TEST(lagi_cajun, ReaderParserErrors) {
json::UnknownElement ue;
std::istringstream missing_comma("[1 2]");
EXPECT_THROW(json::Reader::Read(ue, missing_comma), json::Exception);
std::istringstream garbage_after_number("123!");
EXPECT_THROW(json::Reader::Read(ue, garbage_after_number), json::Exception);
std::istringstream unexpected_eof("[");
EXPECT_THROW(json::Reader::Read(ue, unexpected_eof), json::Exception);
std::istringstream bad_initial_token("]");
EXPECT_THROW(json::Reader::Read(ue, bad_initial_token), json::Exception);
std::istringstream garbage_after_end("[]a");
EXPECT_THROW(json::Reader::Read(ue, garbage_after_end), json::Exception);
std::istringstream empty_str("");
EXPECT_THROW(json::Reader::Read(ue, empty_str), json::Exception);
std::istringstream dupe_keys("{\"a\": [], \"a\": 0}");
EXPECT_THROW(json::Reader::Read(ue, dupe_keys), json::Exception);
std::istringstream unique_keys("{\"a\": [], \"b\": 0}");
EXPECT_NO_THROW(json::Reader::Read(ue, unique_keys));
}
TEST(lagi_cajun, ReaderScanErrors) {
json::UnknownElement ue;
std::istringstream doc("[true, false, thiswontwork]");
EXPECT_THROW(json::Reader::Read(ue, doc), json::Exception);
std::istringstream garbage_after_number("123abc");
EXPECT_THROW(json::Reader::Read(ue, garbage_after_number), json::Exception);
std::istringstream bad_escape("\"\\j\"");
EXPECT_THROW(json::Reader::Read(ue, bad_escape), json::Exception);
std::istringstream unexpected_eof("\"abc");
EXPECT_THROW(json::Reader::Read(ue, unexpected_eof), json::Exception);
}
unsigned bs_fill_byte(struct bitstream_st *bs, int eofok)
{
unsigned n;
assert(INRANGE(bs->byte_end,
bs->byte_window, AFTER_OF(bs->byte_window)));
assert(INRANGE(bs->byte_p, bs->byte_window, bs->byte_end));
n = bs_read(bs, bs->byte_window, sizeof(bs->byte_window));
bs->eof = n != sizeof(bs->byte_window);
bs->byte_p = bs->byte_window;
bs->byte_end = &bs->byte_window[n];
if (!n && !eofok)
unexpected_eof(bs);
return n;
} /* bs_fill_byte */
/**
* \brief Loads the memo database from disk
*/
void readMemoData(void)
{
RegNickList *nick = NULL;
RegNickList *from, *rnlb;
MemoList *newmemo;
char *command;
char *topic;
int done = 0;
unsigned long linenum = 0;
db.ms = fopen(MS_DB, "r");
if (db.ms == NULL)
return;
while (!done) {
if (!(sfgets(dbLine, 2048, db.ms))) {
if (!done) {
unexpected_eof(MS_DB);
}
done = 1;
fclose(db.ms);
return;
}
linenum++;
if (parse_init(&state, dbLine) != 0) {
/*! \bug XXX be nicer here... */
abort();
}
command = parse_getarg(&state);
if (strcmp(command, "data") == 0) {
nick = getRegNickData(parse_getarg(&state));
/*! \bug Increment the arguments.. we REALLY need to fix the dbs */
(void)parse_getarg(&state);
(void)parse_getarg(&state);
if (nick) {
nick->memos->flags = atoi(parse_getarg(&state));
nick->memos->max = atoi(parse_getarg(&state));
if (nick->memos->max <= 0)
nick->memos->max = MS_DEF_RCV_MAX;
}
} else if (strcmp(command, "mblock") == 0) {
MemoBlock *mbitem;
if (nick && nick->memos) {
char *nickToBlock;
