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parse.c
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/* name: parse.c */
/* author: J. Michael Word date written: 2/29/96 */
/* purpose: build a parse tree from an input string. */
/* based on "Compilers", Aho, Sethi, and Ullman */
/*****************************************************************/
/* NOTICE: This is free software and the source code is freely */
/* available. You are free to redistribute or modify under the */
/* conditions that (1) this notice is not removed or modified */
/* in any way and (2) any modified versions of the program are */
/* also available for free. */
/* ** Absolutely no Warranty ** */
/* Copyright (C) 1999 J. Michael Word */
/*****************************************************************/
#include <stdlib.h> /*060902 needs this for malloc() */
#include <string.h>
#include <ctype.h>
#include "utility.h"
#include "parse.h"
static symbolEntry SymTable[LEXSYMMAX] = {0};
static char *inputStr = 0;
static int tokenval = 0;
static float realtokval = 0.0;
static int lookahead = 0;
static char lexbuf[LXBUFSZ+1] = {0};
static char Lexemes[LEXSTRINGMAX] = {0};
static int LastLexChar = -1;
static int LastSymEntry = 0;
static int ParseError = FALSE;
pattern* parseArg(char *s) { /*called by select.c/getPat() */
pattern *pat;
inputStr = s;
lookahead = lexan();
ParseError = FALSE;
pat = exprItem();
matchTok(DONE_TOK);
if (ParseError == TRUE) {
pat = freePattern(pat);
}
return pat;
}
pattern* freePattern(pattern *pat) {
if (pat) {
pat->lhs = freePattern(pat->lhs);
pat->rhs = freePattern(pat->rhs);
free(pat);
}
return NULL;
}
pattern* exprItem() {
pattern *lhs, *rhs;
lhs = setItem();
for (;;) {
if (lookahead == '|') {
matchTok('|');
rhs = setItem();
lhs = makeNode(lhs, rhs, OR_NODE);
}
else {
break;
}
}
return lhs;
}
pattern* setItem() {
pattern *lhs, *rhs;
lhs = limitItem();
for (;;) {
if((lookahead == '(') /* a limitItem must begin with a feature! */
|| (lookahead == NOT_TOK)
|| (lookahead == NUM_TOK)
|| (lookahead == ID_TOK)
|| (lookahead == WITHIN_TOK)
|| (lookahead == '-')) {
rhs = limitItem();
lhs = makeNode(lhs, rhs, AND_NODE);
}
else {
break;
}
}
return lhs;
}
pattern* limitItem() {
pattern *lhs, *rhs;
lhs = featureItem();
for (;;) {
if (lookahead == ',') {
matchTok(',');
rhs = featureItem();
lhs = makeNode(lhs, rhs, OR_NODE);
}
else {
break;
}
}
return lhs;
}
pattern* featureItem() {
pattern *f = NULL;
if (lookahead == '(') {
matchTok('(');
f = exprItem();
matchTok(')');
}
else if (lookahead == NOT_TOK) {
matchTok(NOT_TOK);
f = featureItem();
f = makeNode(f, NULL, NOT_NODE);
}
else if (lookahead == NUM_TOK) {
f = numericItem(+1);
}
else if (lookahead == ID_TOK) {
f = idItem();
}
else if (lookahead == WITHIN_TOK) {
f = distItem();
}
/* if an item starts with a minus */
/* it is a negative residue number */
