 |
+- std::string atomNames = fileline.substr(0,11); |
1142 |
++ //while (fileline != "") { |
1143 |
++ while (stripString(fileline, " ") != "") { |
1144 |
++ |
1145 |
++//std::cout << "\n " << fileline << std::endl; |
1146 |
++ |
1147 |
++//std::cout << fileline.substr(0,12) << std::endl; |
1148 |
++ |
1149 |
++// snip = str.substr(0,12); |
1150 |
++//(3) erase the substring of 0..where str.erase(0,where); |
1151 |
++ |
1152 |
++ std::string atTypes = fileline.substr(0,12); |
1153 |
+ std::vector<std::string> splitLine; |
1154 |
+- splitString(atomNames, "-", splitLine, 0); |
1155 |
+- if (splitLine.size() == 4) { |
1156 |
+- for (unsigned int i = 0; i < 4; i++) { |
1157 |
+- splitLine[i] = stripString(splitLine[i]," "); |
1158 |
+- } |
1159 |
++ splitString(atTypes, "-", splitLine, 0); |
1160 |
++ |
1161 |
++/*for (unsigned int i = 0; i < splitLine.size(); i++) { |
1162 |
++ std::cout << splitLine[i] << std::endl; |
1163 |
++}*/ |
1164 |
++ |
1165 |
++ fileline.erase(0,12); |
1166 |
++ |
1167 |
++ std::vector<std::string> splitLine2; |
1168 |
++ splitString(fileline, " ", splitLine2, 0); |
1169 |
++/* |
1170 |
++for (unsigned int i = 0; i < splitLine2.size(); i++) { |
1171 |
++ std::cout << splitLine2[i] << std::endl; |
1172 |
++}*/ |
1173 |
++ |
1174 |
++ //std::string atomNames = fileline.substr(0,11); |
1175 |
++ //std::vector<std::string> splitLine; |
1176 |
++ //splitString(atomNames, "-", splitLine, 0); |
1177 |
++ |
1178 |
++ //if (splitLine.size() == 4) { |
1179 |
++ //for (unsigned int i = 0; i < 4; i++) { |
1180 |
++ //splitLine[i] = stripString(splitLine[i], " "); |
1181 |
++ //} |
1182 |
+ pTorsionParam = pParameters->addTorsionParam(); |
1183 |
+ pTorsionParam->groupName = this->groupName; |
1184 |
+- pTorsionParam->atomType1 = std::string(splitLine[0]); |
1185 |
+- pTorsionParam->atomType2 = std::string(splitLine[1]); |
1186 |
+- pTorsionParam->atomType3 = std::string(splitLine[2]); |
1187 |
+- pTorsionParam->atomType4 = std::string(splitLine[3]); |
1188 |
+- pTorsionParam->npth = atoi(fileline.substr(11,4).c_str()); |
1189 |
+- pTorsionParam->Vn = strtod(fileline.substr(18,8).c_str(), 0); |
1190 |
+- pTorsionParam->gamma = strtod(fileline.substr(31,8).c_str(), 0) * DEG2RAD; |
1191 |
+- pTorsionParam->Nt = strtod(fileline.substr(42,12).c_str(), 0); |
1192 |
++ pTorsionParam->atomType1 = stripString(splitLine[0], " "); |
1193 |
++ pTorsionParam->atomType2 = stripString(splitLine[1], " "); |
1194 |
++ pTorsionParam->atomType3 = stripString(splitLine[2], " "); |
1195 |
++ pTorsionParam->atomType4 = stripString(splitLine[3], " "); |
1196 |
++ |
1197 |
++ pTorsionParam->npth = string2Int(splitLine2[0]); |
1198 |
++ pTorsionParam->Vn = string2Double(splitLine2[1]); |
1199 |
++ pTorsionParam->gamma = string2Double(splitLine2[2]) * DEG2RAD; |
1200 |
++ pTorsionParam->Nt = string2Double(splitLine2[3]); |
1201 |
++ |
1202 |
++ //pTorsionParam->npth = atoi(fileline.substr(11,4).c_str()); |
1203 |
++ //pTorsionParam->Vn = strtod(fileline.substr(18,8).c_str(), 0); |
1204 |
++ //pTorsionParam->gamma = strtod(fileline.substr(31,8).c_str(), 0) * DEG2RAD; |
1205 |
++ //pTorsionParam->Nt = strtod(fileline.substr(42,12).c_str(), 0); |
1206 |
++ |
1207 |
++//std::cout << " DIHE " << pTorsionParam->atomType1 << " " << pTorsionParam->atomType2 << " " << pTorsionParam->atomType3 << " " << pTorsionParam->atomType4 << " " << pTorsionParam->npth << " " << pTorsionParam->Vn << " " << string2Double(splitLine2[2]) << " " << pTorsionParam->Nt << std::endl; |
1208 |
++ |
1209 |
+ getline(ifrcmod,fileline); |
1210 |
+- } |
1211 |
++//std::cout << " DIHE LINE: " << fileline << std::endl; |
1212 |
++ //} |
1213 |
+ } |
1214 |
+ } |
1215 |
+ |
1216 |
+ if (bIMPROPER) { |
1217 |
+ getline(ifrcmod,fileline); |
1218 |
+- while (fileline != "") { |
1219 |
+- std::string atomNames = fileline.substr(0,11); |
1220 |
++ //while (fileline != "") { |
1221 |
++ while (stripString(fileline, " ") != "") { |
1222 |
++ |
1223 |
++ std::string atTypes = fileline.substr(0,12); |
1224 |
+ std::vector<std::string> splitLine; |
1225 |
+- splitString(atomNames, "-", splitLine, 0); |
1226 |
+- if (splitLine.size() == 4) { |
1227 |
+- for (unsigned int i = 0; i < 4; i++) { |
1228 |
+- splitLine[i] = stripString(splitLine[i]," "); |
1229 |
+- } |
1230 |
++ splitString(atTypes, "-", splitLine, 0); |
1231 |
++ |
1232 |
++ fileline.erase(0,12); |
1233 |
++ |
1234 |
++ std::vector<std::string> splitLine2; |
1235 |
++ splitString(fileline, " ", splitLine2, 0); |
1236 |
++ |
1237 |
++// std::vector<std::string> splitLine; |
1238 |
++// splitString(fileline, "-", splitLine, 0); |
1239 |
++ |
1240 |
++// std::vector<std::string> splitLine2; |
1241 |
++// splitString(splitLine[3], " ", splitLine2, 0); |
1242 |
++ |
1243 |
++ //std::string atomNames = fileline.substr(0,11); |
1244 |
++ //std::vector<std::string> splitLine; |
1245 |
++ //splitString(atomNames, "-", splitLine, 0); |
1246 |
++ //if (splitLine.size() == 4) { |
1247 |
++ //for (unsigned int i = 0; i < 4; i++) { |
1248 |
++ //splitLine[i] = stripString(splitLine[i]," "); |
1249 |
++ //} |
1250 |
+ pImproperParam = pParameters->addImproperParam(); |
1251 |
+ pImproperParam->groupName = this->groupName; |
1252 |
+- pImproperParam->atomType1 = std::string(splitLine[0]); |
1253 |
+- pImproperParam->atomType2 = std::string(splitLine[1]); |
1254 |
+- pImproperParam->atomType3 = std::string(splitLine[2]); |
1255 |
+- pImproperParam->atomType4 = std::string(splitLine[3]); |
1256 |
+- pImproperParam->Vn = strtod(fileline.substr(18,8).c_str(), 0); |
1257 |
+- pImproperParam->gamma = strtod(fileline.substr(31,8).c_str(), 0) * DEG2RAD; |
1258 |
+- pImproperParam->Nt = strtod(fileline.substr(42,12).c_str(), 0); |
1259 |
++ pImproperParam->atomType1 = stripString(splitLine[0], " "); |
1260 |
++ pImproperParam->atomType2 = stripString(splitLine[1], " "); |
1261 |
++ pImproperParam->atomType3 = stripString(splitLine[2], " "); |
1262 |
++ pImproperParam->atomType4 = stripString(splitLine[3], " "); |
1263 |
++ |
1264 |
++ pImproperParam->Vn = string2Double(splitLine2[0]); |
1265 |
++ pImproperParam->gamma = string2Double(splitLine2[1]) * DEG2RAD; |
1266 |
++ pImproperParam->Nt = string2Double(splitLine2[2]); |
1267 |
++ |
1268 |
++ //pImproperParam->Vn = strtod(fileline.substr(18,8).c_str(), 0); |
1269 |
++ //pImproperParam->gamma = strtod(fileline.substr(31,8).c_str(), 0) * DEG2RAD; |
1270 |
++ //pImproperParam->Nt = strtod(fileline.substr(42,12).c_str(), 0); |
1271 |
++ |
1272 |
++//std::cout << "\n " << fileline << std::endl; |
1273 |
++//std::cout << " IMPR " << pImproperParam->atomType1 << " " << pImproperParam->atomType2 << " " << pImproperParam->atomType3 << " " << pImproperParam->atomType4 << " " << pImproperParam->Vn << " " << string2Double(splitLine2[1]) << " " << pImproperParam->Nt << std::endl; |
1274 |
++ |
1275 |
+ getline(ifrcmod,fileline); |
1276 |
+- } |
1277 |
++ //} |
1278 |
+ } |
1279 |
+ } |
1280 |
+ if (bNONBON) { |
1281 |
++ getline(ifrcmod,fileline); |
1282 |
++//std::cout << fileline << std::endl; |
1283 |
++ //while (fileline != "") { |
1284 |
++ while (stripString(fileline, " ") != "") { |
1285 |
++ std::vector<std::string> splitLine; |
1286 |
++ splitString(fileline, " ", splitLine, 0); |
1287 |
++ if (splitLine.size() >= 3) { |
1288 |
++ for (unsigned int i = 0; i < 3; i++) { |
1289 |
++ splitLine[i] = stripString(splitLine[i], " "); |
1290 |
++ } |
1291 |
++//std::cout << " |" << splitLine[0] << "|" << std::endl; |
1292 |
++ |
1293 |
++//std::cout << "\n " << fileline << std::endl; |
1294 |
++ |
1295 |
++ pAtomType = pParameters->getAtomType(stripString(splitLine[0], " ")); |
1296 |
++ if (pAtomType) { |
1297 |
++ pAtomType->rvalue = string2Double(splitLine[1]); |
1298 |
++ pAtomType->evalue = string2Double(splitLine[2]); |
1299 |
+ |
1300 |
++//std::cout << pAtomType->name << " " << pAtomType->rvalue << " " << pAtomType->evalue << std::endl; |
1301 |
++ |
1302 |
++ } |
1303 |
++ else { |
1304 |
++ std::cout << " Can't find atom type " << std::endl; |
1305 |
++ } |
1306 |
++ getline(ifrcmod,fileline); |
1307 |
++ } |
1308 |
++ } |
1309 |
+ } |
1310 |
+ } |
1311 |
++ |
1312 |
+ ifrcmod.close(); |
1313 |
+ } |
1314 |
+ |
1315 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/gaussianParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/gaussianParser.cpp |
1316 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/gaussianParser.cpp 2011-04-14 15:30:18.000000000 +0300 |
1317 |
++++ amber11/AmberTools/src/mtkpp/src/Parsers/gaussianParser.cpp 2012-03-03 20:03:01.408032569 +0200 |
1318 |
+@@ -84,7 +84,7 @@ |
1319 |
+ |
1320 |
+ this->bMem = 0; |
1321 |
+ |
1322 |
+- this->bnProc = 0; |
1323 |
++ this->bNProc = 0; |
1324 |
+ |
1325 |
+ this->bWriteInternalCoords = true; |
1326 |
+ this->bWriteCartCoords = false; |
1327 |
+@@ -168,7 +168,7 @@ |
1328 |
+ while (igau) { |
1329 |
+ getline(igau,fileline); |
1330 |
+ |
1331 |
+- if (containsSubStr(fileline, "modredundant")) { |
1332 |
++ if (containsSubStr(fileline, "ModRedundant")) { |
1333 |
+ bModRedundant = true; |
1334 |
+ } |
1335 |
+ if (fileline.substr(0,59) == " Redundant internal coordinates taken from checkpoint file:") { |
1336 |
+@@ -626,6 +626,7 @@ |
1337 |
+ void gaussianParser::Write(const std::string &gaussfile, molecule* pMolecule, |
1338 |
+ std::vector< vector3d > &coordinates) |
1339 |
+ { |
1340 |
++ std::string routecard; |
1341 |
+ std::ofstream ogauss; |
1342 |
+ ogauss.open(gaussfile.c_str()); |
1343 |
+ |
1344 |
+@@ -643,52 +644,64 @@ |
1345 |
+ return; |
1346 |
+ } |
1347 |
+ |
1348 |
+- ogauss << "$rungauss" << std::endl; |
1349 |
++ ogauss << "$RunGauss" << std::endl; |
1350 |
+ |
1351 |
+ if (bChkPt) { |
1352 |
+- ogauss << "%chk=" << this->itsChkPtFile << std::endl; |
1353 |
++ ogauss << "%Chk=" << this->itsChkPtFile << std::endl; |
1354 |
+ } |
1355 |
+ if (bMem) { |
1356 |
+- ogauss << "%mem=" << this->itsMem << std::endl; |
1357 |
++ ogauss << "%Mem=" << this->itsMem << std::endl; |
1358 |
+ } |
1359 |
+- if (bnProc) { |
1360 |
+- ogauss << "%nproc=" << this->itsnProc << std::endl; |
1361 |
++ if (bNProc) { |
1362 |
++ ogauss << "%NProcShared=" << this->itsNProc << std::endl; |
1363 |
+ } |
1364 |
+ |
1365 |
+- ogauss << "#" << this->itsVerbosity << " " << this->itsTheory << "/" << this->itsBasisSet << " "; |
1366 |
++ routecard = "#" + this->itsVerbosity + " " + this->itsTheory + "/" + this->itsBasisSet; |
1367 |
+ |
1368 |
+ if (!itsCommandOptions.empty()) { |
1369 |
+ for (mapIterator p = itsCommandOptions.begin(); p != itsCommandOptions.end(); p++) { |
1370 |
+ std::string c = p->first; |
1371 |
+ std::vector<std::string> o = p->second; |
1372 |
++ std::string opts = ""; |
1373 |
+ if (o.size() == 1) { |
1374 |
+- if ( p->second[0] == "NONE") { |
1375 |
+- ogauss << p->first << " "; |
1376 |
+- } |
1377 |
+- else { |
1378 |
+- ogauss << p->first << "=" << p->second[0] << " "; |
1379 |
++ if ( p->second[0] != "NONE") { |
1380 |
++ opts = "=" + p->second[0]; |
1381 |
+ } |
1382 |
+ } |
1383 |
+ else { |
1384 |
+- ogauss << p->first << "("; |
1385 |
++ opts = "("; |
1386 |
+ for (unsigned int i = 0; i < o.size(); i++) { |
1387 |
+- if (i == o.size()-1) { |
1388 |
+- ogauss << o[i]; |
1389 |
++ opts = opts + o[i]; |
1390 |
++ if (i != o.size()-1) { |
1391 |
++ opts = opts + ","; |
1392 |
+ } |
1393 |
+- else { |
1394 |
+- ogauss << o[i] << ","; |
1395 |
+ } |
1396 |
++ opts = opts + ")"; |
1397 |
+ } |
1398 |
+- ogauss << ")" << " "; |
1399 |
++ |
1400 |
++ if (routecard.length() + c.length() + opts.length() < 72) { |
1401 |
++ routecard = routecard + " " + c + opts; |
1402 |
++ } else { |
1403 |
++ if (routecard.length() != 0) { |
1404 |
++ ogauss << routecard << std::endl; |
1405 |
++ } |
1406 |
++ routecard = c + opts; |
1407 |
+ } |
1408 |
+ } |
1409 |
+ } |
1410 |
+ for (unsigned int i = 0; i < this->iops.size(); i++) { |
1411 |
+- ogauss << this->iops[i] << " "; |
1412 |
++ if (routecard.length() + this->iops[i].length() < 72) { |
1413 |
++ routecard = routecard + " " + this->iops[i]; |
1414 |
++ } else { |
1415 |
++ if (routecard.length() != 0) { |
1416 |
++ ogauss << routecard << std::endl; |
1417 |
++ } |
1418 |
++ routecard = this->iops[i]; |
1419 |
++ } |
1420 |
+ } |
1421 |
+ |
1422 |
+ // Flush command block and follow with a blank line |
1423 |
+- ogauss << "\n" << std::endl; |
1424 |
++ ogauss << routecard << "\n" << std::endl; |
1425 |
+ |
1426 |
+ // Write name (if required) and follow with a blank line |
1427 |
+ if (bWriteMoleculeName) { |
1428 |
+@@ -740,11 +753,11 @@ |
1429 |
+ ogauss << std::endl; |
1430 |
+ } |
1431 |
+ |
1432 |
+- std::vector<std::string> optOptions = this->getCommandOption("opt"); |
1433 |
++ std::vector<std::string> optOptions = this->getCommandOption("Opt"); |
1434 |
+ if (optOptions.size() > 0) { |
1435 |
+ bool bMD = 0; |
1436 |
+ for (unsigned int x = 0; x < optOptions.size(); x++) { |
1437 |
+- if (optOptions[x] == "modredundant") { |
1438 |
++ if (optOptions[x] == "ModRedundant") { |
1439 |
+ bMD = 1; |
1440 |
+ } |
1441 |
+ } |
1442 |
