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/* name: atomprops.c */
/* author: J. Michael Word date written: 6/12/97 */
/* purpose: define atom properties */
/*****************************************************************/
/* 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 <stdio.h>
#include <string.h> /*060902 needs this for strlen() */
#include <ctype.h>
#define INIT_ATOM_TABLE 1
#include "atomprops.h"
static atomProp* AtomTblIndex[NUMATOMTYPES];
static float ExplMaxRad = 0.0;
static float ImplMaxRad = 0.0;
void initalizeAtomTbl() {
int i;
atomProp *ap;
ExplMaxRad = 0.0;
ImplMaxRad = 0.0;
for(i=0; i < NUMATOMTYPES; i++) { /* default to noAtom */
AtomTblIndex[i] = &(AtomTbl[0]);
}
for(i=0; i < NUMATOMTYPES; i++) {
ap = &(AtomTbl[i]);
AtomTblIndex[ap->type] = ap;
if (ap->iRad > ImplMaxRad){ ImplMaxRad = ap->iRad; }
if (ap->eRad > ExplMaxRad){ ExplMaxRad = ap->eRad; }
}
}
int getAtno(int a) { return AtomTblIndex[a]->atno; }
char* getAtomName(int a) { return AtomTblIndex[a]->name; }
float getExplRad(int a) { return AtomTblIndex[a]->eRad; }
float getImplRad(int a) { return AtomTblIndex[a]->iRad; }
float getCovRad(int a) { return AtomTblIndex[a]->covRad; }
char* getColor(int a) { return AtomTblIndex[a]->color; }
float getMaxRadius(int isImpl){
return (isImpl? ImplMaxRad : ExplMaxRad);
}
int atomHasProp(int a, int f) {
return AtomTblIndex[a]->flags & f;
}
int fixAtomName(const char* atomname, char resname[], int position) { /* no bool in C */
char resn[6];
char name[5] = " ";
int i;
sprintf(resn, ":%-3.3s:", resname);
for (i = 0; i < 4; i++) { /* uppercase the input */
if (atomname[i] == '\0') { break; }
name[i] = toupper(atomname[i]);
}
name[i] = '\0';
switch(name[position]) {
case 'E': if (strstr(HE_RESNAMES, resn) != NULL) { return 1; }
case 'F': if (strstr(HF_RESNAMES, resn) != NULL) { return 1; }
case 'G': if (strstr(HG_RESNAMES, resn) != NULL) { return 1; }
case 'O': if (strstr(HO_RESNAMES, resn) != NULL) { return 1; }
case 'S': if (strstr(HS_RESNAMES, resn) != NULL) { return 1; }
default: break;
}
return 0;
}
int identifyAtom(char* name, char resname[], int Verbose) { /*dcr041007 allow warning choice*/
int n = -1, emitWarning = 0;
switch(name[0]) {
case '*': case '\'': case '"': case '`': case '_':
case '+': case '-': case ' ':
case '0': case '1': case '2': case '3': case '4':
case '5': case '6': case '7': case '8': case '9':
switch(name[1]) {
case 'A':
switch(name[3]) {
case '1': n = atomO; emitWarning = 1; break;
case '2': n = atomN; emitWarning = 1; break;
} break;
case 'B': n = atomB; break;
case 'C': n = atomC; break;
case 'D': n = atomH; break;
case 'F': n = atomF; break;
case 'H':
switch(name[2]) {
case 'E': n = fixAtomName(name,resname,2) ? atomHe : atomH; break;
case 'F': n = fixAtomName(name,resname,2) ? atomHf : atomH; break;
case 'G': n = fixAtomName(name,resname,2) ? atomHg : atomH; break;
case 'O': n = fixAtomName(name,resname,2) ? atomHo : atomH; break;
/* case 'S': n = fixAtomName(name,resname,2) ? atomHs : atomH; break; */
default : n = atomH; break;
} break;
case 'I': n = atomI; break;
case 'K': n = atomK; break;
case 'N': n = atomN; break;
case 'O': n = atomO; break;
case 'P': n = atomP; break;
/*case 'S': n = atomS; break;*/
case 'S':
if(name[0] == ' ' && name[2] == 'E')
{/*_SE likely refmac,cns missplaced Selenium atom name dcr041007*/
n = atomSe; emitWarning = 1; break;
}
else {n = atomS; break;} /*050121 NO warning for other S*/
case 'U': n = atomU; break;
case 'V': n = atomV; break;
case 'W': n = atomW; break;
case 'Y': n = atomY; break;
} break;
case 'A':
switch(name[1]) {
case 'C': n = atomC; emitWarning = 1;break;/*nonstd!*/