else if (lookahead == '-') {
matchTok('-');
if (lookahead == NUM_TOK) {
f = numericItem(-1);
}
else {
char msg[100];
describeLookahead(msg,"syntax: minus sign requires a number ");
errmsg(msg);
ParseError = TRUE;
}
}
else {
char msg[100];
describeLookahead(msg,"syntax: improper feature ");
errmsg(msg);
ParseError = TRUE;
}
return f;
}
pattern* numericItem(int signFactor) {
pattern *lhs, *rhs, *rrs;
int inscode = 0;
lhs = makeTerminal(RES_NODE, signFactor*tokenval);
inscode = lexbuf[0];
matchTok(NUM_TOK);
if (isalpha(inscode) || inscode == ' ') { /* combine res# with insert code */
rhs = makeTerminal(INS_NODE, inscode);
lhs = makeNode(lhs, rhs, AND_NODE);
}
if (lookahead == '-') { /* first dash is the range separator */
matchTok('-');
signFactor = +1;
if (lookahead == '-') { /* this dash specifies a negative num */
matchTok('-');
signFactor = -1;
}
rhs = makeTerminal(RES_NODE, signFactor*tokenval);
inscode = lexbuf[0];
matchTok(NUM_TOK);
if (isalpha(inscode) || inscode == ' ') { /* combine res# with insert code */
rrs = makeTerminal(INS_NODE, inscode);
rhs = makeNode(rhs, rrs, AND_NODE);
}
if ((lhs->type == AND_NODE)|| (rhs->type == AND_NODE)) {
/* more than just a span of numbers */
/* includes insert codes */
lhs = makeNode(lhs, rhs, INS_RANGE_NODE);
}
else {
lhs = makeNode(lhs, rhs, RANGE_NODE);
}
}
return lhs;
}
pattern* idItem() {
pattern *lhs = NULL;
int type = 0, val = 0;
char *s, *tmpstr;
s = SymTable[tokenval].lexptr;
if ((strncmp(s, "FILE", 4) == 0) && isdigit(s[4])) {
type = FILE_NODE; val = parseInteger(s,4,10);
}
else if ((strncmp(s, "CHAIN", 5) == 0) && (isalnum(s[5])||(s[5]=='_'))) {
type = CHAIN_NODE;
for(tmpstr = s+5; *tmpstr; tmpstr++) { /* substitute blank for _ */
if (*tmpstr == '_') {*tmpstr = ' ';}
}
if (s[6] == '\0') {
s[4] = ' ';
val = lookup(s+4); if(val == 0) val = insert(s+4, ID_TOK);
}
else {
val = lookup(s+5); if(val == 0) val = insert(s+5, ID_TOK);
}
/* type = CHAIN_NODE; val = (unsigned char)s[5]; */
}
else if ((strncmp(s, "ALT", 3) == 0) && (isalnum(s[3])||(s[3]=='_'))) {
if (s[3] == '_') {s[3] = ' ';}
type = ALT_NODE; val = (unsigned char)s[3];
}
else if ((strncmp(s, "MODEL", 5) == 0) && isdigit(s[5])) {
type = MODEL_NODE; val = parseInteger(s,5,10);
}
else if ((strncmp(s, "ATOM", 4) == 0) && (isalnum(s[4])||(s[4]=='_'))) {
type = ANAME_NODE;
for(tmpstr = s+4; *tmpstr; tmpstr++) { /* substitute blank for _ */
if (*tmpstr == '_') {*tmpstr = ' ';}
}
val = lookup(s+4); if(val == 0) val = insert(s+4, ID_TOK);
}
else if ((strncmp(s, "SEG", 3) == 0) && (isalnum(s[3])||(s[3]=='_'))) {
type = SEGID_NODE;
for(tmpstr = s+3; *tmpstr; tmpstr++) { /* substitute blank for _ */
if (*tmpstr == '_') {*tmpstr = ' ';}
}
val = lookup(s+3); if(val == 0) val = insert(s+3, ID_TOK);
}
else if (strcmp(s, "ALL") == 0) {
type = TRUE_NODE; val = 0;
}
else if (strcmp(s, "NONE") == 0) {
type = FALSE_NODE; val = 0;
