source: branches/nanovis2/packages/vizservers/pymolproxy/pymolproxy2.c @ 3305

/*
 * ----------------------------------------------------------------------
 * proxypymol2.c
 *
 *      This module creates the Tcl interface to the pymol server.  It acts as
 *      a go-between establishing communication between a molvisviewer widget
 *      and the pymol server. The communication protocol from the molvisviewer
 *      widget is the Tcl language.  Commands are then relayed to the pymol
 *      server.  Responses from the pymol server are translated into Tcl
 *      commands and send to the molvisviewer widget. For example, resulting
 *      image rendered offscreen is returned as ppm-formatted image data.
 *
 *  Copyright (c) 2004-2012  HUBzero Foundation, LLC
 *
 *  See the file "license.terms" for information on usage and
 *  redistribution of this file, and for a DISCLAIMER OF ALL WARRANTIES.
 * ======================================================================
 */

/*
 * Notes:   The proxy should not maintain any state information from the
 *          client, other that what it needs for event (rotate, pan, zoom,
 *          atom scale, bond thickness, etc.) compression.  This is because 
 *          the connection is periodically broken (timeout, error, etc.).
 *          It's the responsibility of the client (molvisviewer) to restore 
 *          the settings of the previous view.  The proxy is just a relay
 *          between the client and the pymol server.
 */
/*
 *   +--------------+          +------------+          +----------+
 *   |              | (stdin)  |            |  (stdin) |          | 
 *   |              |--------->|            |--------->|          |
 *   | molvisviewer |          | pymolproxy |          | pymol    |
 *   |  (client)    |          |            |          | (server) |(stderr)
 *   |              | (stdout) |            | (stdout) |          |-------> file
 *   |              |<---------|            |<---------|          | 
 *   +--------------+          +------------+          +----------+
 * 
 * We're using a simple 2 thread setup: one for read client requests and
 * relaying them to the pymol server, another reading pymol server output,
 * and sending images by to the client.  The reason is because the client
 * blocks on writes.  While it is sending requests or data, the proxy
 * must be available to accept it.  Likewise, the proxy buffers images in a
 * linked list when the client isn't ready to receive them.
 *
 * Reader thread:
 * The communication between the pymol server and proxy is asynchronous.  
 * The proxy translates commands from the client and sends them to the
 * server without waiting for a response.  It watches the server's
 * stdout in a separate thread snooping for image data.  
 *
 * Writer thread:
 * The communication between the client and the proxy is also asynchronous.  
 * The client commands are read when they become available on the socket.  
 * The proxy writes images to the client when it can, otherwise it stores
 * them in a list in memory.  This should prevent deadlocks from occuring:
 * the client sends a request, while the proxy is writing an image.
 */

#include <assert.h>
#include <ctype.h>
#include <errno.h>
#include <fcntl.h>
#include <getopt.h>
#include <poll.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include <sys/time.h>
#include <sys/times.h>
#include <sys/types.h>
#include <sys/wait.h>
#include <time.h>
#include <syslog.h>
#include <unistd.h>
#include <tcl.h>
#include <pthread.h>

#undef INLINE
#ifdef __GNUC__
#  define INLINE __inline__
#else
#  define INLINE
#endif

#define FALSE 0
#define TRUE  1

static int debug = FALSE;
static char stderrFile[200];
static FILE *fdebug;
static FILE *frecord;
static int recording = FALSE;
static int pymolIsAlive = TRUE;

#define WANT_DEBUG      0
#define READ_DEBUG      0
#define WRITE_DEBUG     0
#define EXEC_DEBUG      0

#define FORCE_UPDATE            (1<<0)
#define CAN_UPDATE              (1<<1)
#define INVALIDATE_CACHE        (1<<3)
#define ATOM_SCALE_PENDING      (1<<4)
#define STICK_RADIUS_PENDING    (1<<5)
#define ROTATE_PENDING          (1<<6)
#define PAN_PENDING             (1<<7)
#define ZOOM_PENDING            (1<<8)
#define UPDATE_PENDING          (1<<9)
#define VIEWPORT_PENDING        (1<<10)

#define IO_TIMEOUT (30000)
#define KEEPSTATS       1
#define CVT2SECS(x)  ((double)(x).tv_sec) + ((double)(x).tv_usec * 1.0e-6)

typedef struct {
    pid_t pid;                          /* Child process. */
    size_t nFrames;                     /* # of frames sent to client. */
    size_t nBytes;                      /* # of bytes for all frames. */
    size_t nCommands;                   /* # of commands executed */
    double cmdTime;                     /* Elapsed time spend executing
                                         * commands. */
    struct timeval start;               /* Start of elapsed time. */
} Stats;

static Stats stats;

typedef struct Image {
    struct Image *nextPtr;              /* Next image in chain of images. The
                                         * list is ordered by the most
                                         * recently received image from the
                                         * pymol server to the least. */
    struct Image *prevPtr;              /* Previous image in chain of
                                         * images. The list is ordered by the
                                         * most recently received image from
                                         * the pymol server to the least. */
    int id;
    ssize_t nWritten;                   /* Number of bytes of image data
                                         * already delivered.*/
    size_t bytesLeft;                   /* Number of bytes of image data left
                                         * to delivered to the client. */
    unsigned char data[1];              /* Start of image data. We allocate
                                         * the size of the Image structure
                                         * plus the size of the image data. */
} Image;

#define BUFFER_SIZE             4096

typedef struct {
    Image *headPtr, *tailPtr;           /* List of images to be delivered to
                                         * the client.  The most recent images
                                         * are in the front of the list. */
} ImageList;

typedef struct {
    const char *ident;
    unsigned char *bytes;
    size_t fill;
    size_t mark;
    size_t newline;
    size_t bufferSize;
    int lastStatus;
    int fd;
} ReadBuffer;

#define BUFFER_OK                0
#define BUFFER_ERROR            -1
#define BUFFER_CONTINUE         -2
#define BUFFER_EOF              -3

typedef struct {
    Tcl_Interp *interp;
    unsigned int flags;                 /* Various flags. */
    int sin, sout;                      /* Server file descriptors. */
    int cin, cout;                      /* Client file descriptors. */
    ReadBuffer client;                  /* Read buffer for client input. */
    ReadBuffer server;                  /* Read buffer for server output. */
    int frame;
    int rockOffset;
    int cacheId;
    int error;
    int status;
    int width, height;                  /* Size of viewport. */
    float xAngle, yAngle, zAngle;       /* Euler angles of pending
                                         * rotation.  */
    float sphereScale;                  /* Atom scale of pending re-scale. */
    float stickRadius;                  /* Bond thickness of pending
                                         * re-scale. */
    float zoom;
    float xPan, yPan;
    pid_t pid;
} PymolProxy;

#if WANT_DEBUG
#define DEBUG(...)      if (debug) PrintToLog(__VA_ARGS__)
#else 
#define DEBUG(...) 
#endif

#define ERROR(...)      SysLog(LOG_ERR, __FILE__, __LINE__, __VA_ARGS__)
#define TRACE(...)      SysLog(LOG_DEBUG, __FILE__, __LINE__, __VA_ARGS__)
#define WARN(...)       SysLog(LOG_WARNING, __FILE__, __LINE__, __VA_ARGS__)
#define INFO(...)       SysLog(LOG_INFO, __FILE__, __LINE__, __VA_ARGS__)

static const char *syslogLevels[] = {
    "emergency",                        /* System is unusable */
    "alert",                            /* Action must be taken immediately */
    "critical",                         /* Critical conditions */
    "error",                            /* Error conditions */
    "warning",                          /* Warning conditions */
    "notice",                           /* Normal but significant condition */
    "info",                             /* Informational */
    "debug",                            /* Debug-level messages */
};