+@@ -766,13 +779,13 @@ |
1443 |
+ } |
1444 |
+ } |
1445 |
+ |
1446 |
+- if (this->itsBasisSet.substr(0,3) == "GEN") { |
1447 |
++ if (this->itsBasisSet.substr(0,3) == "Gen") { |
1448 |
+ std::ifstream iBSFile; |
1449 |
+ iBSFile.open(this->itsBasisSetFile.c_str()); |
1450 |
+ |
1451 |
+ if (!iBSFile) { |
1452 |
+ std::cout << "\nERROR!" |
1453 |
+- << "\nBasis set \"GEN\" requires a custom file." |
1454 |
++ << "\nBasis set \"Gen\" requires a custom file." |
1455 |
+ << "\nFile \"" << this->itsBasisSetFile << "\" is missing or unreadable." |
1456 |
+ << "\nPlease choose another file. For instructions, consult your program's" |
1457 |
+ << "\ndocumentation." |
1458 |
+@@ -789,13 +802,13 @@ |
1459 |
+ } |
1460 |
+ |
1461 |
+ // +BPR |
1462 |
+- if (this->getCommandOption("pseudo").size() > 0) { |
1463 |
++ if (this->getCommandOption("Pseudo").size() > 0) { |
1464 |
+ std::ifstream iPseudoFile; |
1465 |
+ iPseudoFile.open(this->itsPseudoPotentialFile.c_str()); |
1466 |
+ |
1467 |
+ if (!iPseudoFile) { |
1468 |
+ std::cout << "\nERROR!" |
1469 |
+- << "\npseudo=read or pseudo=cards requires a custom file." |
1470 |
++ << "\nPseudo=Read or Pseudo=Cards requires a custom file." |
1471 |
+ << "\nFile \"" << this->itsPseudoPotentialFile << "\" is missing or unreadable." |
1472 |
+ << "\nPlease choose another file. For instructions, consult your program's" |
1473 |
+ << "\ndocumentation." |
1474 |
+@@ -812,7 +825,7 @@ |
1475 |
+ } |
1476 |
+ // -BPR |
1477 |
+ |
1478 |
+- if (this->getCommandOption("pop").size() > 0) { |
1479 |
++ if (this->getCommandOption("Pop").size() > 0) { |
1480 |
+ if (!itsMKRadii.empty()) { |
1481 |
+ for (dMapIterator p = itsMKRadii.begin(); p != itsMKRadii.end(); p++) { |
1482 |
+ ogauss << p->first << "=" << p->second << "\n"; |
1483 |
+@@ -1037,14 +1050,14 @@ |
1484 |
+ } |
1485 |
+ |
1486 |
+ // ============================================================ |
1487 |
+-// Function : setnProc |
1488 |
++ // Function : setNProc |
1489 |
+ // ------------------------------------------------------------ |
1490 |
+ // |
1491 |
+ // ============================================================ |
1492 |
+-void gaussianParser::setnProc(const std::string &n) |
1493 |
++ void gaussianParser::setNProc(const std::string &n) |
1494 |
+ { |
1495 |
+- this->bnProc = 1; |
1496 |
+- this->itsnProc = n; |
1497 |
++ this->bNProc = 1; |
1498 |
++ this->itsNProc = n; |
1499 |
+ } |
1500 |
+ |
1501 |
+ // ============================================================ |
1502 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/gaussianParser.h amber11/AmberTools/src/mtkpp/src/Parsers/gaussianParser.h |
1503 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/gaussianParser.h 2011-04-14 15:30:18.000000000 +0300 |
1504 |
++++ amber11/AmberTools/src/mtkpp/src/Parsers/gaussianParser.h 2012-03-03 20:03:01.408032569 +0200 |
1505 |
+@@ -196,9 +196,9 @@ |
1506 |
+ |
1507 |
+ /*! |
1508 |
+ \brief Set number of processors to use |
1509 |
+- \param n nprocs |
1510 |
++ \param n number of processors |
1511 |
+ */ |
1512 |
+- void setnProc(const std::string &n); |
1513 |
++ void setNProc(const std::string &n); |
1514 |
+ |
1515 |
+ /*! |
1516 |
+ \brief Set level of theory |
1517 |
+@@ -354,10 +354,10 @@ |
1518 |
+ bool bMem; |
1519 |
+ |
1520 |
+ //! number of processors |
1521 |
+- std::string itsnProc; |
1522 |
++ std::string itsNProc; |
1523 |
+ |
1524 |
+- //! Turn on mem |
1525 |
+- bool bnProc; |
1526 |
++ //! Turn on number of processors |
1527 |
++ bool bNProc; |
1528 |
+ |
1529 |
+ //! Use internal or cartesian coordinates |
1530 |
+ bool bWriteInternalCoords; |
1531 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/Makefile.am amber11/AmberTools/src/mtkpp/src/Parsers/Makefile.am |
1532 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/Makefile.am 2011-04-14 15:30:18.000000000 +0300 |
1533 |
++++ amber11/AmberTools/src/mtkpp/src/Parsers/Makefile.am 2012-03-03 20:03:01.406032569 +0200 |
1534 |
+@@ -1,15 +1,15 @@ |
1535 |
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics/$(SRCDIR) |
1536 |
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR) |
1537 |
+ DIAGNOSTICS_LIB=-lDiagnostics |
1538 |
+-MOLECULE_LD=-L$(top_builddir)/src/Molecule/$(SRCDIR) |
1539 |
++MOLECULE_LD=-L$(abs_top_builddir)/src/Molecule/$(SRCDIR) |
1540 |
+ MOLECULE_LIB=-lMolecule |
1541 |
+-GA_LD=-L$(top_builddir)/src/GA/$(SRCDIR) |
1542 |
++GA_LD=-L$(abs_top_builddir)/src/GA/$(SRCDIR) |
1543 |
+ GA_LIB=-lGA |
1544 |
+-LOG_LD=-L$(top_builddir)/src/Log/$(SRCDIR) |
1545 |
++LOG_LD=-L$(abs_top_builddir)/src/Log/$(SRCDIR) |
1546 |
+ LOG_LIB=-lLog |
1547 |
+-STATS_LD=-L$(top_builddir)/src/Statistics/$(SRCDIR) |
1548 |
++STATS_LD=-L$(abs_top_builddir)/src/Statistics/$(SRCDIR) |
1549 |
+ STATS_LIB=-lStatistics |
1550 |
+ |
1551 |
+-TINYXML_LD=-L$(top_builddir)/src/tinyxml/$(SRCDIR) |
1552 |
++TINYXML_LD=-L$(abs_top_builddir)/src/tinyxml/$(SRCDIR) |
1553 |
+ TINYXML_LIB=-ltinyxml |
1554 |
+ |
1555 |
+ if USE_XERCES |
1556 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/Makefile.in amber11/AmberTools/src/mtkpp/src/Parsers/Makefile.in |
1557 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/Makefile.in 2011-04-14 15:30:18.000000000 +0300 |
1558 |
++++ amber11/AmberTools/src/mtkpp/src/Parsers/Makefile.in 2012-03-03 20:03:01.407032569 +0200 |
1559 |
+@@ -267,17 +267,17 @@ |
1560 |
+ top_builddir = @top_builddir@ |
1561 |
+ top_srcdir = @top_srcdir@ |
1562 |
+ xerces_path = @xerces_path@ |
1563 |
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics/$(SRCDIR) |
1564 |
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR) |
1565 |
+ DIAGNOSTICS_LIB = -lDiagnostics |
1566 |
+-MOLECULE_LD = -L$(top_builddir)/src/Molecule/$(SRCDIR) |
1567 |
++MOLECULE_LD = -L$(abs_top_builddir)/src/Molecule/$(SRCDIR) |
1568 |
+ MOLECULE_LIB = -lMolecule |
1569 |
+-GA_LD = -L$(top_builddir)/src/GA/$(SRCDIR) |
1570 |
++GA_LD = -L$(abs_top_builddir)/src/GA/$(SRCDIR) |
1571 |
+ GA_LIB = -lGA |
1572 |
+-LOG_LD = -L$(top_builddir)/src/Log/$(SRCDIR) |
1573 |
++LOG_LD = -L$(abs_top_builddir)/src/Log/$(SRCDIR) |
1574 |
+ LOG_LIB = -lLog |
1575 |
+-STATS_LD = -L$(top_builddir)/src/Statistics/$(SRCDIR) |
1576 |
++STATS_LD = -L$(abs_top_builddir)/src/Statistics/$(SRCDIR) |
1577 |
+ STATS_LIB = -lStatistics |
1578 |
+-TINYXML_LD = -L$(top_builddir)/src/tinyxml/$(SRCDIR) |
1579 |
++TINYXML_LD = -L$(abs_top_builddir)/src/tinyxml/$(SRCDIR) |
1580 |
+ TINYXML_LIB = -ltinyxml |
1581 |
+ @USE_XERCES_TRUE@XERCES_LD = -L@xerces_path@/lib/ |
1582 |
+ @USE_XERCES_TRUE@XERCES_LIB = -lxerces-c |
1583 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/mtkppParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/mtkppParser.cpp |
1584 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/mtkppParser.cpp 2011-04-14 15:30:18.000000000 +0300 |
1585 |
++++ amber11/AmberTools/src/mtkpp/src/Parsers/mtkppParser.cpp 2012-03-03 20:03:01.409032568 +0200 |
1586 |
+@@ -1769,6 +1769,15 @@ |
1587 |
+ atomElem->SetAttribute("type", int2String(pAtom->getType())); |
1588 |
+ atomElem->SetAttribute("formalCharge", int2String(pAtom->getFormalCharge())); |
1589 |
+ |
1590 |
++ // Coordinates |
1591 |
++ TiXmlElement* coordElem = new TiXmlElement("coord"); |
1592 |
++ atomElem->LinkEndChild(coordElem); |
1593 |
++ |
1594 |
++ coordElem->SetAttribute("x", double2String(pAtom->getX())); |
1595 |
++ coordElem->SetAttribute("y", double2String(pAtom->getY())); |
1596 |
++ coordElem->SetAttribute("z", double2String(pAtom->getZ())); |
1597 |
++ |
1598 |
++ // Properties |
1599 |
+ std::map<std::string, double> atomDMap = pAtom->getPropertyMap(); |
1600 |
+ std::map<std::string, int> atomIMap = pAtom->getIntPropertyMap(); |
1601 |
+ |
1602 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/paramParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/paramParser.cpp |
1603 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/paramParser.cpp 2011-04-14 15:30:18.000000000 +0300 |
1604 |
++++ amber11/AmberTools/src/mtkpp/src/Parsers/paramParser.cpp 2012-03-03 20:03:01.410032567 +0200 |
1605 |
+@@ -144,6 +144,10 @@ |
1606 |
+ pAtomType->evalue = string2Double(element->Attribute("potentialWellDepth")); |
1607 |
+ } |
1608 |
+ |
1609 |
++ if (element->Attribute("atomPolarizability")) { |
1610 |
++ pAtomType->atomPolarizability = string2Double(element->Attribute("atomPolarizability")); |
1611 |
++ } |
1612 |
++ |
1613 |
+ if (element->Attribute("element")) { |
1614 |
+ pAtomType->element = element->Attribute("element"); |
1615 |
+ } |
1616 |
+@@ -1808,6 +1812,7 @@ |
1617 |
+ entry->SetAttribute("mass" , double2String(pAtomType->mass).c_str()); |
1618 |
+ entry->SetAttribute("vdwRadius" , double2String(pAtomType->rvalue).c_str()); |
1619 |
+ entry->SetAttribute("potentialWellDepth" , double2String(pAtomType->evalue).c_str()); |
1620 |
++ entry->SetAttribute("atomPolarizability" , double2String(pAtomType->atomPolarizability).c_str()); |
1621 |
+ entry->SetAttribute("element" , pAtomType->element); |
1622 |
+ entry->SetAttribute("hybridization" , pAtomType->hybridization); |
1623 |
+ entry->SetAttribute("groupName" , pAtomType->groupName); |
1624 |
+@@ -2035,6 +2040,7 @@ |
1625 |
+ typeElem->setAttribute(X("mass"), X(double2String(pAtomType->mass).c_str())); |
1626 |
+ typeElem->setAttribute(X("vdwRadius"), X(double2String(pAtomType->rvalue).c_str())); |
1627 |
+ typeElem->setAttribute(X("potentialWellDepth"), X(double2String(pAtomType->evalue).c_str())); |
1628 |
++ typeElem->setAttribute(X("atomPolarizability"), X(double2String(pAtomType->atomPolarizability).c_str())); |
1629 |
+ typeElem->setAttribute(X("element"), X(pAtomType->element.c_str())); |
1630 |
+ typeElem->setAttribute(X("hybridization"), X(pAtomType->hybridization.c_str())); |
1631 |
+ typeElem->setAttribute(X("groupName"), X(pAtomType->groupName.c_str())); |
1632 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/pdbParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/pdbParser.cpp |
1633 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/pdbParser.cpp 2011-04-14 15:30:18.000000000 +0300 |
1634 |
++++ amber11/AmberTools/src/mtkpp/src/Parsers/pdbParser.cpp 2012-03-03 20:03:01.410032567 +0200 |
1635 |
+@@ -840,6 +840,7 @@ |
1636 |
+ for (atomIterator a = atomList.begin(); a != atomList.end(); a++) { |
1637 |
+ pAtom = *a; |
1638 |
+ pSubMolecule = pAtom->getParent(); |
1639 |
++ //std::cout << pSubMolecule->getColIndex() << std::endl; |
1640 |
+ char temp[100]; |
1641 |
+ |
1642 |
+ char tmp_element[3]; |
1643 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/prepParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/prepParser.cpp |
1644 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/prepParser.cpp 2011-04-14 15:30:18.000000000 +0300 |
1645 |
++++ amber11/AmberTools/src/mtkpp/src/Parsers/prepParser.cpp 2012-03-03 20:03:01.411032567 +0200 |
1646 |
+@@ -66,71 +66,106 @@ |
1647 |
+ prepParser::~prepParser() {} |
1648 |
+ |
1649 |
+ // ========================================================= |
1650 |
+-// Function : Read |
1651 |
+-// --------------------------------------------------------- |
1652 |
+-// parsers a prep file |
1653 |
+-// --------------------------------------------------------- |
1654 |
+-// Format : |
1655 |
+-// ========================================================= |
1656 |
+-void prepParser::Read(const std::string &prepfile, stdGroup* pStdGroup) |
1657 |
+-{ |
1658 |
+- std::string errorMessage = " Reading " + prepfile + " " + |
1659 |
+- pStdGroup->getName() + " ... implement "; |
1660 |
+- errorLogger.throwError("prepParser", errorMessage, 1); |
1661 |
+-} |
1662 |
+- |
1663 |
+-// ========================================================= |
1664 |
+-// Function : Read |
1665 |
++// Function : openFile |
1666 |
+ // --------------------------------------------------------- |
1667 |
+-// parsers a prep file |
1668 |
++// open a prep file |
1669 |
+ // --------------------------------------------------------- |
1670 |
+ // Format : |
1671 |
+ // ========================================================= |
1672 |
+-void prepParser::Read(const std::string &prepfile, stdFrag* pStdFrag) |
1673 |
++int prepParser::openFile(const std::string &prepfile) |
1674 |
+ { |
1675 |
+- errorLogger.throwError("prepParser", "Read", INFO); |
1676 |
+- |
1677 |
+- std::ifstream iprep; |
1678 |
+ iprep.open(prepfile.c_str()); |
1679 |
+ |
1680 |
++ //std::cout << "\n\n prepParser::openFile " << prepfile << std::endl; |
1681 |
+ if (!iprep) { |
1682 |
+ setError(1); |
1683 |
+ std::string errorMessage = " Error, Can't Find " + prepfile; |
1684 |
+ setErrorMessage(errorMessage); |
1685 |
+ errorLogger.throwError("prepParser::Read", errorMessage, 1); |
1686 |
+- return; |
1687 |
++ return 1; |
1688 |
+ } |
1689 |
+ |
1690 |
+ std::string fileline; |
1691 |
+- std::string title; |
1692 |
+- std::string atom; |
1693 |
+- std::string buffer(80,'*'); |
1694 |
+ |
1695 |
+ // SKIP FIRST TWO LINES |
1696 |
+ getline(iprep,fileline); |
1697 |
+ getline(iprep,fileline); |
1698 |
++ |
1699 |
++ return 0; |
1700 |
