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RasMol2
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Announce,
ChangeLog,
ChangeLog.1,
ChangeLog.2,
ChangeLog.3,
ChangeLog.4,
ChangeLog.5,
ChangeLog.6,
INSTALL,
Imakefile,
Makefile,
Makefile.bak,
Makefile.in,
Makefile.nt,
Makefile.pc,
PROJECTS,
README,
TODO,
abstree.c,
abstree.h,
abstree.o,
applemac.c,
bitmaps.h,
cexio.c,
command.c,
command.h,
command.o,
data,
doc,
font.h,
graphics.h,
infile.c,
infile.h,
infile.o,
mac,
molecule.c,
molecule.h,
molecule.o,
mswin,
mswin31.c,
outfile.c,
outfile.h,
outfile.o,
pixutils.c,
pixutils.h,
pixutils.o,
rasmac.c,
rasmol.c,
rasmol.h,
rasmol.hlp,
rasmol.o,
rasmol.sh,
raswin.c,
render.c,
render.h,
render.o,
repres.c,
repres.h,
repres.o,
script.c,
script.h,
script.o,
tokens.h,
transfor.c,
transfor.h,
transfor.o,
vms,
x11win.c,
x11win.o,
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/* abstree.h
* RasMol2 Molecular Graphics
* Roger Sayle, August 1995
* Version 2.6
*/
#define OpCode(x) (((x)->type)&0x0f)
/* Operator Types */
#define OpAnd 0x01
#define OpOr 0x02
#define OpNot 0x03
#define OpEqual 0x04
#define OpNotEq 0x05
#define OpLess 0x06
#define OpMore 0x07
#define OpLessEq 0x08
#define OpMoreEq 0x09
#define OpConst 0x0a
#define OpWithin 0x0b
#define OpMember 0xac
#define OpLftProp 0x10
#define OpLftVal 0x20
#define OpRgtProp 0x40
#define OpRgtVal 0x80
/* Property fields */
#define PropIdent 1
#define PropXCord 2
#define PropYCord 3
#define PropZCord 4
#define PropTemp 5
#define PropRad 6
#define PropResId 7
#define PropName 8
#define PropChain 9
#define PropResName 10
#define PropSelect 11
#define PropElemNo 12
#define PropModel 13
#define PredAbsOrd(x) ((x)-20)
#define PredAbsChr(x) ((x)+20)
#define PredAlpha 20
#define PredAmino 21
#define PredAT 22
#define PredBonded 23
#define PredCG 24
#define PredCystine 25
#define PredDNA 26
#define PredHelix 27
#define PredHetero 28
#define PredHydrogen 29
#define PredIon 30
#define PredLigand 31
#define PredMainChain 32
#define PredNucleic 33
#define PredProtein 34
#define PredPurine 35
#define PredPyrimidine 36
#define PredRNA 37
#define PredSelected 38 /* Unused! */
#define PredSheet 39
#define PredSidechain 40
#define PredSolvent 41
#define PredTurn 42
#define PredWater 43
#define PredAcidic 44
#define PredAcyclic 45
#define PredAliphatic 46
#define PredAromatic 47
#define PredBasic 48
#define PredBuried 49
#define PredCharged 50
#define PredCyclic 51
#define PredHydrophobic 52
#define PredLarge 53
#define PredMedium 54
#define PredNeutral 55
#define PredPolar 56