}
else if (strcmp(s, "ALPHA") == 0) {
type = PROP_NODE; val = ALPHA_PROP;
}
else if (strcmp(s, "BETA") == 0) {
type = PROP_NODE; val = BETA_PROP;
}
else if ((strcmp(s, "MAINCHAIN") == 0) || (strcmp(s, "MC") == 0)
|| (strcmp(s, "BACKBONE") == 0)) {
type = PROP_NODE; val = MC_PROP;
}
else if ((strcmp(s, "SIDECHAIN") == 0) || (strcmp(s, "SC") == 0)
|| (strcmp(s, "BASE") == 0)) {
type = PROP_NODE; val = SC_PROP;
}
else if (strcmp(s, "NITROGEN") == 0) {
type = PROP_NODE; val = N_PROP;
}
else if (strcmp(s, "CARBON") == 0) {
type = PROP_NODE; val = C_PROP;
}
else if (strcmp(s, "OXYGEN") == 0) {
type = PROP_NODE; val = O_PROP;
}
else if (strcmp(s, "SULFUR") == 0) {
type = PROP_NODE; val = S_PROP;
}
else if (strcmp(s, "PHOSPHORUS") == 0) {
type = PROP_NODE; val = P_PROP;
}
else if (strcmp(s, "HYDROGEN") == 0) {
type = PROP_NODE; val = H_PROP;
}
else if ((strcmp(s, "H2O") == 0) || (strcmp(s, "WATER") == 0)) {
type = PROP_NODE; val = WATER_PROP;
}
else if ((strcmp(s, "HET") == 0) || (strcmp(s, "HETATM") == 0)) {
type = PROP_NODE; val = HET_PROP;
}
else if ((strcmp(s, "PROTEIN") == 0) || (strcmp(s, "PEPTIDE") == 0)) {
type = PROP_NODE; val = PROT_PROP;
}
else if ((strcmp(s, "DNA") == 0) || (strcmp(s, "RNA") == 0)) {
type = PROP_NODE; val = DNA_PROP;
}
else if (strcmp(s, "METAL") == 0) {
type = PROP_NODE; val = METAL_PROP;
}
else if (strcmp(s, "METHYLENE") == 0) {
type = PROP_NODE; val = METHYLENE_PROP;
}/*longer name first*/
else if (strcmp(s, "METHYL") == 0) {
type = PROP_NODE; val = METHYL_PROP;
}
else if (strcmp(s, "DONOR") == 0) {
type = PROP_NODE; val = DONOR_PROP;
}
else if (strcmp(s, "ACCEPTOR") == 0) {
type = PROP_NODE; val = ACCEPTOR_PROP;
}
else if ((strcmp(s, "NONPOLAR") == 0) || (strcmp(s, "HYDROPHOBIC") == 0)
|| (strcmp(s, "HPHOBIC")== 0)|| (strcmp(s, "PHOBIC") == 0)) {
type = PROP_NODE; val = RHPHOBIC_PROP;
}
else if ((strcmp(s, "POLAR") == 0) || (strcmp(s, "HYDROPHILIC") == 0)
|| (strcmp(s, "HPHILIC")== 0)|| (strcmp(s, "PHILIC") == 0)) {
type = PROP_NODE; val = RHPHILIC_PROP;
}
else if ((strcmp(s, "CHARGED") == 0) || (strcmp(s, "CHARGE") == 0)) {
type = PROP_NODE; val = RCHARGED_PROP;
}
else if (strcmp(s, "AROMATIC") == 0) {
type = PROP_NODE; val = AROMATIC_PROP;
}
else if ((strcmp(s, "GLY") == 0) || (strcmp(s, "G") == 0)) {
type = RTYPE_NODE;
val = lookup("GLY"); if(val == 0) val = insert("GLY", ID_TOK);
}
else if ((strcmp(s, "ALA") == 0) || (strcmp(s, "A") == 0)) {
type = RTYPE_NODE;
val = lookup("ALA"); if(val == 0) val = insert("ALA", ID_TOK);
}
else if ((strcmp(s, "VAL") == 0) || (strcmp(s, "V") == 0)) {
type = RTYPE_NODE;
val = lookup("VAL"); if(val == 0) val = insert("VAL", ID_TOK);
}
else if ((strcmp(s, "PHE") == 0) || (strcmp(s, "F") == 0)) {
type = RTYPE_NODE;
val = lookup("PHE"); if(val == 0) val = insert("PHE", ID_TOK);
}
else if ((strcmp(s, "PRO") == 0) || (strcmp(s, "P") == 0)) {
