diff --git a/scripts/config2c.pl b/scripts/config2c.pl index 7b1fe364..06b726c9 100644 --- a/scripts/config2c.pl +++ b/scripts/config2c.pl @@ -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); @@ -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; diff --git a/scripts/rsa/ARG.pdb b/scripts/rsa/ARG.pdb index 026acac0..73ff7870 100644 --- a/scripts/rsa/ARG.pdb +++ b/scripts/rsa/ARG.pdb @@ -23,6 +23,8 @@ 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 @@ -30,6 +32,4 @@ 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 diff --git a/scripts/rsa/ASP.pdb b/scripts/rsa/ASP.pdb index 5bed3e76..d22745d3 100644 --- a/scripts/rsa/ASP.pdb +++ b/scripts/rsa/ASP.pdb @@ -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 diff --git a/scripts/rsa/GLU.pdb b/scripts/rsa/GLU.pdb index ad59964f..d1279658 100644 --- a/scripts/rsa/GLU.pdb +++ b/scripts/rsa/GLU.pdb @@ -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 diff --git a/scripts/rsa/LEU.pdb b/scripts/rsa/LEU.pdb index c1484661..72e5028f 100644 --- a/scripts/rsa/LEU.pdb +++ b/scripts/rsa/LEU.pdb @@ -15,6 +15,8 @@ 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 @@ -22,6 +24,4 @@ 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 diff --git a/scripts/rsa/PHE.pdb b/scripts/rsa/PHE.pdb index 3e8c7ef2..1a7602fd 100644 --- a/scripts/rsa/PHE.pdb +++ b/scripts/rsa/PHE.pdb @@ -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 diff --git a/src/classifier_naccess.c b/src/classifier_naccess.c index 5f10c38b..08a78d13 100644 --- a/src/classifier_naccess.c +++ b/src/classifier_naccess.c @@ -3,9 +3,9 @@ /* Autogenerated code from the script config2c.pl */ static const char *naccess_residue_name[] = {"A", "ALA", "ANY", "ARG", "ASN", "ASP", "C", "CYS", "DA", "DC", "DG", "DI", "DT", "DU", "G", "GLN", "GLU", "GLY", "HIS", "I", "ILE", "LEU", "LYS", "MET", "PHE", "PRO", "SEC", "SER", "T", "THR", "TRP", "TYR", "U", "VAL", }; -static const char *naccess_A_atom_name[] = {"N1", "N3", "C2", "C6", "N7", "C8", "C4", "N6", "C5", "N9", }; -static double naccess_A_atom_radius[] = {1.60, 1.60, 1.80, 1.80, 1.60, 1.80, 1.80, 1.60, 1.80, 1.60, }; -static int naccess_A_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_A_atom_name[] = {"C4", "C6", "N9", "N6", "C5", "N7", "C2", "N1", "N3", "C8", }; +static double naccess_A_atom_radius[] = {1.80, 1.80, 1.60, 1.60, 1.80, 1.60, 1.80, 1.60, 1.60, 1.80, }; +static int naccess_A_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_A_cfg = { .name = "A", .n_atoms = 10, .atom_name = (char**) naccess_A_atom_name, @@ -22,12 +22,12 @@ static struct classifier_residue naccess_ALA_cfg = { .atom_name = (char**) naccess_ALA_atom_name, .atom_radius = (double*) naccess_ALA_atom_radius, .atom_class = (freesasa_atom_class*) naccess_ALA_atom_class, - .max_area = {.name = "ALA", .total = 102.31, .main_chain = 46.96, .side_chain = 55.35, .polar = 28.51, .apolar = 73.80}, + .max_area = {.name = "ALA", .total = 107.89, .main_chain = 43.94, .side_chain = 63.94, .polar = 36.71, .apolar = 71.17}, }; -static const char *naccess_ANY_atom_name[] = {"O2'", "OP2", "C2'", "OXT", "O5'", "CA", "O4'", "O3'", "C1'", "C3'", "P", "OP3", "O", "C5'", "N", "C4'", "CB", "C", "OP1", }; -static double naccess_ANY_atom_radius[] = {1.40, 1.40, 1.80, 1.40, 1.40, 1.87, 1.40, 1.40, 1.80, 1.80, 1.90, 1.40, 1.40, 1.80, 1.65, 1.80, 1.87, 1.76, 1.40, }; -static int naccess_ANY_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_ANY_atom_name[] = {"CA", "OP2", "P", "C3'", "C4'", "OXT", "C", "O", "C5'", "OP3", "O5'", "C1'", "N", "C2'", "O3'", "O2'", "CB", "OP1", "O4'", }; +static double naccess_ANY_atom_radius[] = {1.87, 1.40, 1.90, 1.80, 1.80, 1.40, 1.76, 1.40, 1.80, 1.40, 1.40, 1.80, 1.65, 1.80, 1.40, 1.40, 1.87, 1.40, 1.40, }; +static int naccess_ANY_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue naccess_ANY_cfg = { .name = "ANY", .n_atoms = 19, .atom_name = (char**) naccess_ANY_atom_name, @@ -36,29 +36,29 @@ static struct classifier_residue naccess_ANY_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *naccess_ARG_atom_name[] = {"CG", "CZ", "CD", "NH1", "NE", "NH2", }; -static double naccess_ARG_atom_radius[] = {1.87, 1.76, 1.87, 1.65, 1.65, 1.65, }; -static int naccess_ARG_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_ARG_atom_name[] = {"NH1", "NH2", "CG", "CD", "NE", "CZ", }; +static double naccess_ARG_atom_radius[] = {1.65, 1.65, 1.87, 1.87, 1.65, 1.76, }; +static int naccess_ARG_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_ARG_cfg = { .name = "ARG", .n_atoms = 6, .atom_name = (char**) naccess_ARG_atom_name, .atom_radius = (double*) naccess_ARG_atom_radius, .atom_class = (freesasa_atom_class*) naccess_ARG_atom_class, - .max_area = {.name = "ARG", .total = 232.08, .main_chain = 45.58, .side_chain = 186.50, .polar = 148.95, .apolar = 83.13}, + .max_area = {.name = "ARG", .total = 238.33, .main_chain = 41.72, .side_chain = 196.61, .polar = 161.10, .apolar = 77.23}, }; -static const char *naccess_ASN_atom_name[] = {"CG", "OD1", "ND2", }; -static double naccess_ASN_atom_radius[] = {1.76, 1.40, 1.65, }; -static int naccess_ASN_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_ASN_atom_name[] = {"ND2", "OD1", "CG", }; +static double naccess_ASN_atom_radius[] = {1.65, 1.40, 1.76, }; +static int naccess_ASN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_ASN_cfg = { .name = "ASN", .n_atoms = 3, .atom_name = (char**) naccess_ASN_atom_name, .atom_radius = (double*) naccess_ASN_atom_radius, .atom_class = (freesasa_atom_class*) naccess_ASN_atom_class, - .max_area = {.name = "ASN", .total = 137.97, .main_chain = 44.26, .side_chain = 93.71, .polar = 87.92, .apolar = 50.05}, + .max_area = {.name = "ASN", .total = 143.97, .main_chain = 41.03, .side_chain = 102.94, .polar = 97.83, .apolar = 46.14}, }; -static const char *naccess_ASP_atom_name[] = {"OD1", "OD2", "CG", }; +static const char *naccess_ASP_atom_name[] = {"OD2", "OD1", "CG", }; static double naccess_ASP_atom_radius[] = {1.40, 1.40, 1.76, }; static int naccess_ASP_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_ASP_cfg = { @@ -66,12 +66,12 @@ static struct classifier_residue naccess_ASP_cfg = { .atom_name = (char**) naccess_ASP_atom_name, .atom_radius = (double*) naccess_ASP_atom_radius, .atom_class = (freesasa_atom_class*) naccess_ASP_atom_class, - .max_area = {.name = "ASP", .total = 134.50, .main_chain = 45.25, .side_chain = 89.25, .polar = 81.36, .apolar = 53.14}, + .max_area = {.name = "ASP", .total = 140.48, .main_chain = 41.76, .side_chain = 98.72, .polar = 91.19, .apolar = 49.29}, }; -static const char *naccess_C_atom_name[] = {"C5", "C4", "O2", "N4", "C6", "N1", "C2", "N3", }; -static double naccess_C_atom_radius[] = {1.80, 1.80, 1.40, 1.60, 1.80, 1.60, 1.80, 1.60, }; -static int naccess_C_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_C_atom_name[] = {"C5", "N4", "C6", "N1", "N3", "C2", "O2", "C4", }; +static double naccess_C_atom_radius[] = {1.80, 1.60, 1.80, 1.60, 1.60, 1.80, 1.40, 1.80, }; +static int naccess_C_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_C_cfg = { .name = "C", .n_atoms = 8, .atom_name = (char**) naccess_C_atom_name, @@ -88,12 +88,12 @@ static struct classifier_residue naccess_CYS_cfg = { .atom_name = (char**) naccess_CYS_atom_name, .atom_radius = (double*) naccess_CYS_atom_radius, .atom_class = (freesasa_atom_class*) naccess_CYS_atom_class, - .max_area = {.name = "CYS", .total = 127.09, .main_chain = 45.71, .side_chain = 81.38, .polar = 28.51, .apolar = 98.58}, + .max_area = {.name = "CYS", .total = 134.24, .main_chain = 41.92, .side_chain = 92.33, .polar = 36.49, .apolar = 97.75}, }; -static const char *naccess_DA_atom_name[] = {"C8", "C4", "C5", "N6", "N9", "C2", "N3", "N1", "C6", "N7", }; -static double naccess_DA_atom_radius[] = {1.80, 1.80, 1.80, 1.60, 1.60, 1.80, 1.60, 1.60, 1.80, 1.60, }; -static int naccess_DA_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_DA_atom_name[] = {"C4", "N9", "C6", "C5", "N6", "N7", "C2", "C8", "N3", "N1", }; +static double naccess_DA_atom_radius[] = {1.80, 1.60, 1.80, 1.80, 1.60, 1.60, 1.80, 1.80, 1.60, 1.60, }; +static int naccess_DA_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue naccess_DA_cfg = { .name = "DA", .n_atoms = 10, .atom_name = (char**) naccess_DA_atom_name, @@ -102,9 +102,9 @@ static struct classifier_residue naccess_DA_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *naccess_DC_atom_name[] = {"C6", "N3", "N1", "C2", "N4", "C5", "C4", "O2", }; -static double naccess_DC_atom_radius[] = {1.80, 1.60, 1.60, 1.80, 1.60, 1.80, 1.80, 1.40, }; -static int naccess_DC_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_DC_atom_name[] = {"C6", "N4", "C5", "C2", "N1", "N3", "C4", "O2", }; +static double naccess_DC_atom_radius[] = {1.80, 1.60, 1.80, 1.80, 1.60, 1.60, 1.80, 1.40, }; +static int naccess_DC_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue naccess_DC_cfg = { .name = "DC", .n_atoms = 8, .atom_name = (char**) naccess_DC_atom_name, @@ -113,9 +113,9 @@ static struct classifier_residue naccess_DC_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *naccess_DG_atom_name[] = {"O6", "N3", "N1", "C2", "C6", "N7", "C8", "C4", "C5", "N2", "N9", }; -static double naccess_DG_atom_radius[] = {1.40, 1.60, 1.60, 1.80, 1.80, 1.60, 1.80, 1.80, 1.80, 1.60, 1.60, }; -static int naccess_DG_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_DG_atom_name[] = {"O6", "C4", "N9", "C6", "C5", "N7", "C2", "N2", "N3", "N1", "C8", }; +static double naccess_DG_atom_radius[] = {1.40, 1.80, 1.60, 1.80, 1.80, 1.60, 1.80, 1.60, 1.60, 1.60, 1.80, }; +static int naccess_DG_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_DG_cfg = { .name = "DG", .n_atoms = 11, .atom_name = (char**) naccess_DG_atom_name, @@ -124,9 +124,9 @@ static struct classifier_residue naccess_DG_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *naccess_DI_atom_name[] = {"C5", "N9", "C4", "C8", "N7", "O6", "C6", "N3", "C2", "N1", }; -static double naccess_DI_atom_radius[] = {1.80, 1.60, 1.80, 1.80, 1.60, 1.40, 1.80, 1.60, 1.80, 1.60, }; -static int naccess_DI_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_DI_atom_name[] = {"O6", "C4", "C2", "N3", "N1", "C8", "N9", "C6", "N7", "C5", }; +static