#define PredSmall 57
#define PredSurface 58
#define SetSize 10
typedef struct _AtomSet {
struct _AtomSet __far *next;
Atom __far *data[SetSize];
int count;
} AtomSet;
typedef union {
AtomSet __far *set;
struct _Expr *ptr;
Long limit;
int val;
} Branch;
typedef struct _Expr {
int type;
Branch rgt;
Branch lft;
} Expr;
/* CPK Colour Indices
* 0 Light Grey 1 Sky Blue 2 Red 3 Yellow
* 4 White 5 Pink 6 Golden Rod 7 Blue
* 8 Orange 9 Dark Grey 10 Brown 11 Purple
* 12 Deep Pink 13 Green 14 Fire Brick 15 Mid Green
*/
#define MAXELEMNO 104
typedef struct {
char symbol[2];
int covalrad;
int vdwrad;
int cpkcol;
char *name;
} ElemStruct;
/* Structures with Implicit Hydrogens */
#define VDWCarbon 468
#define VDWNitrogen 375
#define VDWOxygen 350
#define VDWSulphur 462
#ifdef ABSTREE
ElemStruct Element[MAXELEMNO] = {
{ { ' ', ' ' }, 170, 360, 12, "" }, /* 0 */
{ { 'H', ' ' }, 80, 275, 4, "HYDROGEN" }, /* 1 */
{ { 'H', 'e' }, 400, 550, 5, "HELIUM" }, /* 2 */
{ { 'L', 'i' }, 170, 305, 14, "LITHIUM" }, /* 3 */
{ { 'B', 'e' }, 88, 157, 12, "BERYLLIUM" }, /* 4 */
{ { 'B', ' ' }, 208, 387, 13, "BORON" }, /* 5 */
{ { 'C', ' ' }, 180, 387, 0, "CARBON" }, /* 6 */
{ { 'N', ' ' }, 170, 350, 1, "NITROGEN" }, /* 7 */
{ { 'O', ' ' }, 170, 337, 2, "OXYGEN" }, /* 8 */
{ { 'F', ' ' }, 160, 325, 6, "FLUORINE" }, /* 9 */
{ { 'N', 'e' }, 280, 505, 12, "NEON" }, /* 10 */
{ { 'N', 'a' }, 243, 550, 7, "SODIUM" }, /* 11 */
{ { 'M', 'g' }, 275, 375, 15, "MAGNESIUM" }, /* 12 */
{ { 'A', 'l' }, 338, 375, 9, "ALUMINIUM" }, /* 13 */
{ { 'S', 'i' }, 300, 550, 6, "SILICON" }, /* 14 */
{ { 'P', ' ' }, 259, 470, 8, "PHOSPHORUS" }, /* 15 */ /* 262? */
{ { 'S', ' ' }, 255, 452, 3, "SULPHUR" }, /* 16 */
{ { 'C', 'l' }, 250, 437, 13, "CHLORINE" }, /* 17 */
{ { 'A', 'r' }, 392, 692, 12, "ARGON" }, /* 18 */
{ { 'K', ' ' }, 332, 597, 12, "POTASSIUM" }, /* 19 */
{ { 'C', 'a' }, 248, 487, 9, "CALCIUM" }, /* 20 */
{ { 'S', 'c' }, 360, 330, 12, "SCANDIUM" }, /* 21 */
{ { 'T', 'i' }, 368, 487, 9, "TITANIUM" }, /* 22 */
{ { 'V', ' ' }, 332, 265, 12, "VANADIUM" }, /* 23 */
{ { 'C', 'r' }, 338, 282, 9, "CHROMIUM" }, /* 24 */
{ { 'M', 'n' }, 338, 297, 9, "MANGANESE" }, /* 25 */
{ { 'F', 'e' }, 335, 487, 8, "IRON" }, /* 26 */
{ { 'C', 'o' }, 332, 282, 12, "COBALT" }, /* 27 */
{ { 'N', 'i' }, 405, 310, 10, "NICKEL" }, /* 28 */ /* >375! */
{ { 'C', 'u' }, 380, 287, 10, "COPPER" }, /* 29 */
{ { 'Z', 'n' }, 362, 287, 10, "ZINC" }, /* 30 */
{ { 'G', 'a' }, 305, 387, 12, "GALLIUM" }, /* 31 */
{ { 'G', 'e' }, 292, 999, 12, "GERMANIUM" }, /* 32 */ /* 1225? */
{ { 'A', 's' }, 302, 207, 12, "ARSENIC" }, /* 33 */