type = RTYPE_NODE;
val = lookup("PRO"); if(val == 0) val = insert("PRO", ID_TOK);
}
else if ((strcmp(s, "MET") == 0) || (strcmp(s, "M") == 0)) {
type = RTYPE_NODE;
val = lookup("MET"); if(val == 0) val = insert("MET", ID_TOK);
}
else if ((strcmp(s, "ILE") == 0) || (strcmp(s, "I") == 0)) {
type = RTYPE_NODE;
val = lookup("ILE"); if(val == 0) val = insert("ILE", ID_TOK);
}
else if ((strcmp(s, "LEU") == 0) || (strcmp(s, "L") == 0)) {
type = RTYPE_NODE;
val = lookup("LEU"); if(val == 0) val = insert("LEU", ID_TOK);
}
else if ((strcmp(s, "ASP") == 0) || (strcmp(s, "D") == 0)) {
type = RTYPE_NODE;
val = lookup("ASP"); if(val == 0) val = insert("ASP", ID_TOK);
}
else if ((strcmp(s, "GLU") == 0) || (strcmp(s, "E") == 0)) {
type = RTYPE_NODE;
val = lookup("GLU"); if(val == 0) val = insert("GLU", ID_TOK);
}
else if ((strcmp(s, "LYS") == 0) || (strcmp(s, "K") == 0)) {
type = RTYPE_NODE;
val = lookup("LYS"); if(val == 0) val = insert("LYS", ID_TOK);
}
else if ((strcmp(s, "ARG") == 0) || (strcmp(s, "R") == 0)) {
type = RTYPE_NODE;
val = lookup("ARG"); if(val == 0) val = insert("ARG", ID_TOK);
}
else if ((strcmp(s, "SER") == 0) || (strcmp(s, "S") == 0)) {
type = RTYPE_NODE;
val = lookup("SER"); if(val == 0) val = insert("SER", ID_TOK);
}
else if ((strcmp(s, "THR") == 0) || (strcmp(s, "T") == 0)) {
type = RTYPE_NODE;
val = lookup("THR"); if(val == 0) val = insert("THR", ID_TOK);
}
else if ((strcmp(s, "TYR") == 0) || (strcmp(s, "Y") == 0)) {
type = RTYPE_NODE;
val = lookup("TYR"); if(val == 0) val = insert("TYR", ID_TOK);
}
else if ((strcmp(s, "HIS") == 0) || (strcmp(s, "H") == 0)) {
type = RTYPE_NODE;
val = lookup("HIS"); if(val == 0) val = insert("HIS", ID_TOK);
}
else if ((strcmp(s, "CYS") == 0) || (strcmp(s, "C") == 0)) {
type = RTYPE_NODE;
val = lookup("CYS"); if(val == 0) val = insert("CYS", ID_TOK);
}
else if ((strcmp(s, "ASN") == 0) || (strcmp(s, "N") == 0)) {
type = RTYPE_NODE;
val = lookup("ASN"); if(val == 0) val = insert("ASN", ID_TOK);
}
else if ((strcmp(s, "GLN") == 0) || (strcmp(s, "Q") == 0)) {
type = RTYPE_NODE;
val = lookup("GLN"); if(val == 0) val = insert("GLN", ID_TOK);
}
else if ((strcmp(s, "TRP") == 0) || (strcmp(s, "W") == 0)) {
type = RTYPE_NODE;
val = lookup("TRP"); if(val == 0) val = insert("TRP", ID_TOK);
}
else if (strcmp(s, "ACE") == 0) {
type = RTYPE_NODE;
val = lookup("ACE"); if(val == 0) val = insert("ACE", ID_TOK);
}
else if (strcmp(s, "ASX") == 0) {
type = RTYPE_NODE;
val = lookup("ASX"); if(val == 0) val = insert("ASX", ID_TOK);
}
else if (strcmp(s, "GLX") == 0) {
type = RTYPE_NODE;
val = lookup("GLX"); if(val == 0) val = insert("GLX", ID_TOK);
}
else if (strcmp(s, "MSE") == 0) {
type = RTYPE_NODE;
val = lookup("MSE"); if(val == 0) val = insert("MSE", ID_TOK);
}
else if (strcmp(s, "PCA") == 0) {
type = RTYPE_NODE;
val = lookup("PCA"); if(val == 0) val = insert("PCA", ID_TOK);