++} |
1701 |
++ |
1702 |
++// ========================================================= |
1703 |
++// Function : read fragment header section |
1704 |
++// --------------------------------------------------------- |
1705 |
++// |
1706 |
++// --------------------------------------------------------- |
1707 |
++// Format : |
1708 |
++// ========================================================= |
1709 |
++int prepParser::readHeader(std::string &name, std::string &symbol, double &charge) |
1710 |
++{ |
1711 |
++ std::string fileline; |
1712 |
++ |
1713 |
+ getline(iprep,fileline); |
1714 |
+- //std::string name = stripString(fileline," "); |
1715 |
+- //pStdFrag->setName(fileline); |
1716 |
++ if (stripString(fileline, " ") == "STOP") return 1; |
1717 |
++ |
1718 |
++ name = stripString(fileline," "); |
1719 |
++ |
1720 |
++ // blank line |
1721 |
+ getline(iprep,fileline); |
1722 |
++ |
1723 |
++ // symbol |
1724 |
+ getline(iprep,fileline); |
1725 |
+ std::vector<std::string> splitLine; |
1726 |
+ splitString(fileline, " ", splitLine, 0); |
1727 |
+- pStdFrag->setSymbol(splitLine[0]); |
1728 |
++ symbol = splitLine[0]; |
1729 |
++ |
1730 |
++ // |
1731 |
+ getline(iprep,fileline); |
1732 |
++ |
1733 |
++ // charge |
1734 |
+ getline(iprep,fileline); |
1735 |
+- //pStdFrag->setCharge(splitLine[0]); |
1736 |
++ charge = string2Double(stripString(fileline, " ")); |
1737 |
++ |
1738 |
++ return 0; |
1739 |
++} |
1740 |
++ |
1741 |
++// ========================================================= |
1742 |
++// Function : read fragment main section |
1743 |
++// --------------------------------------------------------- |
1744 |
++// |
1745 |
++// --------------------------------------------------------- |
1746 |
++// Format : |
1747 |
++// ========================================================= |
1748 |
++void prepParser::readFragment(stdFrag* pStdFrag) |
1749 |
++{ |
1750 |
++ std::string fileline; |
1751 |
++ |
1752 |
++ std::vector<stdBond*> todos; |
1753 |
+ |
1754 |
+ while (iprep) { |
1755 |
+ getline(iprep,fileline); |
1756 |
+- if (fileline == "") break; |
1757 |
++ |
1758 |
++ std::string filelineTest = stripString(fileline, " "); |
1759 |
++ if (filelineTest == "") break; |
1760 |
++ |
1761 |
++//std::cout << "|" << fileline << "|" << std::endl; |
1762 |
+ |
1763 |
+ std::vector<std::string> splitstring; |
1764 |
+ splitString(fileline, " ", splitstring, 0); |
1765 |
+ if (atoi(splitstring[0].c_str()) > 3) { |
1766 |
+ stdAtom* pStdAtom = pStdFrag->addStdAtom(); |
1767 |
+ int atIndex = atoi(splitstring[0].c_str()) - 3; |
1768 |
+- std::string atomName = fileline.substr(6,4); |
1769 |
++ |
1770 |
++//////// |
1771 |
++ //std::string atomName = fileline.substr(6,4); |
1772 |
++ std::string atomName = splitstring[1]; |
1773 |
++ if (atomName.size() == 1) atomName = " " + atomName + " "; |
1774 |
++ else if (atomName.size() == 2) atomName = " " + atomName + " "; |
1775 |
++ else if (atomName.size() == 3) atomName = " " + atomName; |
1776 |
++ |
1777 |
++//std::cout << "|" << atomName << "|" << std::endl; |
1778 |
++///////// |
1779 |
++ |
1780 |
+ std::string atomType = splitstring[2]; |
1781 |
+ std::string atomChain = splitstring[3]; |
1782 |
+ |
1783 |
+@@ -170,32 +205,54 @@ |
1784 |
+ pStdBond->atom1 = pStdAtom->index; |
1785 |
+ pStdBond->atom2 = pStdAtom->bond12; |
1786 |
+ pStdBond->type = 1; |
1787 |
++ |
1788 |
+ if (pStdAtom->atSymbol == "H") { |
1789 |
+ if (pStdAtom->bond12 > 0) { |
1790 |
+ stdAtom* pStdBondedAtom = pStdFrag->getStdAtom(pStdAtom->bond12); |
1791 |
++ |
1792 |
++ if (pStdBondedAtom) { |
1793 |
+ std::string bondedAtomSymbol = pStdBondedAtom->atSymbol; |
1794 |
+ if (bondedAtomSymbol == "N" or bondedAtomSymbol == "O" or bondedAtomSymbol == "S") { |
1795 |
+ pStdBond->kind = 1; |
1796 |
+ } |
1797 |
+ } |
1798 |
++ else { |
1799 |
++ todos.push_back(pStdBond); |
1800 |
++ } |
1801 |
++ } |
1802 |
+ } |
1803 |
+ else { |
1804 |
+ pStdBond->kind = 0; |
1805 |
+ } |
1806 |
++ |
1807 |
+ pStdBond->topology = 2; |
1808 |
+ pStdBond->stereo = 0; |
1809 |
+ pStdBond->length = pStdAtom->bondLength; |
1810 |
+ } |
1811 |
+ } |
1812 |
+ |
1813 |
++ for (unsigned int x = 0; x < todos.size(); x++) { |
1814 |
++ stdAtom* pStdBondedAtom1 = pStdFrag->getStdAtom(todos[x]->atom1); |
1815 |
++ stdAtom* pStdBondedAtom2 = pStdFrag->getStdAtom(todos[x]->atom2); |
1816 |
++ if (pStdBondedAtom1 and pStdBondedAtom2) { |
1817 |
++ std::string bondedAtomSymbol = pStdBondedAtom2->atSymbol; |
1818 |
++ if (bondedAtomSymbol == "N" or bondedAtomSymbol == "O" or bondedAtomSymbol == "S") { |
1819 |
++ todos[x]->kind = 1; |
1820 |
++ } |
1821 |
++ } |
1822 |
++ } |
1823 |
++ |
1824 |
+ // Read charge, alias, loop, and improper data |
1825 |
+ while (iprep) { |
1826 |
+ getline(iprep,fileline); |
1827 |
++//std::cout << "!" << fileline << "!" << std::endl; |
1828 |
+ if (fileline != "") { |
1829 |
+ if (fileline.substr(0,6) == "CHARGE") { |
1830 |
+ while (iprep) { |
1831 |
+ getline(iprep,fileline); |
1832 |
+- if (fileline == "") break; |
1833 |
++ |
1834 |
++ std::string filelineTest = stripString(fileline, " "); |
1835 |
++ if (filelineTest == "") break; |
1836 |
+ } |
1837 |
+ } |
1838 |
+ else if (fileline.substr(0,5) == "ALIAS") { |
1839 |
+@@ -252,7 +309,7 @@ |
1840 |
+ else { |
1841 |
+ std::string errorMessage = " ALIAS Tag Error ... exiting "; |
1842 |
+ errorLogger.throwError("prepParser::Read", errorMessage, 1); |
1843 |
+- //exit(0); |
1844 |
++ |
1845 |
+ std::stringstream ss; |
1846 |
+ ss << "prepParser::Read"<< errorMessage; |
1847 |
+ throw MTKException(ss.str()); |
1848 |
+@@ -263,11 +320,20 @@ |
1849 |
+ else if (fileline.substr(0,4) == "LOOP") { |
1850 |
+ while (iprep) { |
1851 |
+ getline(iprep,fileline); |
1852 |
+- if (fileline == "") break; |
1853 |
++ |
1854 |
++ std::string filelineTest = stripString(fileline, " "); |
1855 |
++ if (filelineTest == "") break; |
1856 |
++ |
1857 |
++ //if (fileline == "") break; |
1858 |
+ |
1859 |
+ std::vector<std::string> atomNames; |
1860 |
+ splitString(fileline, " ", atomNames, 0); |
1861 |
+- |
1862 |
++/* |
1863 |
++for (unsigned int x = 0; x <atomNames.size();x++){ |
1864 |
++ std::cout << atomNames[x] <<std::endl; |
1865 |
++} |
1866 |
++pStdFrag->print(); |
1867 |
++*/ |
1868 |
+ std::vector< std::vector<std::string> > possibleNames; |
1869 |
+ for (int d = 0; d < 2; d++) { |
1870 |
+ int atNameSize = atomNames[d].size(); |
1871 |
+@@ -315,17 +381,22 @@ |
1872 |
+ else { |
1873 |
+ std::string errorMessage = " LOOP Tag Error ... exiting "; |
1874 |
+ errorLogger.throwError("prepParser::Read", errorMessage, 1); |
1875 |
+- //exit(0); |
1876 |
+- |
1877 |
+ std::stringstream ss; |
1878 |
+ ss << "prepParser::Read"<< errorMessage; |
1879 |
+ throw MTKException(ss.str()); |
1880 |
+ } |
1881 |
+ } |
1882 |
+ } |
1883 |
++ else if (fileline.substr(0,4) == "DONE") { |
1884 |
++ break; |
1885 |
++ } |
1886 |
+ else if (fileline.substr(0,8) == "IMPROPER") { |
1887 |
+ while (iprep) { |
1888 |
+ getline(iprep,fileline); |
1889 |
++ |
1890 |
++ std::string filelineTest = stripString(fileline, " "); |
1891 |
++ if (filelineTest == "") break; |
1892 |
++ |
1893 |
+ if (fileline == "") break; |
1894 |
+ |
1895 |
+ std::vector<std::string> atomNames; |
1896 |
+@@ -424,7 +495,6 @@ |
1897 |
+ else { |
1898 |
+ std::string errorMessage = " IMPROPER Tag Error ... exiting "; |
1899 |
+ errorLogger.throwError("prepParser::Read", errorMessage, 1); |
1900 |
+- //exit(0); |
1901 |
+ |
1902 |
+ std::stringstream ss; |
1903 |
+ ss << "prepParser::Read" << errorMessage; |
1904 |
+@@ -642,8 +712,112 @@ |
1905 |
+ } |
1906 |
+ // QBio end |
1907 |
+ } |
1908 |
+- |
1909 |
+ errorLogger.throwError("prepParser::Read", eMessage, INFO); |
1910 |
++} |
1911 |
++ |
1912 |
++// ========================================================= |
1913 |
++// Function : Read |
1914 |
++// --------------------------------------------------------- |
1915 |
++// parsers a prep file |
1916 |
++// --------------------------------------------------------- |
1917 |
++// Format : |
1918 |
++// ========================================================= |
1919 |
++void prepParser::Read(const std::string &prepfile, stdGroup* pStdGroup) |
1920 |
++{ |
1921 |
++ int r = openFile(prepfile); |
1922 |
++ if (r == 1) return; |
1923 |
++ |
1924 |
++ while(iprep) { |
1925 |
++ std::string name = ""; |
1926 |
++ std::string symbol = ""; |
1927 |
++ double charge = 0.0; |
1928 |
++ int h = readHeader(name, symbol, charge); |
1929 |
++ if (h == 1) break; |
1930 |
++ |
1931 |
++ stdFrag* pStdFrag = pStdGroup->addStdFrag(); |
1932 |
++ if (!pStdFrag) { |
1933 |
++ setError(1); |
1934 |
++ std::string errorMessage = " Error creating fragment "; |
1935 |
++ setErrorMessage(errorMessage); |
1936 |
++ errorLogger.throwError("prepParser::Read", errorMessage, 1); |
1937 |
++ return; |
1938 |
++ } |
1939 |
++ |
1940 |
++ if (symbol.size() == 1) symbol = symbol + " "; |
1941 |
++ if (symbol.size() == 2) symbol = symbol + " "; |
1942 |
++ if (symbol.size() > 3) symbol = symbol.substr(1,3); |
1943 |
++ |
1944 |
++ pStdFrag->setSymbol(symbol); // 3L code |
1945 |
++ //pStdFrag->setCode("P2XML"+name); // 8L code |
1946 |
++ pStdFrag->setName(name); // long name |
1947 |
++ pStdFrag->setType("m"); // fragment type |
1948 |
++ |
1949 |
++ //std::cout << " prepParser::Read " << name << " charge " << charge << " symbol " << symbol << std::endl; |
1950 |
++ readFragment(pStdFrag); |
1951 |
++ } |
1952 |
++ |
1953 |
++ iprep.close(); |
1954 |
++ |
1955 |
++ return; |
1956 |
++} |
1957 |
++ |
1958 |
++// ========================================================= |
1959 |
++// Function : Read |
1960 |
++// --------------------------------------------------------- |
1961 |
++// parsers a prep file |
1962 |
++// --------------------------------------------------------- |
1963 |
++// Format : |
1964 |
++// ========================================================= |
1965 |
++void prepParser::Read(const std::string &prepfile, stdFrag* pStdFrag) |
1966 |
++{ |
1967 |
++ errorLogger.throwError("prepParser", "Read", INFO); |
1968 |
++/* |
1969 |
++ std::ifstream iprep; |
1970 |
++ iprep.open(prepfile.c_str()); |
1971 |
++ |
1972 |
++ if (!iprep) { |
1973 |
++ setError(1); |
1974 |
++ std::string errorMessage = " Error, Can't Find " + prepfile; |
1975 |
++ setErrorMessage(errorMessage); |
1976 |
++ errorLogger.throwError("prepParser::Read", errorMessage, 1); |
1977 |
++ return; |
1978 |
++ } |
1979 |
++*/ |
1980 |
++ |
1981 |
++ int r = openFile(prepfile); |
1982 |
++ if (r == 1) return; |
1983 |
++ |
1984 |
++ std::string fileline; |
1985 |
++ std::string title; |
1986 |
++ std::string atom; |
1987 |
++ //std::string buffer(80,'*'); |
1988 |
++ |
1989 |
++ // SKIP FIRST TWO LINES |
1990 |
++ //getline(iprep,fileline); |
1991 |
++ //getline(iprep,fileline); |
1992 |
++ |
1993 |
++/* |
1994 |
++ getline(iprep,fileline); |
1995 |
++ //std::string name = stripString(fileline," "); |
1996 |
++ //pStdFrag->setName(fileline); |
1997 |
++ getline(iprep,fileline); |
1998 |
++ getline(iprep,fileline); |
1999 |
++ std::vector<std::string> splitLine; |
2000 |
++ splitString(fileline, " ", splitLine, 0); |
2001 |
++ pStdFrag->setSymbol(splitLine[0]); |
2002 |
++ getline(iprep,fileline); |
2003 |
++ getline(iprep,fileline); |
2004 |
++ //pStdFrag->setCharge(splitLine[0]); |
2005 |
++*/ |
2006 |
++ |
2007 |
++ std::string name = ""; |
2008 |
++ std::string symbol = ""; |
2009 |
++ double charge = 0.0; |
2010 |
++ readHeader(name, symbol, charge); |
2011 |
++ |
2012 |
++ pStdFrag->setSymbol(symbol); |
2013 |
++ |
2014 |
++ readFragment(pStdFrag); |
2015 |
+ |
2016 |
+ iprep.close(); |
2017 |
+ } |
2018 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/prepParser.h amber11/AmberTools/src/mtkpp/src/Parsers/prepParser.h |
2019 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/prepParser.h 2011-04-14 15:30:18.000000000 +0300 |
2020 |
++++ amber11/AmberTools/src/mtkpp/src/Parsers/prepParser.h 2012-03-03 20:03:01.411032567 +0200 |
2021 |
+@@ -89,6 +89,25 @@ |
2022 |
+ ~prepParser(); |
2023 |
+ |
2024 |
+ /*! |
2025 |
++ \brief open prep file |
2026 |
++ \param i input file |
2027 |
++ */ |
2028 |
++ int openFile(const std::string &i); |
2029 |
++ |
2030 |
++ /*! |
2031 |
++ \brief read fragment header section |
2032 |
++ \param name fragment name |
2033 |
++ \param symbol fragment symbol |
2034 |
++ \param charge fragment charge |
2035 |
++ */ |
2036 |
++ int readHeader(std::string &name, std::string &symbol, double &charge); |
2037 |
++ |
2038 |
++ /*! |
2039 |
++ \brief read fragment main section |
2040 |
++ */ |
2041 |
++ void readFragment(stdFrag* pStdFrag); |
2042 |
++ |
2043 |
++ /*! |
2044 |
+ \brief Read prep file |
2045 |
+ \param i input file |
2046 |
+ \param g stdGroup pointer |
2047 |
+@@ -127,6 +146,9 @@ |
2048 |
+ |
2049 |
+ //! atom pointer |
2050 |
+ atom* pAtom; |
2051 |
++ |
2052 |
++ //! file handler |
2053 |
++ std::ifstream iprep; |
2054 |
+ }; |
2055 |
+ |
2056 |
+ } // MTKpp namespace |