{ { 'S', 'e' }, 305, 225, 12, "SELENIUM" }, /* 34 */
{ { 'B', 'r' }, 302, 437, 10, "BROMINE" }, /* 35 */
{ { 'K', 'r' }, 400, 475, 12, "KRYPTON" }, /* 36 */
{ { 'R', 'b' }, 368, 662, 12, "RUBIDIUM" }, /* 37 */
{ { 'S', 'r' }, 280, 505, 12, "STRONTIUM" }, /* 38 */
{ { 'Y', ' ' }, 445, 402, 12, "YTTRIUM" }, /* 39 */
{ { 'Z', 'r' }, 390, 355, 12, "ZIRCONIUM" }, /* 40 */
{ { 'N', 'b' }, 370, 332, 12, "NIOBIUM" }, /* 41 */
{ { 'M', 'o' }, 368, 437, 12, "MOLYBDENUM" }, /* 42 */
{ { 'T', 'c' }, 338, 450, 12, "TECHNETIUM" }, /* 43 */
{ { 'R', 'u' }, 350, 300, 12, "RUTHENIUM" }, /* 44 */
{ { 'R', 'h' }, 362, 305, 12, "RHODIUM" }, /* 45 */
{ { 'P', 'd' }, 375, 360, 12, "PALLADIUM" }, /* 46 */
{ { 'A', 'g' }, 398, 387, 9, "SILVER" }, /* 47 */
{ { 'C', 'd' }, 422, 437, 12, "CADMIUM" }, /* 48 */
{ { 'I', 'n' }, 408, 362, 12, "INDIUM" }, /* 49 */
{ { 'S', 'n' }, 365, 417, 12, "TIN", }, /* 50 */
{ { 'S', 'b' }, 365, 280, 12, "ANTIMONY" }, /* 51 */
{ { 'T', 'e' }, 368, 315, 12, "TELLURIUM" }, /* 52 */
{ { 'I', ' ' }, 350, 437, 11, "IODINE" }, /* 53 */
{ { 'X', 'e' }, 425, 525, 12, "XENON" }, /* 54 */
{ { 'C', 's' }, 418, 752, 12, "CAESIUM" }, /* 55 */
{ { 'B', 'a' }, 335, 602, 8, "BARIUM" }, /* 56 */
{ { 'L', 'a' }, 468, 457, 12, "LANTHANUM" }, /* 57 */
{ { 'C', 'e' }, 458, 465, 12, "CERIUM" }, /* 58 */
{ { 'P', 'r' }, 455, 405, 12, "PRASEODYMIUM" }, /* 59 */
{ { 'N', 'd' }, 452, 447, 12, "NEODYMIUM" }, /* 60 */
{ { 'P', 'm' }, 450, 440, 12, "PROMETHIUM" }, /* 61 */
{ { 'S', 'm' }, 450, 435, 12, "SAMARIUM" }, /* 62 */
{ { 'E', 'u' }, 498, 490, 12, "EUROPIUM" }, /* 63 */
{ { 'G', 'd' }, 448, 422, 12, "GADOLINIUM" }, /* 64 */
{ { 'T', 'b' }, 440, 415, 12, "TERBIUM" }, /* 65 */
{ { 'D', 'y' }, 438, 407, 12, "DYSPROSIUM" }, /* 66 */
{ { 'H', 'o' }, 435, 402, 12, "HOLMIUM" }, /* 67 */
{ { 'E', 'r' }, 432, 397, 12, "ERBIUM" }, /* 68 */
{ { 'T', 'm' }, 430, 392, 12, "THULIUM" }, /* 69 */
{ { 'Y', 'b' }, 485, 385, 12, "YTTERBIUM" }, /* 70 */
{ { 'L', 'u' }, 430, 382, 12, "LUTETIUM" }, /* 71 */
{ { 'H', 'f' }, 392, 350, 12, "HAFNIUM" }, /* 72 */
{ { 'T', 'a' }, 358, 305, 12, "TANTALUM" }, /* 73 */
{ { 'W', ' ' }, 342, 315, 12, "TUNGSTEN" }, /* 74 */
{ { 'R', 'e' }, 338, 325, 12, "RHENIUM" }, /* 75 */
{ { 'O', 's' }, 342, 395, 12, "OSMIUM" }, /* 76 */
{ { 'I', 'r' }, 330, 305, 12, "IRIDIUM" }, /* 77 */
{ { 'P', 't' }, 375, 387, 12, "PLATINUM" }, /* 78 */
{ { 'A', 'u' }, 375, 362, 6, "GOLD" }, /* 79 */
{ { 'H', 'g' }, 425, 495, 12, "MERCURY" }, /* 80 */
{ { 'T', 'l' }, 388, 427, 12, "THALLIUM" }, /* 81 */
