Merge branch 'dev'

.gitignore

@@ -43,3 +43,4 @@ doc/doxygen
 bindings/python/*.c
 doc/html/
 tests/libtest
+tests/test-cli.sh

configure.ac

@@ -2,7 +2,7 @@
 # Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.68])
-AC_INIT([FreeSASA], [0.3.3.1])
+AC_INIT([FreeSASA], [0.3.4])
 AM_INIT_AUTOMAKE([foreign])
 AC_CONFIG_SRCDIR([src/freesasa.c])
 AC_CONFIG_HEADERS([config.h])

src/Makefile.am

@@ -1,10 +1,8 @@
 if COND_GCOV
 AM_CFLAGS = --coverage
 AM_LDFLAGS = -lgcov
-GCOV_FILES = *.gcda *.gcno *.gcov
-else
-GCOV_FILES =
 endif
+GCOV_FILES = *.gcda *.gcno *.gcov
 
 bin_PROGRAMS = freesasa
 lib_LIBRARIES = libfreesasa.a
@@ -21,4 +19,4 @@ freesasa_LDADD = libfreesasa.a
 example_LDADD = libfreesasa.a
 
 
-CLEANFILES = $(GCOV_FILES)
+CLEANFILES = $(GCOV_FILES) *~

src/classify.c

@@ -36,13 +36,15 @@ static const char *residue_names[] = {
     "MET","PHE","PRO","SER",
     "THR","TRP","TYR","VAL",
     "CSE","ASX","GLX",
+    "ACE","NH2",
     "UNK",
     //DNA
     "DA","DC","DG","DT","DU","DI",
     //RNA
     "A","C","G","U","I","T",
     //General nuceleotide
     "N"
+
 };
 
 
@@ -112,6 +114,8 @@ const freesasa_classifier freesasa_residue_classifier = {
 
 double freesasa_classify_radius(const char *res_name, const char *atom_name)
 {
+    if (freesasa_classify_element(atom_name) == freesasa_hydrogen) 
+        return freesasa_classify_element_radius(freesasa_hydrogen);
     int res = freesasa_classify_residue(res_name);
     if (freesasa_classify_is_aminoacid(res)) {
         return freesasa_classify_oons_radius(freesasa_classify_oons(res_name,
@@ -215,6 +219,7 @@ int freesasa_classify_element(const char *atom_name)
         case 'N': return freesasa_nitrogen;
         case 'S': return freesasa_sulfur;
         case 'P': return freesasa_phosphorus;
+        case 'H': return freesasa_hydrogen;
             // what about Se?
         default:
             freesasa_warn("%s: atom '%s' unknown.\n",__func__,atom_name);
@@ -252,7 +257,7 @@ double freesasa_classify_element_radius(int element)
     case freesasa_sulfur: return 1.8;
     case freesasa_phosphorus: return 1.8;
     case freesasa_selenium: return 1.9;
-        //case freesasa_hydrogen: return 1.2;
+    case freesasa_hydrogen: return 0.0; // the exception
     case freesasa_element_unknown:
     default:
         return 0.0;
@@ -319,6 +324,18 @@ static int classify_oons_cse(const char* a)
     return freesasa_oons_unknown;
 }
 
+static int classify_oons_nh2(const char* a) 
+{
+    if (a[1] == 'N' && a[2] == 'H' && a[3] == '2') return freesasa_amide_N;
+    return freesasa_oons_unknown;
+}
+
+static int classify_oons_ace(const char* a)
+{
+    if (a[1] == 'C' && a[2] == 'H' && a[3] == '3') return freesasa_aliphatic_C;
+    return freesasa_oons_unknown;
+}
+
 /** Main OONS function */
 int freesasa_classify_oons(const char *res_name, const char *a)
 {
@@ -376,6 +393,8 @@ int freesasa_classify_oons(const char *res_name, const char *a)
     case freesasa_ASX: return classify_oons_ND(a);
     case freesasa_GLX: return classify_oons_QE(a);
     case freesasa_CSE: return classify_oons_cse(a);
+    case freesasa_ACE: return classify_oons_ace(a);
+    case freesasa_NH2: return classify_oons_nh2(a);
     default:
         return freesasa_oons_unknown;
     }

src/classify.h

@@ -57,6 +57,9 @@ enum freesasa_residue {
     freesasa_THR, freesasa_TRP, freesasa_TYR, freesasa_VAL,
     //some non-standard ones
     freesasa_CSE, freesasa_ASX, freesasa_GLX,
+    //capping N- and C-terminal groups (usually HETATM)
+    freesasa_ACE, freesasa_NH2,
+    //residue unknown
     freesasa_UNK,
     //DNA
     freesasa_DA, freesasa_DC, freesasa_DG, freesasa_DT,

src/freesasa.c

@@ -255,10 +255,11 @@ int freesasa_log(FILE *log,
     // return value. 
     errno = 0;
 
-    fprintf(log,"## %s %s ##\n",freesasa_name,freesasa_version);
     if (name == NULL) fprintf(log,"name: unknown\n");
     else              fprintf(log,"name: %s\n",name);
 
+    fprintf(log,"n_atoms: %d\n",result->n_atoms);
+
     fprintf(log,"algorithm: %s\nprobe-radius: %f A\n",
             freesasa_alg_names[p->alg],
             p->probe_radius);

src/freesasa.h

@@ -93,7 +93,14 @@
     using freesasa_classifier_from_file() (see @ref Config-file).
 
