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/* abstree.c
* RasMol2 Molecular Graphics
* Roger Sayle, August 1995
* Version 2.6
*/
#include "rasmol.h"
#ifdef IBMPC
#include <malloc.h>
#endif
#ifndef sun386
#include <stdlib.h>
#endif
#include <string.h>
#include <ctype.h>
#include <stdio.h>
#include <math.h>
#define ABSTREE
#include "molecule.h"
#include "abstree.h"
#define ExprPool 16
#define SetPool 4
typedef struct _SymEntry {
struct _SymEntry __far *lft;
struct _SymEntry __far *rgt;
AtomSet __far *defn;
char *ident;
} SymEntry;
static SymEntry __far *SymbolTable;
static SymEntry __far *FreeEntry;
static AtomSet __far *FreeSet;
static Expr *FreeExpr;
static Expr FalseExpr;
static Expr TrueExpr;
/* Macros for commonly used loops */
#define ForEachAtom for(chain=Database->clist;chain;chain=chain->cnext) \
for(group=chain->glist;group;group=group->gnext) \
for(aptr=group->alist;aptr;aptr=aptr->anext)
#define BitAcidic 0x001
#define BitAliphatic 0x002
#define BitAromatic 0x004
#define BitBasic 0x008
#define BitBuried 0x010
#define BitCyclic 0x020
#define BitHydrophobic 0x040
#define BitMedium 0x080
#define BitNeutral 0x100
#define BitSmall 0x200
#define BitCharged 0x009
#define BitNotLarge 0x280
/* Acyclic = !Cyclic */
/* Large = !Medium && !Small */
/* Polar = !Hydrophobic */
/* Surface = !Buried */
#define AminoCodeMax 28
static char *AminoCode = "AGLSVTKDINEPRFQYHCMWBZPPACGTX";
static int AminoProp[] = {
/*ALA*/ BitAliphatic | BitBuried | BitHydrophobic | BitNeutral |
BitSmall,
/*GLY*/ BitAliphatic | BitHydrophobic | BitNeutral | BitSmall,
/*LEU*/ BitAliphatic | BitBuried | BitHydrophobic | BitNeutral,
/*SER*/ BitNeutral | BitSmall,
/*VAL*/ BitAliphatic | BitBuried | BitHydrophobic | BitMedium |
BitNeutral,
/*THR*/ BitMedium | BitNeutral,
/*LYS*/ BitBasic,
/*ASP*/ BitAcidic | BitMedium,
/*ILE*/ BitAliphatic | BitBuried | BitHydrophobic | BitNeutral,
/*ASN*/ BitMedium | BitNeutral,
/*GLU*/ BitAcidic,
/*PRO*/ BitCyclic | BitHydrophobic | BitMedium | BitNeutral,
/*ARG*/ BitBasic,
/*PHE*/ BitAromatic | BitBuried | BitCyclic | BitHydrophobic |
BitNeutral,
/*GLN*/ BitNeutral,
/*TYR*/ BitAromatic | BitCyclic | BitNeutral,
/*HIS*/ BitAromatic | BitBasic | BitCyclic | BitNeutral,
/*CYS*/ BitBuried | BitMedium | BitNeutral,
/*MET*/ BitBuried | BitHydrophobic | BitNeutral,
/*TRP*/ BitAromatic | BitBuried | BitCyclic | BitHydrophobic |
BitNeutral,
/*ASX*/ BitMedium | BitNeutral,
/*GLX*/ BitNeutral,
/*PCA*/ BitCyclic | BitHydrophobic | BitMedium | BitNeutral,
/*HYP*/ BitCyclic | BitMedium | BitNeutral
};
static void FatalExprError(ptr)
char *ptr;
{
char buffer[80];
sprintf(buffer,"Expression Error: %s!",ptr);
RasMolFatalExit(buffer);
}
#ifdef FUNCPROTO
/* Function Prototypes */
static AtomSet __far *SetInsert( AtomSet __far*, Atom __far* );
static int IsWithinRadius( AtomSet __far*, Long );
static int IsSetMember( AtomSet __far* );
#endif
static AtomSet __far *SetInsert( ptr, item )
AtomSet __far *ptr; Atom __far *item;
{
register AtomSet __far *temp;
register int i;
if( ptr && (ptr->count<SetSize) )
{ ptr->data[ptr->count] = item;
ptr->count++;
return( ptr );
}
if( !FreeSet )
{ temp = (AtomSet __far*)_fmalloc( SetPool*sizeof(AtomSet) );
if( !temp ) FatalExprError("Memory allocation failed");
for( i=1; i<SetPool; i++ )
{ temp->next = FreeSet;
FreeSet = temp++;
}
} else