#if WANT_DEBUG
static void
PrintToLog TCL_VARARGS_DEF(const char *, arg1)
{
    const char *format;
    va_list args;
    
    format = TCL_VARARGS_START(const char *, arg1, args);
    fprintf(fdebug, "pymolproxy: ");
    vfprintf(fdebug, format, args);
    fprintf(fdebug, "\n");
    fflush(fdebug);
}
#endif

void
SysLog(int priority, const char *path, int lineNum, const char* fmt, ...)
{
#define MSG_LEN (2047)
    char message[MSG_LEN+1];
    const char *s;
    int length;
    va_list lst;

    va_start(lst, fmt);
    s = strrchr(path, '/');
    if (s == NULL) {
        s = path;
    } else {
        s++;
    }
    length = snprintf(message, MSG_LEN, "pymolproxy2 (%d) %s: %s:%d ", 
        getpid(), syslogLevels[priority],  s, lineNum);
    length += vsnprintf(message + length, MSG_LEN - length, fmt, lst);
    message[MSG_LEN] = '\0';
    if (debug) {
        DEBUG("%s\n", message);
    } else {
        syslog(priority, message, length);
    }
}

static void
Record TCL_VARARGS_DEF(const char *, arg1)
{
    const char *format;
    va_list args;
    
    format = TCL_VARARGS_START(const char *, arg1, args);
    vfprintf(frecord, format, args);
    fflush(frecord);
}

static int
SendCmd(PymolProxy *proxyPtr, const char *format, ...)
{
    va_list ap;
    char buffer[BUFSIZ];
    int result;
    ssize_t nWritten;
    size_t length;

    if (proxyPtr->error) {
        return TCL_ERROR;
    }
    
    va_start(ap, format);
    result = vsnprintf(buffer, BUFSIZ-1, format, ap);
    va_end(ap);
    
#ifdef EXEC_DEBUG
    DEBUG("to-pymol>(%s) code=%d", buffer, result);
#endif
    if (recording) {
        Record("%s\n", buffer);
    }
    
    /* Write the command out to the server. */
    length = strlen(buffer);
    nWritten = write(proxyPtr->sin, buffer, length);
    if (nWritten != length) {
        ERROR("short write to pymol (wrote=%d, should have been %d): %s",
              nWritten, length, strerror(errno));
    }
    return  proxyPtr->status;
}



/* -*- mode: c++; c-basic-offset: 4; indent-tabs-mode: nil -*- */
/*
 * Copyright (C) 2011, Purdue Research Foundation
 *
 * Author: George A. Howlett <gah@purdue.edu>
 */

static void
FlushReadBuffer(ReadBuffer *bp)
{
    bp->fill = bp->mark = 0;
    bp->newline = 0;
}

/**
 * \param[in] fd File descriptor to read
 * \param[in] bufferSize Block size to use in internal buffer
 */

static void
InitReadBuffer(ReadBuffer *bp, const char *id, int fd, size_t bufferSize)
{
    bp->ident = id;
    bp->bufferSize = bufferSize;
    bp->fd = fd;
    bp->lastStatus = BUFFER_OK;
    bp->bytes = malloc(bufferSize);
    FlushReadBuffer(bp);
}

/**
 * \brief Checks if a new line is currently in the buffer.
 *
 * \return the index of the character past the new line.
 */
static size_t
NextLine(ReadBuffer *bp)
{
    /* Check for a newline in the current buffer. */

    if (bp->newline > 0) {
        return bp->newline;
    } else {
        unsigned char *p;
        size_t newline;

        p = (unsigned char *)memchr(bp->bytes + bp->mark, '\n', 
                                    bp->fill - bp->mark);
        if (p == NULL) {
            newline = 0;
        } else {
            newline = (p - bp->bytes + 1);
        }
        bp->newline = newline;
        return newline;
    }
}

/**  
 * \brief Fills the buffer with available data.
 * 
 * Any existing data in the buffer is moved to the front of the buffer, 
 * then the channel is read to fill the rest of the buffer.
 *
 * \return If an error occur when reading the channel, then ERROR is
 * returned. ENDFILE is returned on EOF.  If the buffer can't be filled, 
 * then CONTINUE is returned.
 */
static int 
FillReadBuffer(ReadBuffer *bp)
{
    ssize_t numRead;
    size_t bytesLeft;

#if READ_DEBUG
    DEBUG("Enter FillReadBuffer for %s: mark=%lu fill=%lu", 
          bp->ident, bp->mark, bp->fill);
#endif
    if (bp->mark >= bp->fill) {
        FlushReadBuffer(bp);    /* Fully consumed buffer */
    }
    if (bp->mark > 0) {
        /* Some data has been consumed. Move the unconsumed data to the front
         * of the buffer. */
#if READ_DEBUG
        DEBUG("memmove %lu bytes", bp->fill - bp->mark);
#endif
        memmove(bp->bytes, bp->bytes + bp->mark, 
                bp->fill - bp->mark);
        bp->fill -= bp->mark;
        bp->mark = 0;
    }

    bytesLeft = bp->bufferSize - bp->fill;
#if READ_DEBUG
    DEBUG("going to read %lu bytes", bytesLeft);
#endif
    numRead = read(bp->fd, bp->bytes + bp->fill, bytesLeft);
    if (numRead == 0) {
        /* EOF */
#if READ_DEBUG
        DEBUG("EOF found reading %s buffer (fill=%d): ", 
              bp->ident, bp->fill);
#endif
        return BUFFER_EOF;
    }
    if (numRead < 0) {
        if (errno != EAGAIN) {
            ERROR("error reading %s buffer: %s", bp->ident, strerror(errno));
            return BUFFER_ERROR;
        }
#if READ_DEBUG
        DEBUG("Short read for buffer");
#endif
        return BUFFER_CONTINUE;
    }
    bp->fill += numRead;
#if READ_DEBUG
    DEBUG("Read %lu bytes", numRead);
#endif
    return ((size_t)numRead == bytesLeft) ? BUFFER_OK : BUFFER_CONTINUE;
}

/**
 * \brief Read the requested number of bytes from the buffer.

 * Fails if the requested number of bytes are not immediately 
 * available. Never should be short. 
 */
static int
ReadFollowingData(ReadBuffer *bp, unsigned char *out, size_t numBytes)
{
#if READ_DEBUG
    DEBUG("Enter ReadFollowingData %s", bp->ident);
#endif
    while (numBytes > 0) {
        size_t bytesLeft;

        bytesLeft = bp->fill - bp->mark;
        if (bytesLeft > 0) {
            int size;

            /* Pull bytes out of the buffer, updating the mark. */
            size = (bytesLeft >  numBytes) ? numBytes : bytesLeft;
            memcpy(out, bp->bytes + bp->mark, size);
            bp->mark += size;
            numBytes -= size;
            out += size;
        }
        if (numBytes == 0) {
            /* Received requested # bytes. */
            return BUFFER_OK;
        }
        /* Didn't get enough bytes, need to read some more. */
        bp->lastStatus = FillReadBuffer(bp);
        if ((bp->lastStatus == BUFFER_ERROR) || 
            (bp->lastStatus == BUFFER_EOF)) {
            return bp->lastStatus;
        }
    }
    return BUFFER_OK;
}

/** 
 * \brief Returns the next available line (terminated by a newline)
 * 
 * If insufficient data is in the buffer, then the channel is
 * read for more data.  If reading the channel results in a
 * short read, CONTINUE is returned and *numBytesPtr is set to 0.
 */
static int
GetLine(ReadBuffer *bp, size_t *numBytesPtr, const char **bytesPtr)
{
#if READ_DEBUG
    DEBUG("Enter GetLine");
#endif
    *numBytesPtr = 0;
    *bytesPtr = NULL;

    bp->lastStatus = BUFFER_OK;
    for (;;) {
        size_t newline;

        newline = NextLine(bp);
        if (newline > 0) {
            /* Start of the line. */
            *bytesPtr = (const char *)(bp->bytes + bp->mark);
            /* Number of bytes in the line. */
            *numBytesPtr = newline - bp->mark;
            bp->mark = newline;
            bp->newline = 0;
            return BUFFER_OK;
        }
        /* Couldn't find a newline, so it may be that we need to read some
         * more. Check first that last read wasn't a short read. */
        if (bp->lastStatus == BUFFER_CONTINUE) {
            /* No complete line just yet. */
            return BUFFER_CONTINUE;
        }
        /* Try to add more data to the buffer. */
        bp->lastStatus = FillReadBuffer(bp);
        if (bp->lastStatus == BUFFER_ERROR ||
            bp->lastStatus == BUFFER_EOF) {
            return bp->lastStatus;
        }
        /* OK or CONTINUE */
    }
    return BUFFER_CONTINUE;
}

static int
IsLineAvailable(ReadBuffer *bp)
{
    return (NextLine(bp) > 0);
}

static int
WaitForNextLine(ReadBuffer *bp, struct timeval *tvPtr)
{
    fd_set readFds;
    int n;

    if (IsLineAvailable(bp)) {
        return 1;
    }
    FD_ZERO(&readFds);
    FD_SET(bp->fd, &readFds);
    n = select(bp->fd+1, &readFds, NULL, NULL, tvPtr);
    return (n > 0);
}