}
else if (strcmp(s, "NH2") == 0) {
type = RTYPE_NODE;
val = lookup("NH2"); if(val == 0) val = insert("NH2", ID_TOK);
}
else if (strcmp(s, "NME") == 0) {
type = RTYPE_NODE;
val = lookup("NME"); if(val == 0) val = insert("NME", ID_TOK);
}
else if (strcmp(s, "FOR") == 0) {
type = RTYPE_NODE;
val = lookup("FOR"); if(val == 0) val = insert("FOR", ID_TOK);
}
else if ((strncmp(s, "RES", 3) == 0) && (isalnum(s[3])||(s[3]=='_'))) {
type = RTYPE_NODE;
for(tmpstr = s+3; *tmpstr; tmpstr++) { /* substitute blank for _ */
if (*tmpstr == '_') {*tmpstr = ' ';}
}
val = lookup(s+3); if(val == 0) val = insert(s+3, ID_TOK);
}
else if ((strncmp(s, "OLT", 3) == 0) && isdigit(s[3])) {
type = OCC_LT_NODE; val = parseInteger(s,3,10);
}
else if ((strncmp(s, "OGT", 3) == 0) && isdigit(s[3])) {
type = OCC_GT_NODE; val = parseInteger(s,3,10);
}
else if ((strncmp(s, "BLT", 3) == 0) && isdigit(s[3])) {
type = B_LT_NODE; val = parseInteger(s,3,10);
}
else if ((strncmp(s, "BGT", 3) == 0) && isdigit(s[3])) {
type = B_GT_NODE; val = parseInteger(s,3,10);
}
else if ((strncmp(s, "INS", 3) == 0) && (isalnum(s[3])||(s[3]=='_'))) {
if (s[3] == '_') {s[3] = ' ';}
type = INS_NODE; val = (unsigned char)s[3];
}
else {
char msg[200];
sprintf(msg,"syntax: unknown identifier: %s", s);
errmsg(msg);
ParseError = TRUE;
type = FALSE_NODE;
val = 0;
}
lhs = makeTerminal(type, val);
matchTok(ID_TOK);
return lhs;
}
pattern* distItem() {
pattern *f;
float dst = 0.0, px = 0.0, py = 0.0, pz = 0.0, signFactor = 0.0;
int ok = 1;
/* within */
f = makeTerminal(DIST_NODE, 0);
matchTok(WITHIN_TOK);
/* distance */
if (ok && lookahead == REALNUM_TOK) {
dst = realtokval;
matchTok(REALNUM_TOK);
}
else if (ok && lookahead == NUM_TOK) {
dst = tokenval;
matchTok(NUM_TOK);
}
else { ok = 0; }
/* of */
if (ok && lookahead == ID_TOK
&& strcmp(SymTable[tokenval].lexptr, "OF") == 0) {
matchTok(ID_TOK);
}
else { ok = 0; }
/* x */
signFactor = 1.0;
if (ok && lookahead == '-') {
matchTok('-');
signFactor = -1.0;
}
if (ok && lookahead == REALNUM_TOK) {
px = signFactor * realtokval;
matchTok(REALNUM_TOK);
}
else if (ok && lookahead == NUM_TOK) {
px = signFactor * tokenval;
matchTok(NUM_TOK);
}
else { ok = 0; }
/* , */
if (ok && lookahead == ',') {
matchTok(',');
}
else { ok = 0; }
/* y */
signFactor = 1.0;
if (ok && lookahead == '-') {
matchTok('-');
signFactor = -1.0;
}
if (ok && lookahead == REALNUM_TOK) {
py = signFactor * realtokval;
matchTok(REALNUM_TOK);
}
else if (ok && lookahead == NUM_TOK) {
py = signFactor * tokenval;
matchTok(NUM_TOK);
}
else { ok = 0; }
/* , */
if (ok && lookahead == ',') {
matchTok(',');
}
else { ok = 0; }
/* z */
signFactor = 1.0;
if (ok && lookahead == '-') {
matchTok('-');
signFactor = -1.0;
}
if (ok && lookahead == REALNUM_TOK) {
pz = signFactor * realtokval;
matchTok(REALNUM_TOK);
}
else if (ok && lookahead == NUM_TOK) {
pz = signFactor * tokenval;