{ temp = FreeSet;
FreeSet = temp->next;
}
temp->data[0] = item;
temp->next = ptr;
temp->count = 1;
return( temp );
}
static int IsWithinRadius( ptr, limit )
AtomSet __far *ptr;
Long limit;
{
register Atom __far *aptr;
register Long dx,dy,dz;
register Long dist;
register int i;
while( ptr )
{ for( i=0; i<ptr->count; i++ )
{ aptr = ptr->data[i];
dx = QAtom->xorg-aptr->xorg; if( (dist=dx*dx)>limit ) continue;
dy = QAtom->yorg-aptr->yorg; if( (dist+=dy*dy)>limit ) continue;
dz = QAtom->zorg-aptr->zorg; if( (dist+=dz*dz)>limit ) continue;
return( True );
}
ptr = ptr->next;
}
return( False );
}
static int IsSetMember( ptr )
AtomSet __far *ptr;
{
register int i;
while( ptr )
{ for( i=0; i<ptr->count; i++ )
if( ptr->data[i] == QAtom )
return( True );
ptr = ptr->next;
}
return( False );
}
void DeleteAtomSet( ptr )
AtomSet __far *ptr;
{
register AtomSet __far *temp;
if( ptr )
{ temp = ptr;
while( temp->next )
temp = temp->next;
temp->next = FreeSet;
FreeSet = ptr;
}
}
Expr *AllocateNode()
{
register Expr *ptr;
register int i;
if( !FreeExpr )
{ ptr = (Expr*)malloc( ExprPool*sizeof(Expr) );
if( !ptr ) FatalExprError("Memory allocation failed");
for( i=1; i<ExprPool; i++ )
{ ptr->rgt.ptr = FreeExpr;
FreeExpr = ptr++;
}
} else
{ ptr = FreeExpr;
FreeExpr = ptr->rgt.ptr;
}
ptr->rgt.ptr = NULL;
ptr->lft.ptr = NULL;
return( ptr );
}
void DeAllocateExpr( expr )
Expr *expr;
{
if( !expr ) return;
if( (expr == &FalseExpr) ||
(expr == &TrueExpr) )
return;
if( expr->type!=OpWithin )
{ if( !(expr->type&(OpLftProp|OpLftVal)) )
DeAllocateExpr( expr->lft.ptr );
if( !(expr->type&(OpRgtProp|OpRgtVal)) )
DeAllocateExpr( expr->rgt.ptr );
} else DeleteAtomSet( expr->rgt.set );
expr->rgt.ptr = FreeExpr;
FreeExpr = expr;
}
int GetElemNumber( group, aptr )
Group __far *group;
Atom __far *aptr;
{
register char ch1,ch2;
register char *ptr;
ptr = ElemDesc[aptr->refno];
if( IsNADGroup(group->refno) || IsCOAGroup(group->refno) )
{ /* Exceptions to Brookhaven Atom Naming! */
ch1 = ' ';
} else
{ ch1 = ptr[0];
/* Handle HG, HD etc.. in Amino Acids! */
if( (ch1=='H') && IsProtein(group->refno) )
return( 1 );
}
ch2 = ptr[1];
switch( ch1 )
{ case(' '): switch( ch2 )
{ case('B'): return( 5 );
case('C'): return( 6 );
case('D'): return( 1 );
case('F'): return( 9 );
case('H'): return( 1 );
case('I'): return( 53 );
case('K'): return( 19 );
case('L'): return( 1 );
case('N'): return( 7 );
case('O'): return( 8 );
case('P'): return( 15 );
case('S'): return( 16 );
case('U'): return( 92 );
case('V'): return( 23 );
case('W'): return( 74 );
case('Y'): return( 39 );
}
break;
case('A'): switch( ch2 )
{ case('C'): return( 89 );
case('G'): return( 47 );
case('L'): return( 13 );
case('M'): return( 95 );
case('R'): return( 18 );
case('S'): return( 33 );
case('T'): return( 85 );
case('U'): return( 79 );
}
break;
case('B'): switch( ch2 )
{ case('A'): return( 56 );
case('E'): return( 4 );
case('I'): return( 83 );
case('K'): return( 97 );
case('R'): return( 35 );
}
break;
case('C'): switch( ch2 )
{ case('A'): return( 20 );
case('D'): return( 48 );
case('E'): return( 58 );
case('F'): return( 98 );
case('L'): return( 17 );
case('M'): return( 96 );
case('O'): return( 27 );
case('R'): return( 24 );
case('S'): return( 55 );
case('U'): return( 29 );
}
break;
case('D'): if( ch2=='Y' )
return( 66 );
break;
case('E'): if( ch2=='R' )
{ return( 68 );
