Support longer chain labels in output.

mittinatten · Feb 22, 2024 · e6783ae · e6783ae
1 parent 17463b8
commit e6783ae
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Showing 6 changed files with 22 additions and 19 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,11 @@
 
 FreeSASA uses semantic versioning. Changelog added for versions 2.x
 
+## Upcoming release
+
+- Breaking: Support 3-letter chain labels (auth_sym_id) in CIF-files. Default and RSA output formats 
+  have changes in whitespace as a consequence, to give space to the larger labels.
+
 ## 2.1.2
 
 - Fix error where CLI options weren't parsed properly on ARM processors.

diff --git a/src/cif.cc b/src/cif.cc
@@ -142,7 +142,7 @@ freesasa_atom_from_site(const gemmi::cif::Table::Row &site)
         auth_atom_id = site[5].c_str();
     }
 
-    return freesasa_cif_atom_lcl {
+    return freesasa_cif_atom_lcl{
         .group_PDB = site[0].c_str(),
         .auth_asym_id = site[1].c_str(),
         .auth_seq_id = site[2].c_str(),

diff --git a/src/log.c b/src/log.c
@@ -57,9 +57,9 @@ write_result(FILE *log,
     fprintf(log, "atoms   : %d\n", freesasa_node_structure_n_atoms(structure));
 
     fprintf(log, "\nRESULTS (A^2)\n");
-    fprintf(log, "Total   : %10.2f\n", area->total);
-    fprintf(log, "Apolar  : %10.2f\n", area->apolar);
-    fprintf(log, "Polar   : %10.2f\n", area->polar);
+    fprintf(log, "Total     : %10.2f\n", area->total);
+    fprintf(log, "Apolar    : %10.2f\n", area->apolar);
+    fprintf(log, "Polar     : %10.2f\n", area->polar);
     if (area->unknown > 0) {
         fprintf(log, "Unknown : %10.2f\n", area->unknown);
     }
@@ -68,7 +68,7 @@ write_result(FILE *log,
     while (chain) {
         area = freesasa_node_area(chain);
         assert(area);
-        fprintf(log, "CHAIN %s : %10.2f\n", freesasa_node_name(chain), area->total);
+        fprintf(log, "CHAIN %3s : %10.2f\n", freesasa_node_name(chain), area->total);
         chain = freesasa_node_next(chain);
     }
 

diff --git a/src/node.c b/src/node.c
@@ -326,15 +326,12 @@ node_chain(const freesasa_structure *structure,
            const freesasa_result *result,
            int chain_index)
 {
-    const char *chains = freesasa_structure_chain_labels(structure);
-    char name[2] = {chains[chain_index], '\0'};
+    const char *name = freesasa_structure_chain_label(structure, chain_index);
     freesasa_node *chain = NULL;
     int first_atom, last_atom, first_residue, last_residue;
 
-    assert(strlen(chains) > chain_index);
-
-    freesasa_structure_chain_atoms(structure, chains[chain_index],
-                                   &first_atom, &last_atom);
+    freesasa_structure_chain_atoms_lcl(structure, name,
+                                       &first_atom, &last_atom);
 
     chain = node_new(name);
     if (chain == NULL) {
@@ -343,8 +340,8 @@ node_chain(const freesasa_structure *structure,
     }
 
     chain->type = FREESASA_NODE_CHAIN;
-    freesasa_structure_chain_residues(structure, name[0],
-                                      &first_residue, &last_residue);
+    freesasa_structure_chain_residues_lcl(structure, name,
+                                          &first_residue, &last_residue);
     chain->properties.chain.n_residues = last_residue - first_residue + 1;
 
     if (node_gen_children(chain, structure, result,

diff --git a/src/rsa.c b/src/rsa.c
@@ -82,12 +82,12 @@ rsa_print_residue(FILE *output,
                   freesasa_node *residue)
 {
     const char *resi_str;
-    char chain;
+    const char *chain;
 
     resi_str = freesasa_node_residue_number(residue);
-    chain = freesasa_node_name(freesasa_node_parent(residue))[0];
+    chain = freesasa_node_name(freesasa_node_parent(residue));
 
-    fprintf(output, "RES %s %c%s ", abs->name, chain, resi_str);
+    fprintf(output, "RES %s %3s%-4s ", 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);
@@ -152,8 +152,8 @@ int freesasa_write_rsa(FILE *output,
         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,
+        fprintf(output, "CHAIN%3d %3s %10.1f   %10.1f   %10.1f   %10.1f   %10.1f\n",
+                chain_index + 1, name, abs->total, abs->side_chain,
                 abs->main_chain, abs->apolar, abs->polar);
 
         ++chain_index;
@@ -162,7 +162,7 @@ int freesasa_write_rsa(FILE *output,
 
     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",
+    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);

diff --git a/tests/test-cli.in b/tests/test-cli.in
@@ -240,6 +240,7 @@ assert_pass "$cli --cif --format=cif --separate-chains $datadir/1ubq.cif > $dump
 assert_pass "$cli --cif --format=cif --separate-chains --separate-models $datadir/1ubq.cif > $dump"
 assert_fail "$cli --cif --format=pdb $datadir/1ubq.cif > $dump"
 assert_fail "$cli --format=cif $datadir/1ubq.pdb > $dump"
+assert_pass $cli --cif $datadir/7cma-assembly1.cif | grep 'CHAIN C-2 :    8980.86'
 
 echo
 echo "== Testing --separate-chains and --separate-models output are equal between cif and pdb"