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use strict;
# Script to generate source code for a classifier based on a
# config-file. Useful for having default classifiers statically in
# memory. It generates a constant classifier that should be placed in
# its own source-file.
# This interpreter has stricter requirements on the input format than
# the one in the C-code, since it is only for internal use. It also
# doesn't do any syntax checks, so it will only work on valid config
# files.
# The script should be run from the same directory as it is stored,
# because it depends on the subdir 'rsa/' to gengerate reference SASA
# values for RSA output. The file classifier_protor.c in the
# source-directory was generated using the command
#
# perl config2c.pl protor ../share/protor.config
#
# where 'protor' will be the variable name prefix and the name used in
# output generated from this classifier. It is also referred to in
# freesasa.h.
# Ideally RSA values should be stored in the configuration file, in a
# separate section. This will be added in the future.
my %types;
my %atoms;
my %residues;
my %rsa;
my $name;
my $n_classes = 0;
my $n_residues = 0;
my $atom_flag = 0;
my $type_flag = 0;
(scalar @ARGV == 2) or die "usage : $0 <variable_prefix> <config-file>\n";
my $prefix = shift @ARGV;
my $config_file = shift @ARGV;
open(my $input, "<$config_file") or die "Can't open $config_file. $!";
while (<$input>) {
next if (/^#/);
chomp;
$_ =~ s/^(.*)#.*/$1/; # strip comments
next if (/^\s*$/);
if (/^types:/) {
$type_flag = 1;
$atom_flag = 0;
next;
}
if (/^atoms:/) {
$type_flag = 0;
$atom_flag = 1;
next;
}
if (/^name:/) {
$_ =~ s/name:\s+(\S+)/$1/;
$name = $_;
next;
}
if ($type_flag) {
my ($name,$radius,$class) = split /\s+/, $_;
my $class_code;
$types{$name}{radius} = $radius;
if ($class =~ /apolar/i) {$class_code = 'FREESASA_ATOM_APOLAR';}
elsif ($class =~ /polar/i) {$class_code = 'FREESASA_ATOM_POLAR';}
else {die "Only classes 'polar' and 'apolar' allowed";}
$types{$name}{class} = $class_code;
}
if ($atom_flag) {
my ($res,$atom,$type) = split /\s+/, $_;
$atoms{$res}{$atom} = $type;
if (! exists $residues{$res}) {
$residues{$res} = $n_residues;
++$n_residues;
}
}
}
close($input);
# generate RSA values
my @pdb = `ls rsa/*.pdb`;
foreach my $p (@pdb) {
chomp $p;
my $name = substr($p,4,3);
my @rsa_atoms = `cat $p`;
my (@pol_atoms, @apol_atoms);
foreach (@rsa_atoms) {
next if (! /^ATOM/);
next if (! (substr($_,25,1) eq '2'));
next if (/H\s*$/); #skip hydrogen
my $atom = substr($_,12,4);
next if (substr($_,1,1) eq "H");
my $c;
$atom =~ s/\s//g;
if (exists $atoms{$name}{$atom}) {
$c = $types{$atoms{$name}{$atom}}{class};
} elsif (exists $atoms{'ANY'}{$atom}) {
$c = $types{$atoms{'ANY'}{$atom}}{class};
} else {
die "Atom $name $atom not in classifier";
}
push(@apol_atoms, $atom) if ($c =~ /FREESASA_ATOM_APOLAR/);
push(@pol_atoms, $atom) if ($c =~ /FREESASA_ATOM_POLAR/);
}
my $select_total = '--select="res2, resi 2"';
my $select_bb = '--select="bb, resi 2 and name c+n+o+ca"';
my $select_sc = '--select="sc, resi 2 and not name c+n+o+ca"';
my ($select_apol, $select_pol);
if (scalar @apol_atoms > 0) {
$select_apol = '--select="apol, resi 2 and name ' . join('+',@apol_atoms) . '"';
}
if (scalar @pol_atoms > 0) {
$select_pol = '--select="pol, resi 2 and name ' . join('+',@pol_atoms) . '"';
}
my @data = `../src/freesasa $p -c $config_file -n 1000 $select_total $select_bb $select_sc $select_apol $select_pol`;
my %subarea;
$subarea{pol} = $subarea{apol} = 0;
$subarea{name} = $name;
foreach (@data) {
if (/^res2 :\ +(\d+.\d+)/) {
$subarea{total} = $1;
}
if (/^bb :\ +(\d+.\d+)/) {
$subarea{bb} = $1;
}
if (/^sc :\ +(\d+.\d+)/) {
$subarea{sc} = $1;
}
if (/^pol :\ +(\d+.\d+)/) {
$subarea{pol} = $1;
}
if (/^apol :\ +(\d+.\d+)/) {
$subarea{apol} = $1;
}
}
$rsa{$name} = "\{\"$name\", $subarea{total}, $subarea{bb}, ".
"$subarea{sc}, $subarea{pol}, $subarea{apol}, 0\}";
}
my @res_array = sort keys %residues;
print "#include \"classifier.h\"\n\n";
print "/* Autogenerated code from the script config2c.pl */\n\n";
print "static const char *$prefix\_residue_name[] = {";
print "\"$_\", "foreach (@res_array);
print "};\n";
foreach my $res (@res_array) {
my @atom_names = keys %{$atoms{$res}};
print "static const char *$prefix\_$res\_atom_name[] = {";
print "\"$_\", " foreach (@atom_names);
print "};\n";
print "static double $prefix\_$res\_atom_radius[] = {";
print $types{$atoms{$res}{$_}}{radius},", " foreach (@atom_names);
print "};\n";
print "static int $prefix\_$res\_atom_class[] = {";
print $types{$atoms{$res}{$_}}{class},", " foreach (@atom_names);
print "};\n";
print "static struct classifier_residue $prefix\_$res\_cfg = {\n";
print " ", scalar keys %{$atoms{$res}}, ",\n";
print " \"$res\",\n";
print " (char**) $prefix\_$res\_atom_name,\n";
print " (double*) $prefix\_$res\_atom_radius,\n";
print " (freesasa_atom_class*) $prefix\_$res\_atom_class,\n";
if (exists $rsa{$res}) {
print " $rsa{$res},";
} else {
print " {NULL, 0, 0, 0, 0, 0},";
}
print"\n};\n\n"
}
print "static struct classifier_residue *$prefix\_residue_cfg[] = {\n ";
foreach my $res (@res_array) {
print "&$prefix\_$res\_cfg, ";
}
print "};\n\n";
print "const freesasa_classifier freesasa_$prefix\_classifier = {\n";
print " $n_residues,";
print " (char**) $prefix\_residue_name,\n";
print " \"$name\",\n";
print " (struct classifier_residue **) $prefix\_residue_cfg,\n";
print "};\n\n";
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