} else if( ch2=='S' )
{ return( 99 );
} else if( ch2=='U' )
return( 63 );
break;
case('F'): if( ch2=='E' )
{ return( 26 );
} else if( ch2=='M' )
{ return( 100 );
} else if( ch2=='R' )
return( 87 );
break;
case('G'): if( ch2=='A' )
{ return( 31 );
} else if( ch2=='D' )
{ return( 64 );
} else if( ch2=='E' )
return( 32 );
break;
case('H'): if( ch2=='E' )
{ return( 2 );
} else if( ch2=='F' )
{ return( 72 );
} else if( ch2=='G' )
{ return( 80 );
} else if( ch2=='O' )
return( 67 );
break;
case('I'): if( ch2=='N' )
{ return( 49 );
} else if( ch2=='R' )
return( 77 );
break;
case('K'): if( ch2=='R' )
return( 36 );
break;
case('L'): if( ch2=='A' )
{ return( 57 );
} else if( ch2=='I' )
{ return( 3 );
} else if( (ch2=='R') || (ch2=='W') )
{ return( 103 );
} else if( ch2=='U' )
return( 71 );
break;
case('M'): if( ch2=='D' )
{ return( 101 );
} else if( ch2=='G' )
{ return( 12 );
} else if( ch2=='N' )
{ return( 25 );
} else if( ch2=='O' )
return( 42 );
break;
case('N'): switch( ch2 )
{ case('A'): return( 11 );
case('B'): return( 41 );
case('D'): return( 60 );
case('E'): return( 10 );
case('I'): return( 28 );
case('O'): return( 102 );
case('P'): return( 93 );
}
break;
case('O'): if( ch2=='S' )
return( 76 );
break;
case('P'): switch( ch2 )
{ case('A'): return( 91 );
case('B'): return( 82 );
case('D'): return( 46 );
case('M'): return( 61 );
case('O'): return( 84 );
case('R'): return( 59 );
case('T'): return( 78 );
case('U'): return( 94 );
}
break;
case('R'): switch( ch2 )
{ case('A'): return( 88 );
case('B'): return( 37 );
case('E'): return( 75 );
case('H'): return( 45 );
case('N'): return( 86 );
case('U'): return( 44 );
}
break;
case('S'): switch( ch2 )
{ case('B'): return( 51 );
case('C'): return( 21 );
case('E'): return( 34 );
case('I'): return( 14 );
case('M'): return( 62 );
case('N'): return( 50 );
case('R'): return( 38 );
}
break;
case('T'): switch( ch2 )
{ case('A'): return( 73 );
case('B'): return( 65 );
case('C'): return( 43 );
case('E'): return( 52 );
case('H'): return( 90 );
case('I'): return( 22 );
case('L'): return( 81 );
case('M'): return( 69 );
}
break;
case('X'): if( ch2=='E' )
return( 54 );
break;
case('Y'): if( ch2=='B' )
return( 70 );
break;
case('Z'): if( ch2=='N' )
{ return( 30 );
} else if( ch2=='R' )
return( 40 );
break;
}
if( (ch1>='0') && (ch1<='9') )
if( (ch2=='H') || (ch2=='D') )
return( 1 ); /* Hydrogen */
return( 0 );
}
int ElemVDWRadius( elem )
int elem;
{
if( !HasHydrogen )
switch( elem )
{ case( 6 ): return( VDWCarbon );
case( 7 ): return( VDWNitrogen );
case( 8 ): return( VDWOxygen );
case( 16 ): return( VDWSulphur );
}
return( Element[elem].vdwrad );
}
static int EvaluateProperty( prop )
int prop;
{
switch( prop )
{ case( PropIdent ): return( QAtom->serno );
case( PropXCord ): return( (int)QAtom->xorg );
case( PropYCord ): return( (int)QAtom->yorg );
case( PropZCord ): return( (int)QAtom->zorg );
case( PropTemp ): return( QAtom->temp );
case( PropName ): return( QAtom->refno );
case( PropResId ): return( QGroup->serno );
case( PropResName ): return( QGroup->refno );
case( PropChain ): return( QChain->ident );
case( PropSelect ): return( QAtom->flag&SelectFlag );
case( PropElemNo ): return( QAtom->elemno );
case( PropModel ): return( QChain->model );
case( PropRad ): if( QAtom->flag&SphereFlag )
{ return( QAtom->radius );
} else return( 0 );
/* Predicates stored in flags */
