mengine/src/pcmod.h

#ifndef True
#define True 1
#define False 0
#endif 

/* TJO to include FILE type definition */
#include <stdio.h>

#include "pcmsiz.h"

/* These flags allow us to choose whether to do the extra calculations */
#define DO_VIBRATION     2
#define DO_DIPOLE        4
#define DO_XLOGP         8
#define DO_ADDH         16 

/* Global to indicate verbose output or not */
EXTERN int VERBOSE;

#define MAXSELBND 50
#define MAXQUERY  100

EXTERN  int     LPTYPE;

#define radian 57.29577951308

#define Retype 122
EXTERN int hitcount;

#define         MMX             1
#define         MM2             2
#define         MM3             3
#define         MM4             4
#define         AMBER           5
#define         CHARMM          6
#define         MMFF94          7
#define         OPLS            8
#define         OPLSAA          9
#define         UNKNOWN         10

// File Information
#define FTYPE_MMX                   102
#define FTYPE_MM2                   103
#define FTYPE_MM3                   104
#define FTYPE_ALC                   106
#define FTYPE_SYBYL                 107
#define FTYPE_MMOD                  108
#define FTYPE_PCM                   109
#define FTYPE_XRA                   110
#define FTYPE_C3D                   111
#define FTYPE_MOL                   112
#define FTYPE_PDB                   115
#define FTYPE_CSD                   118
#define FTYPE_SDF                   123
#define FTYPE_TINKER                124
#define FTYPE_MOL2                  125

#define FTYPE_MOP                   105
#define FTYPE_ARC                   114
#define FTYPE_GAU                   113   // read gaussian output
#define FTYPE_GAUSOUT               119   // write gaussian job file
#define FTYPE_GAU_IRC               122
#define FTYPE_GAUSFCHK              128
#define FTYPE_PSGVBIN               116
#define FTYPE_PSGVBOUT              117
#define FTYPE_GAMES                 120
#define FTYPE_GAMESOUT              121
#define FTYPE_EHT                   126
#define FTYPE_HONDO                 127
#define FTYPE_HONDOPUN              131
#define FTYPE_TURBOMOLE             129
#define FTYPE_ADF                   130

#define FTYPE_SMILES                131
#define FTYPE_CHEMDRAW              132
#define FTYPE_XML                   133
#define FTYPE_CML                   134

#define SUB_MOVE                        0
#define SUB_HIDE                        1
#define SUB_MINIMIZE                    2

//  flags definitions
#define PI_MASK                 0
#define HBOND_MASK              1
#define AROMATIC_MASK           2
//  metal flags
#define METCOORD_MASK           3
#define SATMET_MASK             4
#define GT18e_MASK              5
#define LOWSPIN_MASK            6
#define SQPLAN_MASK             7

// type rules
#define NO_RETYPE               8
//  invisible
#define VIS_MASK                9
//  minimize 
#define MIN_MASK                10
// cpk surface
#define CPK_SURF                11
//  dotsurf
#define DOT_SURF                12
// Nterm, CNterm, Oterm, COterm, DUMMY
#define NTERM                   13
#define CNTERM                  14
#define OTERM                   15
#define COTERM                  16
#define DUMMY                   17
#define P5                      18
#define P3                      19
// Ring Size
#define RING3                   20
#define RING4                   21
#define RING5                   22
#define RING6                   23

/*  PCMODEL specific definitions */
#ifndef ATOMTYPE
typedef struct {
                        double x,y,z;
                        int type;
                        int tclass;
                        int mmx_type;
                        int mm3_type;
                        int amber_type;
                        int mmff_type;
                        int charm_type;
                        int opls_type;
                        int atomnum;
                        int serno;
                        int molecule;
                        int residue;
                        int biotype;
                        double atomwt;
                        float energy;
                        int use;
                        int color;
                        int chrg_color;
                        int iat[MAXIAT];
                        int bo[MAXIAT];
                        char name[3];
                        double charge;
                        float formal_charge;
                        float sigma_charge;
                        float radius;
                        float vdw_radius;
                        long int flags;
                        long int substr[MAXSSCLASS];
                        } ATOMTYPE;
#endif

