File size: 6,056 Bytes
e5f7066 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 | #if HAVE_CONFIG_H
#include <config.h>
#endif
#include <assert.h>
#include <errno.h>
#include <math.h>
#include <stdlib.h>
#include "classifier.h"
#include "freesasa_internal.h"
#include "pdb.h"
void freesasa_residue_rel_nodearea(freesasa_nodearea *rel,
const freesasa_nodearea *abs,
const freesasa_nodearea *ref)
{
rel->total = 100. * abs->total / ref->total;
rel->side_chain = 100. * abs->side_chain / ref->side_chain;
rel->main_chain = 100. * abs->main_chain / ref->main_chain;
rel->polar = 100. * abs->polar / ref->polar;
rel->apolar = 100. * abs->apolar / ref->apolar;
rel->name = abs->name;
}
static void
rsa_print_header(FILE *output,
const char *config_name,
const char *protein_name,
const char *chains,
const freesasa_parameters *parameters,
int options)
{
freesasa_algorithm alg = parameters->alg;
#ifdef PACKAGE_VERSION
fprintf(output, "REM FreeSASA " PACKAGE_VERSION "\n");
#else
fprintf(output, "REM FreeSASA\n");
#endif
fprintf(output, "REM Absolute and relative SASAs for %s\n", protein_name);
if (!(options & FREESASA_OUTPUT_SKIP_REL))
fprintf(output, "REM Atomic radii and reference values for relative SASA: %s\n", config_name);
else
fprintf(output, "REM No reference values available to calculate relative SASA\n");
fprintf(output, "REM Chains: %s\n", chains);
fprintf(output, "REM Algorithm: %s\n", freesasa_alg_name(alg));
fprintf(output, "REM Probe-radius: %.2f\n", parameters->probe_radius);
if (alg == FREESASA_LEE_RICHARDS) {
fprintf(output, "REM Slices: %d\n", parameters->lee_richards_n_slices);
} else if (alg == FREESASA_SHRAKE_RUPLEY) {
fprintf(output, "REM Test-points: %d\n", parameters->shrake_rupley_n_points);
}
fprintf(output, "REM RES _ NUM All-atoms Total-Side Main-Chain Non-polar All polar\n");
fprintf(output, "REM ABS REL ABS REL ABS REL ABS REL ABS REL\n");
}
static inline void
rsa_print_abs_rel(FILE *output,
double abs,
double rel)
{
fprintf(output, "%7.2f", abs);
if (isfinite(rel))
fprintf(output, "%6.1f", rel);
else
fprintf(output, " N/A");
}
static inline void
rsa_print_abs_only(FILE *output,
double abs)
{
fprintf(output, "%7.2f", abs);
fprintf(output, " N/A");
}
static int
rsa_print_residue(FILE *output,
int iaa,
const freesasa_nodearea *abs,
const freesasa_nodearea *rel,
freesasa_node *residue)
{
const char *resi_str;
char chain;
resi_str = freesasa_node_residue_number(residue);
chain = freesasa_node_name(freesasa_node_parent(residue))[0];
fprintf(output, "RES %s %c%s ", abs->name, chain, resi_str);
if (rel->name != NULL) {
rsa_print_abs_rel(output, abs->total, rel->total);
rsa_print_abs_rel(output, abs->side_chain, rel->side_chain);
rsa_print_abs_rel(output, abs->main_chain, rel->main_chain);
rsa_print_abs_rel(output, abs->apolar, rel->apolar);
rsa_print_abs_rel(output, abs->polar, rel->polar);
} else {
rsa_print_abs_only(output, abs->total);
rsa_print_abs_only(output, abs->side_chain);
rsa_print_abs_only(output, abs->main_chain);
rsa_print_abs_only(output, abs->apolar);
rsa_print_abs_only(output, abs->polar);
}
fprintf(output, "\n");
return FREESASA_SUCCESS;
}
int freesasa_write_rsa(FILE *output,
freesasa_node *tree,
int options)
{
freesasa_node *residue, *chain, *structure_node, *result_node;
const freesasa_nodearea *abs, *reference;
freesasa_nodearea rel;
int res_index, chain_index;
const freesasa_parameters *parameters;
assert(output);
assert(tree);
result_node = freesasa_node_children(tree);
parameters = freesasa_node_result_parameters(result_node);
structure_node = freesasa_node_children(result_node);
chain = freesasa_node_children(structure_node);
rsa_print_header(output, freesasa_node_classified_by(result_node),
freesasa_node_name(result_node), freesasa_node_name(structure_node), parameters, options);
res_index = chain_index = 0;
while (chain) {
residue = freesasa_node_children(chain);
while (residue) {
abs = freesasa_node_area(residue);
reference = freesasa_node_residue_reference(residue);
if (reference && !(options & FREESASA_OUTPUT_SKIP_REL)) {
freesasa_residue_rel_nodearea(&rel, abs, reference);
} else {
rel = freesasa_nodearea_null;
}
rsa_print_residue(output, res_index, abs, &rel, residue);
++res_index;
residue = freesasa_node_next(residue);
}
chain = freesasa_node_next(chain);
}
fprintf(output, "END Absolute sums over single chains surface\n");
chain = freesasa_node_children(structure_node);
chain_index = 0;
while (chain) {
const char *name = freesasa_node_name(chain);
abs = freesasa_node_area(chain);
fprintf(output, "CHAIN%3d %c %10.1f %10.1f %10.1f %10.1f %10.1f\n",
chain_index + 1, name[0], abs->total, abs->side_chain,
abs->main_chain, abs->apolar, abs->polar);
++chain_index;
chain = freesasa_node_next(chain);
}
abs = freesasa_node_area(structure_node);
fprintf(output, "END Absolute sums over all chains\n");
fprintf(output, "TOTAL %10.1f %10.1f %10.1f %10.1f %10.1f\n",
abs->total, abs->side_chain, abs->main_chain, abs->apolar, abs->polar);
fflush(output);
if (ferror(output)) {
return fail_msg(strerror(errno));
}
return FREESASA_SUCCESS;
}
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