case( PredBonded ): return( !(QAtom->flag&NonBondFlag) );
case( PredHydrogen ): return( QAtom->flag&HydrogenFlag );
case( PredHetero ): return( QAtom->flag&HeteroFlag );
case( PredCystine ): return( QGroup->flag&CystineFlag );
case( PredHelix ): return( QGroup->struc&HelixFlag );
case( PredSheet ): return( QGroup->struc&SheetFlag );
case( PredTurn ): return( QGroup->struc&TurnFlag );
/* Residue type predicates */
case( PredDNA ): return( IsDNA(QGroup->refno) );
case( PredRNA ): return( IsRNA(QGroup->refno) );
case( PredNucleic ): return( IsNucleo(QGroup->refno) );
case( PredProtein ): return( IsProtein(QGroup->refno) );
case( PredAmino ): return( IsAmino(QGroup->refno) );
case( PredWater ): return( IsWater(QGroup->refno) );
case( PredSolvent ): return( IsSolvent(QGroup->refno) );
case( PredIon ): return( IsIon(QGroup->refno) );
/* General Predicates */
case( PredAlpha ): return( IsAmino(QGroup->refno) &&
IsAlphaCarbon(QAtom->refno) );
case( PredMainChain ): return( (IsAmino(QGroup->refno) &&
IsAminoBackbone(QAtom->refno)) ||
(IsNucleo(QGroup->refno) &&
IsNucleicBackbone(QAtom->refno)) );
case( PredSidechain ): return( IsAmino(QGroup->refno) &&
!IsAminoBackbone(QAtom->refno) );
case( PredLigand ): return( (QAtom->flag&HeteroFlag) &&
!IsSolvent(QGroup->refno) );
/* Nucleic Acid Classifications */
case( PredAT ): return( IsAdenine(QGroup->refno) ||
IsThymine(QGroup->refno) );
case( PredCG ): return( IsCytosine(QGroup->refno) ||
IsGuanine(QGroup->refno) );
case( PredPyrimidine ): return( IsPyrimidine(QGroup->refno) );
case( PredPurine ): return( IsPurine(QGroup->refno) );
/* Amino Acid Classifications */
case( PredAcidic ): return( IsAmino(QGroup->refno) &&
AminoProp[QGroup->refno]&BitAcidic );
case( PredAcyclic ): return( IsAmino(QGroup->refno) &&
!(AminoProp[QGroup->refno]&BitCyclic) );
case( PredAliphatic ): return( IsAmino(QGroup->refno) &&
AminoProp[QGroup->refno]&BitAliphatic );
case( PredAromatic ): return( IsAmino(QGroup->refno) &&
AminoProp[QGroup->refno]&BitAromatic );
case( PredBasic ): return( IsAmino(QGroup->refno) &&
AminoProp[QGroup->refno]&BitBasic );
case( PredBuried ): return( IsAmino(QGroup->refno) &&
AminoProp[QGroup->refno]&BitBuried );
case( PredCharged ): return( IsAmino(QGroup->refno) &&
AminoProp[QGroup->refno]&BitCharged );
case( PredCyclic ): return( IsAmino(QGroup->refno) &&
AminoProp[QGroup->refno]&BitCyclic );
case( PredHydrophobic ): return( IsAmino(QGroup->refno) &&
AminoProp[QGroup->refno]&BitHydrophobic );
case( PredLarge ): return( IsAmino(QGroup->refno) &&
!(AminoProp[QGroup->refno]&BitNotLarge) );
case( PredMedium ): return( IsAmino(QGroup->refno) &&
AminoProp[QGroup->refno]&BitMedium );
case( PredNeutral ): return( IsAmino(QGroup->refno) &&
AminoProp[QGroup->refno]&BitNeutral );
case( PredPolar ): return( IsAmino(QGroup->refno) &&
!(AminoProp[QGroup->refno]&BitHydrophobic) );
case( PredSmall ): return( IsAmino(QGroup->refno) &&
AminoProp[QGroup->refno]&BitSmall );
case( PredSurface ): return( IsAmino(QGroup->refno) &&
!(AminoProp[QGroup->refno]&BitBuried) );
}
return( True );
}
int EvaluateExpr( expr )
Expr *expr;
{
register int lft, rgt;
if( !expr )
return( True );
if( expr->type==OpWithin )
{ if( expr->lft.limit )
{ return( IsWithinRadius(expr->rgt.set,expr->lft.limit) );
} else return( IsSetMember(expr->rgt.set) );