matchTok(NUM_TOK);
}
else { ok = 0; }
/* info is packed into the floating-point vector */
if (ok) {
f->fvec[0] = dst;
f->fvec[1] = px;
f->fvec[2] = py;
f->fvec[3] = pz;
}
else {
char msg[100];
describeLookahead(msg,"syntax: parsing WITHIN: ");
errmsg(msg);
ParseError = TRUE;
}
return f;
}
pattern* makeNode(pattern *lhs, pattern *rhs, int type) {
pattern *node;
node = (pattern *)malloc(sizeof(pattern));
if (node) {
node->lhs = lhs;
node->rhs = rhs;
node->type = type;
node->val = 0;
node->fvec[0] = 0.0;
node->fvec[1] = 0.0;
node->fvec[2] = 0.0;
node->fvec[3] = 0.0;
}
else {
halt("out of memory in makeNode()");
}
return node;
}
pattern* makeTerminal(int type, int val) {
pattern *term;
term = (pattern *)malloc(sizeof(pattern));
if (term) {
term->lhs = NULL;
term->rhs = NULL;
term->type = type;
term->val = val;
term->fvec[0] = 0.0;
term->fvec[1] = 0.0;
term->fvec[2] = 0.0;
term->fvec[3] = 0.0;
}
else {
halt("out of memory in makeTerminal()");
}
return term;
}
void matchTok(int t) {
if (lookahead == t) {
lookahead = lexan();
}
else {
char msg[100];
describeLookahead(msg,"improper syntax ");
errmsg(msg);
sprintf(msg,"expect match code: %d", t);
errmsg(msg);
ParseError = TRUE;
}
}
char* lexString(int p) {
return SymTable[p].lexptr;
}
int lexan() {
int p, t, rc, cnt;
for (;;) {
t = toupper(*inputStr++);
if (t == ' ' || t == '\t' || t == '\n' || t == '\r') {
/* skip over whitespace */
}
else if (isdigit(t) || t == '.') {
int insCode = 0;
int fractional = (t == '.');
lexbuf[cnt = 0] = t;
while ( isdigit(*inputStr)
|| ( (*inputStr == '.' ||
isalpha(*inputStr) || *inputStr == '_')
&& ! (insCode || fractional)) ) {
if (*inputStr == '.') { fractional = 1; }
else if (isalpha(*inputStr)) { insCode = toupper(*inputStr); }
else if (*inputStr == '_') { insCode = ' '; }
if (cnt >= LXBUFSZ-1) { halt("number too long"); }
lexbuf[++cnt] = toupper(*inputStr++);
}
lexbuf[++cnt] = '\0';
if (fractional) {
realtokval = parseReal(lexbuf, 0, cnt);
tokenval = 0;
rc = REALNUM_TOK;
}
else { /* need to save insCode */
tokenval = parseInteger(lexbuf, 0, cnt);
cnt = 0;
if (insCode) { lexbuf[cnt++] = insCode; }
lexbuf[cnt] = '\0';
rc = NUM_TOK;
}
break;
}
else if (t == 'N' && toupper(inputStr[0]) == 'O'
&& toupper(inputStr[1]) == 'T' && !isalnum(inputStr[2]) ) {
inputStr++;
inputStr++;
tokenval = 0;
rc = NOT_TOK;
break;
}
else if (t == 'W' && toupper(inputStr[0]) == 'I'
&& toupper(inputStr[1]) == 'T' && toupper(inputStr[2]) == 'H'
&& toupper(inputStr[3]) == 'I' && toupper(inputStr[4]) == 'N'
&& !isalnum(inputStr[5]) ) {
inputStr += 5;
tokenval = 0;
rc = WITHIN_TOK;
break;
}
else if (isalpha(t)) {
lexbuf[cnt = 0] = t;
while (isalnum(*inputStr) || (*inputStr == '_')
|| (*inputStr == '*') || (*inputStr == '\'')
|| (*inputStr == '"')) {
if (cnt >= LXBUFSZ-1) { halt("symbol too long"); }
lexbuf[++cnt] = toupper(*inputStr++);
}