EXTERN struct {
                int numbonds;
                int ia1[MAXATOM], ia2[MAXATOM], bondorder[MAXATOM];
                } bonds;

EXTERN struct {
                int   istereo;
                int   noh;
                int   immx;
                int   minimized;
                int   modified;
                float dielc;
                float avleg;
                int   rescale;
                int   nohyd; } flags;

EXTERN struct {
                int nquery, qatom[MAXQUERY][4],qtype[MAXQUERY];
                float qxpos[MAXQUERY],qypos[MAXQUERY];
                int queryon;
                } query;

EXTERN ATOMTYPE         atom[MAXATOM];
EXTERN int              selatom[MAXATOM];
EXTERN int              selbnd[MAXSELBND][2];
EXTERN int              last_atom;
EXTERN int              natom;
EXTERN int              DrawAtoms, DrawBonds;
EXTERN long             StrScale;
EXTERN long             MaxAtomRadius;
EXTERN float            currentx,currenty,currentz;
EXTERN int              curtype;
EXTERN int              cur_label;
EXTERN int              curmetal;
EXTERN int              cur_color;
EXTERN char             Struct_Title[100];
EXTERN FILE             *pcmoutfile, *PSfile, *HPGLfile;
EXTERN char             pcwindir[80];
EXTERN int              hbond_flag;
EXTERN int              cmap[225][3];
EXTERN int              Mopac_Charges;
EXTERN int              use_external_chrg;
EXTERN int              use_gast_chrg;
EXTERN int              default_intype, default_outtype;
Revision:	20
Committed:	Mon Jun 30 22:00:43 2008 UTC (13 years, 10 months ago) by tjod
Original Path:	*trunk/smi23d/src/mengine/pcmod.h*
File size:	6189 byte(s)
Log Message:	Add -a switch to cause H atoms to be added, deleting existing ones. With -a, mengine behaves as the original. Formal charges are not always preserved, by the original or the modified mengine with or without the -a switch. It appears that negative charges are preserved (benzoic acid). A positive charge on a N atom (an amine) is not preserved. Charges are recognized in CHG records and in atom records. Charges are output only in atom records.
Line	File contents
1	#ifndef True
2	#define True 1
3	#define False 0
4	#endif
5
6	/* TJO to include FILE type definition */
7	#include <stdio.h>
8
9	#include "pcmsiz.h"
10
11	/* These flags allow us to choose whether to do the extra calculations */
12	#define DO_VIBRATION 2
13	#define DO_DIPOLE 4
14	#define DO_XLOGP 8
15	#define DO_ADDH 16
16
17	/* Global to indicate verbose output or not */
18	EXTERN int VERBOSE;
19
20	#define MAXSELBND 50
21	#define MAXQUERY 100
22
23	EXTERN int LPTYPE;
24
25	#define radian 57.29577951308
26
27	#define Retype 122
28	EXTERN int hitcount;
29
30	#define MMX 1
31	#define MM2 2
32	#define MM3 3
33	#define MM4 4
34	#define AMBER 5
35	#define CHARMM 6
36	#define MMFF94 7
37	#define OPLS 8
38	#define OPLSAA 9
39	#define UNKNOWN 10
40
41	// File Information
42	#define FTYPE_MMX 102
43	#define FTYPE_MM2 103
44	#define FTYPE_MM3 104
45	#define FTYPE_ALC 106
46	#define FTYPE_SYBYL 107
47	#define FTYPE_MMOD 108
48	#define FTYPE_PCM 109
49	#define FTYPE_XRA 110
50	#define FTYPE_C3D 111
51	#define FTYPE_MOL 112
52	#define FTYPE_PDB 115
53	#define FTYPE_CSD 118
54	#define FTYPE_SDF 123
