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# Simple script to read an entry from the Chemical Component
# Dictionary (ftp://ftp.wwpdb.org/pub/pdb/data/monomers) and create
# lines for a classifier using the ProtOr classes in the paper by Tsai
# et al. (http://www.ncbi.nlm.nih.gov/pubmed/10388571).
## Example ##
# Using the entry for ALA
#
# RESIDUE ALA 13
# CONECT N 3 CA H H2
# CONECT CA 4 N C CB HA
# CONECT C 3 CA O OXT
# CONECT O 1 C
# CONECT CB 4 CA HB1 HB2 HB3
# CONECT OXT 2 C HXT
# CONECT H 1 N
# CONECT H2 1 N
# CONECT HA 1 CA
# CONECT HB1 1 CB
# CONECT HB2 1 CB
# CONECT HB3 1 CB
# CONECT HXT 1 OXT
# END
# HET ALA 13
# HETNAM ALA ALANINE
# FORMUL ALA C3 H7 N1 O2
#
# We get the output
#
# ALA N N3H2
# ALA CA C4H1
# ALA C C3H0
# ALA O O1H0
# ALA CB C4H3
# ALA OXT O2H1
#
# These lines can be added to the atoms-section of a classifier
# config-file, and then the types N3H2, C4H1 need to be defined in the
# types-section. See share/protor.config for a template including
# all the standard amino acids, nucleic acids, plus some common
# non-standard entries. In the setting of a polypeptide chain the
# N-atom should be N3H1, since it is linked to the next residue, but
# since N3H1 and N3H2 have the same radius this doesn't necessarily
# have to be fixed.
#
# The script does not do anything clever, so if your entry contains
# some unusual elements the output should be checked (the atom SE in
# SEC becomes S2H1 for instance).
#
use strict;
my $res;
while (<>) {
if (/RESIDUE\s+(\w+)/) { $res = $1; next }
if (/CONECT/) {
my @fields = split /\s+/, $_;
shift @fields;
my $atom = shift @fields;
next if ($atom =~ m/^H/);
my $val = shift @fields;
my $nh = 0;
foreach (@fields) {
++$nh if ($_ =~ m/^H/);
}
print "$res $atom ",substr($atom,0,1),$val,"H$nh\n";
}
}
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