2057 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Parsers/stdLibParser.cpp amber11/AmberTools/src/mtkpp/src/Parsers/stdLibParser.cpp |
2058 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Parsers/stdLibParser.cpp 2011-04-14 15:30:18.000000000 +0300 |
2059 |
++++ amber11/AmberTools/src/mtkpp/src/Parsers/stdLibParser.cpp 2012-03-03 20:03:01.412032567 +0200 |
2060 |
+@@ -3280,7 +3280,7 @@ |
2061 |
+ // ------------------------------------------------------------ |
2062 |
+ // Write xml files using tinyxml |
2063 |
+ // ------------------------------------------------------------ |
2064 |
+-void stdLibParser::Write(std::string fileName) |
2065 |
++void stdLibParser::Write(std::string fileName) // TinyXML |
2066 |
+ { |
2067 |
+ std::string errMessage = " Writing " + fileName; |
2068 |
+ errorLogger.throwError("stdLibParser", errMessage, INFO); |
2069 |
+@@ -3512,6 +3512,7 @@ |
2070 |
+ TiXmlElement* impElem = new TiXmlElement("improper"); |
2071 |
+ frag->LinkEndChild(impElem); |
2072 |
+ |
2073 |
++ /* |
2074 |
+ if (improperList[k]->atom1 == -1) { |
2075 |
+ impElem->SetAttribute("Atom1", "p1"); |
2076 |
+ } |
2077 |
+@@ -3520,7 +3521,8 @@ |
2078 |
+ } |
2079 |
+ else { |
2080 |
+ impElem->SetAttribute("Atom1", int2String(improperList[k]->atom1)); |
2081 |
+- } |
2082 |
++ }*/ |
2083 |
++ impElem->SetAttribute("Atom1", int2String(improperList[k]->atom1)); |
2084 |
+ impElem->SetAttribute("Atom2", int2String(improperList[k]->atom2)); |
2085 |
+ impElem->SetAttribute("Atom3", int2String(improperList[k]->atom3)); |
2086 |
+ impElem->SetAttribute("Atom4", int2String(improperList[k]->atom4)); |
2087 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Statistics/Makefile.am amber11/AmberTools/src/mtkpp/src/Statistics/Makefile.am |
2088 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Statistics/Makefile.am 2011-04-14 15:30:18.000000000 +0300 |
2089 |
++++ amber11/AmberTools/src/mtkpp/src/Statistics/Makefile.am 2012-03-03 20:03:01.413032567 +0200 |
2090 |
+@@ -1,4 +1,4 @@ |
2091 |
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics/$(SRCDIR) |
2092 |
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR) |
2093 |
+ DIAGNOSTICS_LIB=-lDiagnostics |
2094 |
+ |
2095 |
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/.. -I$(top_srcdir)/src/eigen3b2 |
2096 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/src/Statistics/Makefile.in amber11/AmberTools/src/mtkpp/src/Statistics/Makefile.in |
2097 |
+--- amber11.orig/AmberTools/src/mtkpp/src/Statistics/Makefile.in 2011-04-14 15:30:18.000000000 +0300 |
2098 |
++++ amber11/AmberTools/src/mtkpp/src/Statistics/Makefile.in 2012-03-03 20:03:01.413032567 +0200 |
2099 |
+@@ -241,7 +241,7 @@ |
2100 |
+ top_builddir = @top_builddir@ |
2101 |
+ top_srcdir = @top_srcdir@ |
2102 |
+ xerces_path = @xerces_path@ |
2103 |
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics/$(SRCDIR) |
2104 |
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics/$(SRCDIR) |
2105 |
+ DIAGNOSTICS_LIB = -lDiagnostics |
2106 |
+ INCLUDES = -I@boost_inc@ -I$(srcdir)/.. -I$(top_srcdir)/src/eigen3b2 |
2107 |
+ lib_LTLIBRARIES = libStatistics.la |
2108 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/tests/Makefile.am amber11/AmberTools/src/mtkpp/tests/Makefile.am |
2109 |
+--- amber11.orig/AmberTools/src/mtkpp/tests/Makefile.am 2011-04-14 15:30:19.000000000 +0300 |
2110 |
++++ amber11/AmberTools/src/mtkpp/tests/Makefile.am 2012-03-03 20:03:01.414032567 +0200 |
2111 |
+@@ -42,25 +42,25 @@ |
2112 |
+ LAPACK_LIB=-llapack -lblas -lg2c |
2113 |
+ endif |
2114 |
+ |
2115 |
+-MOLECULE_LD=-L$(top_builddir)/src/Molecule |
2116 |
++MOLECULE_LD=-L$(abs_top_builddir)/src/Molecule |
2117 |
+ MOLECULE_LIB=-lMolecule |
2118 |
+-DIAGNOSTICS_LD=-L$(top_builddir)/src/Diagnostics |
2119 |
++DIAGNOSTICS_LD=-L$(abs_top_builddir)/src/Diagnostics |
2120 |
+ DIAGNOSTICS_LIB=-lDiagnostics |
2121 |
+-LOG_LD=-L$(top_builddir)/src/Log |
2122 |
++LOG_LD=-L$(abs_top_builddir)/src/Log |
2123 |
+ LOG_LIB=-lLog |
2124 |
+-GRAPH_LD=-L$(top_builddir)/src/Graph |
2125 |
++GRAPH_LD=-L$(abs_top_builddir)/src/Graph |
2126 |
+ GRAPH_LIB=-lGraph |
2127 |
+-GA_LD=-L$(top_builddir)/src/GA |
2128 |
++GA_LD=-L$(abs_top_builddir)/src/GA |
2129 |
+ GA_LIB=-lGA |
2130 |
+-MM_LD=-L$(top_builddir)/src/MM |
2131 |
++MM_LD=-L$(abs_top_builddir)/src/MM |
2132 |
+ MM_LIB=-lMM |
2133 |
+-MINIMIZERS_LD=-L$(top_builddir)/src/Minimizers |
2134 |
++MINIMIZERS_LD=-L$(abs_top_builddir)/src/Minimizers |
2135 |
+ MINIMIZERS_LIB=-lMinimizers |
2136 |
+-PARSERS_LD=-L$(top_builddir)/src/Parsers |
2137 |
++PARSERS_LD=-L$(abs_top_builddir)/src/Parsers |
2138 |
+ PARSERS_LIB=-lParsers |
2139 |
+-STATS_LD=-L$(top_builddir)/src/Statistics |
2140 |
++STATS_LD=-L$(abs_top_builddir)/src/Statistics |
2141 |
+ STATS_LIB=-lStatistics |
2142 |
+-TINYXML_LD=-L$(top_builddir)/src/tinyxml |
2143 |
++TINYXML_LD=-L$(abs_top_builddir)/src/tinyxml |
2144 |
+ TINYXML_LIB=-ltinyxml |
2145 |
+ |
2146 |
+ # INCLUDES = -I@boost_inc@ -I@xerces_path@/include -I$(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) |
2147 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/tests/Makefile.in amber11/AmberTools/src/mtkpp/tests/Makefile.in |
2148 |
+--- amber11.orig/AmberTools/src/mtkpp/tests/Makefile.in 2011-04-14 15:30:19.000000000 +0300 |
2149 |
++++ amber11/AmberTools/src/mtkpp/tests/Makefile.in 2012-03-03 20:03:01.414032567 +0200 |
2150 |
+@@ -303,25 +303,25 @@ |
2151 |
+ @USE_QT_TRUE@tmpQT_LIBS = $(QT_LIBS) |
2152 |
+ @IS_LINUX_TRUE@LAPACK_LD = -L/usr/lib64 |
2153 |
+ @IS_LINUX_TRUE@LAPACK_LIB = -llapack -lblas -lg2c |
2154 |
+-MOLECULE_LD = -L$(top_builddir)/src/Molecule |
2155 |
++MOLECULE_LD = -L$(abs_top_builddir)/src/Molecule |
2156 |
+ MOLECULE_LIB = -lMolecule |
2157 |
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics |
2158 |
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics |
2159 |
+ DIAGNOSTICS_LIB = -lDiagnostics |
2160 |
+-LOG_LD = -L$(top_builddir)/src/Log |
2161 |
++LOG_LD = -L$(abs_top_builddir)/src/Log |
2162 |
+ LOG_LIB = -lLog |
2163 |
+-GRAPH_LD = -L$(top_builddir)/src/Graph |
2164 |
++GRAPH_LD = -L$(abs_top_builddir)/src/Graph |
2165 |
+ GRAPH_LIB = -lGraph |
2166 |
+-GA_LD = -L$(top_builddir)/src/GA |
2167 |
++GA_LD = -L$(abs_top_builddir)/src/GA |
2168 |
+ GA_LIB = -lGA |
2169 |
+-MM_LD = -L$(top_builddir)/src/MM |
2170 |
++MM_LD = -L$(abs_top_builddir)/src/MM |
2171 |
+ MM_LIB = -lMM |
2172 |
+-MINIMIZERS_LD = -L$(top_builddir)/src/Minimizers |
2173 |
++MINIMIZERS_LD = -L$(abs_top_builddir)/src/Minimizers |
2174 |
+ MINIMIZERS_LIB = -lMinimizers |
2175 |
+-PARSERS_LD = -L$(top_builddir)/src/Parsers |
2176 |
++PARSERS_LD = -L$(abs_top_builddir)/src/Parsers |
2177 |
+ PARSERS_LIB = -lParsers |
2178 |
+-STATS_LD = -L$(top_builddir)/src/Statistics |
2179 |
++STATS_LD = -L$(abs_top_builddir)/src/Statistics |
2180 |
+ STATS_LIB = -lStatistics |
2181 |
+-TINYXML_LD = -L$(top_builddir)/src/tinyxml |
2182 |
++TINYXML_LD = -L$(abs_top_builddir)/src/tinyxml |
2183 |
+ TINYXML_LIB = -ltinyxml |
2184 |
+ |
2185 |
+ # INCLUDES = -I@boost_inc@ -I@xerces_path@/include -I$(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) |
2186 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/tools/Makefile.am amber11/AmberTools/src/mtkpp/tools/Makefile.am |
2187 |
+--- amber11.orig/AmberTools/src/mtkpp/tools/Makefile.am 2011-04-14 15:30:19.000000000 +0300 |
2188 |
++++ amber11/AmberTools/src/mtkpp/tools/Makefile.am 2012-03-03 20:03:01.417032565 +0200 |
2189 |
+@@ -25,7 +25,7 @@ |
2190 |
+ tmpQT_LIBS = $(QT_LIBS) |
2191 |
+ endif |
2192 |
+ |
2193 |
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics |
2194 |
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics |
2195 |
+ DIAGNOSTICS_LIB = -lDiagnostics |
2196 |
+ MOLECULE_LD = -L$(top_builddir)/src/Molecule |
2197 |
+ MOLECULE_LIB = -lMolecule |
2198 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/tools/Makefile.in amber11/AmberTools/src/mtkpp/tools/Makefile.in |
2199 |
+--- amber11.orig/AmberTools/src/mtkpp/tools/Makefile.in 2011-04-14 15:30:19.000000000 +0300 |
2200 |
++++ amber11/AmberTools/src/mtkpp/tools/Makefile.in 2012-03-03 20:03:01.417032565 +0200 |
2201 |
+@@ -392,7 +392,7 @@ |
2202 |
+ @USE_XERCES_TRUE@XERCES_LIB = -lxerces-c |
2203 |
+ @USE_QT_TRUE@tmpQT_INCPATH = $(QT_INCPATH) |
2204 |
+ @USE_QT_TRUE@tmpQT_LIBS = $(QT_LIBS) |
2205 |
+-DIAGNOSTICS_LD = -L$(top_builddir)/src/Diagnostics |
2206 |
++DIAGNOSTICS_LD = -L$(abs_top_builddir)/src/Diagnostics |
2207 |
+ DIAGNOSTICS_LIB = -lDiagnostics |
2208 |
+ MOLECULE_LD = -L$(top_builddir)/src/Molecule |
2209 |
+ MOLECULE_LIB = -lMolecule |
2210 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/tools/MCPB.cpp amber11/AmberTools/src/mtkpp/tools/MCPB.cpp |
2211 |
+--- amber11.orig/AmberTools/src/mtkpp/tools/MCPB.cpp 2011-04-14 15:30:19.000000000 +0300 |
2212 |
++++ amber11/AmberTools/src/mtkpp/tools/MCPB.cpp 2012-03-03 20:03:01.416032566 +0200 |
2213 |
+@@ -67,6 +67,7 @@ |
2214 |
+ #include "Parsers/mtkppParser.h" |
2215 |
+ #include "Parsers/dMParser.h" |
2216 |
+ #include "Parsers/commLineOptions.h" |
2217 |
++#include "Parsers/StringManip.h" |
2218 |
+ |
2219 |
+ // - Log |
2220 |
+ #include "Log/errorHandler.h" |
2221 |
+@@ -84,6 +85,12 @@ |
2222 |
+ |
2223 |
+ using namespace MTKpp; |
2224 |
+ |
2225 |
++std::string getEnvVar(std::string const& key) |
2226 |
++{ |
2227 |
++ char const* val = getenv(key.c_str()); |
2228 |
++ return val == NULL ? std::string() : std::string(val); |
2229 |
++} |
2230 |
++ |
2231 |
+ void printFunctionList() |
2232 |
+ { |
2233 |
+ std::string functionList = "\n MCPB Functions:\n"; |
2234 |
+@@ -181,32 +188,32 @@ |
2235 |
+ functionList += " Find all metal centers in the collection\n"; |
2236 |
+ functionList += " syntax: findMetalCenters\n"; |
2237 |
+ functionList += "\n"; |
2238 |
+- functionList += " g03Charges\n"; |
2239 |
++ functionList += " gaussianCharges\n"; |
2240 |
+ functionList += " Generate a Gaussian input file for partial-charge computation\n"; |
2241 |
+ functionList += " Optional: set the Gaussian job file name\n"; |
2242 |
+- functionList += " syntax: g03Charges //cuCYM4 cuCYM4.com\n"; |
2243 |
++ functionList += " syntax: gaussianCharges //cuCYM4 cuCYM4.com\n"; |
2244 |
+ functionList += "\n"; |
2245 |
+- functionList += " g03Mem\n"; |
2246 |
+- functionList += " Set amount of memory requested for g03\n"; |
2247 |
+- functionList += " syntax: g03Mem 3600MB\n"; |
2248 |
++ functionList += " gaussianMem\n"; |
2249 |
++ functionList += " Set amount of memory requested for Gaussian\n"; |
2250 |
++ functionList += " syntax: gaussianMem 3600MB\n"; |
2251 |
+ functionList += "\n"; |
2252 |
+- functionList += " g03MoldenFormat\n"; |
2253 |
++ functionList += " gaussianMoldenFormat\n"; |
2254 |
+ functionList += " Request Gaussian log files formatted for viewing in Molden\n"; |
2255 |
+- functionList += " (adds the GFINPUT and IOP(6/7=3) keywords)\n"; |
2256 |
+- functionList += " syntax: g03MoldenFormat\n"; |
2257 |
++ functionList += " (adds the GFInput and IOp(6/7=3) keywords)\n"; |
2258 |
++ functionList += " syntax: gaussianMoldenFormat\n"; |
2259 |
+ functionList += "\n"; |
2260 |
+- functionList += " g03nProc\n"; |
2261 |
+- functionList += " Set number of processors requested for g03\n"; |
2262 |
+- functionList += " syntax: g03nProc 2\n"; |
2263 |
++ functionList += " gaussianNProc\n"; |
2264 |
++ functionList += " Set number of processors requested for Gaussian\n"; |
2265 |
++ functionList += " syntax: gaussianNProc 2\n"; |
2266 |
+ functionList += "\n"; |
2267 |
+- functionList += " g03OptAndFC\n"; |
2268 |
++ functionList += " gaussianOptAndFC\n"; |
2269 |
+ functionList += " Generate Gaussian input files for optimisation and force constants\n"; |
2270 |
+ functionList += " Optional: set the Gaussian job file name\n"; |
2271 |
+- functionList += " syntax: g03OptAndFC //cuCYM4 cuCYM4.com\n"; |
2272 |
++ functionList += " syntax: gaussianOptAndFC //cuCYM4 cuCYM4.com\n"; |
2273 |
+ functionList += "\n"; |
2274 |
+- functionList += " g03Verbosity\n"; |
2275 |
++ functionList += " gaussianVerbosity\n"; |
2276 |
+ functionList += " Set the verbosity of Gaussian output ([T]erse, [N]ormal, [P]rolix)\n"; |
2277 |
+- functionList += " syntax: g03Verbosity [T|N|P]\n"; |
2278 |
++ functionList += " syntax: gaussianVerbosity [T|N|P]\n"; |
2279 |
+ functionList += "\n"; |
2280 |
+ functionList += " levelOfTheory\n"; |
2281 |
+ functionList += " Set Gaussian Theory Level\n"; |
2282 |
+@@ -256,9 +263,9 @@ |
2283 |
+ functionList += " Read Formatted Checkpoint file\n"; |
2284 |
+ functionList += " syntax: readFormattedChkPtFile file.fchk\n"; |
2285 |
+ functionList += "\n"; |
2286 |
+- functionList += " readG03Output\n"; |
2287 |
+- functionList += " Read G03 Output\n"; |
2288 |
+- functionList += " syntax: readG03Output cuCYM4.log\n"; |
2289 |
++ functionList += " readGaussianOutput\n"; |
2290 |
++ functionList += " Read Gaussian Output\n"; |
2291 |
++ functionList += " syntax: readGaussianOutput cuCYM4.log\n"; |
2292 |
+ functionList += "\n"; |
2293 |
+ functionList += " readMolZmatMapping\n"; |