if ((nickToBlock = parse_getarg(&state))
&& (rnlb = getRegNickData(nickToBlock))) {
mbitem = (MemoBlock *) oalloc(sizeof(MemoBlock));
mbitem->blockId = rnlb->regnum;
mbitem->next = nick->memos->firstMblock;
nick->memos->firstMblock = mbitem;
}
}
} else if (strcmp(command, "redirect") == 0) {
nick = getRegNickData(parse_getarg(&state));
if (nick != NULL)
nick->memos->forward =
getRegNickData(parse_getarg(&state));
} else if (strcmp(command, "memo") == 0) {
char *cn;
cn = parse_getarg(&state);
nick = getRegNickData(cn);
if (nick == NULL) {
printf("memo: %s not valid\n", cn);
continue;
}
newmemo = (MemoList *) oalloc(sizeof(MemoList));
newmemo->realto = nick;
/*! \bug Increment the argument 1, we need to fix the db */
(void)parse_getarg(&state);
newmemo->flags = atoi(parse_getarg(&state));
newmemo->sent = (time_t) atol(parse_getarg(&state));
/* Memo expiration code */
if ((time(NULL) - newmemo->sent) >= NICKDROPTIME
&& !(newmemo->flags & MEMO_SAVE)) {
FREE(newmemo);
continue;
}
strncpyzt(newmemo->from, parse_getarg(&state), NICKLEN);
from = getRegNickData(newmemo->from);
strncpyzt(newmemo->to, parse_getarg(&state), CHANLEN);
/* Read the memo, skipping the leading : */
topic = parse_getallargs(&state);
if (topic == NULL) {
FREE(newmemo);
continue;
}
newmemo->memotxt = strdup(topic);
/* Add the memo to the users memobox */
LIST_ENTRY_INIT(newmemo, ml_lst);
LIST_INSERT_HEAD(&nick->memos->mb_memos, newmemo, ml_lst);
if (from && newmemo->flags & MEMO_UNREAD)
LIST_INSERT_HEAD(&from->memos->mb_sent, newmemo, ml_sent);
nick->memos->memocnt++;
} else if (strcmp(command, "done") == 0) {
done = 1;
} else {
fprintf(stderr, "Error in reading memo data (%s) %lu\n",
dbLine, linenum);
sshutdown(-1);
}
#ifdef DBDEBUG
sSend(":%s PRIVMSG " DEBUGCHAN " :Read memo data (%s)", MemoServ,
dbLine);
#endif
parse_cleanup(&state);
}
fclose(db.ms);
}
/**
* \brief Loads the ChanServ database from disk
*/
void readChanData()
{
RegChanList *rcl;
RegNickList *rnl;
char *command;
int done = 0, db_version = 1;
int line_num = 0;
char *pass;
char *topic;
rcl = NULL;
rnl = NULL;
db.cs = fopen(CS_DIR "chanserv.db", "r");
if (db.cs == NULL)
return;
while (!done) {
if ((sfgets(dbLine, 2048, db.cs)) == 0) {
if (!done) {
unexpected_eof(CS_DB);
}
done = 1;
fclose(db.cs);
return;
}
line_num++;
if (parse_init(&state, dbLine) != 0) {
fprintf(stderr,
CS_DIR "chanserv.db:%d: " " Fatal error during read "
" (Null line?) \n", line_num);
abort();
}
command = parse_getarg(&state);
if (!strcmp(command, "version")) {
db_version = atoi(parse_getarg(&state));
}
else if (!strcmp(command, "channel")) {
char *sChannelName, *sFounderNick;
rcl = (RegChanList *) oalloc(sizeof(RegChanList));
sChannelName = parse_getarg(&state);
sFounderNick = parse_getarg(&state);
initRegChanData(rcl);
if (strlen(sChannelName) >= CHANLEN) {
fprintf(stderr,
CS_DIR "chanserv.db:%d: "
" Channel name '%.80s' exceeds " " CHANLEN.\n",
line_num, sChannelName);
sshutdown(-1);
} else if (strlen(sFounderNick) >= NICKLEN) {