     The default classifier is available as a global const variable
-    ::freesasa_default_classifier.
+    ::freesasa_default_classifier. This uses the classes and radii,
+    defined in the paper by Ooi et al.  ([PNAS 1987, 84:
+    3086](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC304812/)) for
+    the standard amino acids and also for some capping groups
+    (ACE/NH2) if HETATM fields are included when the PDB input is
+    read. For other residues such as Nucleic Acids or nonstandard
+    amino acids, or unrecognized HETATM entries the VdW radius of
+    the element is used. Warnings are emitted in this case.
 
     @subsubsection Config-file Classifier configuration files
 
@@ -199,7 +206,6 @@ typedef enum {
     FREESASA_NUCLEICACID, FREESASA_CLASS_UNKNOWN
 } freesasa_class;
 
-
 // Default parameters
 #define FREESASA_DEF_PROBE_RADIUS 1.4 //!< Default probe radius (in Ångström) @ingroup API
 #define FREESASA_DEF_SR_N 100 //!< Default number of test points in S&R @ingroup API
@@ -209,6 +215,13 @@ typedef enum {
 #define FREESASA_FAIL -1 //!< Something went seriously wrong. @ingroup API
 #define FREESASA_WARN -2 //!< Something went wrong, but results might still be meaningful @ingroup API
 
+// Parameters for reading structure from PDB
+#define FREESASA_INCLUDE_HETATM 1 //!< Include HETATM entries
+#define FREESASA_INCLUDE_HYDROGEN 2 //!< Include hydrogen atoms
+#define FREESASA_SEPARATE_MODELS 4 //!< Read MODELs as separate structures
+#define FREESASA_SEPARATE_CHAINS 8 //!< Read separate chains as separate structures
+#define FREESASA_JOIN_MODELS 16 //!< Read MODELs as part of one big structure
+
 //! Struct to store parameters for SASA calculation @ingroup API
 typedef struct {
     freesasa_algorithm alg;     //!< Algorithm
@@ -535,24 +548,62 @@ freesasa_structure* freesasa_structure_new(void);
     Automatically skips hydrogens. If an atom has alternative
     coordinates, only the first alternative is used. If a file has
     more than one `MODEL` (as in NMR structures) only the first model
-    is used. User specifies if `HETATM` entries should be included. If
-    non-default behavior is wanted, the PDB-file needs to be modified
-    before calling this function, or atoms can be added manually one
-    by one using freesasa_structure_add_atom().
+    is used. User specifies if `HETATM` entries and/or hydrogen atoms
+    should be included. It is also possible to specify that all MODELs
+    should be joined to one large structure. If more fine-grained
+    control over which atoms to include is needed, the PDB-file needs
+    to be modified before calling this function, or atoms can be added
+    manually one by one using freesasa_structure_add_atom().
 
     Return value is dynamically allocated, should be freed with
     freesasa_structure_free().
 
     @param pdb Input PDB-file.
-    @param include_hetatm The value 0 means only read `ATOM` entries, 1
-    means also include `HETATM` entries.
-    @return The generated structure. Returns `NULL` and prints error if
-    input is invalid.
+    @param options Bitfield. 0 means only use non-hydrogen `ATOM`
+      entries, first MODEL only. ::FREESASA_INCLUDE_HETATM and
+      ::FREESASA_INCLUDE_HYDROGEN can be used to include more
+      atoms. ::FREESASA_JOIN_MODELS can be used if input has several
+      models that should be considered part of the same structure. The
+      options can be included using `|`, for example
+      `FREESASA_INCLUDE_HETATM | FREESASA_INCLUDE_HYDROGEN` means
+      include both hydrogens and HETATMs.
+    @return The generated structure. Returns `NULL` and prints error
+      if input is invalid.
 
     @ingroup StructureAPI
 */
 freesasa_structure* freesasa_structure_from_pdb(FILE *pdb,
-                                                int include_hetatm);
+                                                int options);
+
+/**
+    Init array of structures from PDB.
+    
+    Either iniatilize one structure per model in multimodel PDB, or
+    one per chain, or both. Otherwise equivalent to
+    freesasa_structure_from_pdb(). 
+
+    Returns dynamically allocated array of size n. Its members should
+    be freed using freesasa_structure_free() and the array itself with
+    free().
+
+    @param pdb Input PDB-file.  
+    
+    @param n Number of structures found are written to this integer.
+    
+    @param options Bitfield. 0 means only use non-hydrogen `ATOM`
+      entries. ::FREESASA_INCLUDE_HETATM and
+      ::FREESASA_INCLUDE_HYDROGEN can be used to include more
+      atoms. ::FREESASA_SEPARATE_MODELS and
+      ::FREESASA_SEPARATE_CHAINS can be used to generate one structure
+      per model and one structure per chain, respectively.  All four
+      options can be combined using `|`, analogously to
+      freesasa_structure_from_pdb().
+      
+    @ingroup StructureAPI
+ */
+freesasa_structure** freesasa_structure_array(FILE *pdb,
+                                              int *n,
+                                              int options);
 
 /**
     Add individual atom to structure.
@@ -624,6 +675,7 @@ void freesasa_structure_free(freesasa_structure* structure);
 double* freesasa_structure_radius(const freesasa_structure *structure,
                                   const freesasa_classifier *classifier);
 
+
 /**
     Get atom name
 
@@ -671,6 +723,15 @@ const char* freesasa_structure_atom_res_number(const freesasa_structure *s,
  */
 char freesasa_structure_atom_chain(const freesasa_structure *s, int i);
 
+/**
+    Get model number for structure.
+
+    Useful if structure was generated with freesasa_structure_array().
+
+    @param structure The structure.  
+    @return The model number. 0 means no model number has been read.
+ */
+int freesasa_structure_model(const freesasa_structure *structure);
 
 #ifdef __cplusplus
 }