2294 |
+ functionList += " Read Molecule <--> Z-Matrix mapping file\n"; |
2295 |
+@@ -470,7 +477,7 @@ |
2296 |
+ else { |
2297 |
+ printHeader(std::cout, prog_name, authors); |
2298 |
+ clo->printUsage(); |
2299 |
+- std::cout << " Please provide a MCPB file " << std::endl; |
2300 |
++ std::cout << " Please provide an MCPB file " << std::endl; |
2301 |
+ return 0; |
2302 |
+ } |
2303 |
+ |
2304 |
+@@ -515,7 +522,9 @@ |
2305 |
+ std::string errorMessage = ""; |
2306 |
+ |
2307 |
+ std::vector<std::vector<std::string> > inputFileContents; |
2308 |
++ |
2309 |
+ int failure = readInputFile(inputFile, inputFileContents); |
2310 |
++ |
2311 |
+ if (failure) { |
2312 |
+ printHeader(std::cout, prog_name, authors); |
2313 |
+ clo->printUsage(); |
2314 |
+@@ -660,7 +669,7 @@ |
2315 |
+ std::vector<std::vector<std::string> > sourceInputFileContents; |
2316 |
+ failure = readInputFile(cur[1], sourceInputFileContents); |
2317 |
+ if (failure) { |
2318 |
+- errorMessage = " Error Reading File " + cur[1]; |
2319 |
++ errorMessage = " Error reading file " + cur[1]; |
2320 |
+ MTKpp::errorLogger.throwError("MCPB::source", errorMessage, 1); |
2321 |
+ exit(1); |
2322 |
+ } |
2323 |
+@@ -668,7 +677,7 @@ |
2324 |
+ sourceInputFileContents.end()); |
2325 |
+ } |
2326 |
+ else { |
2327 |
+- errorMessage = " Error Reading File " + cur[1]; |
2328 |
++ errorMessage = " Error reading file " + cur[1]; |
2329 |
+ MTKpp::errorLogger.throwError("MCPB::source", errorMessage, 1); |
2330 |
+ exit(1); |
2331 |
+ } |
2332 |
+@@ -742,6 +751,20 @@ |
2333 |
+ \endcode |
2334 |
+ */ |
2335 |
+ if ((inputFileContents[i].size() == 3)) { |
2336 |
++ //std::cout << "SET COMMAND " << inputFileContents[i][2] << std::endl; |
2337 |
++ if (inputFileContents[i][2].compare(0,1,"$") == 0) { |
2338 |
++ std::string envVariable = ""; |
2339 |
++ std::string tVar = inputFileContents[i][2]; |
2340 |
++ envVariable = getEnvVar(tVar.substr(1,tVar.size()-1)); |
2341 |
++ if (envVariable == "") { |
2342 |
++ std::cout << " Environment variable " << tVar.substr(1,tVar.size()-1) |
2343 |
++ << " is unset " << std::endl; |
2344 |
++ exit(1); |
2345 |
++ } |
2346 |
++ //std::cout << "Environment variable = " << envVariable << std::endl; |
2347 |
++ inputFileContents[i][2] = envVariable; |
2348 |
++ } |
2349 |
++ |
2350 |
+ variableMap[inputFileContents[i][1]] = inputFileContents[i][2]; |
2351 |
+ for (unsigned int j = i+1; j < inputFileContents.size(); j++) { |
2352 |
+ bool bReplaced = false; |
2353 |
+@@ -813,6 +836,115 @@ |
2354 |
+ } |
2355 |
+ } |
2356 |
+ |
2357 |
++ else if (inputFileContents[i][0] == "printGroupCharge") { |
2358 |
++ /*! |
2359 |
++ @ingroup MCPB_commands |
2360 |
++ \code |
2361 |
++ Function: printFrag |
2362 |
++ |
2363 |
++ Description: Print fragment details |
2364 |
++ |
2365 |
++ syntax: printGroupCharge Zn-CCCC |
2366 |
++ |
2367 |
++ \endcode |
2368 |
++ */ |
2369 |
++ if ((inputFileContents[i].size() != 2) or (!pCollection)) { |
2370 |
++ MTKpp::errorLogger.throwError("MCPB::printGroupCharge", " Incorrect use of printGroupCharge ... exiting", MTK_ERROR); |
2371 |
++ exit(1); |
2372 |
++ } |
2373 |
++ else { |
2374 |
++ stdLibrary* pStdLibrary = pCollection->getStdLibrary(); |
2375 |
++ if (pStdLibrary) { |
2376 |
++ stdGroup* pStdGroup = pStdLibrary->getStdGroup(inputFileContents[i][1]); |
2377 |
++ std::cout << " Group " << pStdGroup->getName() << "\n"; |
2378 |
++ if (pStdGroup) { |
2379 |
++ molecule* pM = pStdGroup->getStdMolecule(); |
2380 |
++ if (pM) { |
2381 |
++ double groupCharge = 0.0; |
2382 |
++ std::vector<submolecule*> pSM = pM->getSubMoleculeList(); |
2383 |
++ //std::cout << " Number of submolecules = " << pSM.size() << "\n"; |
2384 |
++ for (unsigned int x = 0; x < pSM.size(); x++) { |
2385 |
++ stdFrag* pSF = pStdGroup->getStdFrag(pSM[x]->getName()); |
2386 |
++ if (pSF) { |
2387 |
++ std::cout << " " << pSF->getSymbol() << "\n"; |
2388 |
++ double fCharge = 0.0; |
2389 |
++ std::vector<atom*> pA = pSM[x]->getAtomList(); |
2390 |
++ for (unsigned int y = 0; y < pA.size(); y++) { |
2391 |
++ stdAtom* pSA = pA[y]->getStdAtom(); |
2392 |
++ if (pSA) { |
2393 |
++ fCharge += pSA->atmCharge; |
2394 |
++ std::cout << " |" << pSA->identity << "| " << pSA->atmCharge << "\n"; |
2395 |
++ } |
2396 |
++ else { |
2397 |
++ std::cout << " Error find std atom " << std::endl; |
2398 |
++ exit(1); |
2399 |
++ } |
2400 |
++ } |
2401 |
++ groupCharge += fCharge; |
2402 |
++ std::cout << " Total Fragment Charge " << pSF->getCharge() << "\n"; |
2403 |
++ } |
2404 |
++ } |
2405 |
++ /*std::vector<stdFrag*> pL = pStdGroup->getStdFragList(); |
2406 |
++ for (unsigned int x = 0; x < pL.size(); x++) { |
2407 |
++ std::cout << " Fragment " << pL[x]->getSymbol() << "\n"; |
2408 |
++ std::vector<stdAtom*> pL2 = pL[x]->getStdAtomList(); |
2409 |
++ double fCharge = 0.0; |
2410 |
++ for (unsigned int y = 0; y < pL2.size(); y++) { |
2411 |
++ fCharge += pL2[y]->atmCharge; |
2412 |
++ std::cout << " Atom " << pL2[y]->identity << " " << pL2[y]->atmCharge << "\n"; |
2413 |
++ } |
2414 |
++ groupCharge += fCharge; |
2415 |
++ //groupCharge += pL[x]->getCharge(); |
2416 |
++ std::cout << " Fragment Charge " << pL[x]->getCharge() << "\n"; |
2417 |
++ } |
2418 |
++ */ |
2419 |
++ |
2420 |
++ std::cout << " Total Charge = " << groupCharge << "\n" << std::endl; |
2421 |
++ } |
2422 |
++ } |
2423 |
++ } |
2424 |
++ } |
2425 |
++ } |
2426 |
++ |
2427 |
++ else if (inputFileContents[i][0] == "printFrag") { |
2428 |
++ /*! |
2429 |
++ @ingroup MCPB_commands |
2430 |
++ \code |
2431 |
++ Function: printFrag |
2432 |
++ |
2433 |
++ Description: Print fragment details |
2434 |
++ |
2435 |
++ syntax: printFrag Zn-CCCC CY1 |
2436 |
++ |
2437 |
++ \endcode |
2438 |
++ */ |
2439 |
++ if ((inputFileContents[i].size() != 3) or (!pCollection)) { |
2440 |
++ MTKpp::errorLogger.throwError("MCPB::printFrag", " Incorrect use of printFrag ... exiting", MTK_ERROR); |
2441 |
++ exit(1); |
2442 |
++ } |
2443 |
++ else { |
2444 |
++ stdLibrary* pStdLibrary = pCollection->getStdLibrary(); |
2445 |
++ if (pStdLibrary) { |
2446 |
++ stdGroup* pStdGroup = pStdLibrary->getStdGroup(inputFileContents[i][1]); |
2447 |
++ |
2448 |
++ double groupCharge = 0.0; |
2449 |
++ std::vector<stdFrag*> pL = pStdGroup->getStdFragList(); |
2450 |
++ for (unsigned int x = 0; x < pL.size(); x++) { |
2451 |
++ groupCharge += pL[x]->getCharge(); |
2452 |
++ |
2453 |
++ } |
2454 |
++ std::cout << " Group " << inputFileContents[i][1] << " charge = " |
2455 |
++ << groupCharge << std::endl; |
2456 |
++ |
2457 |
++ stdFrag* pStdFrag = pStdGroup->getStdFrag(inputFileContents[i][2]); |
2458 |
++ if (pStdFrag) { |
2459 |
++ std::cout << " Fragment " << inputFileContents[i][2] << " charge = " |
2460 |
++ << pStdFrag->getCharge() << std::endl; |
2461 |
++ } |
2462 |
++ } |
2463 |
++ } |
2464 |
++ } |
2465 |
++ |
2466 |
+ else if (inputFileContents[i][0] == "readPdb") { |
2467 |
+ /*! |
2468 |
+ @ingroup MCPB_commands |
2469 |
+@@ -2227,7 +2359,8 @@ |
2470 |
+ double resCharge = 0.0; |
2471 |
+ for (unsigned int y = 0; y < residueAtoms.size(); y++) { |
2472 |
+ stdAtom* pLStdAtom = residueAtoms[y]->getStdAtom(); |
2473 |
+- std::cout << " " << residueAtoms[y]->getName() << " " << residueAtoms[y]->getFileID() |
2474 |
++ std::cout << " " |
2475 |
++ << residueAtoms[y]->getName() << " " << residueAtoms[y]->getFileID() |
2476 |
+ << " " << residueAtoms[y]->getType() << " " << residueAtoms[y]->getValence() |
2477 |
+ << " " << residueAtoms[y]->getHybridization() << " "; |
2478 |
+ if (pLStdAtom) { |
2479 |
+@@ -2437,6 +2570,11 @@ |
2480 |
+ molecule* selMol = pSel->getMol(); |
2481 |
+ pPdbParser->Write(inputFileContents[i][2], selMol); |
2482 |
+ } |
2483 |
++ else { |
2484 |
++ MTKpp::errorLogger.throwError("MCPB::writePdb", |
2485 |
++ " Error molecule was not selected ... exiting ", MTK_ERROR); |
2486 |
++ exit(1); |
2487 |
++ } |
2488 |
+ } |
2489 |
+ } |
2490 |
+ |
2491 |
+@@ -2674,7 +2812,6 @@ |
2492 |
+ |
2493 |
+ syntax: basisSet GEN bs.txt |
2494 |
+ syntax: basisSet GEN.6D.7F bs.txt |
2495 |
+- syntax: basisSet GENECP bs.txt pseudo.txt |
2496 |
+ \endcode |
2497 |
+ */ |
2498 |
+ if (inputFileContents[i].size() == 2) { |
2499 |
+@@ -2685,6 +2822,11 @@ |
2500 |
+ pGParser->setBasisSet(inputFileContents[i][1]); |
2501 |
+ pGParser->setBasisSetFile(inputFileContents[i][2]); |
2502 |
+ } |
2503 |
++ else { |
2504 |
++ MTKpp::errorLogger.throwError("MCPB::basisSet", |
2505 |
++ " Incorrect use ... exiting ", MTK_ERROR); |
2506 |
++ exit(1); |
2507 |
++ } |
2508 |
+ } |
2509 |
+ |
2510 |
+ else if (inputFileContents[i][0] == "pseudoPotentials") { |
2511 |
+@@ -2698,8 +2840,15 @@ |
2512 |
+ syntax: pseudoPotential pseudo.txt |
2513 |
+ \endcode |
2514 |
+ */ |
2515 |
+- pGParser->addCommandOption("pseudo","read"); |
2516 |
++ if (inputFileContents[i].size() == 2) { |
2517 |
++ pGParser->addCommandOption("Pseudo","Read"); |
2518 |
+ pGParser->setPseudoPotentialFile(inputFileContents[i][1]); |
2519 |
++ } else { |
2520 |
++ MTKpp::errorLogger.throwError("MCPB::pseudoPotentials", |
2521 |
++ " Incorrect use ... exiting ", MTK_ERROR); |
2522 |
++ exit(1); |
2523 |
++ } |
2524 |
++ |
2525 |
+ } |
2526 |
+ |
2527 |
+ else if (inputFileContents[i][0] == "modRedundant") { |
2528 |
+@@ -2713,8 +2862,14 @@ |
2529 |
+ syntax: modRedundant modred.txt |
2530 |
+ \endcode |
2531 |
+ */ |
2532 |
+- pGParser->addCommandOption("opt","modredundant"); |
2533 |
++ if (inputFileContents[i].size() == 2) { |
2534 |
++ pGParser->addCommandOption("Opt","ModRedundant"); |
2535 |
+ pGParser->setModRedundantFile(inputFileContents[i][1]); |
2536 |
++ } else { |
2537 |
++ MTKpp::errorLogger.throwError("MCPB::modRedundant", |
2538 |
++ " Incorrect use ... exiting ", MTK_ERROR); |
2539 |
++ exit(1); |
2540 |
++ } |
2541 |
+ } |
2542 |
+ |
2543 |
+ else if (inputFileContents[i][0] == "clusterCharge") { |
2544 |
+@@ -2728,7 +2883,13 @@ |
2545 |
+ syntax: clusterCharge cuCYM4 -3 |
2546 |
+ \endcode |
2547 |
+ */ |
2548 |
++ if (inputFileContents[i].size() == 3) { |
2549 |
+ pGParser->setCharge(atoi(inputFileContents[i][2].c_str())); |
2550 |
++ } else { |
2551 |
++ MTKpp::errorLogger.throwError("MCPB::clusterCharge", |
2552 |
++ " Incorrect use ... exiting ", MTK_ERROR); |
2553 |
++ exit(1); |
2554 |
++ } |
2555 |
+ } |
2556 |
+ |
2557 |
+ else if (inputFileContents[i][0] == "clusterSpin") { |
2558 |
+@@ -2742,76 +2903,94 @@ |
2559 |
+ syntax: clusterSpin 0 |
2560 |
+ \endcode |
2561 |
+ */ |
2562 |
++ if (inputFileContents[i].size() == 2) { |
2563 |
+ pGParser->setMultiplicity(atoi(inputFileContents[i][1].c_str())); |
2564 |
++ } else { |
2565 |
++ MTKpp::errorLogger.throwError("MCPB::clusterSpin", |
2566 |
++ " Incorrect use ... exiting ", MTK_ERROR); |
2567 |
++ exit(1); |
2568 |
++ } |
2569 |
+ } |
2570 |
+ |
2571 |
+- else if (inputFileContents[i][0] == "g03MoldenFormat") { |
2572 |
++ else if (inputFileContents[i][0] == "gaussianMoldenFormat") { |
2573 |
+ /*! |
2574 |
+ @ingroup MCPB_commands |
2575 |
+ \code |
2576 |
+- Function: g03MoldenFormat |
2577 |
++ Function: gaussianMoldenFormat |
2578 |
+ |
2579 |
+ Description: Use Molden formatted output in log file. Print out |
2580 |
+ details of the basis set and the molecular orbitals. |
2581 |
+ |
2582 |
+- syntax: g03MoldenFormat (bare word) |
2583 |
++ syntax: gaussianMoldenFormat (bare word) |
2584 |
+ \endcode |
2585 |
+ */ |
2586 |
+- pGParser->addCommandOption("gfinput"); |
2587 |
+- pGParser->addIop("iop(6/7=3)"); |
2588 |
++ pGParser->addCommandOption("GFInput"); |
2589 |
++ pGParser->addIop("IOp(6/7=3)"); |
2590 |
+ } |
2591 |
+ |
2592 |
+- else if (inputFileContents[i][0] == "g03Verbosity") { |
2593 |
++ else if (inputFileContents[i][0] == "gaussianVerbosity") { |
2594 |
+ if (inputFileContents[i].size() == 2) { |
2595 |
+ pGParser->setVerbosity(inputFileContents[i][1]); |
2596 |
++ } else { |
2597 |
++ MTKpp::errorLogger.throwError("MCPB::gaussianVerbosity", |
2598 |
++ " Incorrect use ... exiting ", MTK_ERROR); |
2599 |
++ exit(1); |
2600 |
+ } |
2601 |
+ } |
2602 |
+ |
2603 |
+- else if (inputFileContents[i][0] == "g03Mem") { |
2604 |
++ else if (inputFileContents[i][0] == "gaussianMem") { |
2605 |
+ /*! |
2606 |
+ @ingroup MCPB_commands |
2607 |
+ \code |
2608 |
+- Function: g03Mem |
2609 |
++ Function: gaussianMem |
2610 |
+ |
2611 |
+- Description: Set amount of memory requested for g03 |
2612 |
++ Description: Set amount of memory requested for Gaussian |
2613 |
+ |
2614 |
+- syntax: g03Mem 3600MB |
2615 |
++ syntax: gaussianMem 3600MB |
2616 |
+ \endcode |
2617 |
+ */ |
2618 |
+ if (inputFileContents[i].size() == 2) { |
2619 |
+ pGParser->setMem(inputFileContents[i][1]); |
2620 |
++ } else { |
2621 |
++ MTKpp::errorLogger.throwError("MCPB::gaussianMem", |
2622 |
++ " Incorrect use ... exiting ", MTK_ERROR); |
2623 |
++ exit(1); |
2624 |
+ } |
2625 |
+ } |
2626 |
+ |
2627 |
+- else if (inputFileContents[i][0] == "g03nProc") { |
2628 |
++ else if (inputFileContents[i][0] == "gaussianNProc") { |
2629 |
+ /*! |
2630 |
+ @ingroup MCPB_commands |