INLINE static void
clear_error(PymolProxy *proxyPtr)
{
    proxyPtr->error = 0;
    proxyPtr->status = TCL_OK;
}


static int
CartoonCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
           const char *argv[])
{
    PymolProxy *p = clientData;
    int bool, defer, push, i;
    const char *model;

    clear_error(p);
    defer = push = FALSE;
    model = "all";
    bool = FALSE;
    for(i = 1; i < argc; i++) {
        if (strcmp(argv[i],"-defer") == 0) {
            defer = TRUE;
        } else if (strcmp(argv[i],"-push") == 0) {
            push = TRUE;
        } else if (strcmp(argv[i],"-model") == 0) {
            if (++i < argc) {
                model = argv[i];
            }
        } else { 
            if (Tcl_GetBoolean(interp, argv[i], &bool) != TCL_OK) {
                return TCL_ERROR;
            }
        }
    }
    p->flags |= INVALIDATE_CACHE;       /* cartoon */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    if (bool) {
        SendCmd(p, "show cartoon,%s\n", model);
    } else {
        SendCmd(p, "hide cartoon,%s\n", model);
    }
    return p->status;
}

static int
CartoonTraceCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
                const char *argv[])
{
    PymolProxy *p = clientData;
    int bool, defer, push, i;
    const char *model;

    clear_error(p);
    defer = push = bool = FALSE;
    model = "all";
    for(i = 1; i < argc; i++) {
        if (strcmp(argv[i],"-defer") == 0) {
            defer = TRUE;
        } else if (strcmp(argv[i],"-push") == 0) {
            push = TRUE;
        } else if (strcmp(argv[i],"-model") == 0) {
            if (++i < argc) {
                model = argv[i];
            }
        } else { 
            if (Tcl_GetBoolean(interp, argv[i], &bool) != TCL_OK) {
                return TCL_ERROR;
            }
        }
    }
    p->flags |= INVALIDATE_CACHE; /* cartoon_trace  */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    SendCmd(p, "set cartoon_trace,%d,%s\n", bool, model);
    return p->status;
}

static int
DisableCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
           const char *argv[])
{
    PymolProxy *p = clientData;
    const char *model = "all";
    int i, defer, push;

    clear_error(p);
    defer = push = FALSE;
    for(i = 1; i < argc; i++) {
        if (strcmp(argv[i], "-defer") == 0 )
            defer = 1;
        else if (strcmp(argv[i], "-push") == 0 )
            push = 1;
        else
            model = argv[i];
    }

    p->flags |= INVALIDATE_CACHE;       /* disable */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    SendCmd(p, "disable %s\n", model);
    return p->status;
}


static int
EnableCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
          const char *argv[])
{
    PymolProxy *p = clientData;
    const char *model;
    int i, defer, push;

    clear_error(p);
    push = defer = FALSE;
    model = "all";
    for(i = 1; i < argc; i++) {
        if (strcmp(argv[i],"-defer") == 0) {
            defer = TRUE;
        } else if (strcmp(argv[i], "-push") == 0) {
            push = TRUE;
        } else {
            model = argv[i];
        }
    }
    p->flags |= INVALIDATE_CACHE; /* enable */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    SendCmd(p, "enable %s\n", model);
    return p->status;
}

static int
FrameCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
         const char *argv[])
{
    PymolProxy *p = clientData;
    int i, push, defer, frame;

    clear_error(p);
    frame = 0;
    push = defer = FALSE;
    for(i = 1; i < argc; i++) { 
        if (strcmp(argv[i],"-defer") == 0) {
            defer = TRUE;
        } else if (strcmp(argv[i],"-push") == 0) {
            push = TRUE;
        } else {
            frame = atoi(argv[i]);
        }
    }
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    p->frame = frame;

    /* Does not invalidate cache? */

    SendCmd(p,"frame %d\n", frame);
    return p->status;
}


static int
LabelCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
         const char *argv[])
{
    PymolProxy *p = clientData;
    int i, push, defer, bool, size;
    const char *model;

    clear_error(p);
    model = "all";
    size = 14;
    bool = TRUE;
    push = defer = FALSE;
    for(i = 1; i < argc; i++) {
        if (strcmp(argv[i],"-defer") == 0) {
            defer = TRUE;
        } else if (strcmp(argv[i],"-push") == 0) {
            push = TRUE;
        } else if (strcmp(argv[i],"-model") == 0) {
            if (++i < argc) {
                model = argv[i];
            }
        } else if (strcmp(argv[i],"-size") == 0) {
            if (++i < argc) {
                size = atoi(argv[i]);
            }
        } else if (Tcl_GetBoolean(interp, argv[i], &bool) != TCL_OK) {
            return TCL_ERROR;
        }
    }
    p->flags |= INVALIDATE_CACHE;       /* label */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    SendCmd(p, "set label_color,white,%s\nset label_size,%d,%s\n", 
            model, size, model);
    if (bool) {
        SendCmd(p, "label %s,\"%%s%%s\" %% (ID,name)\n", model);
    } else {
        SendCmd(p, "label %s\n", model);
    }
    return p->status;
}

/* 
 * LoadPDBCmd --
 *
 *      Load a PDB into pymol.  We write the pdb data into a temporary file
 *      and then let pymol read it and delete it.  There is no good way to
 *      load PDB data into pymol without using a file.  The specially created
 *      routine "loadandremovepdbfile" in pymol will remove the file after
 *      loading it.  
 *
 */
static int
LoadPDBCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
           const char *argv[])
{
    PymolProxy *p = clientData;
    const char *string;
    const char *name;
    unsigned char *allocated;
    int state, defer, push;
    size_t numBytes;
    int i, j;
    int status;

    if (p == NULL){
        return TCL_ERROR;
    }
    clear_error(p);
    defer = push = FALSE;
    for(i = j = 1; i < argc; i++) {
        if (strcmp(argv[i],"-defer") == 0) {
            defer = TRUE;
        } else if (strcmp(argv[i],"-push") == 0) {
            push = TRUE;
        } else {
            if (j < i) {
                argv[j] = argv[i];
            }
            j++;
        }
    }
    argc = j;
    if (argc < 4) {
        Tcl_AppendResult(interp, "wrong # arguments: should be \"", argv[0],
                         " <data>|follows <model> <state> ?<nBytes>?\"",
                         (char *)NULL);
        return TCL_ERROR;
    }
    string = argv[1];
    name   = argv[2];
    if (Tcl_GetInt(interp, argv[3], &state) != TCL_OK) {
        return TCL_ERROR;
    }
    numBytes = 0;
    status = BUFFER_ERROR;
    if (strcmp(string, "follows") == 0) {
        int n;

        if (argc != 5) {
            Tcl_AppendResult(interp, "wrong # arguments: should be \"", argv[0],
                         " follows <model> <state> <nBytes>\"", (char *)NULL);
            return TCL_ERROR;
        }
        if (Tcl_GetInt(interp, argv[4], &n) != TCL_OK) {
            return TCL_ERROR;
        }
        if (n < 0) {
            Tcl_AppendResult(interp, "bad value for # bytes \"", argv[4],
                         "\"", (char *)NULL);
            return TCL_ERROR;
        }
        numBytes = (size_t)n;
    }
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    p->cacheId = state;

    /* Does not invalidate cache? */

    allocated = NULL;
    allocated = malloc(sizeof(char) * numBytes);
    if (allocated == NULL) {
        Tcl_AppendResult(interp, "can't allocate buffer for pdbdata.",
                         (char *)NULL);
        return TCL_ERROR;
    }
    status = ReadFollowingData(&p->client, allocated, numBytes);
    if (status != BUFFER_OK) {
        Tcl_AppendResult(interp, "can't read pdbdata from client.",
                         (char *)NULL);
        free(allocated);
        return TCL_ERROR;
    }
    string = (const char *)allocated;
    {
        int f;
        ssize_t nWritten;
        char fileName[200];

        strcpy(fileName, "/tmp/pdb.XXXXXX");
        p->status = TCL_ERROR;
        f = mkstemp(fileName);
        if (f < 0) {
            Tcl_AppendResult(interp, "can't create temporary file \"", 
                fileName, "\":", Tcl_PosixError(interp), (char *)NULL);
            goto error;
        } 
        nWritten = write(f, string, numBytes);
        if (numBytes != nWritten) {
            Tcl_AppendResult(interp, "can't write PDB data to \"",
                fileName, "\": ", Tcl_PosixError(interp), (char *)NULL);
            close(f);
            goto error;
        }
        close(f);
        SendCmd(p, "loadandremovepdbfile %s,%s,%d\n", fileName, name, state);
        p->status = TCL_OK;
    }
 error:
    if (allocated != NULL) {
        free(allocated);
    }
    return p->status;
}

static int
OrthoscopicCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
              const char *argv[])
{
    PymolProxy *p = clientData;
    int bool, defer, push, i;

    clear_error(p);
    defer = push = FALSE;
    bool = FALSE;
    for(i = 1; i < argc; i++) {
        if (strcmp(argv[i],"-defer") == 0) {
            defer = TRUE;
        } else if (strcmp(argv[i],"-push") == 0) {
            push = TRUE;
        } else { 
            if (Tcl_GetBoolean(interp, argv[i], &bool) != TCL_OK) {
                return TCL_ERROR;
            }
        }
    }
    p->flags |= INVALIDATE_CACHE; /* orthoscopic */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    SendCmd(p, "set orthoscopic=%d\n", bool);
    return p->status;
}

