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/*
A* -------------------------------------------------------------------
B* This file contains source code for the PyMOL computer program
C* copyright Schrodinger, LLC.
D* -------------------------------------------------------------------
E* It is unlawful to modify or remove this copyright notice.
F* -------------------------------------------------------------------
G* Please see the accompanying LICENSE file for further information.
H* -------------------------------------------------------------------
I* Additional authors of this source file include:
-*
-*
-*
Z* -------------------------------------------------------------------
*/
#ifndef _H_AtomInfoHistory
#define _H_AtomInfoHistory
#include <map>
#include"AtomInfo.h"
#include"Util.h"
#include"Lex.h"
typedef struct AtomInfoType_1_7_6 {
int resv;
int customType;
int priority;
float b, q, vdw, partialCharge;
int selEntry;
int color;
int id; // PDB ID
unsigned int flags;
int temp1; /* kludge fields - to remove */
int unique_id; /* introduced in version 0.77 */
int discrete_state; /* state+1 for atoms in discrete objects */
float elec_radius; /* radius for PB calculations */
int rank;
int textType;
int custom;
int label;
int visRep; /* bitmask for all reps */
/* be careful not to write at these as (int*) */
signed char formalCharge; // values typically in range -2..+2
signed char stereo; /* for 2D representation */
signed char mmstereo; /* from MMStereo */
signed char cartoon; /* 0 = default which is auto (use ssType) */
// boolean flags
signed char hetatm;
signed char bonded;
signed char chemFlag; // 0,1,2
signed char geom; // cAtomInfo*
signed char valence;
// boolean flags
signed char deleteFlag;
signed char masked;
signed char protekted; // 0,1,2
signed char protons; /* atomic number */
// boolean flags
signed char hb_donor;
signed char hb_acceptor;
signed char has_setting; /* setting based on unique_id */
int chain;
SegIdent segi;
AtomName name;
ElemName elem; // redundant with "protons" ?
ResIdent resi;
char has_prop;
SSType ssType; /* blank or 'L' = turn/loop, 'H' = helix, 'S' = beta-strand/sheet */
Chain alt;
ResName resn;
// replace with pointer?
float U11, U22, U33, U12, U13, U23;
int oldid; // for undo
int prop_id;
bool has_anisou() const { return U11 || U22 || U33 || U12 || U13 || U23; }
const float * get_anisou() const { return &U11; } // for copying
float * get_anisou() { return &U11; } // for copying
inline void setResi(int resv_, char inscode_) {
resv = resv_;
AtomResiFromResv(resi, sizeof(resi), resv, inscode_);
}
inline char getInscode() const {
int i = strlen(resi) - 1;
if (i >= 0 && (resi[i] < '0' || '9' < resi[i]))
return resi[i];
return '\0';
}
} AtomInfoType_1_7_6;
typedef struct AtomInfoType_1_7_7 {
union {
float * anisou; // only allocate with get_anisou
int64_t dummyanisou;
};
int resv;
int customType;
int priority;
float b, q, vdw, partialCharge;
int selEntry;
int color;
int id; // PDB ID
unsigned int flags;
int temp1; /* kludge fields - to remove */
int unique_id; /* introduced in version 0.77 */
int discrete_state; /* state+1 for atoms in discrete objects */
float elec_radius; /* radius for PB calculations */
int rank;
int textType;
int custom;
int label;
int visRep; /* bitmask for all reps */
int oldid; // for undo
int prop_id;
// boolean flags
bool hetatm : 1;
bool bonded : 1;
bool deleteFlag : 1;
bool masked : 1;
bool hb_donor : 1;
bool hb_acceptor : 1;
bool has_setting : 1; /* setting based on unique_id */
bool has_prop : 1;
/* be careful not to write at these as (int*) */
signed char formalCharge; // values typically in range -2..+2
signed char mmstereo; /* from MMStereo */
signed char cartoon; /* 0 = default which is auto (use ssType) */
signed char geom; // cAtomInfo*
signed char valence; // 0-4
signed char protons; /* atomic number */
int chain;
SegIdent segi;
AtomName name;
ElemName elem; // redundant with "protons" ?
