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Fix atom order in a few PDB files
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Update classifier files

Update config2c.pl and CLI tests to match new reference input
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@mittinatten
mittinatten committed Sep 5, 2017
1 parent 4c791a2 commit aef643b
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Showing 10 changed files with 289 additions and 289 deletions.
10 changes: 5 additions & 5 deletions scripts/config2c.pl
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Expand Up @@ -105,6 +105,7 @@
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);
Expand All @@ -114,14 +115,13 @@
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 -R $select_bb $select_sc $select_apol $select_pol`;
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} = $name;
foreach (@data) {
if (/^SEQ A\ +2 (\w\w\w) :\ + (\d+.\d+)/) {
($name == $1) or die "inconsistency";
$subarea{name} = $1;
$subarea{total} = $2;
if (/^res2 :\ +(\d+.\d+)/) {
$subarea{total} = $1;
}
if (/^bb :\ +(\d+.\d+)/) {
$subarea{bb} = $1;
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4 changes: 2 additions & 2 deletions scripts/rsa/ARG.pdb
View file
Expand Up @@ -23,13 +23,13 @@ ATOM 20 HH1 ARG S 2 3.197 9.689 5.564 1.00 0.00 H
ATOM 21 HH1 ARG S 2 4.218 9.487 4.180 1.00 0.00 H
ATOM 22 HH2 ARG S 2 1.814 7.973 6.235 1.00 0.00 H
ATOM 23 HH2 ARG S 2 1.795 6.481 5.354 1.00 0.00 H
ATOM 31 NH2 ARG S 2 3.531 9.124 4.809 1.00 0.00 1 N
ATOM 32 NH1 ARG S 2 2.148 7.409 5.480 1.00 0.00 2 N
ATOM 24 N ALA S 3 5.780 3.736 0.278 1.00 0.00 N
ATOM 25 CA ALA S 3 7.237 3.764 0.353 1.00 0.00 C
ATOM 26 C ALA S 3 7.803 5.167 0.269 1.00 0.00 C
ATOM 27 O ALA S 3 8.338 5.522 -0.779 1.00 0.00 O
ATOM 28 CB ALA S 3 7.779 2.922 -0.804 1.00 0.00 C
ATOM 29 OXT ALA S 3 7.706 5.898 1.254 1.00 0.00 O1-
ATOM 30 H ALA S 3 5.288 4.338 -0.352 1.00 0.00 H
ATOM 31 NH2 ARG S 2 3.531 9.124 4.809 1.00 0.00 1 N
ATOM 32 NH1 ARG S 2 2.148 7.409 5.480 1.00 0.00 2 N
END
4 changes: 2 additions & 2 deletions scripts/rsa/ASP.pdb
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Expand Up @@ -11,12 +11,12 @@ ATOM 8 C ASP S 2 5.135 2.883 1.077 1.00 0.00 C
ATOM 9 O ASP S 2 5.701 2.131 1.861 1.00 0.00 O
ATOM 10 CB ASP S 2 3.015 3.651 2.128 1.00 0.00 C
ATOM 11 CG ASP S 2 3.609 5.040 2.235 1.00 0.00 C
ATOM 18 OD2 ASP S 2 3.240 5.767 3.155 1.00 0.00 1 O
ATOM 19 OD1 ASP S 2 4.440 5.388 1.397 1.00 0.00 2 O
ATOM 12 N ALA S 3 5.780 3.736 0.278 1.00 0.00 N
ATOM 13 CA ALA S 3 7.237 3.764 0.353 1.00 0.00 C
ATOM 14 C ALA S 3 7.803 5.167 0.269 1.00 0.00 C
ATOM 15 O ALA S 3 8.338 5.522 -0.779 1.00 0.00 O
ATOM 16 CB ALA S 3 7.779 2.922 -0.804 1.00 0.00 C
ATOM 17 OXT ALA S 3 7.706 5.898 1.254 1.00 0.00 O1-
ATOM 18 OD2 ASP S 2 3.240 5.767 3.155 1.00 0.00 1 O