/* 
 * PanCmd --
 *
 *      Issue "move" commands for changes in the x and y coordinates of the
 *      camera.  The problem here is that there is no event compression.
 *      Consecutive "pan" commands are not compressed into a single
 *      directive.  The means that the pymol server will render scenes that
 *      are not used by the client.
 *
 *      Need to 1) defer the "move" commands until we find the next command
 *      isn't a "pan". 2) Track the x and y coordinates as they are
 *      compressed.
 */
static int
PanCmd(ClientData clientData, Tcl_Interp *interp, int argc, const char *argv[])
{
    PymolProxy *p = clientData;
    double x, y;
    int i;
    int defer, push;

    clear_error(p);
    defer = push = FALSE;
    for (i = 1; i < argc; i++) {
        if (strcmp(argv[i],"-defer") == 0) {
            defer = 1;
        } else if (strcmp(argv[i],"-push") == 0) {
            push = 1;
        } else { 
            break;
        }
    }
    if ((Tcl_GetDouble(interp, argv[i], &x) != TCL_OK) ||
        (Tcl_GetDouble(interp, argv[i+1], &y) != TCL_OK)) {
        return TCL_ERROR;
    }
    p->flags |= INVALIDATE_CACHE;       /* pan */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    if ((x != 0.0f) || (y != 0.0f)) {
        p->xPan = x * 0.05;
        p->yPan = -y * 0.05;
        p->flags |= PAN_PENDING;
    }
    return p->status;
}

static int
PngCmd(ClientData clientData, Tcl_Interp *interp, int argc, const char *argv[])
{
    PymolProxy *p = clientData;

    clear_error(p);

    /* Force pymol to update the current scene. */
    SendCmd(p, "refresh\n");
    /* This is a hack. We're encoding the filename to pass extra information
     * to the MyPNGWrite routine inside of pymol. Ideally these would be
     * parameters of a new "molvispng" command that would be passed all the
     * way through to MyPNGWrite.
     *
     * The extra information is contained in the token we get from the
     * molvisviewer client, the frame number, and rock offset. */
    SendCmd(p, "png -:%d:%d:%d\n", p->cacheId, p->frame, p->rockOffset);
    return p->status;
}


static int
PpmCmd(ClientData clientData, Tcl_Interp *interp, int argc, const char *argv[])
{
    PymolProxy *p = clientData;

    clear_error(p);

    /* Force pymol to update the current scene. */
    SendCmd(p, "refresh\n");
    /* This is a hack. We're encoding the filename to pass extra information
     * to the MyPNGWrite routine inside of pymol. Ideally these would be
     * parameters of a new "molvispng" command that would be passed all the
     * way through to MyPNGWrite.
     *
     * The extra information is contained in the token we get from the
     * molvisviewer client, the frame number, and rock offset. */
    SendCmd(p, "png -:%d:%d:%d,format=1\n", p->cacheId, p->frame, 
            p->rockOffset);
    p->flags &= ~(UPDATE_PENDING|FORCE_UPDATE);
    return p->status;
}


static int
PrintCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
         const char *argv[])
{
    PymolProxy *p = clientData;
    int width, height;
    const char *token, *bgcolor;

    clear_error(p);

    if (argc != 5) {
        Tcl_AppendResult(interp, "wrong # arguments: should be \"", 
                         argv[0], " token width height color\"", (char *)NULL);
        return TCL_ERROR;
    }
    token = argv[1];
    if (Tcl_GetInt(interp, argv[2], &width) != TCL_OK) {
        return TCL_ERROR;
    }
    if (Tcl_GetInt(interp, argv[3], &height) != TCL_OK) {
        return TCL_ERROR;
    }
    bgcolor = argv[4];
    /* Force pymol to update the current scene. */
    if (strcmp(bgcolor, "none") == 0) {
        SendCmd(p, "set ray_opaque_background,off\n");
        SendCmd(p, "refresh\n", bgcolor);
    } else {
        SendCmd(p, "set ray_opaque_background,on\n");
        SendCmd(p, "bg_color %s\nrefresh\n", bgcolor);
    }
    /* This is a hack. We're encoding the filename to pass extra information
     * to the MyPNGWrite routine inside of pymol. Ideally these would be
     * parameters of a new "molvispng" command that would be passed all the
     * way through to MyPNGWrite.  
     *
     * The extra information is contained in the token we get from the
     * molvisviewer client, the frame number, and rock offset.
     */
    SendCmd(p, "png -:%s:0:0,width=%d,height=%d,ray=1,dpi=300\n", 
            token, width, height);
    SendCmd(p, "bg_color black\n");
    return p->status;
}

static int
RawCmd(ClientData clientData, Tcl_Interp *interp, int argc, const char *argv[])
{
    PymolProxy *p = clientData;
    int arg, defer = 0, push = 0;
    const char *cmd;
    clear_error(p);

    cmd = NULL;
    defer = push = FALSE;
    for(arg = 1; arg < argc; arg++) {
        if (strcmp(argv[arg], "-defer") == 0)
            defer = 1;
        else if (strcmp(argv[arg], "-push") == 0)
            push = 1;
        else {
            cmd = argv[arg];
        }
    }

    p->flags |= INVALIDATE_CACHE; /* raw */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    SendCmd(p,"%s\n", cmd);
    return p->status;
}

static int
ResetCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
         const char *argv[])
{
    PymolProxy *p = clientData;
    int arg, push = 0, defer = 0;

    clear_error(p);
    defer = push = 0;
    for(arg = 1; arg < argc; arg++) {
        if ( strcmp(argv[arg],"-defer") == 0 )
            defer = 1;
        else if (strcmp(argv[arg],"-push") == 0 )
            push = 1;
    }
                
    p->flags |= INVALIDATE_CACHE; /* reset */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    SendCmd(p, "reset\nzoom complete=1\n");
    return p->status;
}

static int
RockCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
        const char *argv[])
{
    PymolProxy *p = clientData;
    float y = 0.0;
    int arg, push, defer;

    clear_error(p);

    defer = push = FALSE;
    for(arg = 1; arg < argc; arg++) {
        if ( strcmp(argv[arg],"-defer") == 0 )
            defer = 1;
        else if (strcmp(argv[arg],"-push") == 0 )
            push = 1;
        else
            y = atof( argv[arg] );
    }
                
