#8 SMILES ERROR

[Anonymous]

I have a SMILES string, and I parse it with Chemistry::Mol. Afterward I ask for the unique SMILES string of that mol. Firstly, such a unique SMILES string is different from the unique SMILES string obtained by http://cactus.nci.nih.gov/services/translate/. And secondly, when I want to parse it again, I get a SMILES ERROR.

Following it is the output:

Clc1ccc(cc1)C(=c1[Cl+]c([Cl+]1)=C(c1ccc(Cl)cc1)c1ccc(Cl)cc1)c1ccc(Cl)cc1 [smiles string]
Clc1ccc(cc1)C(=c1[cl+]c([cl+]1)=C(c1ccc(Cl)cc1)c1ccc(Cl)cc1)c1ccc(Cl)cc1 [unique smiles string]
Clc1ccc(cc1)C(=C2[Cl+]C([Cl+]2)=C(c3ccc(Cl)cc3)c4ccc(Cl)cc4)c5ccc(Cl)cc5 [unique smiles string from http://cactus.nci.nih.gov/services/translate/\]

parsing new unique smiles from perl:

Clc1ccc(cc1)C(=c1[cl+]c([cl+]1)=C(c1ccc(Cl)cc1)c1ccc(Cl)cc1)c1ccc(Cl)cc1

SMILES ERROR: '[cl+]c([cl+]1)=C(c1ccc(Cl)cc1)c1ccc(Cl)cc1)c1ccc(Cl)cc1 in Clc1ccc(cc1)C(=c1[cl+]c([cl+]1)=C(c1ccc(Cl)cc1)c1ccc(Cl)cc1)c1ccc(Cl)cc1'

at parse-error.pl line 17

Versions for Chemistry::Mol and Chemistry::File::SMILES are:

Chemistry::Mol v0.36
Chemistry::File::SMILES v0.44

The output for perl -V is:

perl -V

Summary of my perl5 (revision 5 version 8 subversion 4) configuration:

Platform:
osname=linux, osvers=2.6.15, archname=i386-linux-thread-multi
uname='linux ninsei 2.6.15 #1 smp preempt sat jan 7 12:47:52 pst 2006 i686 gnulinux '
config_args='-Dusethreads -Duselargefiles -Dccflags=-DDEBIAN -Dcccdlflags=-fPIC -Darchname=i386-linux -Dprefix=/usr -Dprivlib=/usr/share/perl/5.8 -Darchlib=/usr/lib/perl/5.8 -Dvendorprefix=/usr -Dvendorlib=/usr/share/perl5 -Dvendorarch=/usr/lib/perl5 -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl/5.8.4 -Dsitearch=/usr/local/lib/perl/5.8.4 -Dman1dir=/usr/share/man/man1 -Dman3dir=/usr/share/man/man3 -Dsiteman1dir=/usr/local/man/man1 -Dsiteman3dir=/usr/local/man/man3 -Dman1ext=1 -Dman3ext=3perl -Dpager=/usr/bin/sensible-pager -Uafs -Ud_csh -Uusesfio -Uusenm -Duseshrplib -Dlibperl=libperl.so.5.8.4 -Dd_dosuid -des'
hint=recommended, useposix=true, d_sigaction=define
usethreads=define use5005threads=undef useithreads=define usemultiplicity=define
useperlio=define d_sfio=undef uselargefiles=define usesocks=undef
use64bitint=undef use64bitall=undef uselongdouble=undef
usemymalloc=n, bincompat5005=undef

Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBIAN -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -DTHREADS_HAVE_PIDS -DDEBIAN -fno-strict-aliasing -I/usr/local/include'
ccversion='', gccversion='3.3.5 (Debian 1:3.3.5-13)', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=4, prototype=define

Linker and Libraries:
ld='cc', ldflags =' -L/usr/local/lib'
libpth=/usr/local/lib /lib /usr/lib
libs=-lgdbm -lgdbm_compat -ldb -ldl -lm -lpthread -lc -lcrypt
perllibs=-ldl -lm -lpthread -lc -lcrypt
libc=/lib/libc-2.3.2.so, so=so, useshrplib=true, libperl=libperl.so.5.8.4
gnulibc_version='2.3.2'

Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -L/usr/local/lib'

Characteristics of this binary (from libperl):

Compile-time options: MULTIPLICITY USE_ITHREADS USE_LARGE_FILES PERL_IMPLICIT_CONTEXT
Built under linux
Compiled at Jan 12 2006 14:54:46

%ENV:
PERL5LIB="/home/usuaris/lfelix/perl-modules/share/perl/5.8.4:/home/usuaris/lfelix/perl-modules/lib/perl/5.8.4:/home/usuaris/lfelix/perl-modules/lib/perl/5.8"

@INC:
/home/usuaris/lfelix/perl-modules/share/perl/5.8.4
/home/usuaris/lfelix/perl-modules/lib/perl/5.8.4
/home/usuaris/lfelix/perl-modules/lib/perl/5.8
/etc/perl
/usr/local/lib/perl/5.8.4
/usr/local/share/perl/5.8.4
/usr/lib/perl5
/usr/share/perl5
/usr/lib/perl/5.8
/usr/share/perl/5.8
/usr/local/lib/site_perl

Thanks in advance,

Liliana Felix
lfelix@lsi.upc.edu

[Nobody/Anonymous]

program to reproduce the SMILES ERROR