55	#define FTYPE_TINKER 124
56	#define FTYPE_MOL2 125
57
58	#define FTYPE_MOP 105
59	#define FTYPE_ARC 114
60	#define FTYPE_GAU 113 // read gaussian output
61	#define FTYPE_GAUSOUT 119 // write gaussian job file
62	#define FTYPE_GAU_IRC 122
63	#define FTYPE_GAUSFCHK 128
64	#define FTYPE_PSGVBIN 116
65	#define FTYPE_PSGVBOUT 117
66	#define FTYPE_GAMES 120
67	#define FTYPE_GAMESOUT 121
68	#define FTYPE_EHT 126
69	#define FTYPE_HONDO 127
70	#define FTYPE_HONDOPUN 131
71	#define FTYPE_TURBOMOLE 129
72	#define FTYPE_ADF 130
73
74	#define FTYPE_SMILES 131
75	#define FTYPE_CHEMDRAW 132
76	#define FTYPE_XML 133
77	#define FTYPE_CML 134
78
79	#define SUB_MOVE 0
80	#define SUB_HIDE 1
81	#define SUB_MINIMIZE 2
82
83	// flags definitions
84	#define PI_MASK 0
85	#define HBOND_MASK 1
86	#define AROMATIC_MASK 2
87	// metal flags
88	#define METCOORD_MASK 3
89	#define SATMET_MASK 4
90	#define GT18e_MASK 5
91	#define LOWSPIN_MASK 6
92	#define SQPLAN_MASK 7
93
94	// type rules
95	#define NO_RETYPE 8
96	// invisible
97	#define VIS_MASK 9
98	// minimize
99	#define MIN_MASK 10
100	// cpk surface
101	#define CPK_SURF 11
102	// dotsurf
103	#define DOT_SURF 12
104	// Nterm, CNterm, Oterm, COterm, DUMMY
105	#define NTERM 13
106	#define CNTERM 14
107	#define OTERM 15
108	#define COTERM 16
109	#define DUMMY 17
110	#define P5 18
111	#define P3 19
112	// Ring Size
113	#define RING3 20
114	#define RING4 21
115	#define RING5 22
116	#define RING6 23
117
118	/* PCMODEL specific definitions */
119	#ifndef ATOMTYPE
120	typedef struct {
121	double x,y,z;
122	int type;
123	int tclass;
124	int mmx_type;
125	int mm3_type;
126	int amber_type;
127	int mmff_type;
128	int charm_type;
129	int opls_type;
130	int atomnum;
131	int serno;
132	int molecule;
133	int residue;
134	int biotype;
135	double atomwt;
136	float energy;
137	int use;
138	int color;
139	int chrg_color;
140	int iat[MAXIAT];
141	int bo[MAXIAT];
142	char name[3];
143	double charge;
144	float formal_charge;
145	float sigma_charge;
146	float radius;
147	float vdw_radius;
148	long int flags;
149	long int substr[MAXSSCLASS];
150	} ATOMTYPE;
151	#endif
152
153	EXTERN struct {
154	int numbonds;
155	int ia1[MAXATOM], ia2[MAXATOM], bondorder[MAXATOM];
156	} bonds;
157
158	EXTERN struct {
159	int istereo;
160	int noh;
161	int immx;
162	int minimized;
163	int modified;
164	float dielc;
165	float avleg;
166	int rescale;
167	int nohyd; } flags;
168
169	EXTERN struct {
170	int nquery, qatom[MAXQUERY][4],qtype[MAXQUERY];
171	float qxpos[MAXQUERY],qypos[MAXQUERY];
172	int queryon;
173	} query;
174
175	EXTERN ATOMTYPE atom[MAXATOM];
176	EXTERN int selatom[MAXATOM];
177	EXTERN int selbnd[MAXSELBND][2];
178	EXTERN int last_atom;
179	EXTERN int natom;
180	EXTERN int DrawAtoms, DrawBonds;
181	EXTERN long StrScale;
182	EXTERN long MaxAtomRadius;
183	EXTERN float currentx,currenty,currentz;
184	EXTERN int curtype;
185	EXTERN int cur_label;
186	EXTERN int curmetal;
187	EXTERN int cur_color;
188	EXTERN char Struct_Title[100];
189	EXTERN FILE pcmoutfile, PSfile, *HPGLfile;
190	EXTERN char pcwindir[80];
191	EXTERN int hbond_flag;
192	EXTERN int cmap[225][3];
193	EXTERN int Mopac_Charges;
194	EXTERN int use_external_chrg;
195	EXTERN int use_gast_chrg;
196	EXTERN int default_intype, default_outtype;