fprintf(stderr,
CS_DIR "chanserv.db:%d: "
" Founder nick name '%.80s' " " (%.80s)"
" exceeds NICKLEN.\n", line_num, sFounderNick,
sChannelName);
sshutdown(-1);
}
if (!sChannelName || !sFounderNick) {
fprintf(stderr,
CS_DIR "chanserv.db:%d: " " Parse error. (%p, %p)",
line_num, sChannelName, sFounderNick);
sshutdown(-1);
}
rnl = getRegNickData(sFounderNick);
strcpy(rcl->name, sChannelName);
if (rnl)
{
rcl->founderId = rnl->regnum;
rnl->chans++;
}
else
rcl->founderId = RegId(0, 0);
rcl->mlock = atol(parse_getarg(&state));
rcl->flags = atol(parse_getarg(&state));
pass = parse_getarg(&state); /*! \bug XXX verify this works */
if (!pass) {
fprintf(stderr,
CS_DIR "chanserv.db:%d: " " Null password?!",
line_num);
sshutdown(-1);
}
if ((db_version < 2) || *pass == '@') {
if (db_version < 2)
strcpy((char *)rcl->password, pass);
else
strcpy((char *)rcl->password, pass + 1);
if (strlen(pass) > (u_int)((db_version < 2) ? PASSLEN : PASSLEN+1)) {
fprintf(stderr,
CS_DIR "chanserv.db:%d: " " password > PASSLEN",
line_num);
sshutdown(-1);
}
xorit((char *)rcl->password);
rcl->flags &= ~CENCRYPT;
}
else {
u_char *tmpup = fromBase64(pass+1, NULL);
int q;
if (!tmpup)
abort();
for(q = 0; q < 16; q++)
rcl->password[q] = tmpup[q];
FREE(tmpup);
rcl->flags |= CENCRYPT;
}
rcl->timereg = (time_t) atol(parse_getarg(&state));
rcl->timestamp = (time_t) atol(parse_getarg(&state));
strncpyzt(rcl->key, parse_getarg(&state), KEYLEN);
rcl->limit = atol(parse_getarg(&state));
rcl->memolevel = atoi(parse_getarg(&state));
rcl->tlocklevel = atoi(parse_getarg(&state));
rcl->restrictlevel = atoi(parse_getarg(&state));
/* The rest of the line - skipping the leading : */
topic = parse_getallargs(&state);
if (topic == NULL)
rcl->desc[0] = '\0';
else
strncpyzt(rcl->desc, topic, CHANDESCBUF);
addRegChan(rcl);
mostchans++;
} else if (!strcmp(command, "topic")) {
rcl = getRegChanData(parse_getarg(&state));
if (rcl == NULL)
continue;
strncpyzt(rcl->tsetby, parse_getarg(&state), NICKLEN);
rcl->ttimestamp = (time_t) atol(parse_getarg(&state));
/* The rest of the topic, skipping the : in it */
topic = parse_getallargs(&state);
if (topic == NULL)
rcl->topic = NULL;
else
rcl->topic = strdup(topic);
} else if (!strcmp(command, "url")) {
rcl = getRegChanData(parse_getarg(&state));
if (rcl == NULL)
continue;
topic = parse_getallargs(&state);
if (topic == NULL)
rcl->url = NULL;
else
rcl->url = strdup(topic);
} else if (!strcmp(command, "autogreet")) {
rcl = getRegChanData(parse_getarg(&state));
if (rcl == NULL)
continue;
topic = parse_getallargs(&state);
if (topic == NULL)
rcl->autogreet = NULL;
else
rcl->autogreet = strdup(topic);
} else if (!strcmp(command, "markby")) {
rcl = getRegChanData(parse_getarg(&state));
if (rcl == NULL)
continue;
topic = parse_getarg(&state);
if (topic == NULL)
rcl->markby = NULL;
else
rcl->markby = strdup(topic);
} else if (strcmp(command, "chkey") == 0) {
char *tmpp = parse_getarg(&state);
if (rcl && tmpp)
rcl->chpw_key = strtoul(tmpp, (char **)0, 16);