    /* Does not invalidate cache. */

    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    SendCmd(p,"turn y, %f\n", y - p->rockOffset);
    p->rockOffset = y;
    return p->status;
}

static int
RepresentationCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
                  const char *argv[])
{
    PymolProxy *p = clientData;
    const char *model;
    const char *rep;
    int defer, push, i;

    clear_error(p);
    defer = push = FALSE;
    model = "all";
    rep = NULL;
    for (i = 1; i < argc; i++) {
        if (strcmp(argv[i],"-defer") == 0 ) {
            defer = TRUE;
        } else if (strcmp(argv[i],"-push") == 0) {
            push = TRUE;
        } else if (strcmp(argv[i],"-model") == 0) {
            if (++i < argc) {
                model = argv[i];
            }
        } else {
            rep = argv[i];
        }
    }
    if (rep == NULL) {
        Tcl_AppendResult(interp, "missing representation argument",
                         (char *)NULL);
        return TCL_ERROR;
    }

    p->flags |= INVALIDATE_CACHE; /* representation */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    if (strcmp(rep, "ballnstick") == 0) { /* Ball 'n Stick */
        SendCmd(p, 
              "set stick_color,white,%s\n"
              "show sticks,%s\n"
              "show spheres,%s\n"
              "hide lines,%s\n"
              "hide cartoon,%s\n",
              model, model, model, model, model);
    } else if (strcmp(rep, "spheres") == 0) { /* spheres */    
        SendCmd(p, 
              "hide sticks,%s\n"
              "show spheres,%s\n"
              "hide lines,%s\n"
              "hide cartoon,%s\n"
              "set sphere_quality,2,%s\n"
              "set ambient,.2,%s\n", 
              model, model, model, model, model, model);
    } else if (strcmp(rep, "none") == 0) { /* nothing */    
        SendCmd(p, 
              "hide sticks,%s\n", 
              "hide spheres,%s\n"
              "hide lines,%s\n"
              "hide cartoon,%s\n",
              model, model, model, model);
    } else if (strcmp(rep, "sticks") == 0) { /* sticks */    
        SendCmd(p, 
              "set stick_color,white,%s\n"
              "show sticks,%s\n"
              "hide spheres,%s\n"
              "hide lines,%s\n"
              "hide cartoon,%s\n",
              model, model, model, model, model);
    } else if (strcmp(rep, "lines") == 0) { /* lines */    
        SendCmd(p, 
              "hide sticks,%s\n"
              "hide spheres,%s\n"
              "show lines,%s\n"
              "hide cartoon,%s\n",
              model, model, model, model);
    } else if (strcmp(rep, "cartoon") == 0) { /* cartoon */    
        SendCmd(p, 
              "hide sticks,%s\n"
              "hide spheres,%s\n"
              "hide lines,%s\n"
              "show cartoon,%s\n", 
              model, model, model, model);
    } 
    return p->status;
}

/* 
 * RotateCmd --
 *
 *      Issue "turn" commands for changes in the angle of the camera.  The
 *      problem here is that there is no event compression.  Consecutive
 *      "rotate" commands are not compressed into a single directive.  The
 *      means that the pymol server will render many scene that are not used
 *      by the client.
 *
 *      Need to 1) defer the "turn" commands until we find the next command
 *      isn't a "rotate". 2) Track the rotation angles as they are compressed.
 */
static int
RotateCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
          const char *argv[])
{
    PymolProxy *p = clientData;
    float xAngle, yAngle, zAngle;
    int defer, push, arg, varg = 1;

    clear_error(p);
    defer = push = 0;
    xAngle = yAngle = zAngle = 0.0f;
    for(arg = 1; arg < argc; arg++) {
        if (strcmp(argv[arg],"-defer") == 0) {
            defer = 1; 
        } else if (strcmp(argv[arg],"-push") == 0) {
            push = 1;
        } else  if (varg == 1) {
            double value;
            if (Tcl_GetDouble(interp, argv[arg], &value) != TCL_OK) {
                return TCL_ERROR;
            }
            xAngle = (float)value;
            varg++;
        } else if (varg == 2) {
            double value;
            if (Tcl_GetDouble(interp, argv[arg], &value) != TCL_OK) {
                return TCL_ERROR;
            }
            yAngle = (float)value;
            varg++;
        } else if (varg == 3) {
            double value;
            if (Tcl_GetDouble(interp, argv[arg], &value) != TCL_OK) {
                return TCL_ERROR;
            }
            zAngle = (float)value;
            varg++;
        }
    } 
    p->flags |= INVALIDATE_CACHE; /* rotate */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    if ((xAngle != 0.0f) || (yAngle != 0.0f) || (zAngle != 0.0f)) {
        p->xAngle += xAngle;
        p->yAngle += yAngle;
        p->zAngle += zAngle;
        p->flags |= ROTATE_PENDING;
    }
    return p->status;
}

static int
ScreenCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
          const char *argv[])
{
    PymolProxy *p = clientData;
    int width = -1, height = -1;
    int defer, push, i, varg;

    clear_error(p);
    defer = push = FALSE;
    varg = 1;
    for(i = 1; i < argc; i++) {
        if ( strcmp(argv[i],"-defer") == 0 ) 
            defer = 1;
        else if ( strcmp(argv[i], "-push") == 0 )
            push = 1;
        else if (varg == 1) {
            width = atoi(argv[i]);
            height = width;
            varg++;
        }
        else if (varg == 2) {
            height = atoi(argv[i]);
            varg++;
        }
    }
    if ((width < 0) || (height < 0)) {
        return TCL_ERROR;
    }
    p->flags |= INVALIDATE_CACHE; /* viewport */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    p->width = width;
    p->height = height;
    p->flags |= VIEWPORT_PENDING;
    return p->status;
}

static int
SphereScaleCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
           const char *argv[])
{
    int defer = 0, push = 0, i;
    double scale;
    const char *model = "all";
    PymolProxy *p = clientData;

    clear_error(p);
    scale = 0.25f;
    for(i = 1; i < argc; i++) {
        if ( strcmp(argv[i],"-defer") == 0 ) {
            defer = 1;
        } else if (strcmp(argv[i],"-push") == 0) {
            push = 1;
        } else if (strcmp(argv[i],"-model") == 0) {
            if (++i < argc) {
                model = argv[i];
            }
        } else {
            if (Tcl_GetDouble(interp, argv[i], &scale) != TCL_OK) {
                return TCL_ERROR;
            }
        }
    }
    p->flags |= INVALIDATE_CACHE;  /* sphere_scale */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    if (strcmp(model, "all") == 0) {
        p->flags |= ATOM_SCALE_PENDING;
        p->sphereScale = scale;
    } else {
        SendCmd(p, "set sphere_scale,%f,%s\n", scale, model);
    }
    return p->status;
}

static int
StickRadiusCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
               const char *argv[])
{
    PymolProxy *p = clientData;
    int defer = 0, push = 0, i;
    double scale;
    const char *model = "all";

    clear_error(p);
    scale = 0.25f;
    for(i = 1; i < argc; i++) {
        if (strcmp(argv[i],"-defer") == 0 ) {
            defer = 1;
        } else if (strcmp(argv[i],"-push") == 0) {
            push = 1;
        } else if (strcmp(argv[i],"-model") == 0) {
            if (++i < argc)
                model = argv[i];
        } else {
            if (Tcl_GetDouble(interp, argv[i], &scale) != TCL_OK) {
                return TCL_ERROR;
            }
        }
    }
    p->flags |= INVALIDATE_CACHE;  /* stick_radius */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }

    if (strcmp(model, "all") == 0) {
        p->flags |= STICK_RADIUS_PENDING;
        p->stickRadius = scale;
    } else {
        SendCmd(p, "set stick_radius,%f,%s\n", scale, model);
    }
    return p->status;
}

static int
TransparencyCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
                const char *argv[])
{
    PymolProxy *p = clientData;
    const char *model;
    float transparency;
    int defer, push;
    int i;

    clear_error(p);
    model = "all";
    defer = push = FALSE;
    transparency = 0.0f;
    for(i = 1; i < argc; i++) {
        if ( strcmp(argv[i],"-defer") == 0 ) {
            defer = 1;
        } else if (strcmp(argv[i],"-push") == 0) {
            push = 1;
        } else if (strcmp(argv[i],"-model") == 0) {
            if (++i < argc) {
                model = argv[i];
            }
        } else {
            transparency = atof(argv[i]);
        }
    }
    p->flags |= INVALIDATE_CACHE; /* transparency */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    } 
    SendCmd(p, 
          "set sphere_transparency,%g,%s\n"
          "set stick_transparency,%g,%s\n"
          "set cartoon_transparency,%g,%s\n",
          transparency, model, transparency, model, 
          transparency, model);
    return p->status;
}

static int
VMouseCmd(ClientData clientData, Tcl_Interp *interp, int argc, 
          const char *argv[])
{
    PymolProxy *p = clientData;
    int i, defer = 0, push = 0, varg = 1;
    int arg1 = 0, arg2 = 0, arg3 = 0, arg4 = 0, arg5 = 0;

    clear_error(p);

    for(i = 1; i < argc; i++) {
        if (strcmp(argv[i], "-defer") == 0)
            defer = 1;
        else if (strcmp(argv[i], "-push") == 0)
            push = 1;
        else if (varg == 1) {
            arg1 = atoi(argv[i]);
            varg++;
        } else if (varg == 2) {
            arg2 = atoi(argv[i]);
            varg++;
        } else if (varg == 3) {
            arg3 = atoi(argv[i]);
            varg++;
        } else if (varg == 4) {
            arg4 = atoi(argv[i]);
            varg++;
        } else if (varg == 5) {
            arg5 = atoi(argv[i]);
            varg++;
        }
    }

    p->flags |= INVALIDATE_CACHE;       /* vmouse */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    SendCmd(p, "vmouse %d,%d,%d,%d,%d\n", arg1, arg2, arg3, arg4, arg5);
    return p->status;
}