lexbuf[++cnt] = '\0';
p = lookup(lexbuf);
if (p == 0) {
p = insert(lexbuf, ID_TOK);
}
tokenval = p;
rc = ID_TOK;
break;
}
else if (t == '\0') {
tokenval = 0;
rc = DONE_TOK;
break;
}
else {
tokenval = 0;
rc = t;
break;
}
}
return rc;
}
int lookup(char *s) {
int p;
for (p = LastSymEntry; p > 0; p--) {
if (strcmp(SymTable[p].lexptr, s) == 0) {
return p;
}
}
return 0;
}
int insert(char *s, int tok) {
int len;
len = strlen(s);
if (LastSymEntry + 1 >= LEXSYMMAX) {
halt("symbol table full");
}
if (LastLexChar + len + 1 >= LEXSTRINGMAX) {
halt("symbol name array full");
}
LastSymEntry++;
SymTable[LastSymEntry].token = tok;
SymTable[LastSymEntry].lexptr = &Lexemes[LastLexChar + 1];
LastLexChar += len + 1;
strcpy(SymTable[LastSymEntry].lexptr, s);
return LastSymEntry;
}
int modelInPattern(pattern *pat)
{
static int model=0;
static int ireturn=0;
if(pat == NULL) {model=0;}
else
{
switch(pat->type)
{
case OR_NODE:
case AND_NODE:
ireturn = modelInPattern(pat->rhs);
case NOT_NODE:
ireturn = modelInPattern(pat->lhs);
break;
case MODEL_NODE:
model = pat->val;
break;
}/*switch*/
}
if(model>0){ireturn = model;}
return(ireturn);
}/*modelInPattern()*/
void printPattern(FILE *outf, pattern *pat) {
if (pat) {
recPrint(outf, pat);
fprintf(outf, "\n");
}
}
void recPrint(FILE *outf, pattern *pat) {
if (pat == NULL) return;
switch(pat->type) {
case OR_NODE:
fprintf(outf, "(");
recPrint(outf, pat->lhs);
fprintf(outf, " or ");
recPrint(outf, pat->rhs);
fprintf(outf, ")");
break;
case AND_NODE:
fprintf(outf, "(");
recPrint(outf, pat->lhs);
fprintf(outf, " and ");
recPrint(outf, pat->rhs);
fprintf(outf, ")");
break;
case NOT_NODE:
fprintf(outf,"not(");
recPrint(outf, pat->lhs);
fprintf(outf,")");
break;
case RANGE_NODE:
fprintf(outf,"%d <= resno <= %d", pat->lhs->val, pat->rhs->val);
break;
case FILE_NODE:
fprintf(outf,"file=%d", pat->val);
break;
case MODEL_NODE:
fprintf(outf,"model=%d", pat->val);
break;
case CHAIN_NODE:
fprintf(outf,"chain=\"%s%s\"", lexString(pat->val),
((strlen(lexString(pat->val))<3)?"*":""));
break;
case ALT_NODE:
fprintf(outf,"alt='%c'", pat->val);
break;
case ANAME_NODE:
fprintf(outf,"atom=\"%s%s\"", lexString(pat->val),
((strlen(lexString(pat->val))<4)?"*":""));
break;
case SEGID_NODE:
fprintf(outf,"segID=\"%s%s\"", lexString(pat->val),
((strlen(lexString(pat->val))<4)?"*":""));
break;
case RES_NODE:
fprintf(outf,"resno=%d", pat->val);
break;
case RTYPE_NODE:
fprintf(outf,"res=\"%s%s\"", lexString(pat->val),
((strlen(lexString(pat->val))<3)?"*":""));
break;
case DIST_NODE:
fprintf(outf,"atoms within %.1f of %.3f, %.3f, %.3f", pat->fvec[0],
pat->fvec[1], pat->fvec[2], pat->fvec[3]);
break;
case PROP_NODE:
switch(pat->val) {
case ALPHA_PROP: fprintf(outf,"alpha"); break;
case BETA_PROP: fprintf(outf,"beta"); break;
case MC_PROP: fprintf(outf,"mainchain"); break;
case SC_PROP: fprintf(outf,"sidechain"); break;