} else if (!strcmp(command, "op")) {
cAccessList *lame;
char *tmpName;
rcl = getRegChanData(parse_getarg(&state));
if (rcl == NULL)
continue;
tmpName = parse_getarg(&state);
if ((rnl = getRegNickData(tmpName)) != NULL)
{
lame = (cAccessList *) oalloc(sizeof(cAccessList));
lame->nickId = rnl->regnum;
lame->uflags = atoi(parse_getarg(&state));
addChanOp(rcl, lame);
}
} else if (!strcmp(command, "akick")) {
cAkickList *lame;
lame = (cAkickList *) oalloc(sizeof(cAkickList));
rcl = getRegChanData(parse_getarg(&state));
if (rcl == NULL)
continue;
strncpyzt(lame->mask, parse_getarg(&state), 70);
lame->added = (time_t) atol(parse_getarg(&state));
/* The rest of the string... */
topic = parse_getallargs(&state);
if (topic == NULL)
lame->reason[0] = '\0';
else {
strncpyzt(lame->reason, topic, NICKLEN + 50);
}
addChanAkick(rcl, lame);
} else if (!strcmp(command, "done"))
done = 1;
else {
fprintf(stderr, "GLOBOPS :Read chan data (%s)", dbLine);
sshutdown(-1);
}
#ifdef DBDEBUG
sSend(":%s PRIVMSG " DEBGUGCHAN " :Read chan data (%s)", ChanServ,
dbLine);
#endif
parse_cleanup(&state);
}
fclose(db.cs);
}
/**
* \brief Loads the NickServ database from disk
*/
void readNickData()
{
RegNickList *rnl = NULL;
char *command, *tmpp;
unsigned char *tmpup;
int done = 0, db_version = 1;
int line_num = 0, do_enc = 0;
#ifdef REQ_EMAIL
readRegData();
#endif
db.ns = fopen(NS_DB, "r");
if (db.ns == NULL) {
logDump(corelog, "Unable to open " NS_DB ": %s", strerror(errno));
return;
}
while (!done) {
if (!(sfgets(dbLine, 1024, db.ns))) {
if (!done) {
unexpected_eof(NS_DB);
}
done = 1;
fclose(db.ns);
return;
}
line_num++;
if (parse_init(&state, dbLine) != 0) {
/*! \bug XXX make a nicer error here! */
abort();
}
command = parse_getarg(&state);
if (strcmp(command, "version") == 0) {
tmpp = parse_getarg(&state);
assert(tmpp);
if (tmpp)
db_version = atoi(tmpp);
}
else
if (strcmp(command, "nick") == 0) {
rnl = (RegNickList *) oalloc(sizeof(RegNickList));
char *sNick, *sUser, *sHost, *sPass;
sNick = parse_getarg(&state);
sUser = parse_getarg(&state);
sHost = parse_getarg(&state);
sPass = parse_getarg(&state);
if (strlen(sNick) >= NICKLEN) {
fprintf(stderr,
NS_DB ":%d: " " Nickname '%.80s' exceeds "
" NICKLEN.\n", line_num, sNick);
sshutdown(-1);
}
strcpy(rnl->nick, sNick);
strncpyzt(rnl->user, sUser, USERLEN);
SetDynBuffer(&rnl->host, sHost);
if (db_version < 2)
{
if (strlen(sPass) > PASSLEN) {
fprintf(stderr,
NS_DB ":%d: " " Password for nick '%s' "
" exceeds PASSLEN.\n", line_num, sNick);
sshutdown(-1);
}
strcpy((char *)rnl->password, xorit(sPass));
}
else {
char encType = *sPass;
if (encType == '@') {
if (strlen(sPass+1) > PASSLEN) {
fprintf(stderr,
NS_DB ":%d: " " Password for nick '%s' "
" exceeds PASSLEN.\n", line_num, sNick);
sshutdown(-1);
}
strcpy((char *)rnl->password, xorit(sPass + 1));
do_enc = 0;
}
else if (encType == '$') {
int q, len;
tmpup = fromBase64(sPass + 1, &len);
assert(tmpup);
for(q = 0; q < 16; q++)
rnl->password[q] = tmpup[q];