ATOM 19 OD1 ASP S 2 4.440 5.388 1.397 1.00 0.00 2 O
END
4 changes: 2 additions & 2 deletions scripts/rsa/GLU.pdb
View file
Expand Up @@ -12,12 +12,12 @@ ATOM 9 O GLU S 2 5.701 2.131 1.861 1.00 0.00 O
ATOM 10 CB GLU S 2 3.015 3.651 2.128 1.00 0.00 C
ATOM 11 CG GLU S 2 3.569 5.066 2.301 1.00 0.00 C
ATOM 12 CD GLU S 2 2.918 5.720 3.503 1.00 0.00 C
ATOM 19 OE2 GLU S 2 3.246 6.869 3.795 1.00 0.00 1 O
ATOM 20 OE1 GLU S 2 2.086 5.078 4.142 1.00 0.00 2 O
ATOM 13 N ALA S 3 5.780 3.736 0.278 1.00 0.00 N
ATOM 14 CA ALA S 3 7.237 3.764 0.353 1.00 0.00 C
ATOM 15 C ALA S 3 7.803 5.167 0.269 1.00 0.00 C
ATOM 16 O ALA S 3 8.338 5.522 -0.779 1.00 0.00 O
ATOM 17 CB ALA S 3 7.779 2.922 -0.804 1.00 0.00 C
ATOM 18 OXT ALA S 3 7.706 5.898 1.254 1.00 0.00 O1-
ATOM 19 OE2 GLU S 2 3.246 6.869 3.795 1.00 0.00 1 O
ATOM 20 OE1 GLU S 2 2.086 5.078 4.142 1.00 0.00 2 O
END
4 changes: 2 additions & 2 deletions scripts/rsa/LEU.pdb
View file
Expand Up @@ -15,13 +15,13 @@ ATOM 12 O LEU S 2 5.701 2.131 1.861 1.00 0.00 O
ATOM 13 CB LEU S 2 3.015 3.651 2.128 1.00 0.00 C
ATOM 14 CG LEU S 2 3.569 5.066 2.301 1.00 0.00 C
ATOM 15 H LEU S 2 3.363 0.853 1.446 1.00 0.00 H
ATOM 23 CD2 LEU S 2 2.956 5.793 3.500 1.00 0.00 1 C
ATOM 24 CD1 LEU S 2 3.304 5.951 1.082 1.00 0.00 2 C
ATOM 16 N ALA S 3 5.780 3.736 0.278 1.00 0.00 N
ATOM 17 CA ALA S 3 7.237 3.764 0.353 1.00 0.00 C
ATOM 18 C ALA S 3 7.803 5.167 0.269 1.00 0.00 C
ATOM 19 O ALA S 3 8.338 5.522 -0.779 1.00 0.00 O
ATOM 20 CB ALA S 3 7.779 2.922 -0.804 1.00 0.00 C
ATOM 21 OXT ALA S 3 7.706 5.898 1.254 1.00 0.00 O1-
ATOM 22 H ALA S 3 5.288 4.338 -0.352 1.00 0.00 H
ATOM 23 CD2 LEU S 2 2.956 5.793 3.500 1.00 0.00 1 C
ATOM 24 CD1 LEU S 2 3.304 5.951 1.082 1.00 0.00 2 C
END
8 changes: 4 additions & 4 deletions scripts/rsa/PHE.pdb
View file
Expand Up @@ -12,14 +12,14 @@ ATOM 9 O PHE S 2 4.935 2.131 3.408 1.00 0.00 O
ATOM 10 CB PHE S 2 2.283 3.651 2.899 1.00 0.00 C
ATOM 11 CG PHE S 2 2.821 5.035 3.170 1.00 0.00 C
ATOM 12 CZ PHE S 2 3.812 7.584 3.668 1.00 0.00 C
ATOM 19 CD2 PHE S 2 2.432 6.101 2.367 1.00 0.00 1 C
ATOM 20 CE2 PHE S 2 2.927 7.376 2.617 1.00 0.00 1 C
ATOM 21 CD1 PHE S 2 3.706 5.244 4.222 1.00 0.00 2 C
ATOM 22 CE1 PHE S 2 4.201 6.518 4.471 1.00 0.00 2 C
ATOM 13 N ALA S 3 5.461 3.736 1.913 1.00 0.00 N
ATOM 14 CA ALA S 3 6.837 3.764 2.400 1.00 0.00 C
ATOM 15 C ALA S 3 7.403 5.167 2.481 1.00 0.00 C
ATOM 16 O ALA S 3 8.215 5.522 1.628 1.00 0.00 O
ATOM 17 CB ALA S 3 7.686 2.922 1.446 1.00 0.00 C
ATOM 18 OXT ALA S 3 7.030 5.898 3.397 1.00 0.00 O1-
ATOM 19 CD2 PHE S 2 2.432 6.101 2.367 1.00 0.00 1 C
ATOM 20 CE2 PHE S 2 2.927 7.376 2.617 1.00 0.00 1 C
ATOM 21 CD1 PHE S 2 3.706 5.244 4.222 1.00 0.00 2 C
ATOM 22 CE1 PHE S 2 4.201 6.518 4.471 1.00 0.00 2 C
END

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