} else if( expr->type==OpMember )
return( IsSetMember(expr->rgt.set) );
if( expr->type & OpLftVal )
{ lft = expr->lft.val;
} else if( expr->type & OpLftProp )
{ lft = EvaluateProperty( expr->lft.val );
} else lft = EvaluateExpr( expr->lft.ptr );
if( OpCode(expr)==OpConst ) return( lft );
if( (OpCode(expr)==OpAnd) && !lft ) return( False );
if( (OpCode(expr)==OpOr) && lft ) return( True );
if( OpCode(expr)==OpNot ) return( !lft );
if( expr->type & OpRgtVal )
{ rgt = expr->rgt.val;
} else if( expr->type & OpRgtProp )
{ rgt = EvaluateProperty( expr->rgt.val );
} else rgt = EvaluateExpr( expr->rgt.ptr );
switch( OpCode(expr) )
{ case(OpOr):
case(OpAnd): return( rgt );
case(OpLess): return( lft<rgt );
case(OpMore): return( lft>rgt );
case(OpEqual): return( lft==rgt );
case(OpNotEq): return( lft!=rgt );
case(OpLessEq): return( lft<=rgt );
case(OpMoreEq): return( lft>=rgt );
}
return( True );
}
AtomSet __far *BuildAtomSet( expr )
Expr *expr;
{
register AtomSet __far *ptr;
ptr = (AtomSet __far*)0;
if( Database )
for( QChain=Database->clist; QChain; QChain=QChain->cnext )
for( QGroup=QChain->glist; QGroup; QGroup=QGroup->gnext )
for( QAtom=QGroup->alist; QAtom; QAtom=QAtom->anext )
if( EvaluateExpr(expr) )
ptr = SetInsert( ptr, QAtom );
return( ptr );
}
int DefineSetExpr( ident, expr )
char *ident; Expr *expr;
{
register SymEntry __far * __far *prev;
register SymEntry __far *ptr;
register AtomSet __far *set;
register int result;
result = True;
prev = &SymbolTable;
while( *prev )
{ ptr = *prev;
result = strcmp(ident,ptr->ident);
if( !result ) break; /* Entry Exists! */
prev = (result<0)? &(ptr->lft) : &(ptr->rgt);
}
if( result )
{ if( FreeEntry )
{ ptr = FreeEntry;
FreeEntry = ptr->rgt;
} else /* Allocate SymEntry! */
{
ptr = (SymEntry __far*)_fmalloc(sizeof(SymEntry));
if( !ptr ) return( False );
}
*prev = ptr;
ptr->ident = ident;
ptr->defn = (void __far*)0;
ptr->lft = (void __far*)0;
ptr->rgt = (void __far*)0;
} else free(ident);
if( expr )
{ set = BuildAtomSet(expr);
if( ptr->defn )
DeleteAtomSet(ptr->defn);
DeAllocateExpr(expr);
ptr->defn = set;
} else ptr->defn = (void __far*)0;
return( True );
}
Expr *LookUpSetExpr( ident )
char *ident;
{
register SymEntry __far *ptr;
register Expr *expr;
register int result;
result = True;
ptr = SymbolTable;
while( ptr )
{ result = strcmp(ident,ptr->ident);
if( !result ) break; /* Entry Exists! */
ptr = (result<0)? ptr->lft : ptr->rgt;
}
if( !result )
{ expr = AllocateNode();
expr->type = OpMember;
expr->rgt.set = ptr->defn;
} else expr = (Expr*)0;
return( expr );
}
static int ElemCompare( ident, elem )
char *ident, *elem;
{
while( *elem )
if( *elem++ != *ident++ )
return( False );
/* Handle Plurals */
if( (ident[0]=='S') && !ident[1] )
return( (elem[-1]!='S') && (elem[-1]!='Y') );
return( !*ident );
}
Expr *LookUpElement( ident )
char *ident;
{
register Expr *expr;
register int elem;
for( elem=1; elem<MAXELEMNO; elem++ )
if( ElemCompare(ident,Element[elem].name) )
break;
/* Handle Difficult Plurals & US Spelling! */
if( elem == MAXELEMNO )
{ if( *ident=='A' )
{ if( ElemCompare(ident,"ALUMINUM") )
{ elem = 13;
} else if( !strcmp(ident,"ANTIMONIES") )
elem = 51;
} else if( *ident=='C' )
{ if( ElemCompare(ident,"CESIUM") )
elem = 55;
} else if( *ident=='M' )
{ if( !strcmp(ident,"MERCURIES") )
elem = 80;
} else if( *ident=='P' )
{ if( !strcmp(ident,"PHOSPHORUSES") )