do_enc = 1;
FREE(tmpup);
}
else
rnl->password[0] = '\0';
}
rnl->timestamp = (time_t) atol(parse_getarg(&state));
rnl->timereg = (time_t) atol(parse_getarg(&state));
rnl->flags = atoi(parse_getarg(&state));
if (db_version >= 3) {
const char *idString = parse_getarg(&state);
int av, bv;
sscanf(idString, "%X*%X", &av, &bv);
rnl->regnum.SetDirect(top_regnick_idnum, av, bv);
}
else {
rnl->regnum.SetNext(top_regnick_idnum);
}
if (do_enc)
rnl->flags |= NENCRYPT;
else
rnl->flags &= ~NENCRYPT;
rnl->opflags = 0;
rnl->idtime = DEF_NDELAY;
ADD_MEMO_BOX(rnl);
addRegNick(rnl);
} else if (strcmp(command, "is") == 0) {
char *data = parse_getarg(&state);
if (rnl && data)
rnl->is_readtime = atol(data);
} else if (strcmp(command, "oper") == 0) {
char *opflags_s;
if (rnl && (rnl == getRegNickData(parse_getarg(&state)))) {
if ((opflags_s = parse_getarg(&state)))
rnl->opflags |=
(strtoul(opflags_s, (char **)0, 10) &
~(OROOT | OSERVOP));
if (rnl->opflags)
addOpData(rnl);
}
} else if (strcmp(command, "url") == 0) {
if (rnl && (rnl == getRegNickData(parse_getarg(&state))))
{
rnl->url = strdup(parse_getarg(&state));
if (strlen(rnl->url) > (URLLEN - 1))
rnl->url[URLLEN - 1] = '\0';
}
} else if (strcmp(command, "gecos") == 0) {
#ifdef TRACK_GECOS
char *gecos = parse_getallargs(&state);
if (gecos != NULL)
rnl->gecos = strdup(gecos);
#endif
} else if (strcmp(command, "akey") == 0) {
#ifdef REQ_EMAIL
if (rnl)
rnl->email_key = atoi(parse_getarg(&state));
#endif
} else if (strcmp(command, "chkey") == 0) {
char *tmpp = parse_getarg(&state);
if (rnl && tmpp)
rnl->chpw_key = strtoul(tmpp, (char **)0, 16);
} else if (strcmp(command, "markby") == 0) {
char *mby;
rnl = getRegNickData(parse_getarg(&state));
if (!rnl || !(mby = parse_getarg(&state)))
continue;
rnl->markby = strdup(mby);
} else if (strcmp(command, "access") == 0) {
rnl = getRegNickData(parse_getarg(&state));
addAccItem(rnl, parse_getarg(&state));
} else if (!strcmp(command, "email")) {
rnl = getRegNickData(parse_getarg(&state));
strncpyzt(rnl->email, parse_getarg(&state), EMAILLEN);
if (!strcmp(rnl->email, "(none)"))
strcat(rnl->email, " ");
} else if (!strcmp(command, "idtime")) {
rnl = getRegNickData(parse_getarg(&state));
rnl->idtime = atoi(parse_getarg(&state));
} else if (!strcmp(command, "done"))
done = 1;
else {
fprintf(stderr, NS_DB ":%d: Error reading nick data (%s)",
line_num, dbLine);
sshutdown(-1);
}
#ifdef DBDEBUG
sSend(":%s PRIVMSG " DEBUGCHAN " :Read nick data (%s)", NICKSERV,
dbLine);
#endif
parse_cleanup(&state);
}
fclose(db.ns);
readMemoData();
}
/**
* \brief Loads the InfoServ database from disk
*/
void readInfoData(void)
{
char *command;
int done = 0;
SomeNews *news, *tmpnews;
is_listhead = NULL;
db.is = fopen(IS_DB, "r");
if (db.is == NULL)
return;
/**
* There was still a crash bug in what was here before...
* cleaning this up .. allocate memory when it's
* needed, don't allocate it in the beginning and
* give it up later if superflous in a linked list
* load.