2631 |
+ \code |
2632 |
+- Function: g03nProc |
2633 |
++ Function: gaussianNProc |
2634 |
+ |
2635 |
+- Description: Set number of processors requested for g03 |
2636 |
++ Description: Set number of processors requested for Gaussian |
2637 |
+ |
2638 |
+- syntax: g03nProc 2 |
2639 |
++ syntax: gaussianNProc 2 |
2640 |
+ \endcode |
2641 |
+ */ |
2642 |
+ if (inputFileContents[i].size() == 2) { |
2643 |
+- pGParser->setnProc(inputFileContents[i][1]); |
2644 |
++ pGParser->setNProc(inputFileContents[i][1]); |
2645 |
++ } else { |
2646 |
++ MTKpp::errorLogger.throwError("MCPB::gaussianNProc", |
2647 |
++ " Incorrect use ... exiting ", MTK_ERROR); |
2648 |
++ exit(1); |
2649 |
+ } |
2650 |
+ } |
2651 |
+ |
2652 |
+- else if (inputFileContents[i][0] == "g03OptAndFC") { |
2653 |
++ else if (inputFileContents[i][0] == "gaussianOptAndFC") { |
2654 |
+ /*! |
2655 |
+ @ingroup MCPB_commands |
2656 |
+ \code |
2657 |
+- Function: g03OptAndFC |
2658 |
++ Function: gaussianOptAndFC |
2659 |
+ |
2660 |
+ Description: Set Gaussian input name |
2661 |
+ |
2662 |
+- syntax: g03OptAndFC //cuCYM4 cuCYM4.com |
2663 |
++ syntax: gaussianOptAndFC //cuCYM4 cuCYM4.com |
2664 |
+ \endcode |
2665 |
+ */ |
2666 |
+ if ((inputFileContents[i].size() != 3) or (!pCollection)) { |
2667 |
+- MTKpp::errorLogger.throwError("MCPB::g03OptAndFC", |
2668 |
++ MTKpp::errorLogger.throwError("MCPB::gaussianOptAndFC", |
2669 |
+ " Incorrect use ... exiting ", MTK_ERROR); |
2670 |
+ exit(1); |
2671 |
+ } |
2672 |
+@@ -2819,7 +2998,7 @@ |
2673 |
+ selection* pSel = new selection(pCollection); |
2674 |
+ failure = pSel->parse(inputFileContents[i][1]); |
2675 |
+ if (failure) { |
2676 |
+- MTKpp::errorLogger.throwError("MCPB::g03OptAndFC", |
2677 |
++ MTKpp::errorLogger.throwError("MCPB::gaussianOptAndFC", |
2678 |
+ " Error in selection parsing ... exiting ", MTK_ERROR); |
2679 |
+ exit(1); |
2680 |
+ } |
2681 |
+@@ -2833,17 +3012,17 @@ |
2682 |
+ pGParser->setCartesian(1); |
2683 |
+ pGParser->setWriteMoleculeName(1); |
2684 |
+ pGParser->setWriteChargeAndMult(1); |
2685 |
+- pGParser->addCommandOption("integral(Grid=UltraFine)"); |
2686 |
++ pGParser->addCommandOption("Integral", "(Grid=UltraFine)"); |
2687 |
+ |
2688 |
+- std::vector<std::string> optOptions = pGParser->getCommandOption("opt"); |
2689 |
++ std::vector<std::string> optOptions = pGParser->getCommandOption("Opt"); |
2690 |
+ if (optOptions.size() == 0) { |
2691 |
+- pGParser->addCommandOption("opt"); |
2692 |
++ pGParser->addCommandOption("Opt"); |
2693 |
+ } |
2694 |
+ |
2695 |
+- pGParser->addCommandOption("scf", "xqc"); |
2696 |
+- pGParser->addCommandOption("geom", "PrintInputOrient"); |
2697 |
++ pGParser->addCommandOption("SCF", "XQC"); |
2698 |
++ pGParser->addCommandOption("Geom", "PrintInputOrient"); |
2699 |
+ pGParser->Write(fileNameBase+"_opt.com", pSelMol); |
2700 |
+- pGParser->removeCommandOption("opt"); |
2701 |
++ pGParser->removeCommandOption("Opt"); |
2702 |
+ |
2703 |
+ // k's |
2704 |
+ // Do not write coordinates, name, charge or multiplicity, |
2705 |
+@@ -2851,40 +3030,40 @@ |
2706 |
+ pGParser->setNoCoords(); |
2707 |
+ pGParser->setWriteMoleculeName(0); |
2708 |
+ pGParser->setWriteChargeAndMult(0); |
2709 |
+- pGParser->addCommandOption("freq", "noraman"); |
2710 |
+- pGParser->addCommandOption("geom", "allcheckpoint"); |
2711 |
+- pGParser->addCommandOption("guess", "read"); |
2712 |
+- pGParser->addIop("iop(7/33=1)"); |
2713 |
++ pGParser->addCommandOption("Freq", "NoRaman"); |
2714 |
++ pGParser->addCommandOption("Geom", "AllCheckpoint"); |
2715 |
++ pGParser->addCommandOption("Guess", "Read"); |
2716 |
++ pGParser->addIop("IOp(7/33=1)"); |
2717 |
+ pGParser->Write(fileNameBase+"_fc.com", pSelMol); |
2718 |
+ pGParser->clearIop(); |
2719 |
+ |
2720 |
+ /* |
2721 |
+ // optimization |
2722 |
+- pGParser->addCommandOption("opt", "z-matrix"); |
2723 |
++ pGParser->addCommandOption("Opt", "Z-Matrix"); |
2724 |
+ pGParser->generateZMatrix(pSelMol); |
2725 |
+ // [molecule index] = zmatrix index; |
2726 |
+ pGParser->writeMappingFile(fileNameBase+"_zmat.map"); |
2727 |
+- pGParser->addCommandOption("geom", "PrintInputOrient"); |
2728 |
++ pGParser->addCommandOption("Geom", "PrintInputOrient"); |
2729 |
+ pGParser->Write(fileNameBase+"_opt.com", pSelMol); |
2730 |
+- pGParser->removeCommandOption("opt"); |
2731 |
++ pGParser->removeCommandOption("Opt"); |
2732 |
+ */ |
2733 |
+ } |
2734 |
+ } |
2735 |
+ } |
2736 |
+ |
2737 |
+- else if (inputFileContents[i][0] == "g03Charges") { |
2738 |
++ else if (inputFileContents[i][0] == "gaussianCharges") { |
2739 |
+ /*! |
2740 |
+ @ingroup MCPB_commands |
2741 |
+ \code |
2742 |
+- Function: g03Charges |
2743 |
++ Function: gaussianCharges |
2744 |
+ |
2745 |
+ Description: Set Gaussian input name |
2746 |
+ |
2747 |
+- syntax: g03Charges //cuCYM4 cuCYM4.com |
2748 |
++ syntax: gaussianCharges //cuCYM4 cuCYM4.com |
2749 |
+ \endcode |
2750 |
+ */ |
2751 |
+ if ((inputFileContents[i].size() != 3) or (!pCollection)) { |
2752 |
+- MTKpp::errorLogger.throwError("MCPB::g03Charges", |
2753 |
++ MTKpp::errorLogger.throwError("MCPB::gaussianCharges", |
2754 |
+ " Incorrect use ... exiting ", MTK_ERROR); |
2755 |
+ exit(1); |
2756 |
+ } |
2757 |
+@@ -2892,7 +3071,7 @@ |
2758 |
+ selection* pSel = new selection(pCollection); |
2759 |
+ failure = pSel->parse(inputFileContents[i][1]); |
2760 |
+ if (failure) { |
2761 |
+- MTKpp::errorLogger.throwError("MCPB::g03Charges", |
2762 |
++ MTKpp::errorLogger.throwError("MCPB::gaussianCharges", |
2763 |
+ " Error in selection parsing ... exiting ", MTK_ERROR); |
2764 |
+ exit(1); |
2765 |
+ } |
2766 |
+@@ -2907,14 +3086,14 @@ |
2767 |
+ |
2768 |
+ // q's |
2769 |
+ std::vector<std::string> popOptions; |
2770 |
+- popOptions.push_back("mk"); |
2771 |
+- popOptions.push_back("readradii"); |
2772 |
+- pGParser->addCommandOption("pop", popOptions); |
2773 |
+- pGParser->removeCommandOption("freq"); |
2774 |
+- pGParser->addIop("iop(6/33=2)"); |
2775 |
++ popOptions.push_back("MK"); |
2776 |
++ popOptions.push_back("ReadRadii"); |
2777 |
++ pGParser->addCommandOption("Pop", popOptions); |
2778 |
++ pGParser->removeCommandOption("Freq"); |
2779 |
++ pGParser->addIop("IOp(6/33=2)"); |
2780 |
+ |
2781 |
+- pGParser->addCommandOption("integral(Grid=UltraFine)"); |
2782 |
+- pGParser->addCommandOption("scf", "xqc"); |
2783 |
++ pGParser->addCommandOption("Integral", "(Grid=UltraFine)"); |
2784 |
++ pGParser->addCommandOption("SCF", "XQC"); |
2785 |
+ |
2786 |
+ pGParser->Write(fileNameBase+"_mk.com", pSelMol); |
2787 |
+ |
2788 |
+@@ -3053,7 +3232,8 @@ |
2789 |
+ result = find(bbb.begin(), bbb.end(), dd); |
2790 |
+ |
2791 |
+ if (result != bbb.end()) { |
2792 |
+- freezingAtoms += "\n BBB " + submols[s]->getName() + " " + int2String(submols[s]->getSubMolId()) + " " + dd; |
2793 |
++ freezingAtoms += "\n BBB " + submols[s]->getName() + " " |
2794 |
++ + int2String(submols[s]->getSubMolId()) + " " + dd; |
2795 |
+ sprintf(temp,"%5d%10.5f", 1, pStdAtom_a->atmCharge); |
2796 |
+ orespAdd << temp << std::endl; |
2797 |
+ sprintf(temp,"%5d%5d", 1, subAtoms[a]->getIndex()); |
2798 |
+@@ -3071,7 +3251,6 @@ |
2799 |
+ MTKpp::errorLogger.throwError("MCPB::respgenAdditions", |
2800 |
+ freezingAtoms, INFO); |
2801 |
+ } |
2802 |
+- |
2803 |
+ orespAdd << "\n" << std::endl; |
2804 |
+ orespAdd.close(); |
2805 |
+ } |
2806 |
+@@ -3099,22 +3278,22 @@ |
2807 |
+ } |
2808 |
+ } |
2809 |
+ |
2810 |
+- else if (inputFileContents[i][0] == "readG03Output") { |
2811 |
++ else if (inputFileContents[i][0] == "readGaussianOutput") { |
2812 |
+ /*! |
2813 |
+ @ingroup MCPB_commands |
2814 |
+ \code |
2815 |
+- Function: readG03Output |
2816 |
++ Function: readGaussianOutput |
2817 |
+ |
2818 |
+- Description: Read G03 Output |
2819 |
++ Description: Read Gaussian Output |
2820 |
+ |
2821 |
+- syntax: readG03Output cuCYM4.log |
2822 |
++ syntax: readGaussianOutput cuCYM4.log |
2823 |
+ \endcode |
2824 |
+ */ |
2825 |
+ if ((inputFileContents[i].size() == 2) or (pGParser)) { |
2826 |
+ pGParser->Read(inputFileContents[i][1], pSheet); |
2827 |
+ } |
2828 |
+ else { |
2829 |
+- MTKpp::errorLogger.throwError("MCPB::readG03Output", |
2830 |
++ MTKpp::errorLogger.throwError("MCPB::readGaussianOutput", |
2831 |
+ " Incorrect use ... exiting ", MTK_ERROR); |
2832 |
+ exit(1); |
2833 |
+ } |
2834 |
+@@ -3481,8 +3660,8 @@ |
2835 |
+ pGParser->setCartesian(0); |
2836 |
+ pGParser->setWriteMoleculeName(1); |
2837 |
+ pGParser->setWriteChargeAndMult(1); |
2838 |
+- pGParser->addCommandOption("freq", "noraman"); |
2839 |
+- pGParser->addIop("iop(7/33=1)"); |
2840 |
++ pGParser->addCommandOption("Freq", "NoRaman"); |
2841 |
++ pGParser->addIop("IOp(7/33=1)"); |
2842 |
+ pGParser->Write(inputFileContents[i][2], pSelMol); |
2843 |
+ pGParser->writeMappingFile(inputFileContents[i][2]+".map"); |
2844 |
+ } |
2845 |
+@@ -3826,6 +4005,7 @@ |
2846 |
+ if (pStdFrag) { |
2847 |
+ bool doIt = pStdGroup->hasStdFrag(pStdFrag->getSymbol()); |
2848 |
+ if (doIt) { |
2849 |
++ //std::cout << " " << pStdFrag->getSymbol() << "\n"; |
2850 |
+ //submolecule* pStdSubmol = pStdMolecule->addSubMolecule(); |
2851 |
+ //pStdSubmol->copy(submolList[t]); |
2852 |
+ std::vector<atom*> lAtomList = submolList[t]->getAtomList(); |
2853 |
+@@ -3834,7 +4014,8 @@ |
2854 |
+ if (pStdAtom) { |
2855 |
+ //std::cout << " |" << lAtomList[r]->getName() << "| " << lAtomList[r]->getZcharge() << "\n"; |
2856 |
+ pStdAtom->atmCharge = lAtomList[r]->getZcharge(); |
2857 |
+- groupCharge += lAtomList[r]->getZcharge(); |
2858 |
++ //groupCharge += lAtomList[r]->getZcharge(); |
2859 |
++ groupCharge += pStdAtom->atmCharge; |
2860 |
+ } |
2861 |
+ } |
2862 |
+ } |
2863 |
+@@ -3861,11 +4042,398 @@ |
2864 |
+ */ |
2865 |
+ } |
2866 |
+ updateRespChargesMessage += " Charge: " + double2String(groupCharge, 2); |
2867 |
++ //std::cout << " Group charge = " << double2String(groupCharge, 2) << "\n"; |
2868 |
+ MTKpp::errorLogger.throwError("MCPB::updateRespCharges", |
2869 |
+ updateRespChargesMessage, INFO); |
2870 |
+ } |
2871 |
+ } |
2872 |
+ |
2873 |
++ else if (inputFileContents[i][0] == "respgen") { |
2874 |
++ /*! |
2875 |
++ @ingroup MCPB_commands |
2876 |
++ \code |
2877 |
++ Function: respgen |
2878 |
++ |
2879 |
++ Description: Create resp1 and resp2 files (recreates functionality of respgen) |
2880 |
++ |
2881 |
++ syntax: respgen /COL/MOL Group fileName |
2882 |
++ \endcode |
2883 |
++ */ |
2884 |
++ |
2885 |
++ if ((inputFileContents[i].size() != 4) or (!pCollection)) { |
2886 |
++ MTKpp::errorLogger.throwError("MCPB::respgen", |
2887 |
++ " Incorrect use ... exiting ", MTK_ERROR); |
2888 |
++ exit(1); |
2889 |
++ } |
2890 |
++ else { |
2891 |
++ selection* pSel = new selection(pCollection); |
2892 |
++ failure = pSel->parse(inputFileContents[i][1]); |
2893 |
++ if (failure) { |
2894 |
++ MTKpp::errorLogger.throwError("MCPB::respgen", |
2895 |
++ " Error in selection parsing ... exiting ", MTK_ERROR); |
2896 |
++ exit(1); |
2897 |
++ } |
2898 |
++ |
2899 |
++ stdLibrary* pStdLibrary = pCollection->getStdLibrary(); |
2900 |
++ stdGroup* pStdGroup = 0; |
2901 |
++ if (pStdLibrary) { |
2902 |
++ pStdGroup = pStdLibrary->getStdGroup(inputFileContents[i][2]); |
2903 |
++ if (!pStdGroup) { |
2904 |
++ MTKpp::errorLogger.throwError("MCPB::respgen", |
2905 |
++ " Can't find stdGroup ... exiting ", MTK_ERROR); |
2906 |
++ exit(1); |
2907 |
++ } |
2908 |
++ } |
2909 |
++ else { |
2910 |
++ MTKpp::errorLogger.throwError("MCPB::respgen", |
2911 |
++ " Error in selection parsing ... exiting ", MTK_ERROR); |
2912 |
++ } |
2913 |
++ |
2914 |
++ if (pSel->getSelectionType() == 1) { |
2915 |
++ molecule* pSelMol = pSel->getMol(); |
2916 |
++ if (!pSelMol) { |
2917 |
++ std::cout << " Error in respgen selection \n"; |
2918 |
++ exit(1); |
2919 |
++ } |
2920 |
++ |
2921 |
++ std::vector<std::string>::iterator result; |
2922 |
++ |
2923 |
++ acParser* pAcParser = new acParser(); |
2924 |
++ pAcParser->Write(inputFileContents[i][3]+".ac", pCollection); |
2925 |
++ delete pAcParser; |
2926 |
++ |
2927 |
++ std::string bb0FileResp1 = inputFileContents[i][3] + "_bb0.resp1"; |
2928 |
++ std::string bb0FileResp2 = inputFileContents[i][3] + "_bb0.resp2"; |
2929 |
++ std::ofstream obb0FileResp1; |
2930 |
++ std::ofstream obb0FileResp2; |
2931 |
++ obb0FileResp1.open(bb0FileResp1.c_str()); |
2932 |
++ obb0FileResp2.open(bb0FileResp2.c_str()); |
2933 |
++ |
2934 |
++ std::string bb1FileResp1 = inputFileContents[i][3] + "_bb1.resp1"; |
2935 |
++ std::string bb1FileResp2 = inputFileContents[i][3] + "_bb1.resp2"; |
2936 |
++ std::ofstream obb1FileResp1; |
2937 |
++ std::ofstream obb1FileResp2; |
2938 |
++ obb1FileResp1.open(bb1FileResp1.c_str()); |
2939 |
++ obb1FileResp2.open(bb1FileResp2.c_str()); |
2940 |
++ |
2941 |
++ std::string bb2FileResp1 = inputFileContents[i][3] + "_bb2.resp1"; |
2942 |
++ std::string bb2FileResp2 = inputFileContents[i][3] + "_bb2.resp2"; |
2943 |
++ std::ofstream obb2FileResp1; |
2944 |
++ std::ofstream obb2FileResp2; |
2945 |
++ obb2FileResp1.open(bb2FileResp1.c_str()); |