elem = 8;
} else if( *ident=='S' )
{ if( ElemCompare(ident,"SULFUR") )
elem = 16;
}
}
if( elem<MAXELEMNO )
{ expr = AllocateNode();
expr->type = OpEqual|OpLftProp|OpRgtVal;
expr->lft.val = PropElemNo;
expr->rgt.val = elem;
} else expr = (Expr*)0;
return( expr );
}
static int MatchWildName( src, dst, size, len )
char *src, *dst; int size, len;
{
register int i, left;
left = size;
while( *dst==' ' )
{ dst++; left--;
}
for( i=0; i<len; i++ )
{ if( left )
{ if( (*dst==*src) || (*src=='?') )
{ dst++; src++; left--;
} else return( False );
} else if( *src++ != '?' )
return( False );
}
while( left )
if( *dst++!=' ' )
{ return( False );
} else left--;
return( True );
}
int ParsePrimitiveExpr( orig )
char **orig;
{
static char NameBuf[4];
register Expr *tmp1,*tmp2;
register Expr *wild;
register char *ptr;
register int i, j;
register int neg;
register int ch;
QueryExpr = &TrueExpr;
ptr = *orig;
ch = *ptr++;
i = 0;
if( ch != ':' )
{ /* Parse Residue Name */
if( ch != '*' )
{ if( ch == '[' )
{ i = 0;
while( (ch = *ptr++) != ']' )
if( ch && (i<3) )
{ NameBuf[i++] = ToUpper(ch);
} else return( False );
ch = *ptr++;
} else
for( i=0; i<3; i++ )
if( isalpha(ch) )
{ NameBuf[i] = ToUpper(ch);
ch = *ptr++;
} else if( (ch=='?') || (ch=='%') )
{ NameBuf[i] = '?';
ch = *ptr++;
} else break;
if( !i ) return( False );
wild = &FalseExpr;
for( j=0; j<ResNo; j++ )
if( MatchWildName(NameBuf,Residue[j],3,i) )
{ tmp1 = AllocateNode();
tmp1->type = OpEqual | OpLftProp | OpRgtVal;
tmp1->lft.val = PropResName;
tmp1->rgt.val = j;
tmp2 = AllocateNode();
tmp2->type = OpOr;
tmp2->lft.ptr = tmp1;
tmp2->rgt.ptr = wild;
wild = tmp2;
}
QueryExpr = wild;
} else ch = *ptr++;
/* Parse Residue Number */
if( ch != '*' )
{ if( ch == '-' )
{ ch = *ptr++;
neg = True;
} else neg = False;
if( isdigit(ch) )
{ i = ch-'0';
while( isdigit(*ptr) )
i = 10*i + (*ptr++)-'0';
tmp1 = AllocateNode();
tmp1->type = OpEqual | OpLftProp | OpRgtVal;
tmp1->rgt.val = neg? -i : i;
tmp1->lft.val = PropResId;
if( QueryExpr != &TrueExpr )
{ tmp2 = AllocateNode();
tmp2->type = OpAnd;
tmp2->rgt.ptr = QueryExpr;
tmp2->lft.ptr = tmp1;
QueryExpr = tmp2;
} else QueryExpr = tmp1;
ch = *ptr++;
} else if( neg )
return( False );
} else ch = *ptr++;
}
/* Parse Chain Ident */
if( ch==':' )
ch = *ptr++;
if( isalnum(ch) )
{ ch = ToUpper(ch);
tmp1 = AllocateNode();
tmp1->type = OpEqual | OpLftProp | OpRgtVal;
tmp1->lft.val = PropChain;
tmp1->rgt.val = ch;
if( QueryExpr != &TrueExpr )
{ tmp2 = AllocateNode();
tmp2->type = OpAnd;
tmp2->rgt.ptr = QueryExpr;
tmp2->lft.ptr = tmp1;
QueryExpr = tmp2;
} else QueryExpr = tmp1;
ch = *ptr++;
} else if( (ch=='?') || (ch=='%') || (ch=='*') )
ch = *ptr++;
/* Parse Model Number */
if( ch == ':' )
{ ch = *ptr++;
if( isdigit(ch) )
{ i = ch-'0';
while( isdigit(*ptr) )
i = 10*i + (*ptr++)-'0';
tmp1 = AllocateNode();
tmp1->type = OpEqual | OpLftProp | OpRgtVal;
tmp1->lft.val = PropModel;
tmp1->rgt.val = i;
if( QueryExpr != &TrueExpr )
{ tmp2 = AllocateNode();
tmp2->type = OpAnd;
tmp2->rgt.ptr = QueryExpr;
tmp2->lft.ptr = tmp1;
QueryExpr = tmp2;
} else QueryExpr = tmp1;
ch = *ptr++;
} else return( False );
}
/* Parse Atom Name */
if( ch == '.' )
{ ch = *ptr++;
if( ch!='*' )
{ for( i=0; i<4; i++ )
if( isalnum(ch) || ch=='\'' || ch=='*' )
{ NameBuf[i] = ToUpper(ch);
ch = *ptr++;
} else if( (ch=='?') || (ch=='%') || (ch=='#') )