{ { 'P', 'b' }, 385, 540, 12, "LEAD" }, /* 82 */
{ { 'B', 'i' }, 385, 432, 12, "BISMUTH" }, /* 83 */
{ { 'P', 'o' }, 420, 302, 12, "POLONIUM" }, /* 84 */
{ { 'A', 't' }, 302, 280, 12, "ASTATINE" }, /* 85 */
{ { 'R', 'n' }, 475, 575, 12, "RADON" }, /* 86 */
{ { 'F', 'r' }, 450, 810, 12, "FRANCIUM" }, /* 87 */
{ { 'R', 'a' }, 358, 642, 12, "RADIUM" }, /* 88 */
{ { 'A', 'c' }, 295, 530, 12, "ACTINIUM" }, /* 89 */
{ { 'T', 'h' }, 255, 460, 12, "THORIUM" }, /* 90 */
{ { 'P', 'a' }, 222, 400, 12, "PROTACTINIUM" }, /* 91 */
{ { 'U', ' ' }, 242, 437, 12, "URANIUM" }, /* 92 */
{ { 'N', 'p' }, 238, 427, 12, "NEPTUNIUM" }, /* 93 */
{ { 'P', 'u' }, 232, 417, 12, "PLUTONIUM" }, /* 94 */
{ { 'A', 'm' }, 230, 415, 12, "AMERICIUM" }, /* 95 */
{ { 'C', 'm' }, 228, 412, 12, "CURIUM" }, /* 96 */
{ { 'B', 'k' }, 225, 410, 12, "BERKELIUM" }, /* 97 */
{ { 'C', 'f' }, 222, 407, 12, "CALIFORNIUM" }, /* 98 */
{ { 'E', 's' }, 220, 405, 12, "EINSTEINIUM" }, /* 99 */
{ { 'F', 'm' }, 218, 402, 12, "FERMIUM" }, /* 100 */
{ { 'M', 'd' }, 215, 400, 12, "MENDELEVIUM" }, /* 101 */
{ { 'N', 'o' }, 212, 397, 12, "NOBELIUM" }, /* 102 */
{ { 'L', 'r' }, 210, 395, 12, "LAWRENCIUM" } /* 103 */ /* Lw? */
};
Expr *QueryExpr;
Chain __far *QChain;
Group __far *QGroup;
Atom __far *QAtom;
#else
extern ElemStruct Element[MAXELEMNO];
extern Expr *QueryExpr;
extern Chain __far *QChain;
extern Group __far *QGroup;
extern Atom __far *QAtom;
#ifdef FUNCPROTO
Expr *AllocateNode();
void DeAllocateExpr( Expr* );
int EvaluateExpr( Expr* );
int DefineSetExpr( char*, Expr* );
Expr *LookUpSetExpr( char* );
AtomSet __far *BuildAtomSet( Expr* );
void DeleteAtomSet( AtomSet __far* );
Expr *LookUpElement( char* );
int ElemVDWRadius( int );
int ParsePrimitiveExpr( char** );
int GetElemNumber( Group __far*, Atom __far* );
void FormatLabel( Chain __far*, Group __far*, Atom __far*, char*, char* );
void InitialiseAbstree();
void ResetSymbolTable();
double CalcTorsion( Atom __far*, Atom __far*, Atom __far*, Atom __far* );
double CalcAngle( Atom __far*, Atom __far*, Atom __far* );
double CalcDistance( Atom __far*, Atom __far* );
#else /* non-ANSI C compiler */
Expr *AllocateNode();
void DeAllocateExpr();
int EvaluateExpr();
int DefineSetExpr();
Expr *LookUpSetExpr();
AtomSet __far *BuildAtomSet();
void DeleteAtomSet();
Expr *LookUpElement();
int ElemVDWRadius();
int ParsePrimitiveExpr();
int GetElemNumber();
void FormatLabel();
void InitialiseAbstree();
void ResetSymbolTable();
double CalcTorsion();
double CalcAngle();
double CalcDistance();
#endif
#endif
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