2946 |
++ obb2FileResp2.open(bb2FileResp2.c_str()); |
2947 |
++ |
2948 |
++ std::string bb3FileResp1 = inputFileContents[i][3] + "_bb3.resp1"; |
2949 |
++ std::string bb3FileResp2 = inputFileContents[i][3] + "_bb3.resp2"; |
2950 |
++ std::ofstream obb3FileResp1; |
2951 |
++ std::ofstream obb3FileResp2; |
2952 |
++ obb3FileResp1.open(bb3FileResp1.c_str()); |
2953 |
++ obb3FileResp2.open(bb3FileResp2.c_str()); |
2954 |
++ |
2955 |
++ if (!obb0FileResp1 or !obb0FileResp2 or !obb1FileResp1 or !obb1FileResp2 or |
2956 |
++ !obb2FileResp1 or !obb2FileResp2 or !obb3FileResp1 or !obb3FileResp2) { |
2957 |
++ MTKpp::errorLogger.throwError("MCPB::respgen", |
2958 |
++ " Unable to open RESP files ... exiting ", MTK_ERROR); |
2959 |
++ exit(1); |
2960 |
++ } |
2961 |
++ |
2962 |
++ std::vector<molecule*> molList = pCollection->getMoleculeList(); |
2963 |
++ |
2964 |
++ std::string terminalFrags = ""; |
2965 |
++ char temp[100]; |
2966 |
++ bool bFirst = true; |
2967 |
++ for (unsigned int m = 0; m < molList.size(); m++) { |
2968 |
++ molecule* pMol = molList[m]; |
2969 |
++ std::vector<submolecule*> submols = pMol->getSubMoleculeList(); |
2970 |
++ for (unsigned int s = 0; s < submols.size(); s++) { |
2971 |
++ if (submols[s]->hasStdFrag()) { |
2972 |
++ stdFrag* pStdFrag = submols[s]->getStdFrag(); |
2973 |
++ if (pStdFrag->getParent()->getName() != inputFileContents[i][2]) { |
2974 |
++ if (bFirst) { |
2975 |
++ sprintf(temp,"%5d%10.5f\n", pStdFrag->numStdAtoms(), 0.0); |
2976 |
++ bFirst = false; |
2977 |
++ } |
2978 |
++ else { |
2979 |
++ sprintf(temp,"\n%5d%10.5f\n", pStdFrag->numStdAtoms(), 0.0); |
2980 |
++ } |
2981 |
++ |
2982 |
++ terminalFrags += std::string(temp); |
2983 |
++ std::vector<atom*> atomList = submols[s]->getAtomList(); |
2984 |
++ char temp2[80]; |
2985 |
++ int counter = 0; |
2986 |
++ for (unsigned int a = 0; a < atomList.size(); a++) { |
2987 |
++ if (counter > 7) { // was 6 |
2988 |
++ terminalFrags += "\n"; |
2989 |
++ counter = 0; |
2990 |
++ } |
2991 |
++ sprintf(temp2,"%5d%5d", 1, atomList[a]->getIndex()); |
2992 |
++ terminalFrags += std::string(temp2); |
2993 |
++ counter++; |
2994 |
++ } |
2995 |
++ //terminalFrags += "\n"; |
2996 |
++ } |
2997 |
++ } |
2998 |
++ } |
2999 |
++ } |
3000 |
++ //std::cout << terminalFrags << std::endl; |
3001 |
++ |
3002 |
++ std::string bb0 = terminalFrags + "\n"; |
3003 |
++ std::string bb1 = terminalFrags + "\n"; |
3004 |
++ std::string bb2 = terminalFrags + "\n"; |
3005 |
++ std::string bb3 = terminalFrags + "\n"; |
3006 |
++ |
3007 |
++ int lInd = 0; |
3008 |
++ for (unsigned int m = 0; m < molList.size(); m++) { |
3009 |
++ molecule* pMol = molList[m]; |
3010 |
++ |
3011 |
++ if (pMol->getName() == "Reference") continue; |
3012 |
++ |
3013 |
++ std::vector<submolecule*> submols = pMol->getSubMoleculeList(); |
3014 |
++ for (unsigned int s = 0; s < submols.size(); s++) { |
3015 |
++ if (submols[s]->hasStdFrag()) { |
3016 |
++ stdFrag* pStdFrag = submols[s]->getStdFrag(); |
3017 |
++ //std::cout << " respgen " << pStdFrag->getParent()->getName() << " " << inputFileContents[i][2] << " \n "; |
3018 |
++ if (pStdFrag->getParent()->getName() != inputFileContents[i][2]) continue; |
3019 |
++ std::vector<atom*> subAtoms = submols[s]->getAtomList(); |
3020 |
++ for (unsigned int a = 0; a < subAtoms.size(); a++) { |
3021 |
++ stdAtom* pStdAtom_a = subAtoms[a]->getStdAtom(); |
3022 |
++ lInd++; |
3023 |
++ // iBB == 1 |
3024 |
++ if (pStdAtom_a) { |
3025 |
++ std::string dd = pStdAtom_a->identity + ":" + pStdAtom_a->type; |
3026 |
++ |
3027 |
++ //result = find(bb_heavy.begin(), bb_heavy.end(), subAtoms[a]->getName()); |
3028 |
++ //result = find(bb_heavy.begin(), bb_heavy.end(), pStdAtom_a->identity); |
3029 |
++ result = find(bb_heavy.begin(), bb_heavy.end(), dd); |
3030 |
++ |
3031 |
++ if (result != bb_heavy.end()) { |
3032 |
++ sprintf(temp,"%5d%10.5f\n", 1, pStdAtom_a->atmCharge); |
3033 |
++ //freezingAtoms += "\n BB Heavy " + submols[s]->getName() + " " + int2String(submols[s]->getSubMolId()) + " " + dd; |
3034 |
++ //std::cout << "\n BB Heavy " + submols[s]->getName() + " " + int2String(submols[s]->getSubMolId()) + " " + dd; |
3035 |
++ //std::cout << dd << " " << subAtoms[a]->getName() << " ---> " << subAtoms[a]->getStdAtom()->type << std::endl; |
3036 |
++ //orespAdd << temp << std::endl; |
3037 |
++ bb1 += std::string(temp); |
3038 |
++ sprintf(temp,"%5d%5d\n", 1, subAtoms[a]->getIndex()); |
3039 |
++ //orespAdd << temp << std::endl; |
3040 |
++ bb1 += std::string(temp); |
3041 |
++ } |
3042 |
++ |
3043 |
++ // iBB == 2 |
3044 |
++ dd = pStdAtom_a->identity + ":" + pStdAtom_a->type; |
3045 |
++ |
3046 |
++ //result = find(bb.begin(), bb.end(), subAtoms[a]->getName()); |
3047 |
++ result = find(bb.begin(), bb.end(), dd); |
3048 |
++ |
3049 |
++ if (result != bb.end()) { |
3050 |
++ //freezingAtoms += "\n BB " + submols[s]->getName() + " " + int2String(submols[s]->getSubMolId()) + " " + dd; |
3051 |
++ sprintf(temp,"%5d%10.5f\n", 1, pStdAtom_a->atmCharge); |
3052 |
++ //orespAdd << temp << std::endl; |
3053 |
++ bb2 += std::string(temp); |
3054 |
++ sprintf(temp,"%5d%5d\n", 1, subAtoms[a]->getIndex()); |
3055 |
++ //orespAdd << temp << std::endl; |
3056 |
++ bb2 += std::string(temp); |
3057 |
++ } |
3058 |
++ // iBB == 3 |
3059 |
++ dd = pStdAtom_a->identity + ":" + pStdAtom_a->type; |
3060 |
++ |
3061 |
++ //result = find(bbb.begin(), bbb.end(), subAtoms[a]->getName()); |
3062 |
++ result = find(bbb.begin(), bbb.end(), dd); |
3063 |
++ |
3064 |
++ if (result != bbb.end()) { |
3065 |
++ //freezingAtoms += "\n BBB " + submols[s]->getName() + " " |
3066 |
++ // + int2String(submols[s]->getSubMolId()) + " " + dd; |
3067 |
++ sprintf(temp,"%5d%10.5f\n", 1, pStdAtom_a->atmCharge); |
3068 |
++ bb3 += std::string(temp); |
3069 |
++ //orespAdd << temp << std::endl; |
3070 |
++ sprintf(temp,"%5d%5d\n", 1, subAtoms[a]->getIndex()); |
3071 |
++ bb3 += std::string(temp); |
3072 |
++ //orespAdd << temp << std::endl; |
3073 |
++ } |
3074 |
++ } |
3075 |
++ else { |
3076 |
++ MTKpp::errorLogger.throwError("MCPB::respgen", |
3077 |
++ " Unknown option ... exiting ", MTK_ERROR); |
3078 |
++ } |
3079 |
++ } |
3080 |
++ } |
3081 |
++ } |
3082 |
++ } |
3083 |
++ |
3084 |
++ std::string resp1 = ""; |
3085 |
++ resp1 += "Resp charges for organic molecule\n"; |
3086 |
++ resp1 += "\n"; |
3087 |
++ resp1 += " &cntrl\n"; |
3088 |
++ resp1 += "\n"; |
3089 |
++ resp1 += " nmol = 1,\n"; |
3090 |
++ resp1 += " ihfree = 1,\n"; |
3091 |
++ resp1 += " ioutopt = 1,\n"; |
3092 |
++ resp1 += "\n"; |
3093 |
++ resp1 += " &end\n"; |
3094 |
++ resp1 += " 1.0\n"; |
3095 |
++ resp1 += "Resp charges for organic molecule\n"; |
3096 |
++ |
3097 |
++ //std::cout << pStdGroup->getCharge() << " " << pSelMol->getNumAtoms() << std::endl; |
3098 |
++ sprintf(temp,"%5d%5d\n", int(pStdGroup->getCharge()), pSelMol->getNumAtoms()); |
3099 |
++ resp1 += std::string(temp); |
3100 |
++ |
3101 |
++ std::vector<submolecule*> sList = pSelMol->getSubMoleculeList(); |
3102 |
++ typedef std::map<std::string, int>::iterator mapIterator; |
3103 |
++ |
3104 |
++ std::map<std::string, int> lMap; |
3105 |
++ int ind = 0; |
3106 |
++ for (unsigned int p = 0; p < sList.size(); p++) { |
3107 |
++ std::vector<atom*> aList = sList[p]->getAtomList(); |
3108 |
++ for (unsigned int a = 0; a < aList.size(); a++) { |
3109 |
++ if (!aList[a]->getStdAtom()) { |
3110 |
++ std::cout << " Error ... exiting()\n"; |
3111 |
++ exit(1); |
3112 |
++ } |
3113 |
++ int elNum = aList[a]->getAtomicNum(); |
3114 |
++ std::string key = ""; |
3115 |
++ if (elNum == 1) { |
3116 |
++ std::vector<atom*> hBondedAtoms = aList[a]->getBondedAtoms(); |
3117 |
++ if (hBondedAtoms.size() == 1) { |
3118 |
++ key = aList[a]->getParent()->getName() + ":" + hBondedAtoms[0]->getName() + ":" + aList[a]->getStdAtom()->type; |
3119 |
++ } |
3120 |
++ else { |
3121 |
++ key = aList[a]->getParent()->getName() + ":" + aList[a]->getStdAtom()->type; |
3122 |
++ } |
3123 |
++ } |
3124 |
++ else { |
3125 |
++ key = aList[a]->getParent()->getName() + ":" + aList[a]->getName(); |
3126 |
++ } |
3127 |
++ |
3128 |
++ mapIterator mi = lMap.find(key); |
3129 |
++ |
3130 |
++ int fg = 0; |
3131 |
++ if (mi != lMap.end()){ |
3132 |
++ fg = lMap[key]+1; |
3133 |
++ } |
3134 |
++ else { |
3135 |
++ lMap[key] = ind; |
3136 |
++ } |
3137 |
++ //sprintf(temp,"%4d %-11s%5d%5d\n", ind+1, key.c_str(), aList[a]->getAtomicNum(), fg); |
3138 |
++ sprintf(temp,"%5d%5d\n", aList[a]->getAtomicNum(), fg); |
3139 |
++ resp1 += std::string(temp); |
3140 |
++ ind++; |
3141 |
++ } |
3142 |
++ } |
3143 |
++ |
3144 |
++ std::string resp2 = ""; |
3145 |
++ |
3146 |
++ resp2 += "Resp charges for organic molecule\n"; |
3147 |
++ resp2 += "\n"; |
3148 |
++ resp2 += " &cntrl\n"; |
3149 |
++ resp2 += "\n"; |
3150 |
++ resp2 += " nmol = 1,\n"; |
3151 |
++ resp2 += " ihfree = 1,\n"; |
3152 |
++ resp2 += " ioutopt = 1,\n"; |
3153 |
++ resp2 += " iqopt = 2,\n"; |
3154 |
++ resp2 += " qwt = 0.001,\n"; |
3155 |
++ resp2 += "\n"; |
3156 |
++ resp2 += " &end\n"; |
3157 |
++ resp2 += " 1.0\n"; |
3158 |
++ resp2 += "Resp charges for organic molecule\n"; |
3159 |
++ |
3160 |
++ sprintf(temp,"%5d%5d\n", int(pStdGroup->getCharge()), pSelMol->getNumAtoms()); |
3161 |
++ resp2 += std::string(temp); |
3162 |
++ |
3163 |
++ ind = 0; |
3164 |
++ std::map<std::string, int> lMap2; |
3165 |
++ |
3166 |
++ for (unsigned int p = 0; p < sList.size(); p++) { |
3167 |
++ std::vector<atom*> aList = sList[p]->getAtomList(); |
3168 |
++ for (unsigned int a = 0; a < aList.size(); a++) { |
3169 |
++ |
3170 |
++ if (!aList[a]->getStdAtom()) { |
3171 |
++ std::cout << " Error ... exiting()\n"; |
3172 |
++ exit(1); |
3173 |
++ } |
3174 |
++ int elNum = aList[a]->getAtomicNum(); |
3175 |
++ std::string key = ""; |
3176 |
++ if (elNum == 1) { |
3177 |
++ std::vector<atom*> hBondedAtoms = aList[a]->getBondedAtoms(); |
3178 |
++ if (hBondedAtoms.size() == 1) { |
3179 |
++ key = aList[a]->getParent()->getName() + ":" + hBondedAtoms[0]->getName() + ":" + |
3180 |
++ aList[a]->getStdAtom()->type; |
3181 |
++ } |
3182 |
++ else { |
3183 |
++ key = aList[a]->getParent()->getName() + ":" + aList[a]->getStdAtom()->type; |
3184 |
++ } |
3185 |
++ } |
3186 |
++ else { |
3187 |
++ key = aList[a]->getParent()->getName() + ":" + aList[a]->getName(); |
3188 |
++ } |
3189 |
++ |
3190 |
++ mapIterator mi = lMap2.find(key); |
3191 |
++ |
3192 |
++ int fg = 0; |
3193 |
++ if (mi != lMap2.end()){ |
3194 |
++ fg = lMap2[key]+1; |
3195 |
++ } |
3196 |
++ else { |
3197 |
++ lMap2[key] = ind; |
3198 |
++ } |
3199 |
++ std::string atName = aList[a]->getName(); |
3200 |
++ std::string atType = aList[a]->getStdAtom()->type; |
3201 |
++ int atNum = aList[a]->getAtomicNum(); |
3202 |
++ |
3203 |
++ if (atName == " CH3" or atName == " CB " or containsSubStr(key, " CB :H1") or |
3204 |
++ containsSubStr(key, " CB :HC") or |
3205 |
++ containsSubStr(key, " CH3:HC") or containsSubStr(key, " CH3:H1") or |
3206 |
++ containsSubStr(key, "GLY: CA ")) {// or (atNum > 16)) { |
3207 |
++ //if (atName == " CH3" or atName == " CB " or atType == "H1" or atType == "HC") { |
3208 |
++ //sprintf(temp,"%4d %-11s%5d%5d\n", ind+1, key.c_str(), aList[a]->getAtomicNum(), fg); |
3209 |
++ sprintf(temp,"%5d%5d\n", aList[a]->getAtomicNum(), fg); |
3210 |
++ } |
3211 |
++ else { |
3212 |
++ //sprintf(temp,"%4d %-11s%5d%5d\n", ind+1, key.c_str(), aList[a]->getAtomicNum(), -99); |
3213 |
++ sprintf(temp,"%5d%5d\n", aList[a]->getAtomicNum(), -99); |
3214 |
++ } |
3215 |
++ resp2 += std::string(temp); |
3216 |
++ |
3217 |
++ ind++; |
3218 |
++ } |
3219 |
++ } |
3220 |
++ |
3221 |
++ std::string twoBlankLine = "\n\n"; |
3222 |
++ bb0 += twoBlankLine; |
3223 |
++ bb1 += twoBlankLine; |
3224 |
++ bb2 += twoBlankLine; |
3225 |
++ bb3 += twoBlankLine; |
3226 |
++ |
3227 |
++ obb0FileResp1 << resp1; |
3228 |
++ obb0FileResp1 << bb0; |
3229 |
++ obb0FileResp2 << resp2; |
3230 |
++ obb0FileResp2 << bb0; |
3231 |
++ |
3232 |
++ obb1FileResp1 << resp1; |
3233 |
++ obb1FileResp1 << bb1; |
3234 |
++ obb1FileResp2 << resp2; |
3235 |
++ obb1FileResp2 << bb1; |
3236 |
++ |
3237 |
++ obb2FileResp1 << resp1; |
3238 |
++ obb2FileResp1 << bb2; |
3239 |
++ obb2FileResp2 << resp2; |
3240 |
++ obb2FileResp2 << bb2; |
3241 |
++ |
3242 |
++ obb3FileResp1 << resp1; |
3243 |
++ obb3FileResp1 << bb3; |
3244 |
++ obb3FileResp2 << resp2; |
3245 |
++ obb3FileResp2 << bb3; |
3246 |
++ |
3247 |
++ obb0FileResp1.close(); |
3248 |
++ obb0FileResp2.close(); |
3249 |
++ obb1FileResp1.close(); |
3250 |
++ obb1FileResp2.close(); |
3251 |
++ obb2FileResp1.close(); |
3252 |
++ obb2FileResp2.close(); |
3253 |
++ obb3FileResp1.close(); |
3254 |
++ obb3FileResp2.close(); |
3255 |
++ } |
3256 |
++ } |
3257 |
++ } |
3258 |
++ |
3259 |
+ else if (inputFileContents[i][0] == "addStdMol") { |
3260 |
+ /*! |
3261 |
+ @ingroup MCPB_commands |
3262 |
+@@ -4496,63 +5064,63 @@ |
3263 |
+ table<double>* nmodeEVectors = pSheet->getTable("NMode EigenVectors"); |
3264 |
+ ublas::matrix<double> &nmodeEVectorsMatrixT = nmodeEVectors->getMatrix(); |