* -Mysidia
*/
while (!done) {
if (!(sfgets(dbLine, 2048, db.is))) {
if (!done) {
unexpected_eof(IS_DB);
}
done = 1;
fclose(db.is);
return;
}
if (parse_init(&state, dbLine) != 0) {
/*! \bug XXX be nicer here... */
abort();
}
command = parse_getarg(&state);
if (!strcmp(command, "article")) {
char *temp;
news = (SomeNews *) oalloc(sizeof(SomeNews));
if (!is_listhead)
is_listhead = news;
else {
for (tmpnews = is_listhead; tmpnews->next;
tmpnews = tmpnews->next);
tmpnews->next = news;
}
news->importance = atoi(parse_getarg(&state));
strncpyzt(news->from, parse_getarg(&state), NICKLEN);
news->timestamp = atol(parse_getarg(&state));
temp = parse_getallargs(&state);
if (temp)
news->header = strdup(temp);
news->content = dbReadString(db.is);
if (news->timestamp > is_last_post_time)
is_last_post_time = news->timestamp;
}
else if (!strcmp(command, "done"))
done = 1;
else
sshutdown(-1);
parse_cleanup(&state);
}
fclose(db.is);
}
/**
* \brief Loads the clone rule database from disk
*/
void readTriggerData(void)
{
CloneRule *rule = NULL;
char *command, *text;
int done = 0;
unsigned long linenum = 0;
db.trigger = fopen(TRG_DB, "r");
if (db.trigger == NULL) {
logDump(corelog,
"Unable to open trigger database for read access: %s",
strerror(errno));
return;
}
while (!done) {
if (!(sfgets(dbLine, 2048, db.trigger))) {
if (!done) {
unexpected_eof(TRG_DB);
}
done = 1;
fclose(db.trigger);
return;
}
linenum++;
if (parse_init(&state, dbLine) != 0) {
/*! \bug XXX be nicer here... */
abort();
}
command = parse_getarg(&state);
if (strcmp(command, "Trigger") == 0) {
rule = NewCrule();
rule->kill_msg = NULL;
rule->warn_msg = NULL;
strncpyzt(rule->mask, parse_getarg(&state),
sizeof(rule->mask));
rule->mask[sizeof(rule->mask) - 1] = '\0';
rule->trigger = atoi(parse_getarg(&state));
rule->utrigger = atoi(parse_getarg(&state));
rule->flags = atol(parse_getarg(&state));
AddCrule(rule, -2); /* -2 is magic for append to end */
} else if (strcmp(command, "Killmsg") == 0) {
text = parse_getallargs(&state);
if (text && rule)
rule->kill_msg = strdup(text);
} else if (strcmp(command, "Warnmsg") == 0) {
text = parse_getallargs(&state);
if (text && rule)
rule->warn_msg = strdup(text);
} else if (strcmp(command, "done") == 0) {
done = 1;
} else {
fprintf(stderr, "Error in reading trigger data (%s) %lu\n",
dbLine, linenum);
parse_cleanup(&state);
return;
}
#ifdef DBDEBUG
sSend(":%s PRIVMSG " DEBUGCHAN " :Read trigger data (%s)",
OperServ, dbLine);
#endif
parse_cleanup(&state);
}
fclose(db.trigger);
}
static bool get_w_conf(FILE *in, char *infile, char *title,
t_atoms *atoms, int *ndec, rvec x[],rvec *v, matrix box)
{
static t_symtab *symtab=NULL;
char name[6];
char line[STRLEN+1],*ptr;
char buf[256];
double x1,y1,z1,x2,y2,z2;
rvec xmin,xmax;
int natoms,i,m,resnr,newres,oldres,ddist,c;
bool bFirst,bVel;
char *p1,*p2,*p3;
newres = 0;
oldres = NOTSET; /* Unlikely number for the first residue! */
ddist = 0;
if (!symtab) {
snew(symtab,1);
open_symtab(symtab);
}
/* Read the title and number of atoms */
get_coordnum_fp(in,title,&natoms);
if (natoms > atoms->nr)
gmx_fatal(FARGS,"gro file contains more atoms (%d) than expected (%d)",