{ NameBuf[i] = '?';
ch = *ptr++;
} else break;
if( !i ) return( False );
wild = &FalseExpr;
for( j=0; j<ElemNo; j++ )
if( MatchWildName(NameBuf,ElemDesc[j],4,i) )
{ tmp1 = AllocateNode();
tmp1->type = OpEqual | OpLftProp | OpRgtVal;
tmp1->lft.val = PropName;
tmp1->rgt.val = j;
tmp2 = AllocateNode();
tmp2->type = OpOr;
tmp2->lft.ptr = tmp1;
tmp2->rgt.ptr = wild;
wild = tmp2;
}
if( (QueryExpr == &TrueExpr) || (wild == &FalseExpr) )
{ DeAllocateExpr(QueryExpr);
QueryExpr=wild;
} else
{ tmp1 = AllocateNode();
tmp1->type = OpAnd;
tmp1->lft.ptr = QueryExpr;
tmp1->rgt.ptr = wild;
QueryExpr = tmp1;
}
} else ch = *ptr++;
}
*orig = --ptr;
return( !ch || isspace(ch) || ispunct(ch) );
}
static char *FormatInteger( ptr, value )
char *ptr; int value;
{
auto char buffer[10];
register char *tmp;
if( value<0 )
{ value = -value;
*ptr++ = '-';
}
if( value>9 )
{ tmp = buffer;
while( value>9 )
{ *tmp++ = (value%10) + '0';
value /= 10;
}
*ptr++ = value + '0';
do { tmp--;
*ptr++ = *tmp;
} while( tmp != buffer );
} else *ptr++ = value + '0';
return( ptr );
}
void FormatLabel( chain, group, aptr, label, ptr )
Chain __far *chain;
Group __far *group;
Atom __far *aptr;
char *label, *ptr;
{
register char ch;
register int i,j;
while( *label )
{ ch = *label++;
if( ch=='%' )
{ ch = *label++;
if( isupper(ch) )
ch = tolower(ch);
switch( ch )
{ case('a'): /* Atom Name */
i = aptr->refno;
for( j=0; j<4; j++ )
if( ElemDesc[i][j]!=' ' )
*ptr++ = ElemDesc[i][j];
break;
case('b'): /* Temperature/B-factor */
case('t'): ptr = FormatInteger(ptr,aptr->temp);
break;
case('c'): /* Chain Identifier */
case('s'): *ptr++ = chain->ident;
break;
case('e'): /* Element Type */
i = aptr->elemno;
*ptr++ = Element[i].symbol[0];
if( Element[i].symbol[1]!=' ' )
*ptr++ = Element[i].symbol[1];
break;
case('i'): /* Atom Number */
ptr = FormatInteger(ptr,aptr->serno);
break;
case('m'): /* Amino (Nucliec) Acid Code */
if( group->refno <= AminoCodeMax )
{ *ptr++ = AminoCode[group->refno];
} else *ptr++ = '?';
break;
case('n'): /* Residue Name */
i = group->refno;
for( j=0; j<3; j++ )
if( Residue[i][j]!=' ' )
*ptr++ = Residue[i][j];
break;
case('r'): /* Residue Number */
ptr = FormatInteger(ptr,group->serno);
break;
case('%'): *ptr++ = '%';
break;
}
} else if( (ch>=' ') && (ch<='~') )
*ptr++ = ch;
}
*ptr = '\0';
}
#ifdef FUNCPROTO
/* Function Prototypes */
static void DeleteSymEntry( SymEntry __far* );
#endif
static void DeleteSymEntry( ptr )
SymEntry __far *ptr;
{
if( ptr->lft )
DeleteSymEntry( ptr->lft );
if( ptr->rgt )
DeleteSymEntry( ptr->rgt );
if( ptr->defn )
DeleteAtomSet( ptr->defn );
free( ptr->ident );
ptr->rgt = FreeEntry;
FreeEntry = ptr;
}
void ResetSymbolTable()
{
if( SymbolTable )
{ DeleteSymEntry(SymbolTable);
SymbolTable = (void __far*)0;
}
}
double CalcDistance( atm1, atm2 )
Atom __far *atm1;
Atom __far *atm2;
{
register Long dx,dy,dz;
register double dist2;
dx = atm1->xorg - atm2->xorg;
dy = atm1->yorg - atm2->yorg;
dz = atm1->zorg - atm2->zorg;
if( dx || dy || dz )
{ dist2 = dx*dx + dy*dy + dz*dz;
return( sqrt(dist2)/250.0 );
} else return( 0.0 );
}
double CalcAngle( atm1, atm2, atm3 )
Atom __far *atm1;
Atom __far *atm2;
Atom __far *atm3;
{
register double ulen2,vlen2;
register double ux,uy,uz;
register double vx,vy,vz;
register double temp;
ux = atm1->xorg - atm2->xorg;
uy = atm1->yorg - atm2->yorg;