case 'G': n = atomAg; break;
case 'H': n = atomH; emitWarning = 1;break;
case 'L': n = atomAl; break;
case 'M': n = atomAm; break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
case 'R': n = atomAr; break;
case 'S': n = atomAs; break;
case 'T': n = atomAt; break;
case 'U': n = atomAu; break;
} break;
case 'B':
switch(name[1]) {
case 'A': n = atomBa; break;
case 'E': n = atomBe; break;
case 'I': n = atomBi; break;
case 'K': n = atomBk; break;
case 'R': n = atomBr; break;
} break;
case 'C':
switch(name[1]) {
case 'A': n = atomCa; break;
case 'C': n = atomC; emitWarning = 1;break;
case 'D': n = atomCd; break;
case 'E': n = atomCe; break;
case 'F': n = atomCf; break;
case 'H': n = atomH; emitWarning = 1;break;
case 'L': n = atomCl; break;
case 'M': n = atomCm; break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomCo; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
case 'R': n = atomCr; break;
case 'S': n = atomCs; break;
case 'U': n = atomCu; break;
default: n = atomC; emitWarning = 1;break;
} break;
case 'D':
switch(name[1]) {
case 'Y': n = atomDy; break;
case 'C': n = atomC; emitWarning = 1;break;
case 'H': n = atomH; emitWarning = 1;break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
default: n = atomH; emitWarning = 1;break;
} break;
case 'E':
switch(name[1]) {
case 'R': n = atomEr; break;
case 'S': n = atomEs; break;
case 'U': n = atomEu; break;
case 'C': n = atomC; emitWarning = 1;break;
case 'H': n = atomH; emitWarning = 1;break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
} break;
case 'F':
switch(name[1]) {
case 'E': n = atomFe; break;
case 'M': n = atomFm; break;
case 'R': n = atomFr; break;
case 'C': n = atomC; emitWarning = 1;break;
case 'H': n = atomH; emitWarning = 1;break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
} break;
case 'G':
switch(name[1]) {
case 'A': n = atomGa; break;
case 'D': n = atomGd; break;
case 'E': n = atomGe; break;
case 'C': n = atomC; emitWarning = 1;break;
case 'H': n = atomH; emitWarning = 1;break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;
case 'P': n = atomP; emitWarning = 1;break;
} break;
case 'H':
switch(name[1]) {
case 'E': n = fixAtomName(name,resname,1) ? atomHe : atomH; break;
case 'F': n = fixAtomName(name,resname,1) ? atomHf : atomH; break;
case 'G': n = fixAtomName(name,resname,1) ? atomHg : atomH; break;
case 'O': n = fixAtomName(name,resname,1) ? atomHo : atomH; break;
/* case 'S': n = fixAtomName(name,resname,1) ? atomHs : atomH; break; */
default : n = atomH; break;
} break;
/* case 'E': */
/* if (isdigit(name[2])) { n = atomH; emitWarning = 1;} */ /* Hepsilon?? */
/* else {n = atomHe; emitWarning = 1;} */
/* break; */
/* case 'F': n = atomHf; emitWarning = 1;break; */
/* case 'G': */
/* if (isdigit(name[2])) { n = atomH; emitWarning = 1;} */ /* Hgamma?? */
/* else {n = atomHg; emitWarning = 1;} */
/* break; */
/* case 'O': n = atomHo; emitWarning = 1;break; */
/* default: n = atomH; emitWarning = 1;break; */
/* } break; */
case 'I':
switch(name[1]) {
case 'N': n = atomIn; break;
case 'R': n = atomIr; break;
} break;
case 'K':
if (name[1] == 'R') n = atomKr; break;
case 'L':
switch(name[1]) {
case 'A': n = atomLa; break;
case 'I': n = atomLi; break;
case 'U': n = atomLu; break;
} break;
case 'M':
switch(name[1]) {
case 'D': n = atomMd; break;
case 'G': n = atomMg; break;
case 'N': n = atomMn; break;
case 'O': n = atomMo; break;
} break;
case 'N':
switch(name[1]) {
case 'A': n = atomNa; emitWarning = 1;break;
case 'B': n = atomNb; emitWarning = 1;break;
case 'C': n = atomC; emitWarning = 1;break;
case 'D': n = atomNd; emitWarning = 1;break;
case 'E': n = atomNe; emitWarning = 1;break;
