:Merge ../GLYLIB_v_0.3.0b

Conflicts:

	lib/ATYPE_init.o
	lib/add_coord.o
	lib/add_vec.o
	lib/amber_prmtop_init.o
	lib/assign_COM.o
	lib/coord_to_vec.o
	lib/dXprint_X.o
	lib/dprint_X.o
	lib/find_molecules.o
	lib/get_COM.o
	lib/get_crossprod.o
	lib/get_dipole.o
	lib/get_dotprod.o
	lib/get_geometric_center.o
	lib/get_magnitude.o
	lib/get_plane.o
	lib/get_rms_alt_X.o
	lib/get_type.o
	lib/init_struct.o
	lib/initialize_GLYstruct.o
	lib/libglylib.a
	lib/load_amber_prmtop.o
	lib/load_atypes.o
	lib/load_dlg_mol.o
	lib/load_pdb.o
	lib/normalize_molecule_vectors.o
	lib/normalize_vec.o
	lib/outputPDB.o
	lib/parse_amber_prmtop.o
	lib/pdb_def.o
	lib/read_amber8_mden.o
	lib/read_amber_prmtop.o
	lib/read_prep.o
	lib/rotate_vector_to_Z.o
	lib/rotation.o
	lib/rwm_line.o
	lib/scalarmult_vec.o
	lib/translate_to_COM.o
	lib/translate_zero_to_coord.o
	lib/vector_movements.o
	lib/write_amber_prmtop.o
	lib/zero_vec_crd.o

inc/geometries.h

@@ -55,5 +55,5 @@ typedef struct {
 	coord_nD *C; ///< nC coordinates (the dimensions are defined inside the structures, and might all be different)
 	int nCD; ///< Number of descriptions defined
 	char **CD; ///< nCD descriptions of the coordinate relevances (e.g, "lower corner" or "A in z=f(A)"). 
-} box_info;
+} boxinfo;
 #endif

inc/geometries.h~

@@ -0,0 +1,59 @@
+/* File geometries.h begun by BLFoley on 20080606
+   Purpose: structures related to geometries of molecules,
+	residues, atoms, etc.  
+   NOTE!!!  This file is loaded with the molecules.h header file by default.
+        It should only be loaded explicitly in a program if, for some reason,
+        you are using it separately. */
+#if !defined(GLYLIB_GEOMETRIES)
+#define GLYLIB_GEOMETRIES
+
+/**************************************************************//**
+			Coordinates 
+******************************************************************/
+// Fixed Dimension
+typedef struct {
+	double i,j,k; ///< Values assigned to the three coordinates.
+} coord_3D; ///< Any 3D coordinate: cartesian, polar, direction cosines, etc.  
+typedef struct {
+	double i,j,k,d; ///< i,j,k vector with magnitude d
+} vectormag_3D; ///< Vector manipulations often require magnitudes, so this struct contains that information.
+
+// Multi-Dimensional
+typedef struct {
+	int nD; ///< Number of dimensions.
+	double *D;///< Values in each of the nD dimensions
+} coord_nD; ///< An n-dimensional coordinate 
+typedef struct {
+	int nDi; ///< Number of dimensions.
+	int *Di;///< Indicies for values in each of the nD dimensions
+} nD_index; ///< Set of indices to n-dimensional coordinate
+typedef struct {
+	int nDp; ///< Number of dimensions.
+	double **Dp;///< Pointers to values in each of the nD dimensions
+} nD_ptrs; ///< Set of pointers to n-dimensional coordinate
+typedef struct {
+	int nD; ///< Number of dimensions.
+	double *D;///< Values in each of the nD dimensions
+	int *Di;///< Indicies for values in each of the nD dimensions
+} coord_nDi; ///< An n-dimensional coordinate 
+
+
+
+/**************************************************************//**
+			Geometrical Objects 
+******************************************************************/
+typedef struct {
+	double A,B,C,D;
+} plane; ///< Standard cartesian plane with equation Ax+By+Cz+D=0
+
+/**************************************************************//**
+			Special Objects 
+******************************************************************/
+typedef struct {
+	char *STYPE,*GTYPE; ///< Types relevant to simulations (e.g., periodic) and to basic geometry (e.g., cubic)
+	int nC; ///< Number of coordinates defined
+	coord_nD *C; ///< nC coordinates (the dimensions are defined inside the structures, and might all be different)
+	int nCD; ///< Number of descriptions defined
+	char **CD; ///< nCD descriptions of the coordinate relevances (e.g, "lower corner" or "A in z=f(A)"). 
+} box_info;
+#endif

inc/molecules.h

@@ -137,6 +137,7 @@ typedef struct {
 	int nOD; // number of other descriptors
 	char **OD; // the nOD descriptors
 	int nVP; // number of void structures
+	char cID; // chain identifier
 	void *VP; // nVP of these, whatever they may be
 } atom; // an actual atom in a residue/molecule
 
@@ -195,10 +196,10 @@ typedef struct {
 	molbond *rb; // nrb of these descriptions of bonds 
 	int nrbs; // number of sets of bonds between residues (for example, linear chains)
 	molbondset *rbs; // nrbs of these sets
-	int nrc; // number of additional reference coordinates (rings, for example)
+	int nrc; // number of additional reference ../inc/molecules.h:265: error: expected specificoordinates (rings, for example)
 	coord_3D *rc; // nrc of these
 	int nBOX; ///< Number of box_info structures defined
-	boxinfo *BOX: ///< The nBOX structures
+	boxinfo *BOX; ///< The nBOX structures
 	//coord_3D boxl,boxh; // box dimensions
 	int noi; // number of other indices
 	int *oi; // other indices, as needed (ni of these)
@@ -262,7 +263,7 @@ typedef struct { // structure for groups of molecules within a larger structure
 	int nmbs; // number of sets of connections between molecules 
 	molbondset *mbs; // nmbs of these sets
 	int nBOX; ///< Number of box_info structures defined
-	boxinfo *BOX: ///< The nBOX structures
+	boxinfo *BOX; ///< The nBOX structures
 	//coord_3D boxl,boxh; // simple box dimensions (limits low & high or just use one for size)
 	//double boxang; // coord_3D is x, y and z -- angle (probably between XY and YZ planes in degrees, maybe).  
 	//char *boxtype; // type of simple box (cubic, trapezoidal, etc.)
@@ -286,7 +287,7 @@ typedef struct { // structure for an entire system of molecules
 	int na; // number of assembly structures
 	assembly *a; // na of these
 	int nBOX; ///< Number of box_info structures defined
-	boxinfo *BOX: ///< The nBOX structures
+	boxinfo *BOX; ///< The nBOX structures
 	//coord_3D boxl,boxh; // box dimensions
 	int nPRM; // number of parameter sets
 	parameter_set *PRM; // pointer to parameter sets