/*
 * pdbsummary.h - contains function prototypes for reading a PDB summary file
 *
 * Update history:
 * 6/9/98       cline   author
 * 6/16/98	cline	added PDB_NUMBER_LENGTH
 */

/*
 * This constant represents the longest expected length of a PDB number
 */
#define PDB_NUMBER_LENGTH	7

/*
 * These constants represent strings in the PDB summary file
 */
#define PDBID_STRING    "PDBID"
#define SEQRES_STRING   "SEQRES"
#define SEQSEQ_STRING   "SEQSEQ"

/*
 * the constant below marks PDB sequence positions with no PDB numbers
 */
#define NO_PDB_NUMBER   "_"

/*
 * Below are constants for lengths of filenames, command buffers, etc.
 */
#define PATHNAME_LENGTH 256
#define COMMAND_BUFFER_LENGTH   256
#define INPUT_BUFFER_LENGTH     337



/*
 * convertNonNumberedPositionsToInserts - for all residues that don't
 *      have real PDB numbers, convert the positions to inserts.
 */
void convertNonNumberedPositionsToInserts(
    int pdbListSize,    /* called with: number of PDB numbers / sequence
                        * positions here */
    char **pdbNumList,  /* called with: list of the PDB numbers */
    char *seqFromPdb);  /* called with: the sequence as it was read
                         * from PDB.  Return with: same sequence, but
                         * with certain states switched to lowercase. */


/*
 * createAlignSummary - make an empty AlignSummary structure to hold
 *                      the specified template sequence.
 */
void createAlignSummary(
    char *templateName,         /* called with: name of the template
                                 * sequence */
    char *templateSeq,          /* called with: the new template sequence */
    char *filename,             /* called with: "filename" for the new
                                 * alignment */
    AlignSummary **newAlign);   /* return with: pointer to a pointer to
                                 * the new AlignSummary struct. */


/*
 * getPdbsumAlignment - read the pdb summary for the specified template
 *      structure.  Store the SEQRES sequence in an AlignSummary structure,
 *      and the list of PDB "numbers" in 2D string array.
 *
 * return value: TRUE if everything worked successfully.  FALSE if
 *   there was a pipe failure, memory failure, pdb-get-summary failure, etc.
 */
int getPdbsumAlignment(
    char *templateName,         /* called with: name of the template
                                 * structure */
    char ***pdbNumberList,      /* return with: pointer to an array
                                 * of PDB numbers */
    int *pdbListSize,           /* return with: number of template
                                 * sequence residues and PDB numbers,
                                 * will be the same (assumed & tested) */
    char **seqReadFromPdb,      /* return with: the sequence as read
                                 * from the PDB, for later error checking */
    AlignSummary **templateSeq); /* return with: an alignsummary structure
                                 * with the template seq in one row, PDB
                                 * numbers in the other row. */


/*
 * readPdbId - read the PDB ID line and check it against the expected PDBID
 *
 * return value: TRUE if we read the expected PDBID, FALSE otherwise.
 */
int readPdbId(
    FILE *fp,                   /* called with: pointer to the PDB summary
                                 * input stream, open for reading */
    char *templateName);        /* called with: expected pdbID */


/*
 * readSeqres - read the SEQRES line of the PDB summary file
 *
 * Read the SEQRES line and return with the sequence it labels
 *
 * Return value: TRUE if we could read and allocate memory for the
 *      sequence, FALSE otherwise.
 */
int readSeqres(
    FILE *fp,                   /* called with: pointer to the PDB summary
                                 * data, open for reading */
    char **templateSeq);        /* return with: the PDB seqres sequence,
                                 * allocated in memory. */


/*
 * readSeqseq - read the seqseq record of the PDB file
 *
 * Read the SEQSEQ record, which contains one PDB number entry for each
 * sequence position in the SEQRES record.  Build
 *
 * Return value: TRUE if we could read and allocate memory for the
 *      sequence, FALSE otherwise.
 */
int readSeqseq(
    FILE *fp,                           /* called with: pointer to the
                                         * pdbsummary input stream */
    int templateSeqLength,              /* called with: length of the
                                         * template sequence */
    char ***pdbNumbers);                /* return with: pointer to an
                                         * array of strings, one cell
                                         * per template seq position,
                                         * containing the PDB number
                                         * for that position. */