Add functions that allow getting chain atom and residue ranges based …

…on string-valued auth_asym_id/chain-labels.

Related to #96.

src/freesasa.h

@@ -1312,6 +1312,28 @@ int freesasa_structure_chain_atoms(const freesasa_structure *structure,
                                    int *first,
                                    int *last);
 
+/**
+    \private
+    Get indices of first and last atoms of a chain
+
+    Uses long form chain labels.
+
+    This is an intermediate function added in the process of migrating to long chain labels.
+    It is not meant to be part of the public API for now.
+
+    @param structure A structure.
+    @param chain The chain label.
+    @param first First atom of `chain` will be stored here.
+    @param last Last atom of `chain` will be stored here.
+    @return ::FREESASA_SUCCESS. ::FREESASA_FAIL if `chain` not found.
+
+    @ingroup structure
+ */
+int freesasa_structure_chain_atoms_lcl(const freesasa_structure *structure,
+                                       const char *chain,
+                                       int *first,
+                                       int *last);
+
 /**
     Get indices of first and last residues of a chain
 
@@ -1328,6 +1350,28 @@ int freesasa_structure_chain_residues(const freesasa_structure *structure,
                                       int *first,
                                       int *last);
 
+/**
+    \private
+    Get indices of first and last residues of a chain
+
+    Uses long form chain labels.
+
+    This is an intermediate function added in the process of migrating to long chain labels.
+    It is not meant to be part of the public API for now.
+
+    @param structure A structure.
+    @param chain The chain label.
+    @param first First residue of `chain` will be stored here.
+    @param last Last residue of `chain` will be stored here.
+    @return ::FREESASA_SUCCESS. ::FREESASA_FAIL if `chain` not found.
+
+    @ingroup structure
+ */
+int freesasa_structure_chain_residues_lcl(const freesasa_structure *structure,
+                                          const char *chain,
+                                          int *first,
+                                          int *last);
+
 /**
     Name of classifier used to generate structure.
 

src/structure.c

@@ -447,7 +447,8 @@ guess_symbol(char *symbol,
 
 int structure_has_chain(freesasa_structure *s, const chain_label_t chain_label)
 {
-    for (int i = 0; i < s->chains.n; ++i) {
+    int i;
+    for (i = 0; i < s->chains.n; ++i) {
         if (strncmp(s->chains.labels[i], chain_label, sizeof(chain_label_t)) == 0) {
             return 1;
         }
@@ -1197,29 +1198,40 @@ int freesasa_structure_n_chains(const freesasa_structure *structure)
     return structure->chains.n;
 }
 
-int freesasa_structure_chain_index(const freesasa_structure *structure,
-                                   char chain)
+int freesasa_structure_chain_index_lcl(const freesasa_structure *structure,
+                                       const char *chain)
 {
     int i;
 
     assert(structure);
 
     for (i = 0; i < structure->chains.n; ++i) {
-        if (structure->chains.labels[i][0] == chain) return i;
+        if (strncmp(structure->chains.labels[i], chain, sizeof(chain_label_t)) == 0) {
+            return i;
+        }
     }
-    return fail_msg("chain %c not found", chain);
+
+    return fail_msg("chain '%s' not found", chain);
 }
 
-int freesasa_structure_chain_atoms(const freesasa_structure *structure,
-                                   char chain,
-                                   int *first,
-                                   int *last)
+/** Not public */
+int freesasa_structure_chain_index(const freesasa_structure *structure,
+                                   char chain)
+{
+    chain_label_t chain_label = {chain, '\0'};
+    return freesasa_structure_chain_index_lcl(structure, chain_label);
+}
+
+int freesasa_structure_chain_atoms_lcl(const freesasa_structure *structure,
+                                       const char *chain,
+                                       int *first,
+                                       int *last)
 {
     int c_i, n;
 
     assert(structure);
 
-    c_i = freesasa_structure_chain_index(structure, chain);
+    c_i = freesasa_structure_chain_index_lcl(structure, chain);
     n = freesasa_structure_n_chains(structure);
 
     if (c_i < 0) return fail_msg("");
@@ -1234,16 +1246,25 @@ int freesasa_structure_chain_atoms(const freesasa_structure *structure,
     return FREESASA_SUCCESS;
 }
 
-int freesasa_structure_chain_residues(const freesasa_structure *structure,
-                                      char chain,
-                                      int *first,
-                                      int *last)
+int freesasa_structure_chain_atoms(const freesasa_structure *structure,
+                                   char chain,
+                                   int *first,
+                                   int *last)
+{
+    chain_label_t chain_label = {chain, '\0'};
+    return freesasa_structure_chain_atoms_lcl(structure, chain_label, first, last);
+}
+
+int freesasa_structure_chain_residues_lcl(const freesasa_structure *structure,
+                                          const char *chain,
+                                          int *first,
+                                          int *last)
 {
     int first_atom, last_atom;
 
     assert(structure);
 
-    if (freesasa_structure_chain_atoms(structure, chain, &first_atom, &last_atom))
+    if (freesasa_structure_chain_atoms_lcl(structure, chain, &first_atom, &last_atom))
         return fail_msg("");
 
     *first = structure->atoms.atom[first_atom]->res_index;
@@ -1252,6 +1273,15 @@ int freesasa_structure_chain_residues(const freesasa_structure *structure,
     return FREESASA_SUCCESS;
 }
 
+int freesasa_structure_chain_residues(const freesasa_structure *structure,
+                                      char chain,
+                                      int *first,
+                                      int *last)
+{
+    chain_label_t chain_label = {chain, '\0'};
+    return freesasa_structure_chain_residues_lcl(structure, chain_label, first, last);
+}
+
 const char *
 freesasa_structure_classifier_name(const freesasa_structure *structure)
 {

tests/test_structure.c

@@ -122,6 +122,7 @@ END_TEST
 
 START_TEST(test_cif)
 {
+    int first, last;
     s = freesasa_structure_new();
     for (int i = 0; i < N; ++i) {
         struct freesasa_cif_atom_lcl atom = {
@@ -151,6 +152,14 @@ START_TEST(test_cif)
     ck_assert_int_eq(freesasa_structure_residue_chain(s, 0), lcl[0][0]);
     ck_assert_str_eq(freesasa_structure_residue_chain_lcl(s, 0), lcl[0]);
 
+    ck_assert_int_eq(freesasa_structure_chain_atoms_lcl(s, "AAA", &first, &last), FREESASA_SUCCESS);
+    ck_assert_int_eq(first, 0);
+    ck_assert_int_eq(last, N - 1);
+
+    ck_assert_int_eq(freesasa_structure_chain_residues_lcl(s, "AAA", &first, &last), FREESASA_SUCCESS);
+    ck_assert_int_eq(first, 0);
+    ck_assert_int_eq(last, 1);
+
     struct freesasa_cif_atom_lcl atom = {
         .group_PDB = "",
         .auth_asym_id = lcl[0],