uz = atm1->zorg - atm2->zorg;
if( !ux && !uy && !uz )
return( 0.0 );
ulen2 = ux*ux + uy*uy + uz*uz;
vx = atm3->xorg - atm2->xorg;
vy = atm3->yorg - atm2->yorg;
vz = atm3->zorg - atm2->zorg;
if( !vx && !vy && !vz )
return( 0.0 );
vlen2 = vx*vx + vy*vy + vz*vz;
temp = (ux*vx + uy*vy + uz*vz)/sqrt(ulen2*vlen2);
return( Rad2Deg*acos(temp) );
}
double CalcTorsion( atm1, atm2, atm3, atm4 )
Atom __far *atm1; Atom __far *atm2;
Atom __far *atm3; Atom __far *atm4;
{
register double ax, ay, az;
register double bx, by, bz;
register double cx, cy, cz;
register double c12,c13,c23;
register double s12,s23;
register double cossq,sgn,om;
register double cosom,sinom;
register double len;
ax = atm2->xorg - atm1->xorg;
ay = atm2->yorg - atm1->yorg;
az = atm2->zorg - atm1->zorg;
if( !ax && !ay && !az )
return( 0.0 );
bx = atm3->xorg - atm2->xorg;
by = atm3->yorg - atm2->yorg;
bz = atm3->zorg - atm2->zorg;
if( !bx && !by && !bz )
return( 0.0 );
cx = atm4->xorg - atm3->xorg;
cy = atm4->yorg - atm3->yorg;
cz = atm4->zorg - atm3->zorg;
if( !cx && !cy && !cz )
return( 0.0 );
len = sqrt(ax*ax + ay*ay + az*az);
ax /= len; ay /= len; az /= len;
len = sqrt(bx*bx + by*by + bz*bz);
bx /= len; by /= len; bz /= len;
len = sqrt(cx*cx + cy*cy + cz*cz);
cx /= len; cy /= len; cz /= len;
c12 = ax*bx + ay*by + az*bz;
c13 = ax*cx + ay*cy + az*cz;
c23 = bx*cx + by*cy + bz*cz;
s12 = sqrt(1.0-c12*c12);
s23 = sqrt(1.0-c23*c23);
cosom = (c12*c23-c13)/(s12*s23);
cossq = cosom*cosom;
if( cossq >= 1.0 )
{ if( cosom < 0.0 )
{ return( 180.0 );
} else return( 0.0 );
}
sinom = sqrt(1.0-cossq);
om = Rad2Deg*atan2(sinom,cosom);
sgn = ax*((by*cz)-(bz*cy));
sgn += ay*((bz*cx)-(bx*cz));
sgn += az*((bx*cy)-(by*cx));
return( (sgn<0)? -om : om );
}
#ifndef ABSTREE
double CalcDihedral( atm1, atm2, atm3, atm4 )
Atom __far *atm1; Atom __far *atm2;
Atom __far *atm3; Atom __far *atm4;
{
return( 180.0 - CalcTorsion(atm1,atm2,atm3,atm4) );
}
/* Note: curr == prev->gnext! */
double CalcPhiAngle( prev, curr )
Group __far *prev;
Group __far *curr;
{
Atom __far *prevc;
Atom __far *currca;
Atom __far *currc;
Atom __far *currn;
if( !(prevc = FindGroupAtom(prev,2)) ) return( 360.0 );
if( !(currca = FindGroupAtom(curr,1)) ) return( 360.0 );
if( !(currc = FindGroupAtom(curr,2)) ) return( 360.0 );
if( !(currn = FindGroupAtom(curr,0)) ) return( 360.0 );
return( CalcDihedral(prevc,currn,currca,currc) );
}
/* Note: next == curr->gnext! */
double CalcPsiAngle( curr, next )
Group __far *curr;
Group __far *next;
{
Atom __far *nextn;
Atom __far *currca;
Atom __far *currc;
Atom __far *currn;
if( !(nextn = FindGroupAtom(next,0)) ) return( 360.0 );
if( !(currca = FindGroupAtom(curr,1)) ) return( 360.0 );
if( !(currc = FindGroupAtom(curr,2)) ) return( 360.0 );
if( !(currn = FindGroupAtom(curr,0)) ) return( 360.0 );
return( CalcDihedral(currn,currca,currc,nextn) );
}
#endif
void InitialiseAbstree()
{
FalseExpr.type = OpConst | OpLftVal | OpRgtVal;
FalseExpr.rgt.val = FalseExpr.lft.val = 0;
TrueExpr.type = OpConst | OpLftVal | OpRgtVal;
TrueExpr.rgt.val = TrueExpr.lft.val = 1;
QChain = (void __far*)0;
QGroup = (void __far*)0;
QAtom = (void __far*)0;
SymbolTable = (void __far*)0;
FreeEntry = (void __far*)0;
FreeSet = (void __far*)0;
FreeExpr = NULL;
}
These are the contents of the former NiCE NeXT User Group NeXTSTEP/OpenStep software archive, currently hosted by Netfuture.ch.