natoms,atoms->nr);
else if (natoms < atoms->nr)
fprintf(stderr,"Warning: gro file contains less atoms (%d) than expected"
" (%d)\n",natoms,atoms->nr);
bFirst=TRUE;
bVel = FALSE;
/* just pray the arrays are big enough */
for (i=0; (i < natoms) ; i++) {
if ((fgets2 (line,STRLEN,in)) == NULL) {
unexpected_eof(infile,i+2);
}
if (strlen(line) < 39)
gmx_fatal(FARGS,"Invalid line in %s for atom %d:\n%s",infile,i+1,line);
/* determine read precision from distance between periods
(decimal points) */
if (bFirst) {
bFirst=FALSE;
p1=strchr(line,'.');
if (p1 == NULL)
gmx_fatal(FARGS,"A coordinate in file %s does not contain a '.'",infile);
p2=strchr(&p1[1],'.');
if (p2 == NULL)
gmx_fatal(FARGS,"A coordinate in file %s does not contain a '.'",infile);
ddist = p2 - p1;
*ndec = ddist - 5;
p3=strchr(&p2[1],'.');
if (p3 == NULL)
gmx_fatal(FARGS,"A coordinate in file %s does not contain a '.'",infile);
if (p3 - p2 != ddist)
gmx_fatal(FARGS,"The spacing of the decimal points in file %s is not consistent for x, y and z",infile);
}
/* residue number*/
memcpy(name,line,5);
name[5]='\0';
sscanf(name,"%d",&resnr);
memcpy(name,line+5,5);
name[5]='\0';
if (resnr != oldres) {
oldres = resnr;
if (newres >= natoms)
gmx_fatal(FARGS,"More residues than atoms in %s (natoms = %d)",
infile,natoms);
atoms->resname[newres] = put_symtab(symtab,name);
newres++;
}
resnr = newres;
atoms->atom[i].resnr = resnr-1;
/* atomname */
memcpy(name,line+10,5);
atoms->atomname[i]=put_symtab(symtab,name);
/* eventueel controle atomnumber met i+1 */
/* coordinates (start after residue shit) */
ptr = line + 20;
/* Read fixed format */
for(m=0; m<DIM; m++) {
for(c=0; (c<ddist && ptr[0]); c++) {
buf[c] = ptr[0];
ptr++;
}
buf[c] = '\0';
if (sscanf (buf,"%lf %lf",&x1,&x2) != 1) {
gmx_fatal(FARGS,"Something is wrong in the coordinate formatting of file %s. Note that gro is fixed format (see the manual)",infile);
} else {
x[i][m] = x1;
}
}
/* velocities (start after residues and coordinates) */
if (v) {
/* Read fixed format */
for(m=0; m<DIM; m++) {
for(c=0; (c<ddist && ptr[0]); c++) {
buf[c] = ptr[0];
ptr++;
}
buf[c] = '\0';
if (sscanf (buf,"%lf",&x1) != 1) {
v[i][m] = 0;
} else {
v[i][m] = x1;
bVel = TRUE;
}
}
}
}
atoms->nres=newres;
/* box */
fgets2 (line,STRLEN,in);
if (sscanf (line,"%lf%lf%lf",&x1,&y1,&z1) != 3) {
sprintf(buf,"Bad box in file %s",infile);
warning(buf);
/* Generate a cubic box */
for(m=0; (m<DIM); m++)
xmin[m]=xmax[m]=x[0][m];
for(i=1; (i<atoms->nr); i++)
for(m=0; (m<DIM); m++) {
xmin[m]=min(xmin[m],x[i][m]);
xmax[m]=max(xmax[m],x[i][m]);
}
for (i=0; i<DIM; i++) for (m=0; m<DIM; m++) box[i][m]=0.0;
for(m=0; (m<DIM); m++)
box[m][m]=(xmax[m]-xmin[m]);
fprintf(stderr,"Generated a cubic box %8.3f x %8.3f x %8.3f\n",
box[XX][XX],box[YY][YY],box[ZZ][ZZ]);
}
else {
/* We found the first three values, the diagonal elements */
box[XX][XX]=x1;
box[YY][YY]=y1;
box[ZZ][ZZ]=z1;
if (sscanf (line,"%*f%*f%*f%lf%lf%lf%lf%lf%lf",
&x1,&y1,&z1,&x2,&y2,&z2) != 6)
x1=y1=z1=x2=y2=z2=0.0;
box[XX][YY] = x1;
box[XX][ZZ] = y1;
box[YY][XX] = z1;
box[YY][ZZ] = x2;
box[ZZ][XX] = y2;
box[ZZ][YY] = z2;
}
close_symtab(symtab);
return bVel;
}