3265 |
+ |
3266 |
+- table<double>* g03EValues = pSheet->getTable("Gaussian EigenValues"); |
3267 |
+- ublas::matrix<double> &g03EValuesMatrix = g03EValues->getMatrix(); |
3268 |
++ table<double>* gaussianEValues = pSheet->getTable("Gaussian EigenValues"); |
3269 |
++ ublas::matrix<double> &gaussianEValuesMatrix = gaussianEValues->getMatrix(); |
3270 |
+ |
3271 |
+- table<double>* g03EVectors = pSheet->getTable("Gaussian EigenVectors"); |
3272 |
+- ublas::matrix<double> &g03EVectorsMatrixT = g03EVectors->getMatrix(); |
3273 |
++ table<double>* gaussianEVectors = pSheet->getTable("Gaussian EigenVectors"); |
3274 |
++ ublas::matrix<double> &gaussianEVectorsMatrixT = gaussianEVectors->getMatrix(); |
3275 |
+ |
3276 |
+ int nRowsNMode = nmodeEValues->getNumRows(); |
3277 |
+- int nRowsG03 = g03EValues->getNumRows(); |
3278 |
++ int nRowsGaussian = gaussianEValues->getNumRows(); |
3279 |
+ |
3280 |
+ int nColsNMode = nmodeEVectors->getNumColumns(); |
3281 |
+- int nColsG03 = g03EVectors->getNumColumns(); |
3282 |
++ int nColsGaussian = gaussianEVectors->getNumColumns(); |
3283 |
+ |
3284 |
+- if (nRowsNMode != nRowsG03 and nColsNMode != nColsG03) { |
3285 |
++ if (nRowsNMode != nRowsGaussian and nColsNMode != nColsGaussian) { |
3286 |
+ std::cout << " PROBLEM " << std::endl; |
3287 |
+ } |
3288 |
+ else { |
3289 |
+ std::cout << " EIGENVALUES " << std::endl; |
3290 |
+ for (int z = 0; z < nRowsNMode; z++) { |
3291 |
+- std::cout << nmodeEValuesMatrix(z, 0) << " " << g03EValuesMatrix(z, 0) << std::endl; |
3292 |
++ std::cout << nmodeEValuesMatrix(z, 0) << " " << gaussianEValuesMatrix(z, 0) << std::endl; |
3293 |
+ } |
3294 |
+ |
3295 |
+ //std::cout << " NMODE " << std::endl; |
3296 |
+ //nmodeEVectors->printMatrix(); |
3297 |
+ |
3298 |
+- //std::cout << " G03 " << std::endl; |
3299 |
+- //g03EVectors->printMatrix(); |
3300 |
++ //std::cout << " Gaussian " << std::endl; |
3301 |
++ //gaussianEVectors->printMatrix(); |
3302 |
+ //std::cout << " \n\n " << std::endl; |
3303 |
+ |
3304 |
+ // Normalize Eigenvector matrices |
3305 |
+ for (int zi = 0; zi < nRowsNMode; zi++) { |
3306 |
+ double normNMode = 0.0; |
3307 |
+- double normG03 = 0.0; |
3308 |
++ double normGaussian = 0.0; |
3309 |
+ for (int zk = 0; zk < nColsNMode; zk++) { |
3310 |
+ normNMode += (nmodeEVectorsMatrixT(zi, zk) * nmodeEVectorsMatrixT(zi, zk)); |
3311 |
+- normG03 += (g03EVectorsMatrixT(zi, zk) * g03EVectorsMatrixT(zi, zk)); |
3312 |
++ normGaussian += (gaussianEVectorsMatrixT(zi, zk) * gaussianEVectorsMatrixT(zi, zk)); |
3313 |
+ } |
3314 |
+ normNMode = sqrt(normNMode); |
3315 |
+- normG03 = sqrt(normG03); |
3316 |
++ normGaussian = sqrt(normGaussian); |
3317 |
+ for (int zk = 0; zk < nColsNMode; zk++) { |
3318 |
+- //std::cout << g03EVectorsMatrixT(zi, zk) << " " << normG03 << " " |
3319 |
+- // << g03EVectorsMatrixT(zi, zk) / normG03 << " "; |
3320 |
++ //std::cout << gaussianEVectorsMatrixT(zi, zk) << " " << normGaussian << " " |
3321 |
++ // << gaussianEVectorsMatrixT(zi, zk) / normGaussian << " "; |
3322 |
+ double newValue1 = nmodeEVectorsMatrixT(zi, zk) / normNMode; |
3323 |
+- double newValue2 = g03EVectorsMatrixT(zi, zk) / normG03; |
3324 |
++ double newValue2 = gaussianEVectorsMatrixT(zi, zk) / normGaussian; |
3325 |
+ nmodeEVectors->setCellValue(zi, zk, newValue1); |
3326 |
+- g03EVectors->setCellValue(zi, zk, newValue2); |
3327 |
+- //std::cout << g03EVectors->getCellValue(zi, zk) << std::endl; |
3328 |
++ gaussianEVectors->setCellValue(zi, zk, newValue2); |
3329 |
++ //std::cout << gaussianEVectors->getCellValue(zi, zk) << std::endl; |
3330 |
+ } |
3331 |
+ } |
3332 |
+ |
3333 |
+ ublas::matrix<double> &nmodeEVectorsMatrix = nmodeEVectors->getMatrix(); |
3334 |
+- ublas::matrix<double> &g03EVectorsMatrix = g03EVectors->getMatrix(); |
3335 |
++ ublas::matrix<double> &gaussianEVectorsMatrix = gaussianEVectors->getMatrix(); |
3336 |
+ |
3337 |
+ //std::cout << " NMODE " << std::endl; |
3338 |
+ //nmodeEVectors->printMatrix(); |
3339 |
+ |
3340 |
+- //std::cout << " G03 " << std::endl; |
3341 |
+- //g03EVectors->printMatrix(); |
3342 |
++ //std::cout << " Gaussian " << std::endl; |
3343 |
++ //gaussianEVectors->printMatrix(); |
3344 |
+ //std::cout << " \n\n " << std::endl; |
3345 |
+ |
3346 |
+ // dot product |
3347 |
+@@ -4563,12 +5131,12 @@ |
3348 |
+ double eN2 = 0.0; |
3349 |
+ double dff = 0.0; |
3350 |
+ for (int zi = 0; zi < nRowsNMode; zi++) { // NMode |
3351 |
+- for (int zj = 0; zj < nRowsNMode; zj++) { // G03 |
3352 |
++ for (int zj = 0; zj < nRowsNMode; zj++) { // Gaussian |
3353 |
+ for (int zk = 0; zk < nColsNMode; zk++) { // Loop over coordinates in Eigenvector |
3354 |
+- //std::cout << nmodeEVectorsMatrix(zi, zk) << " " << g03EVectorsMatrix(zj, zk) << " "; |
3355 |
++ //std::cout << nmodeEVectorsMatrix(zi, zk) << " " << gaussianEVectorsMatrix(zj, zk) << " "; |
3356 |
+ eN += (nmodeEVectorsMatrix(zi, zk) * nmodeEVectorsMatrix(zi, zk)); |
3357 |
+- eN2 += (g03EVectorsMatrix(zj, zk) * g03EVectorsMatrix(zj, zk)); |
3358 |
+- dotProduct += (nmodeEVectorsMatrix(zi, zk) * g03EVectorsMatrix(zj, zk)); |
3359 |
++ eN2 += (gaussianEVectorsMatrix(zj, zk) * gaussianEVectorsMatrix(zj, zk)); |
3360 |
++ dotProduct += (nmodeEVectorsMatrix(zi, zk) * gaussianEVectorsMatrix(zj, zk)); |
3361 |
+ } |
3362 |
+ //std::cout << " eN = " << sqrt(eN) << " eN2 = " << sqrt(eN2) << " "; |
3363 |
+ std::cout << zi << " - " << zj << " " << dotProduct << " " << dotProductMax << std::endl; |
3364 |
+@@ -4582,11 +5150,11 @@ |
3365 |
+ } |
3366 |
+ dotProduct = 0.0; |
3367 |
+ } |
3368 |
+- double dffL = nmodeEValuesMatrix(zi, 0) - g03EValuesMatrix(dotProductMaxIndex, 0); |
3369 |
++ double dffL = nmodeEValuesMatrix(zi, 0) - gaussianEValuesMatrix(dotProductMaxIndex, 0); |
3370 |
+ dffL *= dffL; |
3371 |
+ std::cout << " nmode index = " << zi << " BestMatch = " << dotProductMaxIndex |
3372 |
+ << " => dotProduct =" << dotProductMax << " EVALUES: " |
3373 |
+- << " " << nmodeEValuesMatrix(zi, 0) << " " << g03EValuesMatrix(dotProductMaxIndex, 0) << " " |
3374 |
++ << " " << nmodeEValuesMatrix(zi, 0) << " " << gaussianEValuesMatrix(dotProductMaxIndex, 0) << " " |
3375 |
+ << dffL |
3376 |
+ << std::endl; |
3377 |
+ |
3378 |
+@@ -4617,7 +5185,7 @@ |
3379 |
+ } |
3380 |
+ |
3381 |
+ else { |
3382 |
+- std::string unknownCommand = " Unknown command " + inputFileContents[i][0]; |
3383 |
++ std::string unknownCommand = " Unknown command: \"" + inputFileContents[i][0] + "\""; |
3384 |
+ MTKpp::errorLogger.throwError("MCPB", unknownCommand, MTK_ERROR); |
3385 |
+ } |
3386 |
+ } |
3387 |
+@@ -4628,4 +5196,3 @@ |
3388 |
+ delete pSheet; |
3389 |
+ return 0; |
3390 |
+ } |
3391 |
+- |
3392 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/tools/prep2xml.cpp amber11/AmberTools/src/mtkpp/tools/prep2xml.cpp |
3393 |
+--- amber11.orig/AmberTools/src/mtkpp/tools/prep2xml.cpp 2011-04-14 15:30:19.000000000 +0300 |
3394 |
++++ amber11/AmberTools/src/mtkpp/tools/prep2xml.cpp 2012-03-03 20:03:01.418032565 +0200 |
3395 |
+@@ -86,6 +86,7 @@ |
3396 |
+ clo->addUsage( " -a log file " ); |
3397 |
+ clo->addUsage( " -l hybridize name \n" ); |
3398 |
+ clo->addUsage( " flags: " ); |
3399 |
++ clo->addUsage( " -c convert only " ); |
3400 |
+ clo->addUsage( " -h help \n" ); |
3401 |
+ |
3402 |
+ // 4. SET THE OPTION STRINGS/CHARACTERS |
3403 |
+@@ -97,6 +98,7 @@ |
3404 |
+ clo->setOption( "hyb", 'l' ); |
3405 |
+ clo->setOption( "log", 'a' ); |
3406 |
+ |
3407 |
++ clo->setFlag ( "convert", 'c' ); |
3408 |
+ clo->setFlag ( "help", 'h' ); |
3409 |
+ |
3410 |
+ // 5. PROVIDE THE COMMANDLINE |
3411 |
+@@ -117,6 +119,11 @@ |
3412 |
+ std::string fragName = ""; |
3413 |
+ std::string molName = ""; |
3414 |
+ std::string logFile = ""; |
3415 |
++ bool bConvertOnly = 0; |
3416 |
++ |
3417 |
++ if ( clo->getFlag( "convert" ) || clo->getFlag( 'c' ) ) { |
3418 |
++ bConvertOnly = 1; |
3419 |
++ } |
3420 |
+ |
3421 |
+ std::string AMBERHOME = getenv("AMBERHOME"); |
3422 |
+ std::string parametersFile = AMBERHOME + "/dat/mtkpp/hybridize/labute.txt"; |
3423 |
+@@ -166,13 +173,13 @@ |
3424 |
+ else if ( clo->getValue( "frag" ) != 0 ) { |
3425 |
+ fragName = clo->getValue( "frag" ); |
3426 |
+ } |
3427 |
+- else { |
3428 |
++/* else { |
3429 |
+ printHeader(std::cout, prog_name, authors); |
3430 |
+ clo->printUsage(); |
3431 |
+ std::cout << " Please provide a fragment name " << std::endl; |
3432 |
+ return 0; |
3433 |
+ } |
3434 |
+- |
3435 |
++*/ |
3436 |
+ if ( clo->getValue( "l" ) != 0 ) { |
3437 |
+ parametersFile = clo->getValue( "l" ); |
3438 |
+ } |
3439 |
+@@ -186,13 +193,14 @@ |
3440 |
+ else if ( clo->getValue( "mol" ) != 0 ) { |
3441 |
+ molName = clo->getValue( "mol" ); |
3442 |
+ } |
3443 |
++/* |
3444 |
+ else { |
3445 |
+ printHeader(std::cout, prog_name, authors); |
3446 |
+ clo->printUsage(); |
3447 |
+ std::cout << " Please provide a molecule name " << std::endl; |
3448 |
+ return 0; |
3449 |
+ } |
3450 |
+- |
3451 |
++*/ |
3452 |
+ if ( clo->getValue( "a" ) != 0 ) { |
3453 |
+ logFile = clo->getValue( "a" ); |
3454 |
+ } |
3455 |
+@@ -307,6 +315,22 @@ |
3456 |
+ std::cout << " Incorrect use of prep2xml " << std::endl; |
3457 |
+ exit(1); |
3458 |
+ } |
3459 |
++ |
3460 |
++ ///////// |
3461 |
++ if (fragName == "") { |
3462 |
++ prepParser* pPrepParser = new prepParser(); |
3463 |
++ pPrepParser->Read(prepFile, pStdGroup); |
3464 |
++ delete pPrepParser; |
3465 |
++ |
3466 |
++ pStdLibParser->Write(libXmlFile, groupName); |
3467 |
++ delete pStdLibParser; |
3468 |
++ |
3469 |
++ // - Clean up - // |
3470 |
++ delete pCollection; |
3471 |
++ return 0; |
3472 |
++ } |
3473 |
++ /////////// |
3474 |
++ |
3475 |
+ stdFrag* pStdFrag = pStdGroup->addStdFrag(); |
3476 |
+ if (!pStdFrag) { |
3477 |
+ std::cout << " Incorrect use of prep2xml " << std::endl; |
3478 |
+@@ -322,6 +346,15 @@ |
3479 |
+ pPrepParser->Read(prepFile, pStdFrag); |
3480 |
+ delete pPrepParser; |
3481 |
+ |
3482 |
++ if (bConvertOnly) { |
3483 |
++ pStdLibParser->Write(libXmlFile, groupName); |
3484 |
++ delete pStdLibParser; |
3485 |
++ |
3486 |
++ // - Clean up - // |
3487 |
++ delete pCollection; |
3488 |
++ return 0; |
3489 |
++ } |
3490 |
++ |
3491 |
+ int f = pStdFrag->generateCoordinates(); |
3492 |
+ if (f) { |
3493 |
+ std::cout << " Incorrect use of prep2xml " << std::endl; |
3494 |
+@@ -443,7 +476,7 @@ |
3495 |
+ // atoms |
3496 |
+ for (unsigned int i = 0; i < atomList.size(); i++) { |
3497 |
+ stdAtoms[i]->kind = atomList[i]->getType(); |
3498 |
+- std::cout << atomList[i]->getIndex() << " " << atomList[i]->getName() << " " << atomList[i]->getType() << std::endl; |
3499 |
++ //std::cout << atomList[i]->getIndex() << " " << atomList[i]->getName() << " " << atomList[i]->getType() << std::endl; |
3500 |
+ } |
3501 |
+ |
3502 |
+ // bonds |
3503 |
+diff -urN amber11.orig/AmberTools/src/mtkpp/tools/stdLib2Sdf.cpp amber11/AmberTools/src/mtkpp/tools/stdLib2Sdf.cpp |
3504 |
+--- amber11.orig/AmberTools/src/mtkpp/tools/stdLib2Sdf.cpp 2011-04-14 15:30:19.000000000 +0300 |
3505 |
++++ amber11/AmberTools/src/mtkpp/tools/stdLib2Sdf.cpp 2012-03-03 20:03:01.418032565 +0200 |
3506 |
+@@ -42,6 +42,9 @@ |
3507 |
+ // - COMMAND LINE OPTIONS |
3508 |
+ #include "Parsers/commLineOptions.h" |
3509 |
+ |
3510 |
++// - Log |
3511 |
++#include "Log/errorHandler.h" |
3512 |
++ |
3513 |
+ // temp |
3514 |
+ #include "time.h" |
3515 |
+ |
3516 |
+@@ -174,7 +177,7 @@ |
3517 |
+ } |
3518 |
+ |
3519 |
+ // Set errorLog stream to the log file |
3520 |
+- //MTKpp::errorLogger.setStream(&oLog); |
3521 |
++ MTKpp::errorLogger.setStream(&oLog); |
3522 |
+ |
3523 |
+ // Print MTK++ copyright message |
3524 |
+ printHeader(oLog, prog_name, authors); |
3525 |
+diff -urN amber11.orig/AmberTools/src/pbsa/pb_list.f amber11/AmberTools/src/pbsa/pb_list.f |
3526 |
+--- amber11.orig/AmberTools/src/pbsa/pb_list.f 2011-04-14 15:30:19.000000000 +0300 |
3527 |
++++ amber11/AmberTools/src/pbsa/pb_list.f 2012-03-03 20:02:55.131034376 +0200 |
3528 |
+@@ -949,7 +949,7 @@ |
3529 |
+ ymin == ZERO .and. ymax == ZERO .and. & |
3530 |
+ zmin == ZERO .and. zmax == ZERO ) newbox = .true. |
3531 |
+ |
3532 |
+- if ( newbox ) then |
3533 |
++ if ( .not. ligand ) then |
3534 |
+ if ( ifcap == 0 .or. ifcap == 5 ) then |
3535 |
+ xmin = 9999.0; ymin = 9999.0; zmin = 9999.0 |
3536 |
+ xmax = -9999.0; ymax = -9999.0; zmax = -9999.0 |
3537 |
+diff -urN amber11.orig/AmberTools/src/rism/safemem.f amber11/AmberTools/src/rism/safemem.f |
3538 |
+--- amber11.orig/AmberTools/src/rism/safemem.f 2012-03-03 22:43:02.986777264 +0200 |
3539 |
++++ amber11/AmberTools/src/rism/safemem.f 2012-03-03 20:02:52.131035237 +0200 |
3540 |
+@@ -62,7 +62,7 @@ |
3541 |
+ !BYTES_PER_KILOBYTES :: used to convert between bytes and KB |
3542 |
+ integer*8,parameter :: BYTES_PER_KB = 1024**1 |
3543 |
+ |
3544 |
+- type(memTracker),private :: totalMem |
3545 |
++ type(memTracker),save,private :: totalMem |
3546 |
+ |
3547 |
+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |
3548 |
+ !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! |