double naccess_DI_atom_radius[] = {1.40, 1.80, 1.80, 1.60, 1.60, 1.80, 1.60, 1.80, 1.60, 1.80, }; +static int naccess_DI_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_DI_cfg = { .name = "DI", .n_atoms = 10, .atom_name = (char**) naccess_DI_atom_name, @@ -135,9 +135,9 @@ static struct classifier_residue naccess_DI_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *naccess_DT_atom_name[] = {"C6", "C2", "N3", "N1", "C4", "O2", "C7", "C5", "O4", }; -static double naccess_DT_atom_radius[] = {1.80, 1.80, 1.60, 1.60, 1.80, 1.40, 1.80, 1.80, 1.40, }; -static int naccess_DT_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_DT_atom_name[] = {"C7", "C4", "O2", "C5", "C6", "O4", "N3", "N1", "C2", }; +static double naccess_DT_atom_radius[] = {1.80, 1.80, 1.40, 1.80, 1.80, 1.40, 1.60, 1.60, 1.80, }; +static int naccess_DT_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_DT_cfg = { .name = "DT", .n_atoms = 9, .atom_name = (char**) naccess_DT_atom_name, @@ -146,9 +146,9 @@ static struct classifier_residue naccess_DT_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *naccess_DU_atom_name[] = {"C6", "C2", "N1", "N3", "C5", "O4", "C4", "O2", }; -static double naccess_DU_atom_radius[] = {1.80, 1.80, 1.60, 1.60, 1.80, 1.40, 1.80, 1.40, }; -static int naccess_DU_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_DU_atom_name[] = {"N3", "O4", "N1", "C2", "C5", "C6", "O2", "C4", }; +static double naccess_DU_atom_radius[] = {1.60, 1.40, 1.60, 1.80, 1.80, 1.80, 1.40, 1.80, }; +static int naccess_DU_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_DU_cfg = { .name = "DU", .n_atoms = 8, .atom_name = (char**) naccess_DU_atom_name, @@ -157,9 +157,9 @@ static struct classifier_residue naccess_DU_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *naccess_G_atom_name[] = {"N2", "C5", "N9", "C4", "C8", "N7", "O6", "C6", "N3", "C2", "N1", }; -static double naccess_G_atom_radius[] = {1.60, 1.80, 1.60, 1.80, 1.80, 1.60, 1.40, 1.80, 1.60, 1.80, 1.60, }; -static int naccess_G_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_G_atom_name[] = {"O6", "C4", "C6", "N9", "N7", "C5", "C2", "N2", "N1", "N3", "C8", }; +static double naccess_G_atom_radius[] = {1.40, 1.80, 1.80, 1.60, 1.60, 1.80, 1.80, 1.60, 1.60, 1.60, 1.80, }; +static int naccess_G_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_G_cfg = { .name = "G", .n_atoms = 11, .atom_name = (char**) naccess_G_atom_name, @@ -168,18 +168,18 @@ static struct classifier_residue naccess_G_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *naccess_GLN_atom_name[] = {"CG", "NE2", "OE1", "CD", }; -static double naccess_GLN_atom_radius[] = {1.87, 1.65, 1.40, 1.76, }; -static int naccess_GLN_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *naccess_GLN_atom_name[] = {"CG", "CD", "NE2", "OE1", }; +static double naccess_GLN_atom_radius[] = {1.87, 1.76, 1.65, 1.40, }; +static int naccess_GLN_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue naccess_GLN_cfg = { .name = "GLN", .n_atoms = 4, .atom_name = (char**) naccess_GLN_atom_name, .atom_radius = (double*) naccess_GLN_atom_radius, .atom_class = (freesasa_atom_class*) naccess_GLN_atom_class, - .max_area = {.name = "GLN", .total = 172.15, .main_chain = 45.58, .side_chain = 126.57, .polar = 117.24, .apolar = 54.91}, + .max_area = {.name = "GLN", .total = 178.24, .main_chain = 41.72, .side_chain = 136.52, .polar = 126.35, .apolar = 51.89}, }; -static const char *naccess_GLU_atom_name[] = {"OE2", "CG", "OE1", "CD", }; +static const char *naccess_GLU_atom_name[] = {"OE1", "CG", "OE2", "CD", }; static double naccess_GLU_atom_radius[] = {1.40, 1.87, 1.40, 1.76, }; static int naccess_GLU_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_GLU_cfg = { @@ -187,7 +187,7 @@ static struct classifier_residue naccess_GLU_cfg = { .atom_name = (char**) naccess_GLU_atom_name, .atom_radius = (double*) naccess_GLU_atom_radius, .atom_class = (freesasa_atom_class*) naccess_GLU_atom_class, - .max_area = {.name = "GLU", .total = 166.09, .main_chain = 45.60, .side_chain = 120.49, .polar = 103.10, .apolar = 63.00}, + .max_area = {.name = "GLU", .total = 172.09, .main_chain = 41.72, .side_chain = 130.37, .polar = 112.13, .apolar = 59.96}, }; static const char *naccess_GLY_atom_name[] = {"CA", }; @@ -198,23 +198,23 @@ static struct classifier_residue naccess_GLY_cfg = { .atom_name = (char**) naccess_GLY_atom_name, .atom_radius = (double*) naccess_GLY_atom_radius, .atom_class = (freesasa_atom_class*) naccess_GLY_atom_class, - .max_area = {.name = "GLY", .total = 71.50, .main_chain = 71.50, .side_chain = 0.00, .polar = 29.80, .apolar = 41.69}, + .max_area = {.name = "GLY", .total = 80.30, .main_chain = 80.30, .side_chain = 0.00, .polar = 42.62, .apolar = 37.69}, }; -static const char *naccess_HIS_atom_name[] = {"NE2", "CD2", "ND1", "CG", "CE1", }; -static double naccess_HIS_atom_radius[] = {1.65, 1.76, 1.65, 1.76, 1.76, }; -static int naccess_HIS_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *naccess_HIS_atom_name[] = {"CE1", "CG", "CD2", "NE2", "ND1", }; +static double naccess_HIS_atom_radius[] = {1.76, 1.76, 1.76, 1.65, 1.65, }; +static int naccess_HIS_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue naccess_HIS_cfg = { .name = "HIS", .n_atoms = 5, .atom_name = (char**) naccess_HIS_atom_name, .atom_radius = (double*) naccess_HIS_atom_radius, .atom_class = (freesasa_atom_class*) naccess_HIS_atom_class, - .max_area = {.name = "HIS", .total = 173.15, .main_chain = 44.71, .side_chain = 128.44, .polar = 68.23, .apolar = 104.92}, + .max_area = {.name = "HIS", .total = 182.75, .main_chain = 38.76, .side_chain = 143.99, .polar = 85.61, .apolar = 97.14}, }; -static const char *naccess_I_atom_name[] = {"N7", "C6", "C2", "N3", "N1", "O6", "C5", "N9", "C4", "C8", }; -static double naccess_I_atom_radius[] = {1.60, 1.80, 1.80, 1.60, 1.60, 1.40, 1.80, 1.60, 1.80, 1.80, }; -static int naccess_I_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *naccess_I_atom_name[] = {"C5", "N7", "C6", "N9", "C8", "N3", "N1", "C2", "C4", "O6", }; +static double naccess_I_atom_radius[] = {1.80, 1.60, 1.80, 1.60, 1.80, 1.60, 1.60, 1.80, 1.80, 1.40, }; +static int naccess_I_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue naccess_I_cfg = { .name = "I", .n_atoms = 10, .atom_name = (char**) naccess_I_atom_name, @@ -223,7 +223,7 @@ static struct classifier_residue naccess_I_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *naccess_ILE_atom_name[] = {"CG1", "CG2", "CD1", }; +static const char *naccess_ILE_atom_name[] = {"CG2", "CG1", "CD1", }; static double naccess_ILE_atom_radius[] = {1.87, 1.87, 1.87, }; static int naccess_ILE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_ILE_cfg = { @@ -231,10 +231,10 @@ static struct classifier_residue naccess_ILE_cfg = { .atom_name = (char**) naccess_ILE_atom_name, .atom_radius = (double*) naccess_ILE_atom_radius, .atom_class = (freesasa_atom_class*) naccess_ILE_atom_class, - .max_area = {.name = "ILE", .total = 166.62, .main_chain = 38.94, .side_chain = 127.68, .polar = 24.25, .apolar = 142.37}, + .max_area = {.name = "ILE", .total = 175.10, .main_chain = 41.16, .side_chain = 133.94, .polar = 36.10, .apolar = 139.00}, }; -static const char *naccess_LEU_atom_name[] = {"CD1", "CD2", "CG", }; +static const char *naccess_LEU_atom_name[] = {"CD1", "CG", "CD2", }; static double naccess_LEU_atom_radius[] = {1.87, 1.87, 1.87, }; static int naccess_LEU_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_LEU_cfg = { @@ -242,10 +242,10 @@ static struct classifier_residue naccess_LEU_cfg = { .atom_name = (char**) naccess_LEU_atom_name, .atom_radius = (double*) naccess_LEU_atom_radius, .atom_class = (freesasa_atom_class*) naccess_LEU_atom_class, - .max_area = {.name = "LEU", .total = 159.40, .main_chain = 45.05, .side_chain = 114.35, .polar = 28.51, .apolar = 130.89}, + .max_area = {.name = "LEU", .total = 178.40, .main_chain = 39.50, .side_chain = 138.90, .polar = 36.45, .apolar = 141.95}, }; -static const char *naccess_LYS_atom_name[] = {"CG", "CE", "CD", "NZ", }; +static const char *naccess_LYS_atom_name[] = {"CE", "CG", "CD", "NZ", }; static double naccess_LYS_atom_radius[] = {1.87, 1.87, 1.87, 1.50, }; static int naccess_LYS_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue naccess_LYS_cfg = { @@ -253,10 +253,10 @@ static struct classifier_residue naccess_LYS_cfg = { .atom_name = (char**) naccess_LYS_atom_name, .atom_radius = (double*) naccess_LYS_atom_radius, .atom_class = (freesasa_atom_class*) naccess_LYS_atom_class, - .max_area = {.name = "LYS", .total = 192.51, .main_chain = 45.59, .side_chain = 146.93, .polar = 77.19, .apolar = 115.32}, + .max_area = {.name = "LYS", .total = 200.21, .main_chain = 41.72, .side_chain = 158.49, .polar = 84.31, .apolar = 115.90}, }; -static const char *naccess_MET_atom_name[] = {"SD", "CG", "CE", }; +static const char *naccess_MET_atom_name[] = {"SD", "CE", "CG", }; static double naccess_MET_atom_radius[] = {1.85, 1.87, 1.87, }; static int naccess_MET_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_MET_cfg = { @@ -264,10 +264,10 @@ static struct classifier_residue naccess_MET_cfg = { .atom_name = (char**) naccess_MET_atom_name, .atom_radius = (double*) naccess_MET_atom_radius, .atom_class = (freesasa_atom_class*) naccess_MET_atom_class, - .max_area = {.name = "MET", .total = 185.85, .main_chain = 45.57, .side_chain = 140.28, .polar = 28.51, .apolar = 157.34}, + .max_area = {.name = "MET", .total = 193.72, .main_chain = 41.72, .side_chain = 152.00, .polar = 36.45, .apolar = 157.27}, }; -static const char *naccess_PHE_atom_name[] = {"CE1", "CG", "CZ", "CE2", "CD1", "CD2", }; +static const char *naccess_PHE_atom_name[] = {"CD1", "CE2", "CD2", "CZ", "CE1", "CG", }; static double naccess_PHE_atom_radius[] = {1.76, 1.76, 1.76, 1.76, 1.76, 1.76, }; static int naccess_PHE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_PHE_cfg = { @@ -275,10 +275,10 @@ static struct classifier_residue naccess_PHE_cfg = { .atom_name = (char**) naccess_PHE_atom_name, .atom_radius = (double*) naccess_PHE_atom_radius, .atom_class = (freesasa_atom_class*) naccess_PHE_atom_class, - .max_area = {.name = "PHE", .total = 193.15, .main_chain = 44.02, .side_chain = 149.13, .polar = 28.51, .apolar = 164.64}, + .max_area = {.name = "PHE", .total = 199.40, .main_chain = 38.12, .side_chain = 161.27, .polar = 34.25, .apolar = 165.14}, }; -static const char *naccess_PRO_atom_name[] = {"CG", "CD", }; +static const char *naccess_PRO_atom_name[] = {"CD", "CG", }; static double naccess_PRO_atom_radius[] = {1.87, 1.87, }; static int naccess_PRO_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_PRO_cfg = { @@ -286,7 +286,7 @@ static struct classifier_residue naccess_PRO_cfg = { .atom_name = (char**) naccess_PRO_atom_name, .atom_radius = (double*) naccess_PRO_atom_radius, .atom_class = (freesasa_atom_class*) naccess_PRO_atom_class, - .max_area = {.name = "PRO", .total = 131.26, .main_chain = 29.75, .side_chain = 101.50, .polar = 14.98, .apolar = 116.27}, + .max_area = {.name = "PRO", .total = 135.84, .main_chain = 27.09, .side_chain = 108.76, .polar = 15.17, .apolar = 120.67}, }; static const char *naccess_SEC_atom_name[] = {"SE", }; @@ -308,12 +308,12 @@ static struct classifier_residue naccess_SER_cfg = { .atom_name = (char**) naccess_SER_atom_name, .atom_radius = (double*) naccess_SER_atom_radius, .atom_class = (freesasa_atom_class*) naccess_SER_atom_class, - .max_area = {.name = "SER", .total = 109.82, .main_chain = 46.67, .side_chain = 63.15, .polar = 54.97, .apolar = 54.85}, + .max_area = {.name = "SER", .total = 116.56, .main_chain = 43.38, .side_chain = 73.18, .polar = 68.03, .apolar = 48.53}, }; -static const char *naccess_T_atom_name[] = {"C2", "N3", "N1", "C6", "C7", "O4", "C5", "O2", "C4", }; -static double naccess_T_atom_radius[] = {1.80, 1.60, 1.60, 1.80, 1.80, 1.40, 1.80, 1.40, 1.80, }; -static int naccess_T_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *naccess_T_atom_name[] = {"C2", "N1", "O4", "N3", "C6", "C5", "O2", "C4", "C7", }; +static double naccess_T_atom_radius[] = {1.80, 1.60, 1.40, 1.60, 1.80, 1.80, 1.40, 1.80, 1.80, }; +static int naccess_T_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_T_cfg = { .name = "T", .n_atoms = 9, .atom_name = (char**) naccess_T_atom_name, @@ -330,34 +330,34 @@ static struct classifier_residue naccess_THR_cfg = { .atom_name = (char**) naccess_THR_atom_name, .atom_radius = (double*) naccess_THR_atom_radius, .atom_class = (freesasa_atom_class*) naccess_THR_atom_class, - .max_area = {.name = "THR", .total = 131.81, .main_chain = 40.30, .side_chain = 91.51, .polar = 47.59, .apolar = 84.22}, + .max_area = {.name = "THR", .total = 139.25, .main_chain = 41.70, .side_chain = 97.55, .polar = 63.50, .apolar = 75.75}, }; -static const char *naccess_TRP_atom_name[] = {"CH2", "CG", "CZ2", "CE3", "NE1", "CD2", "CE2", "CZ3", "CD1", }; -static double naccess_TRP_atom_radius[] = {1.76, 1.76, 1.76, 1.76, 1.65, 1.76, 1.76, 1.76, 1.76, }; -static int naccess_TRP_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *naccess_TRP_atom_name[] = {"NE1", "CH2", "CZ3", "CD1", "CG", "CE3", "CZ2", "CD2", "CE2", }; +static double naccess_TRP_atom_radius[] = {1.65, 1.76, 1.76, 1.76, 1.76, 1.76, 1.76, 1.76, 1.76, }; +static int naccess_TRP_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_TRP_cfg = { .name = "TRP", .n_atoms = 9, .atom_name = (char**) naccess_TRP_atom_name, .atom_radius = (double*) naccess_TRP_atom_radius, .atom_class = (freesasa_atom_class*) naccess_TRP_atom_class, - .max_area = {.name = "TRP", .total = 226.33, .main_chain = 40.90, .side_chain = 185.43, .polar = 58.94, .apolar = 167.40}, + .max_area = {.name = "TRP", .total = 248.97, .main_chain = 42.38, .side_chain = 206.59, .polar = 59.83, .apolar = 189.14}, }; -static const char *naccess_TYR_atom_name[] = {"CD2", "CD1", "OH", "CG", "CE1", "CE2", "CZ", }; -static double naccess_TYR_atom_radius[] = {1.76, 1.76, 1.40, 1.76, 1.76, 1.76, 1.76, }; -static int naccess_TYR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *naccess_TYR_atom_name[] = {"CZ", "CE1", "CG", "CD2", "CE2", "CD1", "OH", }; +static double naccess_TYR_atom_radius[] = {1.76, 1.76, 1.76, 1.76, 1.76, 1.76, 1.40, }; +static int naccess_TYR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue naccess_TYR_cfg = { .name = "TYR", .n_atoms = 7, .atom_name = (char**) naccess_TYR_atom_name, .atom_radius = (double*) naccess_TYR_atom_radius, .atom_class = (freesasa_atom_class*) naccess_TYR_atom_class, - .max_area = {.name = "TYR", .total = 206.14, .main_chain = 43.99, .side_chain = 162.14, .polar = 70.47, .apolar = 135.66}, + .max_area = {.name = "TYR", .total = 212.23, .main_chain = 38.13, .side_chain = 174.10, .polar = 76.34, .apolar = 135.89}, }; -static const char *naccess_U_atom_name[] = {"C4", "O2", "C5", "O4", "C6", "C2", "N1", "N3", }; -static double naccess_U_atom_radius[] = {1.80, 1.40, 1.80, 1.40, 1.80, 1.80, 1.60, 1.60, }; -static int naccess_U_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *naccess_U_atom_name[] = {"O2", "C4", "C5", "C6", "O4", "N1", "N3", "C2", }; +static double naccess_U_atom_radius[] = {1.40, 1.80, 1.80, 1.80, 1.40, 1.60, 1.60, 1.80, }; +static int naccess_U_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue naccess_U_cfg = { .name = "U", .n_atoms = 8, .atom_name = (char**) naccess_U_atom_name, @@ -374,7 +374,7 @@ static struct classifier_residue naccess_VAL_cfg = { .atom_name = (char**) naccess_VAL_atom_name, .atom_radius = (double*) naccess_VAL_atom_radius, .atom_class = (freesasa_atom_class*) naccess_VAL_atom_class, - .max_area = {.name = "VAL", .total = 146.03, .main_chain = 44.72, .side_chain = 101.31, .polar = 28.51, .apolar = 117.52}, + .max_area = {.name = "VAL", .total = 151.40, .main_chain = 41.17, .side_chain = 110.23, .polar = 36.12, .apolar = 115.28}, }; static struct classifier_residue *naccess_residue_cfg[] = { diff --git a/src/classifier_oons.c b/src/classifier_oons.c index c8a2c554..d7002329 100644 --- a/src/classifier_oons.c +++ b/src/classifier_oons.c @@ -14,9 +14,9 @@ static struct classifier_residue oons_ACE_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *oons_ANY_atom_name[] = {"OXT", "O5'", "C7", "P", "O2'", "N9", "C3'", "N", "C4'", "N4", "C", "N2", "C5'", "C5", "OP1", "C2'", "CM2", "N6", "C8", "C6", "O2", "OP2", "O6", "C4", "CB", "C1'", "O4", "O4'", "OP3", "O", "O3'", "CA", "N7", "C2", "N3", "N1", }; -static double oons_ANY_atom_radius[] = {1.40, 1.40, 1.75, 1.80, 1.40, 1.55, 1.75, 1.55, 1.75, 1.55, 1.55, 1.55, 2.00, 1.75, 1.40, 1.75, 2.00, 1.55, 1.75, 1.75, 1.40, 1.40, 1.40, 1.75, 2.00, 1.75, 1.40, 1.40, 1.40, 1.40, 1.40, 2.00, 1.55, 1.75, 1.55, 1.55, }; -static int oons_ANY_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *oons_ANY_atom_name[] = {"C5", "N", "O4", "C4", "C8", "OP1", "N1", "OP2", "C3'", "CM2", "P", "N9", "C6", "O2", "CA", "OXT", "O4'", "C5'", "C7", "O3'", "OP3", "O6", "N4", "N7", "C1'", "C", "C4'", "CB", "N2", "C2'", "O2'", "N3", "O", "O5'", "N6", "C2", }; +static double oons_ANY_atom_radius[] = {1.75, 1.55, 1.40, 1.75, 1.75, 1.40, 1.55, 1.40, 1.75, 2.00, 1.80, 1.55, 1.75, 1.40, 2.00, 1.40, 1.40, 2.00, 1.75, 1.40, 1.40, 1.40, 1.55, 1.55, 1.75, 1.55, 1.75, 2.00, 1.55, 1.75, 1.40, 1.55, 1.40, 1.40, 1.55, 1.75, }; +static int oons_ANY_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue oons_ANY_cfg = { .name = "ANY", .n_atoms = 36, .atom_name = (char**) oons_ANY_atom_name, @@ -25,26 +25,26 @@ static struct classifier_residue oons_ANY_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *oons_ARG_atom_name[] = {"NH1", "NE", "CZ", "CD", "NH2", "CG", }; -static double oons_ARG_atom_radius[] = {1.55, 1.55, 2.00, 2.00, 1.55, 2.00, }; -static int oons_ARG_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *oons_ARG_atom_name[] = {"CG", "NH2", "NE", "CZ", "CD", "NH1", }; +static double oons_ARG_atom_radius[] = {2.00, 1.55, 1.55, 2.00, 2.00, 1.55, }; +static int oons_ARG_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue oons_ARG_cfg = { .name = "ARG", .n_atoms = 6, .atom_name = (char**) oons_ARG_atom_name, .atom_radius = (double*) oons_ARG_atom_radius, .atom_class = (freesasa_atom_class*) oons_ARG_atom_class, - .max_area = {.name = "ARG", .total = 228.79, .main_chain = 41.90, .side_chain = 186.89, .polar = 115.26, .apolar = 113.52}, + .max_area = {.name = "ARG", .total = 235.30, .main_chain = 38.31, .side_chain = 196.99, .polar = 125.27, .apolar = 110.03}, }; -static const char *oons_ASN_atom_name[] = {"CG", "ND2", "OD1", }; -static double oons_ASN_atom_radius[] = {1.55, 1.55, 1.40, }; +static const char *oons_ASN_atom_name[] = {"OD1", "CG", "ND2", }; +static double oons_ASN_atom_radius[] = {1.40, 1.55, 1.55, }; static int oons_ASN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue oons_ASN_cfg = { .name = "ASN", .n_atoms = 3, .atom_name = (char**) oons_ASN_atom_name, .atom_radius = (double*) oons_ASN_atom_radius, .atom_class = (freesasa_atom_class*) oons_ASN_atom_class, - .max_area = {.name = "ASN", .total = 136.22, .main_chain = 41.04, .side_chain = 95.18, .polar = 86.37, .apolar = 49.85}, + .max_area = {.name = "ASN", .total = 143.47, .main_chain = 38.26, .side_chain = 105.21, .polar = 97.51, .apolar = 45.97}, }; static const char *oons_ASP_atom_name[] = {"OD2", "CG", "OD1", }; @@ -55,10 +55,10 @@ static struct classifier_residue oons_ASP_cfg = { .atom_name = (char**) oons_ASP_atom_name, .atom_radius = (double*) oons_ASP_atom_radius, .atom_class = (freesasa_atom_class*) oons_ASP_atom_class, - .max_area = {.name = "ASP", .total = 134.24, .main_chain = 41.82, .side_chain = 92.43, .polar = 84.12, .apolar = 50.13}, + .max_area = {.name = "ASP", .total = 141.20, .main_chain = 38.87, .side_chain = 102.33, .polar = 95.17, .apolar = 46.03}, }; -static const char *oons_ASX_atom_name[] = {"AD2", "CG", "XD2", "AD1", "XD1", }; +static const char *oons_ASX_atom_name[] = {"XD2", "CG", "XD1", "AD1", "AD2", }; static double oons_ASX_atom_radius[] = {1.5, 1.55, 1.5, 1.5, 1.5, }; static int oons_ASX_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue oons_ASX_cfg = { @@ -88,10 +88,10 @@ static struct classifier_residue oons_CYS_cfg = { .atom_name = (char**) oons_CYS_atom_name, .atom_radius = (double*) oons_CYS_atom_radius, .atom_class = (freesasa_atom_class*) oons_CYS_atom_class, - .max_area = {.name = "CYS", .total = 132.58, .main_chain = 41.94, .side_chain = 90.64, .polar = 85.30, .apolar = 47.28}, + .max_area = {.name = "CYS", .total = 140.29, .main_chain = 38.44, .side_chain = 101.85, .polar = 98.30, .apolar = 41.99}, }; -static const char *oons_GLN_atom_name[] = {"CD", "CG", "NE2", "OE1", }; +static const char *oons_GLN_atom_name[] = {"NE2", "CG", "CD", "OE1", }; static double oons_GLN_atom_radius[] = {1.55, 2.00, 1.55, 1.40, }; static int oons_GLN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue oons_GLN_cfg = { @@ -99,23 +99,23 @@ static struct classifier_residue oons_GLN_cfg = { .atom_name = (char**) oons_GLN_atom_name, .atom_radius = (double*) oons_GLN_atom_radius, .atom_class = (freesasa_atom_class*) oons_GLN_atom_class, - .max_area = {.name = "GLN", .total = 169.64, .main_chain = 41.90, .side_chain = 127.74, .polar = 115.00, .apolar = 54.64}, + .max_area = {.name = "GLN", .total = 176.23, .main_chain = 38.31, .side_chain = 137.92, .polar = 122.17, .apolar = 54.06}, }; -static const char *oons_GLU_atom_name[] = {"OE1", "OE2", "CG", "CD", }; -static double oons_GLU_atom_radius[] = {1.40, 1.40, 2.00, 1.55, }; -static int oons_GLU_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *oons_GLU_atom_name[] = {"CG", "CD", "OE1", "OE2", }; +static double oons_GLU_atom_radius[] = {2.00, 1.55, 1.40, 1.40, }; +static int oons_GLU_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue oons_GLU_cfg = { .name = "GLU", .n_atoms = 4, .atom_name = (char**) oons_GLU_atom_name, .atom_radius = (double*) oons_GLU_atom_radius, .atom_class = (freesasa_atom_class*) oons_GLU_atom_class, - .max_area = {.name = "GLU", .total = 166.01, .main_chain = 41.93, .side_chain = 124.09, .polar = 108.99, .apolar = 57.02}, + .max_area = {.name = "GLU", .total = 172.43, .main_chain = 38.31, .side_chain = 134.11, .polar = 115.92, .apolar = 56.51}, }; -static const char *oons_GLX_atom_name[] = {"XE2", "CG", "CD", "AE1", "AE2", "XE1", }; -static double oons_GLX_atom_radius[] = {1.5, 2.00, 1.55, 1.5, 1.5, 1.5, }; -static int oons_GLX_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *oons_GLX_atom_name[] = {"XE2", "CD", "CG", "AE2", "XE1", "AE1", }; +static double oons_GLX_atom_radius[] = {1.5, 1.55, 2.00, 1.5, 1.5, 1.5, }; +static int oons_GLX_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue oons_GLX_cfg = { .name = "GLX", .n_atoms = 6, .atom_name = (char**) oons_GLX_atom_name, @@ -124,7 +124,7 @@ static struct classifier_residue oons_GLX_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *oons_HIS_atom_name[] = {"CG", "NE2", "ND1", "CD2", "CE1", }; +static const char *oons_HIS_atom_name[] = {"CD2", "ND1", "NE2", "CE1", "CG", }; static double oons_HIS_atom_radius[] = {1.75, 1.55, 1.55, 1.75, 1.75, }; static int oons_HIS_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue oons_HIS_cfg = { @@ -132,7 +132,7 @@ static struct classifier_residue oons_HIS_cfg = { .atom_name = (char**) oons_HIS_atom_name, .atom_radius = (double*) oons_HIS_atom_radius, .atom_class = (freesasa_atom_class*) oons_HIS_atom_class, - .max_area = {.name = "HIS", .total = 170.73, .main_chain = 41.47, .side_chain = 129.27, .polar = 56.97, .apolar = 113.76}, + .max_area = {.name = "HIS", .total = 180.78, .main_chain = 36.04, .side_chain = 144.74, .polar = 73.26, .apolar = 107.52}, }; static const char *oons_HOH_atom_name[] = {"O", }; @@ -146,7 +146,7 @@ static struct classifier_residue oons_HOH_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *oons_ILE_atom_name[] = {"CG1", "CG2", "CD1", }; +static const char *oons_ILE_atom_name[] = {"CD1", "CG2", "CG1", }; static double oons_ILE_atom_radius[] = {2.00, 2.00, 2.00, }; static int oons_ILE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue oons_ILE_cfg = { @@ -154,10 +154,10 @@ static struct classifier_residue oons_ILE_cfg = { .atom_name = (char**) oons_ILE_atom_name, .atom_radius = (double*) oons_ILE_atom_radius, .atom_class = (freesasa_atom_class*) oons_ILE_atom_class, - .max_area = {.name = "ILE", .total = 173.24, .main_chain = 36.90, .side_chain = 136.34, .polar = 20.58, .apolar = 152.66}, + .max_area = {.name = "ILE", .total = 182.12, .main_chain = 37.96, .side_chain = 144.16, .polar = 31.67, .apolar = 150.45}, }; -static const char *oons_LEU_atom_name[] = {"CD1", "CG", "CD2", }; +static const char *oons_LEU_atom_name[] = {"CG", "CD1", "CD2", }; static double oons_LEU_atom_radius[] = {2.00, 2.00, 2.00, }; static int oons_LEU_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue oons_LEU_cfg = { @@ -165,18 +165,18 @@ static struct classifier_residue oons_LEU_cfg = { .atom_name = (char**) oons_LEU_atom_name, .atom_radius = (double*) oons_LEU_atom_radius, .atom_class = (freesasa_atom_class*) oons_LEU_atom_class, - .max_area = {.name = "LEU", .total = 166.51, .main_chain = 41.95, .side_chain = 124.56, .polar = 25.02, .apolar = 141.50}, + .max_area = {.name = "LEU", .total = 185.43, .main_chain = 35.34, .side_chain = 150.08, .polar = 31.73, .apolar = 153.69}, }; -static const char *oons_LYS_atom_name[] = {"CG", "NZ", "CE", "CD", }; -static double oons_LYS_atom_radius[] = {2.00, 1.55, 2.00, 2.00, }; -static int oons_LYS_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *oons_LYS_atom_name[] = {"CD", "CE", "CG", "NZ", }; +static double oons_LYS_atom_radius[] = {2.00, 2.00, 2.00, 1.55, }; +static int oons_LYS_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue oons_LYS_cfg = { .name = "LYS", .n_atoms = 4, .atom_name = (char**) oons_LYS_atom_name, .atom_radius = (double*) oons_LYS_atom_radius, .atom_class = (freesasa_atom_class*) oons_LYS_atom_class, - .max_area = {.name = "LYS", .total = 197.76, .main_chain = 41.90, .side_chain = 155.86, .polar = 72.37, .apolar = 125.39}, + .max_area = {.name = "LYS", .total = 205.80, .main_chain = 38.31, .side_chain = 167.49, .polar = 78.02, .apolar = 127.78}, }; static const char *oons_MET_atom_name[] = {"SD", "CG", "CE", }; @@ -187,7 +187,7 @@ static struct classifier_residue oons_MET_cfg = { .atom_name = (char**) oons_MET_atom_name, .atom_radius = (double*) oons_MET_atom_radius, .atom_class = (freesasa_atom_class*) oons_MET_atom_class, - .max_area = {.name = "MET", .total = 193.52, .main_chain = 41.88, .side_chain = 151.64, .polar = 71.52, .apolar = 122.00}, + .max_area = {.name = "MET", .total = 201.66, .main_chain = 38.31, .side_chain = 163.35, .polar = 78.68, .apolar = 122.98}, }; static const char *oons_NH2_atom_name[] = {"NH2", }; @@ -201,7 +201,7 @@ static struct classifier_residue oons_NH2_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *oons_PHE_atom_name[] = {"CG", "CE2", "CZ", "CD2", "CD1", "CE1", }; +static const char *oons_PHE_atom_name[] = {"CD2", "CE2", "CG", "CE1", "CD1", "CZ", }; static double oons_PHE_atom_radius[] = {1.75, 1.75, 1.75, 1.75, 1.75, 1.75, }; static int oons_PHE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue oons_PHE_cfg = { @@ -209,10 +209,10 @@ static struct classifier_residue oons_PHE_cfg = { .atom_name = (char**) oons_PHE_atom_name, .atom_radius = (double*) oons_PHE_atom_radius, .atom_class = (freesasa_atom_class*) oons_PHE_atom_class, - .max_area = {.name = "PHE", .total = 192.02, .main_chain = 40.38, .side_chain = 151.64, .polar = 25.21, .apolar = 166.81}, + .max_area = {.name = "PHE", .total = 199.28, .main_chain = 35.20, .side_chain = 164.08, .polar = 30.08, .apolar = 169.20}, }; -static const char *oons_PRO_atom_name[] = {"CG", "CB", "CD", }; +static const char *oons_PRO_atom_name[] = {"CB", "CD", "CG", }; static double oons_PRO_atom_radius[] = {1.75, 1.75, 1.75, }; static int oons_PRO_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue oons_PRO_cfg = { @@ -220,12 +220,12 @@ static struct classifier_residue oons_PRO_cfg = { .atom_name = (char**) oons_PRO_atom_name, .atom_radius = (double*) oons_PRO_atom_radius, .atom_class = (freesasa_atom_class*) oons_PRO_atom_class, - .max_area = {.name = "PRO", .total = 123.92, .main_chain = 33.48, .side_chain = 90.44, .polar = 14.54, .apolar = 109.38}, + .max_area = {.name = "PRO", .total = 128.18, .main_chain = 31.08, .side_chain = 97.10, .polar = 13.95, .apolar = 114.23}, }; -static const char *oons_PYL_atom_name[] = {"CG", "CD2", "CB2", "CE", "CD", "O2", "N2", "CG2", "NZ", "CE2", "CA2", "C2", }; -static double oons_PYL_atom_radius[] = {2.00, 1.75, 2.00, 2.00, 2.00, 1.40, 1.55, 1.75, 1.55, 1.75, 1.75, 1.55, }; -static int oons_PYL_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *oons_PYL_atom_name[] = {"C2", "O2", "N2", "CA2", "CD2", "CD", "CE", "CG", "CE2", "NZ", "CG2", "CB2", }; +static double oons_PYL_atom_radius[] = {1.55, 1.40, 1.55, 1.75, 1.75, 2.00, 2.00, 2.00, 1.75, 1.55, 1.75, 2.00, }; +static int oons_PYL_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue oons_PYL_cfg = { .name = "PYL", .n_atoms = 12, .atom_name = (char**) oons_PYL_atom_name, @@ -253,40 +253,40 @@ static struct classifier_residue oons_SER_cfg = { .atom_name = (char**) oons_SER_atom_name, .atom_radius = (double*) oons_SER_atom_radius, .atom_class = (freesasa_atom_class*) oons_SER_atom_class, - .max_area = {.name = "SER", .total = 111.52, .main_chain = 43.53, .side_chain = 67.99, .polar = 48.36, .apolar = 63.16}, + .max_area = {.name = "SER", .total = 118.43, .main_chain = 40.20, .side_chain = 78.23, .polar = 60.41, .apolar = 58.02}, }; -static const char *oons_THR_atom_name[] = {"CG2", "OG1", }; -static double oons_THR_atom_radius[] = {2.00, 1.40, }; -static int oons_THR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *oons_THR_atom_name[] = {"OG1", "CG2", }; +static double oons_THR_atom_radius[] = {1.40, 2.00, }; +static int oons_THR_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue oons_THR_cfg = { .name = "THR", .n_atoms = 2, .atom_name = (char**) oons_THR_atom_name, .atom_radius = (double*) oons_THR_atom_radius, .atom_class = (freesasa_atom_class*) oons_THR_atom_class, - .max_area = {.name = "THR", .total = 135.14, .main_chain = 38.84, .side_chain = 96.29, .polar = 41.22, .apolar = 93.91}, + .max_area = {.name = "THR", .total = 142.41, .main_chain = 38.32, .side_chain = 104.08, .polar = 56.42, .apolar = 85.99}, }; -static const char *oons_TRP_atom_name[] = {"CG", "CZ3", "CD2", "CZ2", "CD1", "CH2", "CE2", "CE3", "NE1", }; -static double oons_TRP_atom_radius[] = {1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.55, }; -static int oons_TRP_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *oons_TRP_atom_name[] = {"CD2", "CZ2", "NE1", "CD1", "CG", "CE2", "CH2", "CE3", "CZ3", }; +static double oons_TRP_atom_radius[] = {1.75, 1.75, 1.55, 1.75, 1.75, 1.75, 1.75, 1.75, 1.75, }; +static int oons_TRP_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue oons_TRP_cfg = { .name = "TRP", .n_atoms = 9, .atom_name = (char**) oons_TRP_atom_name, .atom_radius = (double*) oons_TRP_atom_radius, .atom_class = (freesasa_atom_class*) oons_TRP_atom_class, - .max_area = {.name = "TRP", .total = 222.80, .main_chain = 37.17, .side_chain = 185.63, .polar = 50.57, .apolar = 172.24}, + .max_area = {.name = "TRP", .total = 247.08, .main_chain = 39.43, .side_chain = 207.65, .polar = 52.90, .apolar = 194.18}, }; -static const char *oons_TYR_atom_name[] = {"CD2", "OH", "CE2", "CZ", "CG", "CE1", "CD1", }; -static double oons_TYR_atom_radius[] = {1.75, 1.40, 1.75, 1.75, 1.75, 1.75, 1.75, }; -static int oons_TYR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *oons_TYR_atom_name[] = {"CZ", "CG", "CE1", "CD1", "CE2", "CD2", "OH", }; +static double oons_TYR_atom_radius[] = {1.75, 1.75, 1.75, 1.75, 1.75, 1.75, 1.40, }; +static int oons_TYR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue oons_TYR_cfg = { .name = "TYR", .n_atoms = 7, .atom_name = (char**) oons_TYR_atom_name, .atom_radius = (double*) oons_TYR_atom_radius, .atom_class = (freesasa_atom_class*) oons_TYR_atom_class, - .max_area = {.name = "TYR", .total = 205.21, .main_chain = 40.35, .side_chain = 164.86, .polar = 67.42, .apolar = 137.79}, + .max_area = {.name = "TYR", .total = 212.31, .main_chain = 35.20, .side_chain = 177.11, .polar = 72.41, .apolar = 139.90}, }; static const char *oons_VAL_atom_name[] = {"CG2", "CG1", }; @@ -297,7 +297,7 @@ static struct classifier_residue oons_VAL_cfg = { .atom_name = (char**) oons_VAL_atom_name, .atom_radius = (double*) oons_VAL_atom_radius, .atom_class = (freesasa_atom_class*) oons_VAL_atom_class, - .max_area = {.name = "VAL", .total = 151.66, .main_chain = 40.79, .side_chain = 110.87, .polar = 25.21, .apolar = 126.45}, + .max_area = {.name = "VAL", .total = 157.64, .main_chain = 37.96, .side_chain = 119.68, .polar = 31.70, .apolar = 125.94}, }; static struct classifier_residue *oons_residue_cfg[] = { diff --git a/src/classifier_protor.c b/src/classifier_protor.c index 8a5b8200..5d9adb9a 100644 --- a/src/classifier_protor.c +++ b/src/classifier_protor.c @@ -3,9 +3,9 @@ /* Autogenerated code from the script config2c.pl */ static const char *protor_residue_name[] = {"A", "ACE", "ALA", "ARG", "ASN", "ASP", "ASX", "C", "CYS", "DA", "DC", "DG", "DI", "DT", "DU", "G", "GLN", "GLU", "GLX", "GLY", "HIS", "HOH", "I", "ILE", "LEU", "LYS", "MET", "NH2", "PHE", "PRO", "PYL", "SEC", "SER", "T", "THR", "TRP", "TYR", "U", "VAL", }; -static const char *protor_A_atom_name[] = {"C5'", "O2'", "OP1", "N6", "O4'", "N9", "C3'", "N3", "OP3", "C2'", "C6", "P", "N1", "OP2", "N7", "C8", "C4'", "C2", "C5", "C1'", "O5'", "C4", "O3'", }; -static double protor_A_atom_radius[] = {1.88, 1.46, 1.42, 1.64, 1.46, 1.64, 1.88, 1.64, 1.46, 1.88, 1.61, 1.8, 1.64, 1.46, 1.64, 1.76, 1.88, 1.76, 1.61, 1.88, 1.46, 1.61, 1.46, }; -static int protor_A_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_A_atom_name[] = {"N6", "C5", "O5'", "C2", "P", "C4", "OP2", "C3'", "N1", "C4'", "C2'", "C8", "C5'", "N7", "O3'", "C6", "N9", "OP1", "C1'", "N3", "OP3", "O2'", "O4'", }; +static double protor_A_atom_radius[] = {1.64, 1.61, 1.46, 1.76, 1.8, 1.61, 1.46, 1.88, 1.64, 1.88, 1.88, 1.76, 1.88, 1.64, 1.46, 1.61, 1.64, 1.42, 1.88, 1.64, 1.46, 1.46, 1.46, }; +static int protor_A_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_A_cfg = { .name = "A", .n_atoms = 23, .atom_name = (char**) protor_A_atom_name, @@ -14,9 +14,9 @@ static struct classifier_residue protor_A_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_ACE_atom_name[] = {"CH3", "C", "O", }; -static double protor_ACE_atom_radius[] = {1.88, 1.76, 1.42, }; -static int protor_ACE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_ACE_atom_name[] = {"CH3", "O", "C", }; +static double protor_ACE_atom_radius[] = {1.88, 1.42, 1.76, }; +static int protor_ACE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_ACE_cfg = { .name = "ACE", .n_atoms = 3, .atom_name = (char**) protor_ACE_atom_name, @@ -25,53 +25,53 @@ static struct classifier_residue protor_ACE_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_ALA_atom_name[] = {"OXT", "O", "CB", "N", "C", "CA", }; -static double protor_ALA_atom_radius[] = {1.46, 1.42, 1.88, 1.64, 1.61, 1.88, }; -static int protor_ALA_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_ALA_atom_name[] = {"OXT", "CA", "N", "O", "C", "CB", }; +static double protor_ALA_atom_radius[] = {1.46, 1.88, 1.64, 1.42, 1.61, 1.88, }; +static int protor_ALA_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_ALA_cfg = { .name = "ALA", .n_atoms = 6, .atom_name = (char**) protor_ALA_atom_name, .atom_radius = (double*) protor_ALA_atom_radius, .atom_class = (freesasa_atom_class*) protor_ALA_atom_class, - .max_area = {.name = "ALA", .total = 103.10, .main_chain = 46.51, .side_chain = 56.60, .polar = 29.89, .apolar = 73.21}, + .max_area = {.name = "ALA", .total = 108.76, .main_chain = 43.96, .side_chain = 64.80, .polar = 37.75, .apolar = 71.01}, }; -static const char *protor_ARG_atom_name[] = {"CA", "N", "CG", "C", "CZ", "O", "NH1", "NH2", "CD", "NE", "OXT", "CB", }; -static double protor_ARG_atom_radius[] = {1.88, 1.64, 1.88, 1.61, 1.61, 1.42, 1.64, 1.64, 1.88, 1.64, 1.46, 1.88, }; -static int protor_ARG_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_ARG_atom_name[] = {"CG", "CA", "NE", "NH2", "NH1", "N", "OXT", "CZ", "CD", "C", "CB", "O", }; +static double protor_ARG_atom_radius[] = {1.88, 1.88, 1.64, 1.64, 1.64, 1.64, 1.46, 1.61, 1.88, 1.61, 1.88, 1.42, }; +static int protor_ARG_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_ARG_cfg = { .name = "ARG", .n_atoms = 12, .atom_name = (char**) protor_ARG_atom_name, .atom_radius = (double*) protor_ARG_atom_radius, .atom_class = (freesasa_atom_class*) protor_ARG_atom_class, - .max_area = {.name = "ARG", .total = 231.99, .main_chain = 45.09, .side_chain = 186.90, .polar = 153.92, .apolar = 78.07}, + .max_area = {.name = "ARG", .total = 238.17, .main_chain = 42.00, .side_chain = 196.17, .polar = 165.00, .apolar = 73.17}, }; -static const char *protor_ASN_atom_name[] = {"ND2", "O", "OD1", "N", "CG", "C", "CA", "CB", "OXT", }; -static double protor_ASN_atom_radius[] = {1.64, 1.42, 1.42, 1.64, 1.61, 1.61, 1.88, 1.88, 1.46, }; -static int protor_ASN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_ASN_atom_name[] = {"OD1", "CG", "CA", "C", "CB", "O", "N", "OXT", "ND2", }; +static double protor_ASN_atom_radius[] = {1.42, 1.61, 1.88, 1.61, 1.88, 1.42, 1.64, 1.46, 1.64, }; +static int protor_ASN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_ASN_cfg = { .name = "ASN", .n_atoms = 9, .atom_name = (char**) protor_ASN_atom_name, .atom_radius = (double*) protor_ASN_atom_radius, .atom_class = (freesasa_atom_class*) protor_ASN_atom_class, - .max_area = {.name = "ASN", .total = 138.45, .main_chain = 43.80, .side_chain = 94.65, .polar = 93.13, .apolar = 45.32}, + .max_area = {.name = "ASN", .total = 145.01, .main_chain = 41.53, .side_chain = 103.48, .polar = 103.46, .apolar = 41.55}, }; -static const char *protor_ASP_atom_name[] = {"CB", "OXT", "O", "OD1", "OD2", "CG", "C", "N", "CA", }; -static double protor_ASP_atom_radius[] = {1.88, 1.46, 1.42, 1.42, 1.46, 1.61, 1.61, 1.64, 1.88, }; -static int protor_ASP_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_ASP_atom_name[] = {"CG", "CA", "OD1", "OD2", "N", "OXT", "C", "CB", "O", }; +static double protor_ASP_atom_radius[] = {1.61, 1.88, 1.42, 1.46, 1.64, 1.46, 1.61, 1.88, 1.42, }; +static int protor_ASP_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_ASP_cfg = { .name = "ASP", .n_atoms = 9, .atom_name = (char**) protor_ASP_atom_name, .atom_radius = (double*) protor_ASP_atom_radius, .atom_class = (freesasa_atom_class*) protor_ASP_atom_class, - .max_area = {.name = "ASP", .total = 135.76, .main_chain = 44.65, .side_chain = 91.11, .polar = 88.93, .apolar = 46.83}, + .max_area = {.name = "ASP", .total = 142.76, .main_chain = 42.29, .side_chain = 100.47, .polar = 100.27, .apolar = 42.49}, }; -static const char *protor_ASX_atom_name[] = {"CG", "C", "N", "CA", "XD1", "XD2", "O", "CB", "OXT", }; -static double protor_ASX_atom_radius[] = {1.61, 1.61, 1.64, 1.88, 1.5, 1.5, 1.42, 1.88, 1.46, }; -static int protor_ASX_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_ASX_atom_name[] = {"XD2", "CA", "CG", "XD1", "OXT", "N", "O", "C", "CB", }; +static double protor_ASX_atom_radius[] = {1.5, 1.88, 1.61, 1.5, 1.46, 1.64, 1.42, 1.61, 1.88, }; +static int protor_ASX_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_ASX_cfg = { .name = "ASX", .n_atoms = 9, .atom_name = (char**) protor_ASX_atom_name, @@ -80,9 +80,9 @@ static struct classifier_residue protor_ASX_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_C_atom_name[] = {"C1'", "O2", "C5", "C4", "O3'", "O5'", "OP2", "C4'", "C2", "C2'", "P", "N1", "C6", "O2'", "C5'", "N4", "OP3", "N3", "C3'", "O4'", "OP1", }; -static double protor_C_atom_radius[] = {1.88, 1.42, 1.76, 1.61, 1.46, 1.46, 1.46, 1.88, 1.61, 1.88, 1.8, 1.64, 1.76, 1.46, 1.88, 1.64, 1.46, 1.64, 1.88, 1.46, 1.42, }; -static int protor_C_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_C_atom_name[] = {"C5", "P", "O2", "C2", "O5'", "C3'", "OP2", "C4", "C2'", "N4", "C4'", "N1", "O3'", "C5'", "C1'", "OP1", "C6", "N3", "O4'", "OP3", "O2'", }; +static double protor_C_atom_radius[] = {1.76, 1.8, 1.42, 1.61, 1.46, 1.88, 1.46, 1.61, 1.88, 1.64, 1.88, 1.64, 1.46, 1.88, 1.88, 1.42, 1.76, 1.64, 1.46, 1.46, 1.46, }; +static int protor_C_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_C_cfg = { .name = "C", .n_atoms = 21, .atom_name = (char**) protor_C_atom_name, @@ -91,20 +91,20 @@ static struct