/* 
 * ZoomCmd --
 *
 *      Issue "move" commands for changes in the z-coordinate of the camera.
 *      The problem here is that there is no event compression.  Consecutive
 *      "zoom" commands are not compressed into a single directive.  The means
 *      that the pymol server will render scenes that are not used by the
 *      client.
 *
 *      Need to 1) defer the "move" commands until we find the next command
 *      isn't a "zoom". 2) Track the z-coordinate as they are compressed.
 */
static int
ZoomCmd(ClientData clientData, Tcl_Interp *interp, int argc, const char *argv[])
{
    PymolProxy *p = clientData;
    double factor = 0.0;
    int defer = 0, push = 0, i, varg = 1;

    clear_error(p);

    for(i = 1; i < argc; i++) {
        if (strcmp(argv[i],"-defer") == 0)
            defer = 1;
        else if (strcmp(argv[i],"-push") == 0)
            push = 1;
        else if (varg == 1) {
            double value;
            if (Tcl_GetDouble(interp, argv[i], &value) != TCL_OK) {
                return TCL_ERROR;
            }
            factor = (float)value;
            varg++;
        }
    }
    p->flags |= INVALIDATE_CACHE; /* Zoom */
    if (!defer || push) {
        p->flags |= UPDATE_PENDING;
    }
    if (push) {
        p->flags |= FORCE_UPDATE;
    }
    if (factor != 0.0) {
        p->zoom = factor;
        p->flags |= ZOOM_PENDING;
    }
    return p->status;
}

        

static int
ExecuteCommand(Tcl_Interp *interp, Tcl_DString *dsPtr) 
{
    struct timeval tv;
    double start, finish;
    int result;

    gettimeofday(&tv, NULL);
    start = CVT2SECS(tv);

#if EXEC_DEBUG
    DEBUG("command from client is (%s)", Tcl_DStringValue(dsPtr));
#endif
    result = Tcl_Eval(interp, Tcl_DStringValue(dsPtr));
    if (result != TCL_OK) {
#if EXEC_DEBUG
        DEBUG("result was %s\n", Tcl_GetString(Tcl_GetObjResult(interp)));
#endif
    }
    gettimeofday(&tv, NULL);
    finish = CVT2SECS(tv);

    stats.cmdTime += finish - start;
    stats.nCommands++;
    Tcl_DStringSetLength(dsPtr, 0);
    return result;
}

static void
SetViewport(PymolProxy *p)
{
    if (p->flags & VIEWPORT_PENDING) {
        SendCmd(p, "viewport %d,%d\n", p->width, p->height);
        SendCmd(p, "refresh\n");
        p->flags &= ~VIEWPORT_PENDING;
    }
}

static void
SetZoom(PymolProxy *p)
{
    if (p->flags & ZOOM_PENDING) {
        SendCmd(p, "move z,%f\n", p->zoom);
        p->flags &= ~ZOOM_PENDING;
    }
}

static void
SetPan(PymolProxy *p)
{
    if (p->flags & PAN_PENDING) {
        SendCmd(p, "move x,%f\nmove y,%f\n", p->xPan, p->yPan);
        p->flags &= ~PAN_PENDING;
    }
}

static void
SetRotation(PymolProxy *p)
{
    if (p->flags & ROTATE_PENDING) {
        /* Every pymol command line generates a new rendering. Execute all
         * three turns as a single command line. */
        SendCmd(p,"turn x,%f\nturn y,%f\nturn z,%f\n", p->xAngle, p->yAngle, 
                p->zAngle);
        p->xAngle = p->yAngle = p->zAngle = 0.0f;
        p->flags &= ~ROTATE_PENDING;
    }
}

static void
SetSphereScale(PymolProxy *p)
{
    if (p->flags & ATOM_SCALE_PENDING) {
        SendCmd(p, "set sphere_scale,%f,all\n", p->sphereScale);
        p->flags &= ~ATOM_SCALE_PENDING;
    }
}

static void
SetStickRadius(PymolProxy *p)
{
    if (p->flags & STICK_RADIUS_PENDING) {
        SendCmd(p, "set stick_radius,%f,all\n", p->stickRadius);
        p->flags &= ~STICK_RADIUS_PENDING;
    }
}

static void
UpdateSettings(PymolProxy *p)
{
    /* Handle all the pending setting changes now. */
    if (p->flags & VIEWPORT_PENDING) {
        SetViewport(p);
    }
    if (p->flags & ROTATE_PENDING) {
        SetRotation(p);
    }
    if (p->flags & PAN_PENDING) {
        SetPan(p);
    }
    if (p->flags & ZOOM_PENDING) {
        SetZoom(p);
    }
    if (p->flags & ATOM_SCALE_PENDING) {
        SetSphereScale(p);
    }
    if (p->flags & STICK_RADIUS_PENDING) {
        SetStickRadius(p);
    }
}

static Image *
NewImage(ImageList *listPtr, size_t dataLength)
{
    Image *imgPtr;
    static int id = 0;

    imgPtr = malloc(sizeof(Image) + dataLength);
    if (imgPtr == NULL) {
        ERROR("can't allocate image of %lu bytes", 
              (unsigned long)(sizeof(Image) + dataLength));
        abort();
    }
    imgPtr->prevPtr = imgPtr->nextPtr = NULL;
    imgPtr->bytesLeft = dataLength;
    imgPtr->id = id++;
#if WRITE_DEBUG
    DEBUG("NewImage: allocating image %d of %d bytes", imgPtr->id, dataLength);
#endif
    if (listPtr->headPtr != NULL) {
        listPtr->headPtr->prevPtr = imgPtr;
    }
    imgPtr->nextPtr = listPtr->headPtr;
    if (listPtr->tailPtr == NULL) {
        listPtr->tailPtr = imgPtr;
    }
    listPtr->headPtr = imgPtr;
    imgPtr->nWritten = 0;
    return imgPtr;
}

INLINE static void
FreeImage(Image *imgPtr)
{
    assert(imgPtr != NULL);
    free(imgPtr);
}


static void
WriteImages(ImageList *listPtr, int fd)
{
    Image *imgPtr, *prevPtr; 

    if (listPtr->tailPtr == NULL) {
        ERROR("Should not be here: no image available to write");
        return;
    }
#if WRITE_DEBUG
        DEBUG("Entering WriteImages");
#endif
    for (imgPtr = listPtr->tailPtr; imgPtr != NULL; imgPtr = prevPtr) {
        ssize_t bytesLeft;

        assert(imgPtr->nextPtr == NULL);
        prevPtr = imgPtr->prevPtr;
#if WRITE_DEBUG
        DEBUG("WriteImages: image %d of %d bytes.", imgPtr->id, 
              imgPtr->bytesLeft);
#endif
        for (bytesLeft = imgPtr->bytesLeft; bytesLeft > 0; /*empty*/) {
            ssize_t nWritten;
#if WRITE_DEBUG
            DEBUG("image %d: bytesLeft=%d", imgPtr->id, bytesLeft);
#endif
            nWritten = write(fd, imgPtr->data + imgPtr->nWritten, bytesLeft);
#if WRITE_DEBUG
            DEBUG("image %d: wrote %d bytes.", imgPtr->id, nWritten);
#endif
            if (nWritten < 0) {
                ERROR("Error writing fd=%d, %s", fd, strerror(errno));
#if WRITE_DEBUG
                DEBUG("Abnormal exit WriteImages");
#endif
                return;
            }
            bytesLeft -= nWritten;
            if (bytesLeft > 0) {
#if WRITE_DEBUG
                DEBUG("image %d, wrote a short buffer, %d bytes left.", 
                      imgPtr->id, bytesLeft);
#endif
                /* Wrote a short buffer, means we would block. */
                imgPtr->nWritten += nWritten;
                imgPtr->bytesLeft = bytesLeft;
#if WRITE_DEBUG
                DEBUG("Abnormal exit WriteImages");
#endif
                return;
            }
            imgPtr->nWritten += nWritten;
        }
        /* Check if image is on the head.  */
        listPtr->tailPtr = prevPtr;
        if (prevPtr != NULL) {
            prevPtr->nextPtr = NULL;
        }
        FreeImage(imgPtr);
    }
    listPtr->headPtr = NULL;
#if WRITE_DEBUG
    DEBUG("Exit WriteImages");
#endif
}