case 'H': n = atomH; emitWarning = 1;break;
case 'I': n = atomNi; break;
case 'N': n = atomN; emitWarning = 1;break;
case 'O': n = atomO; emitWarning = 1;break;/*nonstd!*/
case 'P': n = atomP; emitWarning = 1;break;/*nonstd!*/
case 'S': n = atomS; emitWarning = 1;break;
default: n = atomN; emitWarning = 1;break;
} break;
case 'O':
switch(name[1]) {
case 'S': n = atomOs; break;
default: n = atomO; emitWarning = 1;break;
} break;
case 'P':
switch(name[1]) {
case 'A': n = atomPa; emitWarning = 1;break;
case 'B': n = atomPb; emitWarning = 1;break;
case 'D': n = atomPd; emitWarning = 1;break;
case 'M': n = atomPm; break;
case 'O': n = atomPo; break;
case 'R': n = atomPr; break;
case 'T': n = atomPt; break;
case 'U': n = atomPu; break;
default: n = atomP; emitWarning = 1;break;
} break;
case 'R':
switch(name[1]) {
case 'A': n = atomRa; break;
case 'B': n = atomRb; break;
case 'E': n = atomRe; break;
case 'H': n = atomRh; break;
case 'N': n = atomRn; break;
case 'U': n = atomRu; break;
} break;
case 'S':
switch(name[1]) {
case 'B': n = atomSb; emitWarning = 1;break;
case 'C': n = atomSc; break;
case 'E': n = atomSe; emitWarning = 1;break;
case 'I': n = atomSi; break;
case 'M': n = atomSm; break;
case 'N': n = atomSn; break;
case 'R': n = atomSr; break;
default: n = atomS; emitWarning = 1;break;
} break;
case 'T':
switch(name[1]) {
case 'A': n = atomTa; break;
case 'B': n = atomTb; break;
case 'C': n = atomTc; break;
case 'E': n = atomTe; break;
case 'H': n = atomTh; break;
case 'I': n = atomTi; break;
case 'L': n = atomTl; break;
case 'M': n = atomTm; break;
} break;
case 'X':
if (name[1] == 'E') n = atomXe; break;
case 'Y':
if (name[1] == 'B') n = atomYb; break;
case 'Z':
switch(name[1]) {
case 'N': n = atomZn; break;
case 'R': n = atomZr; break;
} break;
default: break;
}
if (n < 0) { emitWarning = 1;
n = atomC;
switch(name[1]) {
case 'H': case 'D': n = atomH; break;
case 'C': n = atomC; break;
case 'N': n = atomN; break;
case 'O': n = atomO; break;
case 'P': n = atomP; break;
case 'S': n = atomS; break;
case 'I': n = atomI; break;
case 'K': n = atomK; break;
case 'V': n = atomV; break;
case 'W': n = atomW; break;
case 'U': n = atomU; break;
case 'A':
switch(name[2]) {
case 'G': n = atomAg; break;
case 'L': n = atomAl; break;
case 'S': n = atomAs; break;
case 'U': n = atomAu; break;
} break;
case 'F':
if (name[2] == 'E') n = atomFe; break;
case 'G':
if (name[2] == 'D') n = atomGd; break;
case 'L':
if (name[2] == 'I') n = atomLi; break;
case 'M':
switch(name[2]) {
case 'G': n = atomMg; break;
case 'N': n = atomMn; break;
case 'O': n = atomMo; break;
} break;
case 'Z':
if (name[2] == 'N') n = atomZn; break;
/* --------- default if we fall through... ---------------------*/
default: n = atomC; break;
}
}
if (emitWarning && Verbose) {/*Verbose controlled dcr041007*/
char warnstr[5]={'_','_','_','_','\0'}; /*dcr041007*/
char warnresn[5]={'_','_','_','_','\0'}; /*rmi070719*/
char* atstr;
int j=0;
while(name[j]!='\0'&&warnstr[j]!='\0')
{/*explicitly show blanks so can understand atom name problem*/
if(name[j]==' ') {warnstr[j]='_';}
else {warnstr[j]=name[j];}
j++;
}
j=0;
while(resname[j]!='\0'&&warnresn[j]!='\0')
{/*explicitly show blanks so can understand residue/atom name problem*/
if(name[j]==' ') {warnresn[j]='_';}
else {warnresn[j]=resname[j];}
j++;
}
atstr = getAtomName(n);
if(strlen(atstr)==1)
{fprintf(stderr,"WARNING: atom %s from resn %s will be treated as %s\n",warnstr,warnresn,atstr);}
else {fprintf(stderr,"WARNING: atom %s from resn %s will be treated as %s\n",warnstr,warnresn,atstr);}
/*name, getAtomName(n));*/
}
return n;
}
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