classifier_residue protor_C_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_CYS_atom_name[] = {"OXT", "O", "CB", "CA", "SG", "N", "C", }; -static double protor_CYS_atom_radius[] = {1.46, 1.42, 1.88, 1.88, 1.77, 1.64, 1.61, }; +static const char *protor_CYS_atom_name[] = {"O", "SG", "C", "CB", "OXT", "N", "CA", }; +static double protor_CYS_atom_radius[] = {1.42, 1.77, 1.61, 1.88, 1.46, 1.64, 1.88, }; static int protor_CYS_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_CYS_cfg = { .name = "CYS", .n_atoms = 7, .atom_name = (char**) protor_CYS_atom_name, .atom_radius = (double*) protor_CYS_atom_radius, .atom_class = (freesasa_atom_class*) protor_CYS_atom_class, - .max_area = {.name = "CYS", .total = 125.02, .main_chain = 45.47, .side_chain = 79.55, .polar = 79.68, .apolar = 45.33}, + .max_area = {.name = "CYS", .total = 132.20, .main_chain = 42.55, .side_chain = 89.66, .polar = 92.74, .apolar = 39.47}, }; -static const char *protor_DA_atom_name[] = {"OP2", "N7", "C8", "C4'", "C2", "C5", "C1'", "O5'", "O3'", "C4", "C5'", "OP1", "N6", "O4'", "N9", "N3", "C3'", "OP3", "C2'", "C6", "P", "N1", }; -static double protor_DA_atom_radius[] = {1.46, 1.64, 1.76, 1.88, 1.76, 1.61, 1.88, 1.46, 1.46, 1.61, 1.88, 1.42, 1.64, 1.46, 1.64, 1.64, 1.88, 1.46, 1.88, 1.61, 1.8, 1.64, }; -static int protor_DA_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_DA_atom_name[] = {"C1'", "N9", "C6", "OP1", "O3'", "N7", "C5'", "C8", "O4'", "OP3", "N3", "P", "C2", "O5'", "N6", "C5", "C4'", "C2'", "N1", "C3'", "OP2", "C4", }; +static double protor_DA_atom_radius[] = {1.88, 1.64, 1.61, 1.42, 1.46, 1.64, 1.88, 1.76, 1.46, 1.46, 1.64, 1.8, 1.76, 1.46, 1.64, 1.61, 1.88, 1.88, 1.64, 1.88, 1.46, 1.61, }; +static int protor_DA_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_DA_cfg = { .name = "DA", .n_atoms = 22, .atom_name = (char**) protor_DA_atom_name, @@ -113,9 +113,9 @@ static struct classifier_residue protor_DA_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_DC_atom_name[] = {"C2", "C4'", "OP2", "O5'", "C4", "O3'", "C5", "C1'", "O2", "OP1", "O4'", "C3'", "N3", "OP3", "N4", "C5'", "C6", "P", "N1", "C2'", }; -static double protor_DC_atom_radius[] = {1.61, 1.88, 1.46, 1.46, 1.61, 1.46, 1.76, 1.88, 1.42, 1.42, 1.46, 1.88, 1.64, 1.46, 1.64, 1.88, 1.76, 1.8, 1.64, 1.88, }; -static int protor_DC_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_DC_atom_name[] = {"OP3", "O4'", "N3", "C6", "OP1", "C1'", "C5'", "O3'", "N1", "N4", "C4'", "C2'", "C4", "OP2", "C3'", "O5'", "C2", "O2", "P", "C5", }; +static double protor_DC_atom_radius[] = {1.46, 1.46, 1.64, 1.76, 1.42, 1.88, 1.88, 1.46, 1.64, 1.64, 1.88, 1.88, 1.61, 1.46, 1.88, 1.46, 1.61, 1.42, 1.8, 1.76, }; +static int protor_DC_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_DC_cfg = { .name = "DC", .n_atoms = 20, .atom_name = (char**) protor_DC_atom_name, @@ -124,9 +124,9 @@ static struct classifier_residue protor_DC_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_DG_atom_name[] = {"O5'", "C4", "O3'", "N2", "C5", "C1'", "N7", "C8", "C4'", "C2", "OP2", "C6", "N1", "P", "C2'", "OP1", "O4'", "N9", "N3", "C3'", "OP3", "C5'", "O6", }; -static double protor_DG_atom_radius[] = {1.46, 1.61, 1.46, 1.64, 1.61, 1.88, 1.64, 1.76, 1.88, 1.61, 1.46, 1.61, 1.64, 1.8, 1.88, 1.42, 1.46, 1.64, 1.64, 1.88, 1.46, 1.88, 1.42, }; -static int protor_DG_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_DG_atom_name[] = {"C1'", "OP1", "O6", "C6", "N9", "C5'", "C8", "O3'", "N7", "N2", "OP3", "O4'", "N3", "O5'", "P", "C2", "C5", "N1", "C2'", "C4'", "C4", "C3'", "OP2", }; +static double protor_DG_atom_radius[] = {1.88, 1.42, 1.42, 1.61, 1.64, 1.88, 1.76, 1.46, 1.64, 1.64, 1.46, 1.46, 1.64, 1.46, 1.8, 1.61, 1.61, 1.64, 1.88, 1.88, 1.61, 1.88, 1.46, }; +static int protor_DG_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_DG_cfg = { .name = "DG", .n_atoms = 23, .atom_name = (char**) protor_DG_atom_name, @@ -135,9 +135,9 @@ static struct classifier_residue protor_DG_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_DI_atom_name[] = {"O5'", "C4", "O3'", "C5", "C1'", "N7", "C2", "C4'", "C8", "OP2", "N1", "P", "C6", "C2'", "N9", "O4'", "OP1", "OP3", "N3", "C3'", "O6", "C5'", }; -static double protor_DI_atom_radius[] = {1.46, 1.61, 1.46, 1.61, 1.88, 1.64, 1.76, 1.88, 1.76, 1.46, 1.64, 1.8, 1.61, 1.88, 1.64, 1.46, 1.42, 1.46, 1.64, 1.88, 1.42, 1.88, }; -static int protor_DI_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_DI_atom_name[] = {"N7", "O3'", "C5'", "C8", "C1'", "C6", "O6", "N9", "OP1", "N3", "O4'", "OP3", "C5", "P", "C2", "O5'", "C3'", "OP2", "C4", "C4'", "C2'", "N1", }; +static double protor_DI_atom_radius[] = {1.64, 1.46, 1.88, 1.76, 1.88, 1.61, 1.42, 1.64, 1.42, 1.64, 1.46, 1.46, 1.61, 1.8, 1.76, 1.46, 1.88, 1.46, 1.61, 1.88, 1.88, 1.64, }; +static int protor_DI_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_DI_cfg = { .name = "DI", .n_atoms = 22, .atom_name = (char**) protor_DI_atom_name, @@ -146,9 +146,9 @@ static struct classifier_residue protor_DI_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_DT_atom_name[] = {"C6", "P", "N1", "C7", "C2'", "OP1", "O4'", "N3", "C3'", "OP3", "C5'", "O5'", "O4", "C4", "O3'", "C5", "O2", "C1'", "C4'", "C2", "OP2", }; -static double protor_DT_atom_radius[] = {1.76, 1.8, 1.64, 1.88, 1.88, 1.42, 1.46, 1.64, 1.88, 1.46, 1.88, 1.46, 1.42, 1.61, 1.46, 1.61, 1.42, 1.88, 1.88, 1.61, 1.46, }; -static int protor_DT_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_DT_atom_name[] = {"C4'", "C2'", "N1", "C3'", "OP2", "C4", "P", "O2", "C2", "O5'", "C5", "O4'", "C7", "OP3", "N3", "O4", "C1'", "C6", "OP1", "O3'", "C5'", }; +static double protor_DT_atom_radius[] = {1.88, 1.88, 1.64, 1.88, 1.46, 1.61, 1.8, 1.42, 1.61, 1.46, 1.61, 1.46, 1.88, 1.46, 1.64, 1.42, 1.88, 1.76, 1.42, 1.46, 1.88, }; +static int protor_DT_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_DT_cfg = { .name = "DT", .n_atoms = 21, .atom_name = (char**) protor_DT_atom_name, @@ -157,9 +157,9 @@ static struct classifier_residue protor_DT_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_DU_atom_name[] = {"OP3", "C3'", "N3", "O4'", "OP1", "C5'", "P", "N1", "C6", "C2'", "C2", "C4'", "OP2", "O3'", "C4", "O4", "O5'", "O2", "C1'", "C5", }; -static double protor_DU_atom_radius[] = {1.46, 1.88, 1.64, 1.46, 1.42, 1.88, 1.8, 1.64, 1.76, 1.88, 1.61, 1.88, 1.46, 1.46, 1.61, 1.42, 1.46, 1.42, 1.88, 1.76, }; -static int protor_DU_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_DU_atom_name[] = {"O5'", "P", "O2", "C2", "C5", "N1", "C2'", "C4'", "C4", "C3'", "OP2", "C1'", "O4", "C6", "OP1", "C5'", "O3'", "OP3", "O4'", "N3", }; +static double protor_DU_atom_radius[] = {1.46, 1.8, 1.42, 1.61, 1.76, 1.64, 1.88, 1.88, 1.61, 1.88, 1.46, 1.88, 1.42, 1.76, 1.42, 1.88, 1.46, 1.46, 1.46, 1.64, }; +static int protor_DU_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_DU_cfg = { .name = "DU", .n_atoms = 20, .atom_name = (char**) protor_DU_atom_name, @@ -168,9 +168,9 @@ static struct classifier_residue protor_DU_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_G_atom_name[] = {"C1'", "C5", "N2", "C4", "O3'", "O5'", "OP2", "C8", "C2", "C4'", "N7", "C2'", "C6", "N1", "P", "O2'", "O6", "C5'", "N3", "C3'", "OP3", "OP1", "N9", "O4'", }; -static double protor_G_atom_radius[] = {1.88, 1.61, 1.64, 1.61, 1.46, 1.46, 1.46, 1.76, 1.61, 1.88, 1.64, 1.88, 1.61, 1.64, 1.8, 1.46, 1.42, 1.88, 1.64, 1.88, 1.46, 1.42, 1.64, 1.46, }; -static int protor_G_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_G_atom_name[] = {"O4'", "N2", "O2'", "OP3", "N3", "C1'", "C6", "O6", "N9", "OP1", "N7", "O3'", "C5'", "C8", "C2'", "C4'", "N1", "C3'", "OP2", "C4", "P", "C2", "O5'", "C5", }; +static double protor_G_atom_radius[] = {1.46, 1.64, 1.46, 1.46, 1.64, 1.88, 1.61, 1.42, 1.64, 1.42, 1.64, 1.46, 1.88, 1.76, 1.88, 1.88, 1.64, 1.88, 1.46, 1.61, 1.8, 1.61, 1.46, 1.61, }; +static int protor_G_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_G_cfg = { .name = "G", .n_atoms = 24, .atom_name = (char**) protor_G_atom_name, @@ -179,31 +179,31 @@ static struct classifier_residue protor_G_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_GLN_atom_name[] = {"O", "NE2", "CA", "C", "CG", "N", "CB", "OXT", "CD", "OE1", }; -static double protor_GLN_atom_radius[] = {1.42, 1.64, 1.88, 1.61, 1.88, 1.64, 1.88, 1.46, 1.61, 1.42, }; -static int protor_GLN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_GLN_atom_name[] = {"N", "CD", "OXT", "C", "CB", "OE1", "O", "CA", "CG", "NE2", }; +static double protor_GLN_atom_radius[] = {1.64, 1.61, 1.46, 1.61, 1.88, 1.42, 1.42, 1.88, 1.88, 1.64, }; +static int protor_GLN_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_GLN_cfg = { .name = "GLN", .n_atoms = 10, .atom_name = (char**) protor_GLN_atom_name, .atom_radius = (double*) protor_GLN_atom_radius, .atom_class = (freesasa_atom_class*) protor_GLN_atom_class, - .max_area = {.name = "GLN", .total = 172.69, .main_chain = 45.09, .side_chain = 127.60, .polar = 123.13, .apolar = 49.56}, + .max_area = {.name = "GLN", .total = 178.83, .main_chain = 42.00, .side_chain = 136.83, .polar = 131.85, .apolar = 46.98}, }; -static const char *protor_GLU_atom_name[] = {"CB", "OXT", "OE2", "CD", "OE1", "O", "C", "CG", "N", "CA", }; -static double protor_GLU_atom_radius[] = {1.88, 1.46, 1.46, 1.61, 1.42, 1.42, 1.61, 1.88, 1.64, 1.88, }; -static int protor_GLU_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_GLU_atom_name[] = {"OE2", "CG", "CA", "OE1", "O", "C", "CB", "CD", "OXT", "N", }; +static double protor_GLU_atom_radius[] = {1.46, 1.88, 1.88, 1.42, 1.42, 1.61, 1.88, 1.61, 1.46, 1.64, }; +static int protor_GLU_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_GLU_cfg = { .name = "GLU", .n_atoms = 10, .atom_name = (char**) protor_GLU_atom_name, .atom_radius = (double*) protor_GLU_atom_radius, .atom_class = (freesasa_atom_class*) protor_GLU_atom_class, - .max_area = {.name = "GLU", .total = 167.95, .main_chain = 45.12, .side_chain = 122.83, .polar = 113.74, .apolar = 54.21}, + .max_area = {.name = "GLU", .total = 174.18, .main_chain = 42.00, .side_chain = 132.18, .polar = 122.48, .apolar = 51.70}, }; -static const char *protor_GLX_atom_name[] = {"XE2", "OXT", "CB", "CD", "XE1", "O", "CG", "N", "C", "CA", }; -static double protor_GLX_atom_radius[] = {1.5, 1.46, 1.88, 1.61, 1.5, 1.42, 1.88, 1.64, 1.61, 1.88, }; -static int protor_GLX_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_GLX_atom_name[] = {"CG", "CA", "N", "OXT", "CD", "XE1", "C", "CB", "O", "XE2", }; +static double protor_GLX_atom_radius[] = {1.88, 1.88, 1.64, 1.46, 1.61, 1.5, 1.61, 1.88, 1.42, 1.5, }; +static int protor_GLX_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_GLX_cfg = { .name = "GLX", .n_atoms = 10, .atom_name = (char**) protor_GLX_atom_name, @@ -212,26 +212,26 @@ static struct classifier_residue protor_GLX_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_GLY_atom_name[] = {"OXT", "O", "CA", "C", "N", }; -static double protor_GLY_atom_radius[] = {1.46, 1.42, 1.88, 1.61, 1.64, }; -static int protor_GLY_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_GLY_atom_name[] = {"CA", "N", "OXT", "C", "O", }; +static double protor_GLY_atom_radius[] = {1.88, 1.64, 1.46, 1.61, 1.42, }; +static int protor_GLY_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_GLY_cfg = { .name = "GLY", .n_atoms = 5, .atom_name = (char**) protor_GLY_atom_name, .atom_radius = (double*) protor_GLY_atom_radius, .atom_class = (freesasa_atom_class*) protor_GLY_atom_class, - .max_area = {.name = "GLY", .total = 71.84, .main_chain = 71.84, .side_chain = 0.00, .polar = 31.58, .apolar = 40.26}, + .max_area = {.name = "GLY", .total = 81.09, .main_chain = 81.09, .side_chain = 0.00, .polar = 44.65, .apolar = 36.44}, }; -static const char *protor_HIS_atom_name[] = {"ND1", "NE2", "O", "N", "CG", "C", "CA", "CD2", "OXT", "CB", "CE1", }; -static double protor_HIS_atom_radius[] = {1.64, 1.64, 1.42, 1.64, 1.61, 1.61, 1.88, 1.76, 1.46, 1.88, 1.76, }; -static int protor_HIS_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_HIS_atom_name[] = {"N", "ND1", "OXT", "CE1", "C", "CB", "O", "CA", "CG", "CD2", "NE2", }; +static double protor_HIS_atom_radius[] = {1.64, 1.64, 1.46, 1.76, 1.61, 1.88, 1.42, 1.88, 1.61, 1.76, 1.64, }; +static int protor_HIS_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_HIS_cfg = { .name = "HIS", .n_atoms = 11, .atom_name = (char**) protor_HIS_atom_name, .atom_radius = (double*) protor_HIS_atom_radius, .atom_class = (freesasa_atom_class*) protor_HIS_atom_class, - .max_area = {.name = "HIS", .total = 173.43, .main_chain = 44.26, .side_chain = 129.18, .polar = 69.25, .apolar = 104.18}, + .max_area = {.name = "HIS", .total = 182.97, .main_chain = 39.09, .side_chain = 143.87, .polar = 85.94, .apolar = 97.03}, }; static const char *protor_HOH_atom_name[] = {"O", }; @@ -245,9 +245,9 @@ static struct classifier_residue protor_HOH_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_I_atom_name[] = {"O5'", "O3'", "C4", "C5", "C1'", "N7", "C8", "C2", "C4'", "OP2", "C6", "P", "N1", "C2'", "OP1", "O4'", "N9", "C3'", "N3", "OP3", "O6", "C5'", "O2'", }; -static double protor_I_atom_radius[] = {1.46, 1.46, 1.61, 1.61, 1.88, 1.64, 1.76, 1.76, 1.88, 1.46, 1.61, 1.8, 1.64, 1.88, 1.42, 1.46, 1.64, 1.88, 1.64, 1.46, 1.42, 1.88, 1.46, }; -static int protor_I_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_I_atom_name[] = {"O5'", "C2", "P", "C5", "N1", "C4'", "C2'", "C4", "OP2", "C3'", "C6", "O6", "N9", "OP1", "C1'", "C8", "C5'", "N7", "O3'", "O2'", "OP3", "O4'", "N3", }; +static double protor_I_atom_radius[] = {1.46, 1.76, 1.8, 1.61, 1.64, 1.88, 1.88, 1.61, 1.46, 1.88, 1.61, 1.42, 1.64, 1.42, 1.88, 1.76, 1.88, 1.64, 1.46, 1.46, 1.46, 1.46, 1.64, }; +static int protor_I_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_I_cfg = { .name = "I", .n_atoms = 23, .atom_name = (char**) protor_I_atom_name, @@ -256,48 +256,48 @@ static struct classifier_residue protor_I_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_ILE_atom_name[] = {"C", "N", "CA", "O", "CD1", "CG1", "CB", "OXT", "CG2", }; -static double protor_ILE_atom_radius[] = {1.61, 1.64, 1.88, 1.42, 1.88, 1.88, 1.88, 1.46, 1.88, }; -static int protor_ILE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_ILE_atom_name[] = {"CB", "C", "O", "N", "OXT", "CD1", "CG1", "CG2", "CA", }; +static double protor_ILE_atom_radius[] = {1.88, 1.61, 1.42, 1.64, 1.46, 1.88, 1.88, 1.88, 1.88, }; +static int protor_ILE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_ILE_cfg = { .name = "ILE", .n_atoms = 9, .atom_name = (char**) protor_ILE_atom_name, .atom_radius = (double*) protor_ILE_atom_radius, .atom_class = (freesasa_atom_class*) protor_ILE_atom_class, - .max_area = {.name = "ILE", .total = 167.30, .main_chain = 39.09, .side_chain = 128.22, .polar = 24.70, .apolar = 142.60}, + .max_area = {.name = "ILE", .total = 175.73, .main_chain = 41.49, .side_chain = 134.23, .polar = 36.85, .apolar = 138.87}, }; -static const char *protor_LEU_atom_name[] = {"CG", "C", "N", "CD2", "CA", "O", "CD1", "OXT", "CB", }; -static double protor_LEU_atom_radius[] = {1.88, 1.61, 1.64, 1.88, 1.88, 1.42, 1.88, 1.46, 1.88, }; -static int protor_LEU_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_LEU_atom_name[] = {"CG", "CA", "CD2", "N", "CD1", "OXT", "C", "CB", "O", }; +static double protor_LEU_atom_radius[] = {1.88, 1.88, 1.88, 1.64, 1.88, 1.46, 1.61, 1.88, 1.42, }; +static int protor_LEU_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_LEU_cfg = { .name = "LEU", .n_atoms = 9, .atom_name = (char**) protor_LEU_atom_name, .atom_radius = (double*) protor_LEU_atom_radius, .atom_class = (freesasa_atom_class*) protor_LEU_atom_class, - .max_area = {.name = "LEU", .total = 160.87, .main_chain = 44.85, .side_chain = 116.01, .polar = 29.89, .apolar = 130.98}, + .max_area = {.name = "LEU", .total = 179.56, .main_chain = 39.78, .side_chain = 139.78, .polar = 37.16, .apolar = 142.39}, }; -static const char *protor_LYS_atom_name[] = {"CD", "NZ", "CB", "OXT", "CA", "C", "CG", "N", "O", "CE", }; -static double protor_LYS_atom_radius[] = {1.88, 1.64, 1.88, 1.46, 1.88, 1.61, 1.88, 1.64, 1.42, 1.88, }; -static int protor_LYS_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_LYS_atom_name[] = {"CD", "OXT", "N", "O", "C", "CB", "CE", "NZ", "CG", "CA", }; +static double protor_LYS_atom_radius[] = {1.88, 1.46, 1.64, 1.42, 1.61, 1.88, 1.88, 1.64, 1.88, 1.88, }; +static int protor_LYS_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_LYS_cfg = { .name = "LYS", .n_atoms = 10, .atom_name = (char**) protor_LYS_atom_name, .atom_radius = (double*) protor_LYS_atom_radius, .atom_class = (freesasa_atom_class*) protor_LYS_atom_class, - .max_area = {.name = "LYS", .total = 197.47, .main_chain = 45.10, .side_chain = 152.38, .polar = 87.44, .apolar = 110.04}, + .max_area = {.name = "LYS", .total = 204.98, .main_chain = 42.00, .side_chain = 162.98, .polar = 93.88, .apolar = 111.10}, }; -static const char *protor_MET_atom_name[] = {"CE", "SD", "O", "CA", "C", "CG", "N", "OXT", "CB", }; -static double protor_MET_atom_radius[] = {1.88, 1.77, 1.42, 1.88, 1.61, 1.88, 1.64, 1.46, 1.88, }; -static int protor_MET_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_MET_atom_name[] = {"O", "CB", "C", "OXT", "N", "SD", "CE", "CA", "CG", }; +static double protor_MET_atom_radius[] = {1.42, 1.88, 1.61, 1.46, 1.64, 1.77, 1.88, 1.88, 1.88, }; +static int protor_MET_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_MET_cfg = { .name = "MET", .n_atoms = 9, .atom_name = (char**) protor_MET_atom_name, .atom_radius = (double*) protor_MET_atom_radius, .atom_class = (freesasa_atom_class*) protor_MET_atom_class, - .max_area = {.name = "MET", .total = 185.43, .main_chain = 45.08, .side_chain = 140.35, .polar = 67.61, .apolar = 117.83}, + .max_area = {.name = "MET", .total = 193.10, .main_chain = 42.00, .side_chain = 151.10, .polar = 75.48, .apolar = 117.62}, }; static const char *protor_NH2_atom_name[] = {"N", }; @@ -311,31 +311,31 @@ static struct classifier_residue protor_NH2_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_PHE_atom_name[] = {"CZ", "O", "CE2", "CD2", "CA", "C", "CG", "N", "OXT", "CE1", "CB", "CD1", }; -static double protor_PHE_atom_radius[] = {1.76, 1.42, 1.76, 1.76, 1.88, 1.61, 1.61, 1.64, 1.46, 1.76, 1.88, 1.76, }; -static int protor_PHE_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_PHE_atom_name[] = {"O", "C", "CB", "CD1", "CZ", "OXT", "CE1", "N", "CE2", "CD2", "CA", "CG", }; +static double protor_PHE_atom_radius[] = {1.42, 1.61, 1.88, 1.76, 1.76, 1.46, 1.76, 1.64, 1.76, 1.76, 1.88, 1.61, }; +static int protor_PHE_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_PHE_cfg = { .name = "PHE", .n_atoms = 12, .atom_name = (char**) protor_PHE_atom_name, .atom_radius = (double*) protor_PHE_atom_radius, .atom_class = (freesasa_atom_class*) protor_PHE_atom_class, - .max_area = {.name = "PHE", .total = 193.68, .main_chain = 43.52, .side_chain = 150.16, .polar = 29.89, .apolar = 163.79}, + .max_area = {.name = "PHE", .total = 199.88, .main_chain = 38.43, .side_chain = 161.45, .polar = 34.94, .apolar = 164.94}, }; -static const char *protor_PRO_atom_name[] = {"CD", "OXT", "CB", "CG", "N", "C", "CA", "O", }; -static double protor_PRO_atom_radius[] = {1.88, 1.46, 1.88, 1.88, 1.64, 1.61, 1.88, 1.42, }; -static int protor_PRO_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_PRO_atom_name[] = {"O", "CB", "C", "OXT", "CD", "N", "CG", "CA", }; +static double protor_PRO_atom_radius[] = {1.42, 1.88, 1.61, 1.46, 1.88, 1.64, 1.88, 1.88, }; +static int protor_PRO_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_PRO_cfg = { .name = "PRO", .n_atoms = 8, .atom_name = (char**) protor_PRO_atom_name, .atom_radius = (double*) protor_PRO_atom_radius, .atom_class = (freesasa_atom_class*) protor_PRO_atom_class, - .max_area = {.name = "PRO", .total = 132.32, .main_chain = 29.83, .side_chain = 102.49, .polar = 16.16, .apolar = 116.16}, + .max_area = {.name = "PRO", .total = 137.21, .main_chain = 27.51, .side_chain = 109.70, .polar = 16.09, .apolar = 121.12}, }; -static const char *protor_PYL_atom_name[] = {"CB2", "N2", "O2", "C2", "CE2", "CE", "CD", "NZ", "CB", "OXT", "CA2", "CG2", "N", "CG", "C", "CA", "CD2", "O", }; -static double protor_PYL_atom_radius[] = {1.88, 1.64, 1.42, 1.61, 1.76, 1.88, 1.88, 1.64, 1.88, 1.46, 1.88, 1.88, 1.64, 1.88, 