#if KEEPSTATS

static int
WriteStats(const char *who, int code) 
{
    double start, finish;
    pid_t pid;
    char buf[BUFSIZ];
    Tcl_DString ds;

    {
        struct timeval tv;

        /* Get ending time.  */
        gettimeofday(&tv, NULL);
        finish = CVT2SECS(tv);
        tv = stats.start;
        start = CVT2SECS(tv);
    }
    /* 
     * Session information:
     *   1. Start date of session in seconds.
     *   2. Process ID
     *   3. Number of frames returned.
     *   4. Number of bytes total returned (in frames).
     *   5. Total elapsed time of all commands.
     *   6. Total elapsed time of session.
     *   7. Exit code of pymol server.
     *   8. User time.  
     *   9. System time.
     *  10. Maximum resident size.
     */ 
    pid = getpid();
    Tcl_DStringInit(&ds);
    
    sprintf(buf, "<session server=\"%s\" ", who);
    Tcl_DStringAppend(&ds, buf, -1);

    strcpy(buf, ctime(&stats.start.tv_sec));

    buf[strlen(buf) - 1] = '\0';
    Tcl_DStringAppend(&ds, "date=\"", -1);
    Tcl_DStringAppend(&ds, buf, -1);
    Tcl_DStringAppend(&ds, "\" ", -1);

    sprintf(buf, "date_secs=\"%ld\" ", stats.start.tv_sec);
    Tcl_DStringAppend(&ds, buf, -1);

    sprintf(buf, "pid=\"%d\" ", pid);
    Tcl_DStringAppend(&ds, buf, -1);
    sprintf(buf, "num_frames=\"%lu\" ", (unsigned long int)stats.nFrames);
    Tcl_DStringAppend(&ds, buf, -1);
    sprintf(buf, "frame_bytes=\"%lu\" ", (unsigned long int)stats.nBytes);
    Tcl_DStringAppend(&ds, buf, -1);
    sprintf(buf, "num_commands=\"%lu\" ", (unsigned long int)stats.nCommands);
    Tcl_DStringAppend(&ds, buf, -1);
    sprintf(buf, "cmd_time=\"%g\" ", stats.cmdTime);
    Tcl_DStringAppend(&ds, buf, -1);
    sprintf(buf, "session_time=\"%g\" ", finish - start);
    Tcl_DStringAppend(&ds, buf, -1);
    sprintf(buf, "status=\"%d\" ", code);
    Tcl_DStringAppend(&ds, buf, -1);
    {
        long clocksPerSec = sysconf(_SC_CLK_TCK);
        double clockRes = 1.0 / clocksPerSec;
        struct tms tms;

        memset(&tms, 0, sizeof(tms));
        times(&tms);
        sprintf(buf, "utime=\"%g\" ", tms.tms_utime * clockRes);
        Tcl_DStringAppend(&ds, buf, -1);
        sprintf(buf, "stime=\"%g\" ", tms.tms_stime * clockRes);
        Tcl_DStringAppend(&ds, buf, -1);
        sprintf(buf, "cutime=\"%g\" ", tms.tms_cutime * clockRes);
        Tcl_DStringAppend(&ds, buf, -1);
        sprintf(buf, "cstime=\"%g\" ", tms.tms_cstime * clockRes);
        Tcl_DStringAppend(&ds, buf, -1);
    }
    Tcl_DStringAppend(&ds, "/>\n", -1);

    {
        int f;
        ssize_t length;
        int result;

#define STATSDIR        "/var/tmp/visservers"
#define STATSFILE       STATSDIR "/" "data.xml"
        if (access(STATSDIR, X_OK) != 0) {
            mkdir(STATSDIR, 0770);
        }
        length = Tcl_DStringLength(&ds);
        f = open(STATSFILE, O_APPEND | O_CREAT | O_WRONLY, 0600);
        result = FALSE;
        if (f < 0) {
            goto error;
        }
        if (write(f, Tcl_DStringValue(&ds), length) != length) {
            goto error;
        }
        result = TRUE;
 error:
        if (f >= 0) {
            close(f);
        }
        Tcl_DStringFree(&ds);
        return result;
    }
}
#endif

static void
ChildHandler(int sigNum) 
{
    ERROR("pymol (%d) died unexpectedly", stats.pid);
    pymolIsAlive = FALSE;
    /*DoExit(1);*/
}

typedef struct {
    const char *name;
    Tcl_CmdProc *proc;
} CmdProc;

static CmdProc cmdProcs[] = {
    { "cartoon",        CartoonCmd        },       
    { "cartoontrace",   CartoonTraceCmd   },  
    { "disable",        DisableCmd        },       
    { "enable",         EnableCmd         },        
    { "frame",          FrameCmd          },         
    { "label",          LabelCmd          },         
    { "loadpdb",        LoadPDBCmd        },       
    { "orthoscopic",    OrthoscopicCmd    },   
    { "pan",            PanCmd            },           
    { "png",            PngCmd            },           
    { "ppm",            PpmCmd            },           
    { "print",          PrintCmd          },         
    { "raw",            RawCmd            },           
    { "representation", RepresentationCmd },
    { "reset",          ResetCmd          },         
    { "rock",           RockCmd           },          
    { "rotate",         RotateCmd         },        
    { "screen",         ScreenCmd         },        
    { "spherescale",    SphereScaleCmd    },   
    { "stickradius",    StickRadiusCmd    },   
    { "transparency",   TransparencyCmd   },  
    { "viewport",       ScreenCmd         },        
    { "vmouse",         VMouseCmd         },        
    { "zoom",           ZoomCmd           },          
    { NULL,             NULL              }
};

static int
InitProxy(PymolProxy *p, const char *fileName, char *const *argv)
{
    int sin[2], sout[2];                /* Pipes to connect to server. */
    pid_t child;
    struct timeval end;

#if DEBUG
    DEBUG("Entering InitProxy\n");
#endif
    /* Create tow pipes for communication with the external application. One
     * each for the applications's: stdin and stdout.  */

    if (pipe(sin) == -1) {
        return -1;
    }
    if (pipe(sout) == -1) {
        close(sin[0]);
        close(sin[1]);
        return -1;
    }

    /* Fork the new process.  Connect I/O to the new socket.  */
    child = fork();
    if (child < 0) {
        ERROR("can't fork process: %s\n", strerror(errno));
        return -3;
    }

    if (child == 0) {                   /* Child process */
        int f;

        /* 
         * Create a new process group, so we can later kill this process and
         * all its children without affecting the process that created this
         * one.
         */
        setpgid(child, 0); 
        
        /* Redirect stdin, stdout, and stderr to pipes before execing */ 

        dup2(sin[0],  0);               /* Server standard input */
        dup2(sout[1], 1);               /* Server standard output */
        f = open(fileName, O_WRONLY | O_CREAT | O_TRUNC, 0600);
        if (f < 0) {
            ERROR("can't open server error file `%s': %s", fileName, 
                  strerror(errno));
            exit(1);
        }
        dup2(f, 2);                     /* Redirect stderr to a file */
        
        /* Close all other descriptors  */        
        for (f = 3; f < FD_SETSIZE; f++) {
            close(f);
        }
        INFO("attempting to start \"%s\"", argv[0]);
        execvp(argv[0], argv);
        ERROR("can't exec `%s': %s", argv[0], strerror(errno));
        exit(-1);
    } else {
        pymolIsAlive = TRUE;
        signal(SIGCHLD, ChildHandler);
    }
    stats.pid = child;

#if DEBUG
    DEBUG("Started %s DISPLAY=%s\n", argv[0], getenv("DISPLAY"));
#endif
    /* close opposite end of pipe, these now belong to the child process  */
    close(sin[0]);
    close(sout[1]);

    memset(p, 0, sizeof(PymolProxy));
    p->sin        = sin[1];
    p->sout       = sout[0];
    p->cin        = fileno(stdout);
    p->cout       = fileno(stdin);
    p->flags      = CAN_UPDATE;
    p->frame      = 1;
    p->pid      = child;
    InitReadBuffer(&p->client, "client", p->cout, 1<<16);
    InitReadBuffer(&p->server, "server", p->sout, 1<<18);