ResIdent resi;
SSType ssType; /* blank or 'L' = turn/loop, 'H' = helix, 'S' = beta-strand/sheet */
Chain alt;
ResName resn;
// small value optimized bitfields
unsigned char stereo : 2; // 0-3 Only for SDF (MOL) format in/out
unsigned char chemFlag : 2; // 0,1,2
unsigned char protekted : 2; // 0,1,2
// no anisou support in 1.8.0
bool has_anisou() const { return false; }
const float * get_anisou() const { return NULL; }
float * get_anisou() { return NULL; }
inline void setResi(int resv_, char inscode_) {
resv = resv_;
AtomResiFromResv(resi, sizeof(resi), resv, inscode_);
}
inline char getInscode() const {
int i = strlen(resi) - 1;
if (i >= 0 && (resi[i] < '0' || '9' < resi[i]))
return resi[i];
return '\0';
}
} AtomInfoType_1_7_7;
/*
* This is not identical to the 1.8.2 AtomInfoType, it's missing all members
* which are not relevant or unsupported with pse_binary_dump (anisou,
* selEntry, temp1, oldid, prop_id, deleteFlag)
*/
typedef int lexidx_int_t;
struct AtomInfoType_1_8_1 {
// contiguous memory instead of pointer ("short" matches PDB precision)
short anisou[6];
lexidx_int_t segi;
lexidx_int_t chain;
lexidx_int_t resn;
lexidx_int_t name;
lexidx_int_t textType;
lexidx_int_t custom;
lexidx_int_t label;
int resv;
int customType;
int priority;
float b, q, vdw, partialCharge;
int color;
int id; // PDB ID
unsigned int flags;
int unique_id; /* introduced in version 0.77 */
int discrete_state; /* state+1 for atoms in discrete objects */
float elec_radius; /* radius for PB calculations */
int rank;
int visRep; /* bitmask for all reps */
// boolean flags
bool hetatm : 1;
bool bonded : 1;
bool masked : 1;
bool hb_donor : 1;
bool hb_acceptor : 1;
bool has_setting : 1; /* setting based on unique_id */
signed char formalCharge; // values typically in range -2..+2
signed char cartoon; /* 0 = default which is auto (use ssType) */
signed char geom; // cAtomInfo*
signed char valence; // 0-4
signed char protons; /* atomic number */
char inscode;
ElemName elem; // redundant with "protons" ?
SSType ssType; /* blank or 'L' = turn/loop, 'H' = helix, 'S' = beta-strand/sheet */
Chain alt;
// small value optimized bitfields
unsigned char stereo : 2; // 0-3 Only for SDF (MOL) format in/out
unsigned char chemFlag : 2; // 0,1,2
unsigned char protekted : 2; // 0,1,2
char getInscode() const { return inscode; }
void setInscode(char c) { inscode = makeInscode(c); }
void setResi(const char * resi) {
if (sscanf(resi, "%d%c", &resv, &inscode) == 1 || inscode <= ' ')
inscode = '\0';
}
void setResi(int resv_, char inscode_) {
resv = resv_;
setInscode(inscode_);
}
bool has_anisou() const { return anisou[0] || anisou[1] || anisou[2] || anisou[3] || anisou[4] || anisou[5]; }
const short * get_anisou() const { return anisou; } // for copying
short * get_anisou() { return anisou; } // for copying
};
class AtomInfoTypeConverter {
PyMOLGlobals * G;
int NAtom;
template <typename D, typename S> void copy1(D *dest, const S *src);
template <typename D, typename S> void copyN(D *dest, const S *src);
template <typename D> D * allocCopy(const AtomInfoType *src);
public:
AtomInfoTypeConverter(PyMOLGlobals * G_, int natom) : G(G_), NAtom(natom) {}
std::map<lexidx_int_t, lexidx_t> lexidxmap;
lexidx_int_t to_lexidx_int(const lexidx_t& idx) {
return idx;
}
void copy(AtomInfoType * dest, const void *src, int srcversion);
void * allocCopy(int destversion, const AtomInfoType * src);
/*
* For copying Lex strings
*/
inline void copy_attr_s(lexidx_t& dest, lexidx_t src) {
if (!lexidxmap.empty())
src = lexidxmap[src];
LexAssign(G, dest, src);
}
inline void copy_attr_s(lexidx_t& dest, const char * src) {
LexAssign(G, dest, src);
}
template <size_t N> inline void copy_attr_s(char (&dest)[N], const lexidx_t& src) {
UtilNCopy(dest, LexStr(G, src), sizeof(dest));
}
};
#endif
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