1.61, 1.88, 1.88, 1.42, }; -static int protor_PYL_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_PYL_atom_name[] = {"CD2", "NZ", "CA", "CG", "N2", "CD", "OXT", "O", "C", "CE", "CB2", "CG2", "CE2", "N", "CA2", "CB", "C2", "O2", }; +static double protor_PYL_atom_radius[] = {1.88, 1.64, 1.88, 1.88, 1.64, 1.88, 1.46, 1.42, 1.61, 1.88, 1.88, 1.88, 1.76, 1.64, 1.88, 1.88, 1.61, 1.42, }; +static int protor_PYL_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_PYL_cfg = { .name = "PYL", .n_atoms = 18, .atom_name = (char**) protor_PYL_atom_name, @@ -344,9 +344,9 @@ static struct classifier_residue protor_PYL_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_SEC_atom_name[] = {"CA", "C", "N", "SE", "CB", "O", "OXT", }; -static double protor_SEC_atom_radius[] = {1.88, 1.61, 1.64, 1.9, 1.88, 1.42, 1.46, }; -static int protor_SEC_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_SEC_atom_name[] = {"OXT", "N", "CA", "O", "SE", "CB", "C", }; +static double protor_SEC_atom_radius[] = {1.46, 1.64, 1.88, 1.42, 1.9, 1.88, 1.61, }; +static int protor_SEC_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_SEC_cfg = { .name = "SEC", .n_atoms = 7, .atom_name = (char**) protor_SEC_atom_name, @@ -355,20 +355,20 @@ static struct classifier_residue protor_SEC_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_SER_atom_name[] = {"CB", "O", "OXT", "CA", "N", "C", "OG", }; -static double protor_SER_atom_radius[] = {1.88, 1.42, 1.46, 1.88, 1.64, 1.61, 1.46, }; -static int protor_SER_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_SER_atom_name[] = {"OXT", "N", "CA", "O", "OG", "C", "CB", }; +static double protor_SER_atom_radius[] = {1.46, 1.64, 1.88, 1.42, 1.46, 1.61, 1.88, }; +static int protor_SER_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_SER_cfg = { .name = "SER", .n_atoms = 7, .atom_name = (char**) protor_SER_atom_name, .atom_radius = (double*) protor_SER_atom_radius, .atom_class = (freesasa_atom_class*) protor_SER_atom_class, - .max_area = {.name = "SER", .total = 111.49, .main_chain = 46.10, .side_chain = 65.39, .polar = 58.63, .apolar = 52.86}, + .max_area = {.name = "SER", .total = 118.34, .main_chain = 43.41, .side_chain = 74.93, .polar = 71.38, .apolar = 46.96}, }; -static const char *protor_T_atom_name[] = {"C5'", "N3", "C3'", "OP3", "OP1", "O4'", "C2'", "C7", "C6", "N1", "P", "OP2", "C4'", "C2", "C1'", "O2", "C5", "O4", "C4", "O3'", "O5'", }; -static double protor_T_atom_radius[] = {1.88, 1.64, 1.88, 1.46, 1.42, 1.46, 1.88, 1.88, 1.76, 1.64, 1.8, 1.46, 1.88, 1.61, 1.88, 1.42, 1.61, 1.42, 1.61, 1.46, 1.46, }; -static int protor_T_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_T_atom_name[] = {"C5'", "O3'", "OP1", "C6", "C1'", "O4", "N3", "OP3", "C7", "O4'", "C5", "O5'", "O2", "C2", "P", "C4", "OP2", "C3'", "N1", "C2'", "C4'", }; +static double protor_T_atom_radius[] = {1.88, 1.46, 1.42, 1.76, 1.88, 1.42, 1.64, 1.46, 1.88, 1.46, 1.61, 1.46, 1.42, 1.61, 1.8, 1.61, 1.46, 1.88, 1.64, 1.88, 1.88, }; +static int protor_T_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_T_cfg = { .name = "T", .n_atoms = 21, .atom_name = (char**) protor_T_atom_name, @@ -377,42 +377,42 @@ static struct classifier_residue protor_T_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_THR_atom_name[] = {"O", "CA", "C", "N", "CB", "CG2", "OXT", "OG1", }; -static double protor_THR_atom_radius[] = {1.42, 1.88, 1.61, 1.64, 1.88, 1.88, 1.46, 1.46, }; -static int protor_THR_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_THR_atom_name[] = {"CG2", "CA", "C", "CB", "O", "N", "OXT", "OG1", }; +static double protor_THR_atom_radius[] = {1.88, 1.88, 1.61, 1.88, 1.42, 1.64, 1.46, 1.46, }; +static int protor_THR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_THR_cfg = { .name = "THR", .n_atoms = 8, .atom_name = (char**) protor_THR_atom_name, .atom_radius = (double*) protor_THR_atom_radius, .atom_class = (freesasa_atom_class*) protor_THR_atom_class, - .max_area = {.name = "THR", .total = 133.09, .main_chain = 40.38, .side_chain = 92.71, .polar = 49.91, .apolar = 83.18}, + .max_area = {.name = "THR", .total = 140.60, .main_chain = 41.96, .side_chain = 98.64, .polar = 66.15, .apolar = 74.45}, }; -static const char *protor_TRP_atom_name[] = {"CB", "OXT", "CZ2", "NE1", "CE3", "CD1", "CH2", "CZ3", "O", "CE2", "CG", "N", "C", "CA", "CD2", }; -static double protor_TRP_atom_radius[] = {1.88, 1.46, 1.76, 1.64, 1.76, 1.76, 1.76, 1.76, 1.42, 1.61, 1.61, 1.64, 1.61, 1.88, 1.61, }; -static int protor_TRP_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_TRP_atom_name[] = {"N", "CD1", "OXT", "CZ2", "C", "CB", "NE1", "O", "CG", "CA", "CH2", "CD2", "CZ3", "CE2", "CE3", }; +static double protor_TRP_atom_radius[] = {1.64, 1.76, 1.46, 1.76, 1.61, 1.88, 1.64, 1.42, 1.61, 1.88, 1.76, 1.61, 1.76, 1.61, 1.76, }; +static int protor_TRP_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_TRP_cfg = { .name = "TRP", .n_atoms = 15, .atom_name = (char**) protor_TRP_atom_name, .atom_radius = (double*) protor_TRP_atom_radius, .atom_class = (freesasa_atom_class*) protor_TRP_atom_class, - .max_area = {.name = "TRP", .total = 226.55, .main_chain = 40.50, .side_chain = 186.05, .polar = 61.19, .apolar = 165.37}, + .max_area = {.name = "TRP", .total = 249.19, .main_chain = 42.59, .side_chain = 206.60, .polar = 61.64, .apolar = 187.55}, }; -static const char *protor_TYR_atom_name[] = {"CB", "CE1", "OXT", "CD1", "CE2", "O", "OH", "CZ", "CA", "CD2", "CG", "C", "N", }; -static double protor_TYR_atom_radius[] = {1.88, 1.76, 1.46, 1.76, 1.76, 1.42, 1.46, 1.61, 1.88, 1.76, 1.61, 1.61, 1.64, }; -static int protor_TYR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_TYR_atom_name[] = {"CB", "C", "O", "N", "OH", "OXT", "CE1", "CD1", "CZ", "CE2", "CG", "CA", "CD2", }; +static double protor_TYR_atom_radius[] = {1.88, 1.61, 1.42, 1.64, 1.46, 1.46, 1.76, 1.76, 1.61, 1.76, 1.61, 1.88, 1.76, }; +static int protor_TYR_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_TYR_cfg = { .name = "TYR", .n_atoms = 13, .atom_name = (char**) protor_TYR_atom_name, .atom_radius = (double*) protor_TYR_atom_radius, .atom_class = (freesasa_atom_class*) protor_TYR_atom_class, - .max_area = {.name = "TYR", .total = 208.08, .main_chain = 43.49, .side_chain = 164.58, .polar = 76.46, .apolar = 131.62}, + .max_area = {.name = "TYR", .total = 214.19, .main_chain = 38.43, .side_chain = 175.76, .polar = 81.12, .apolar = 133.07}, }; -static const char *protor_U_atom_name[] = {"OP2", "C4'", "C2", "C1'", "O2", "C5", "C4", "O3'", "O4", "O5'", "O2'", "C5'", "OP3", "C3'", "N3", "O4'", "OP1", "C2'", "N1", "P", "C6", }; -static double protor_U_atom_radius[] = {1.46, 1.88, 1.61, 1.88, 1.42, 1.76, 1.61, 1.46, 1.42, 1.46, 1.46, 1.88, 1.46, 1.88, 1.64, 1.46, 1.42, 1.88, 1.64, 1.8, 1.76, }; -static int protor_U_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, }; +static const char *protor_U_atom_name[] = {"C5", "O2", "C2", "P", "O5'", "OP2", "C3'", "C4", "C4'", "C2'", "N1", "O3'", "C5'", "C6", "OP1", "C1'", "O4", "N3", "O4'", "OP3", "O2'", }; +static double protor_U_atom_radius[] = {1.76, 1.42, 1.61, 1.8, 1.46, 1.46, 1.88, 1.61, 1.88, 1.88, 1.64, 1.46, 1.88, 1.76, 1.42, 1.88, 1.42, 1.64, 1.46, 1.46, 1.46, }; +static int protor_U_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, }; static struct classifier_residue protor_U_cfg = { .name = "U", .n_atoms = 21, .atom_name = (char**) protor_U_atom_name, @@ -421,15 +421,15 @@ static struct classifier_residue protor_U_cfg = { .max_area = {NULL, 0, 0, 0, 0, 0}, }; -static const char *protor_VAL_atom_name[] = {"CG2", "OXT", "CB", "CG1", "CA", "N", "C", "O", }; -static double protor_VAL_atom_radius[] = {1.88, 1.46, 1.88, 1.88, 1.88, 1.64, 1.61, 1.42, }; -static int protor_VAL_atom_class[] = {FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, }; +static const char *protor_VAL_atom_name[] = {"N", "OXT", "CB", "C", "O", "CA", "CG2", "CG1", }; +static double protor_VAL_atom_radius[] = {1.64, 1.46, 1.88, 1.61, 1.42, 1.88, 1.88, 1.88, }; +static int protor_VAL_atom_class[] = {FREESASA_ATOM_POLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, FREESASA_ATOM_APOLAR, }; static struct classifier_residue protor_VAL_cfg = { .name = "VAL", .n_atoms = 8, .atom_name = (char**) protor_VAL_atom_name, .atom_radius = (double*) protor_VAL_atom_radius, .atom_class = (freesasa_atom_class*) protor_VAL_atom_class, - .max_area = {.name = "VAL", .total = 146.72, .main_chain = 44.24, .side_chain = 102.48, .polar = 29.89, .apolar = 116.83}, + .max_area = {.name = "VAL", .total = 151.97, .main_chain = 41.50, .side_chain = 110.46, .polar = 36.87, .apolar = 115.09}, }; static struct classifier_residue *protor_residue_cfg[] = { diff --git a/tests/test-cli.in b/tests/test-cli.in index 63756745..66d683c4 100644 --- a/tests/test-cli.in +++ b/tests/test-cli.in @@ -161,7 +161,7 @@ assert_pass "$cli -L -n 10 < $smallpdb > $dump" assert_fail "$cli -L -n 0 < $smallpdb > $dump" echo echo "== Testing option --chain-groups ==" -assert_pass "$cli -g A -S -n 10 $smallpdb > $dump" +assert_pass "$cli -g S -S -n 10 $smallpdb > $dump" assert_fail "$cli -g B -S -n 10 $smallpdb > $dump" assert_pass "$cli -g AB -S -n 10 $datadir/2jo4.pdb > $dump" assert_fail "$cli -g E -S -n 10 $datadir/2jo4.pdb > $dump" @@ -227,7 +227,7 @@ for r in protor naccess do for p in $(ls $datadir/rsa/*.pdb) do - rel=$($cli -L -n 1000 $p --format=rsa --radii=$r | grep "A 2" | sed "s/[[:space:]]\{1,\}/ /g" | cut -f 6,8,10,12,14 -d ' ') + rel=$($cli -L -n 1000 $p --format=rsa --radii=$r | grep "S 2" | sed "s/[[:space:]]\{1,\}/ /g" | cut -f 6,8,10,12,14 -d ' ') if [[ $p == *"GLY"* ]] then assert_pass "test '$rel' = '100.0 N/A 100.0 100.0 100.0' && test $p" @@ -239,7 +239,7 @@ done assert_fail "$cli --format=rsa -C $smallpdb" assert_fail "$cli --format=rsa -M $smallpdb" assert_pass "$cli -L -n 1000 --format=rsa -O -w $datadir/rsa/ALA.pdb > tmp/no_rel" -rel=$(grep "A 2" tmp/no_rel | sed "s/[[:space:]]\{1,\}/ /g" | cut -f 6,8,10,12,14 -d ' ') +rel=$(grep "S 2" tmp/no_rel | sed "s/[[:space:]]\{1,\}/ /g" | cut -f 6,8,10,12,14 -d ' ') assert_pass "test '$rel' = 'N/A N/A N/A N/A N/A'" # deprecated assert_pass "$cli --rsa $datadir/1ubq.pdb > $dump"