    /* Create safe interpreter and add pymol-specific commands to it. */
    {
        Tcl_Interp *interp;
        CmdProc *cp;

        interp = Tcl_CreateInterp();
        Tcl_MakeSafe(interp);

        for (cp = cmdProcs; cp->name != NULL; cp++) {
#if DEBUG
            DEBUG("Adding command %s\n", cp->name);
#endif
            Tcl_CreateCommand(interp, cp->name, cp->proc, p, NULL);
        }
        p->interp = interp;
    }
    gettimeofday(&end, NULL);
    stats.start = end;
    return 1;
}

static int
FreeProxy(PymolProxy *p)
{
    int result, status;

#if DEBUG
    DEBUG("Enter FreeProxy");
#endif
    close(p->cout);
    close(p->sout);
    close(p->cin);
    close(p->sin);

    Tcl_DeleteInterp(p->interp);
#if KEEPSTATS
    WriteStats("pymolproxy", 0);
#endif

#if DEBUG
    DEBUG("Waiting for pymol server to exit");
#endif
    alarm(5);
    if (waitpid(p->pid, &result, 0) < 0) {
        ERROR("error waiting on pymol server to exit: %s", strerror(errno));
    }
#if DEBUG
    DEBUG("attempting to signal (SIGTERM) pymol server.");
#endif
    kill(-p->pid, SIGTERM);             // Kill process group
    alarm(5);
    
#if DEBUG
    DEBUG("Waiting for pymol server to exit after SIGTERM");
#endif
    if (waitpid(p->pid, &result, 0) < 0) {
        if (errno != ECHILD) {
            ERROR("error waiting on pymol server to exit after SIGTERM: %s", 
                  strerror(errno));
        }
    }
    status = -1;
    while ((status == -1) && (errno == EINTR)) {
#if DEBUG
        DEBUG("Attempting to signal (SIGKILL) pymol server.");
#endif
        kill(-p->pid, SIGKILL);         // Kill process group
        alarm(10);
#if DEBUG
        DEBUG("Waiting for pymol server to exit after SIGKILL");
#endif
        status = waitpid(p->pid, &result, 0);
        alarm(0); 
    }
    INFO("pymol server process ended (result=%d)", result);

    if (WIFEXITED(result)) {
        result = WEXITSTATUS(result);
    }
    unlink(stderrFile);
    return result;
}


static void *
ClientToServer(void *clientData)
{
    PymolProxy *p = clientData;
    Tcl_DString command;
    struct timeval tv, *tvPtr;

#if READ_DEBUG
    DEBUG("Reader thread started");
#endif
    Tcl_DStringInit(&command);
    while (pymolIsAlive) {
        tvPtr = NULL;
#if READ_DEBUG
        DEBUG("Start I/O set");
#endif
        while ((pymolIsAlive) && (WaitForNextLine(&p->client, tvPtr))) {
            size_t numBytes;
            const char *line;
            int status;

            status = GetLine(&p->client, &numBytes, &line);
            if (status != BUFFER_OK) {
                ERROR("can't read client stdout (nBytes=%d): %s\n", numBytes,
                      strerror(errno));
                goto done;
            }
            Tcl_DStringAppend(&command, line, numBytes);
            if (Tcl_CommandComplete(Tcl_DStringValue(&command))) {
                int result;
                    
                /* May execute more than one command. */
                result = ExecuteCommand(p->interp, &command);
                if (result == TCL_BREAK) {
#if READ_DEBUG
                    DEBUG("TCL_BREAK found");
#endif
                    break;              /* This was caused by a "imgflush"
                                         * command. Break out of the read loop
                                         * and allow a new image to be
                                         * rendered. */
                }
                if (p->flags & FORCE_UPDATE) {
#if READ_DEBUG
                    DEBUG("FORCE_UPDATE set");
#endif
                    break;
                }
            }
            tv.tv_sec = 0L;
            tv.tv_usec = 0L;    /* On successive reads, we break
                                         *  out * if no data is
                                         *  available. */
            tvPtr = &tv;                        
        }
#if READ_DEBUG
        DEBUG("Finish I/O set");
#endif
        /* Handle all the pending setting changes now. */
        UpdateSettings(p);

        /* We might want to refresh the image if we're not currently
         * transmitting an image back to the client. The image will be
         * refreshed after the image has been completely transmitted. */
        if (p->flags & UPDATE_PENDING) {
#if READ_DEBUG
            DEBUG("calling ppm because of update");
#endif
            Tcl_Eval(p->interp, "ppm");
            p->flags &= ~(UPDATE_PENDING|FORCE_UPDATE);
        }
    }
 done:
#if READ_DEBUG
    DEBUG("Leaving Reader thread");
#endif
    return NULL;
}

static void *
ServerToClient(void *clientData)
{
    ReadBuffer *bp = clientData;
    ImageList list;

#if WRITE_DEBUG
    DEBUG("Writer thread started");
#endif
    list.headPtr = list.tailPtr = NULL;
    while (pymolIsAlive) {
        while (WaitForNextLine(bp, NULL)) {
            Image *imgPtr;
            const char *line;
            char header[200];
            size_t len;
            int numBytes;
            size_t hdrLength;
            int frameNum, rockOffset;
            char cacheId[200];

            /* Keep reading lines untils we find a "image follows:" line */
            if (GetLine(bp, &len, &line) != BUFFER_OK) {
#if WRITE_DEBUG
                DEBUG("Leaving Writer thread");
#endif
                return NULL;
            }
#if WRITE_DEBUG
            DEBUG("Writer: line found is %s\n", line);
#endif
            if (strncmp(line, "image follows: ", 15) != 0) {
                continue;
            }
            if (sscanf(line, "image follows: %d %s %d %d\n", &numBytes, cacheId,
                       &frameNum, &rockOffset) != 4) {
                ERROR("can't get # bytes from \"%s\"", line);
                DEBUG("Leaving Writer thread");
                return NULL;
            } 
#if WRITE_DEBUG
            DEBUG("found image line \"%.*s\"", numBytes, line);
#endif
            sprintf(header, "nv>image %d %s %d %d\n", numBytes, cacheId, 
                    frameNum, rockOffset);
            hdrLength = strlen(header);
#if WRITE_DEBUG
            DEBUG("Queueing image numBytes=%d cacheId=%s, frameNum=%d, rockOffset=%d size=%d\n", numBytes, cacheId, frameNum, rockOffset, numBytes + hdrLength);
#endif
            imgPtr = NewImage(&list, numBytes + hdrLength);
            memcpy(imgPtr->data, header, hdrLength);
            if (ReadFollowingData(bp, imgPtr->data + hdrLength, 
                        (size_t)numBytes) != BUFFER_OK) {
                ERROR("can't read %d bytes for \"image follows\" buffer: %s", 
                      numBytes, strerror(errno));
#if WRITE_DEBUG
                DEBUG("Leaving Writer thread");
#endif
                return NULL;
            }
            stats.nFrames++;
            stats.nBytes += numBytes;
            {
                struct timeval tv;
                fd_set writeFds;
                int fd;

                tv.tv_sec = tv.tv_usec = 0L;
                FD_ZERO(&writeFds);
                fd = fileno(stdout);
                FD_SET(fd, &writeFds);
                if (select(fd+1, NULL, &writeFds, NULL, &tv) > 0) {
                    WriteImages(&list, fd);
                }
            }
        }
    }
#if WRITE_DEBUG
    DEBUG("Leaving Writer thread");
#endif
    return NULL;
}

int
main(int argc, char **argv)
{
    PymolProxy proxy;
    pthread_t thread1, thread2;

    sprintf(stderrFile, "/tmp/pymol%d.stderr", getpid());
    fdebug = stderr;
    if (debug) {
        fdebug = fopen("/tmp/pymolproxy.log", "w");
    }    
    frecord = NULL;
    if (recording) {
        char fileName[200];

        sprintf(fileName, "/tmp/pymolproxy%d.py", getpid());
        frecord = fopen(fileName, "w");
    }    
    fprintf(stdout, "PyMol 1.0\n");
    fflush(stdout);

    INFO("Starting pymolproxy (threaded version)");

    InitProxy(&proxy, stderrFile, argv + 1);
    if (pthread_create(&thread1, NULL, &ClientToServer, &proxy) < 0) {
        ERROR("Can't create reader thread: %s", strerror(errno));
    }
    if (pthread_create(&thread2, NULL, &ServerToClient, &proxy.server) < 0) {
        ERROR("Can't create writer thread: %s", strerror(errno));
    }
    if (pthread_join(thread1, NULL) < 0) {
        ERROR("Can't join reader thread: %s", strerror(errno));
    } 
    return FreeProxy(&proxy);
}