case N_PROP: fprintf(outf,"Nitrogen"); break;
case C_PROP: fprintf(outf,"Carbon"); break;
case O_PROP: fprintf(outf,"Oxygen"); break;
case S_PROP: fprintf(outf,"Sulfur"); break;
case P_PROP: fprintf(outf,"Phosphorus"); break;
case H_PROP: fprintf(outf,"Hydrogen"); break;
case WATER_PROP: fprintf(outf,"H2O"); break;
case HET_PROP: fprintf(outf,"het-group"); break;
case PROT_PROP: fprintf(outf,"protein"); break;
case DNA_PROP: fprintf(outf,"dna/rna"); break;
case METAL_PROP: fprintf(outf,"metal"); break;
case METHYL_PROP: fprintf(outf,"methyl"); break;
case METHYLENE_PROP: fprintf(outf,"methylene"); break; /*20111210dcr*/
case DONOR_PROP: fprintf(outf,"donor"); break;
case ACCEPTOR_PROP: fprintf(outf,"acceptor"); break;
case RHPHOBIC_PROP:
fprintf(outf,"A,V,L,I,M,C,F,W,Y (but not G,P!)"); break;
case RHPHILIC_PROP: fprintf(outf,"S,T,N,Q"); break;
case RCHARGED_PROP: fprintf(outf,"D,E,K,R(+H)"); break;
case AROMATIC_PROP:fprintf(outf,"aromatic-atoms");break;
default: fprintf(outf,"property=%d",pat->val); break;
}
break;
case TRUE_NODE:
fprintf(outf,"all");
break;
case FALSE_NODE:
fprintf(outf,"none");
break;
case OCC_LT_NODE:
fprintf(outf,"occupancy < %.2f", pat->val/100.0);
break;
case OCC_GT_NODE:
fprintf(outf,"occupancy > %.2f", pat->val/100.0);
break;
case B_LT_NODE:
fprintf(outf,"Bval < %d", pat->val);
break;
case B_GT_NODE:
fprintf(outf,"Bval > %d", pat->val);
break;
case INS_NODE:
fprintf(outf,"insert='%c'", pat->val);
break;
case INS_RANGE_NODE:
if (pat->lhs->type == RES_NODE) {
fprintf(outf,"%d", pat->rhs->val);
}
else if (pat->lhs->type == AND_NODE) {
fprintf(outf,"%d%c", pat->lhs->lhs->val,
pat->lhs->rhs->val);
}
else {
errmsg("***INTERNAL DEFECT - EXPECT AND***");
fprintf(outf, "(");
recPrint(outf, pat->lhs);
fprintf(outf, ")");
}
fprintf(outf," <= resno <= ");
if (pat->rhs->type == RES_NODE) {
fprintf(outf,"%d", pat->rhs->val);
}
else if (pat->rhs->type == AND_NODE) {
fprintf(outf,"%d%c", pat->rhs->lhs->val,
pat->rhs->rhs->val);
}
else {
errmsg("***INTERNAL DEFECT - EXPECT AND***");
fprintf(outf, "(");
recPrint(outf, pat->rhs);
fprintf(outf, ")");
}
fprintf(outf," /* warning: insert codes ignored in ranges */");
break;
default:
fprintf(outf,"<<bad type: %d>>", pat->type);
}
}/*recPrint()*/
char* describeLookahead(char formatstring[], char *s) {
if (lookahead == ID_TOK) {
sprintf(formatstring,"%s\"%s\"", s, lexString(tokenval));
}
else if (lookahead == NUM_TOK) {
sprintf(formatstring,"%s%d", s, tokenval);
}
else if (lookahead == REALNUM_TOK) {
sprintf(formatstring,"%s%g", s, realtokval);
}
else if (lookahead == NOT_TOK) {
sprintf(formatstring,"%sNOT", s);
}
else if (lookahead == WITHIN_TOK) {
sprintf(formatstring,"%sWITHIN", s);
}
else if (lookahead == DONE_TOK) {
sprintf(formatstring,"%s(end of pattern)", s);
}
else {
sprintf(formatstring,"%s\'%c\'", s, lookahead);
}
return formatstring;
}