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/* name: atomprops.h */
/* 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 */
/*****************************************************************/
#ifndef ATOMPROPS_H
#define ATOMPROPS_H 1
#define HE_RESNAMES \
"currently there are none RMI 070711"
#define HF_RESNAMES \
":PHF:HF3:HF5:"
#define HG_RESNAMES \
": HG:HG2:HGB:HGC:HGI:MAC:MBO:MMC:PHG:PMB:AAS:AMS:BE7:CMH:EMC:EMT:"
#define HO_RESNAMES \
": HO:HO3:"
#define HS_RESNAMES \
"currently there are none RMI 070711"
typedef struct atomProp_t {
int type; /* atom identifier */
int atno; /* atomic number */
char* name; /* atom name */
float eRad; /* (explicit H) ecloud VDW radius */
float eRad_nuc; /* (explicit H) nuclear VDW radius */
float iRad; /* (implicit H) VDW radius */
float covRad; /* covalent radius */
char* color; /* dot color */
int flags; /* element features */
} atomProp;
void initalizeAtomTbl(void);
int fixAtomName(const char* atomname, char resname[], int position); /*rmi070719 add resname info to identifyAtom*/
int identifyAtom(char* name, char resname[], int Verbose); /*dcr041007 allow warning choice*/
int getAtno(int a);
char* getAtomName(int a);
float getExplRad(int a);
float getImplRad(int a);
float getCovRad(int a);
char* getColor(int a);
float getMaxRadius(int isImplicit);
int atomHasProp(int a, int f);
/* Each atom identifier (except endAtomTypes) must be in the AtomTbl */
/* A new atom must also be added to the function identifyAtomName() and */
/* may need to be entered in setProperties() */
enum atomIdentifiers {
noAtom=0, ignoreAtom,
atomH, atomHarom, atomHpolar, atomHOd,
atomC, atomCarom, atomN, atomO, atomF, atomS, atomP,
atomAc, atomAg, atomAl, atomAm, atomAr, atomAs, atomAt, atomAu,
atomB, atomBa, atomBe, atomBi, atomBk, atomBr, atomCa, atomCd,
atomCe, atomCf, atomCl, atomCm, atomCo, atomCr, atomCs, atomCu,
atomDy, atomEr, atomEs, atomEu, atomFe, atomFm, atomFr, atomGa,
atomGd, atomGe, atomHe, atomHf, atomHg, atomHo, atomI, atomIn,
atomIr, atomK, atomKr, atomLa, atomLi, atomLu, atomMd, atomMg,
atomMn, atomMo, atomNa, atomNb, atomNd, atomNe, atomNi, atomNo,
atomNp, atomOs, atomPa, atomPb, atomPd, atomPm, atomPo, atomPr,
atomPt, atomPu, atomRa, atomRb, atomRe, atomRh, atomRn, atomRu,
atomSb, atomSc, atomSe, atomSi, atomSm, atomSn, atomSr, atomTa,
atomTb, atomTc, atomTe, atomTh, atomTi, atomTl, atomTm, atomU,
atomV, atomW, atomXe, atomY, atomYb, atomZn, atomZr,
/* base identifiers are used in a real hack to paint nucleic acid */
/* contacts with colors for bases as an alternative to atom colors */
/* (dots are catagorized in a table NUMATOMTYPES wide) */
baseA, baseTU, baseC, baseG, baseOther, nonBase,
endAtomTypes
};
#define isHatom(atype) (getAtno(atype) == 1)
#define isCatom(atype) (getAtno(atype) == 6)
#define NUMATOMTYPES endAtomTypes
#define COVRADFUDGE 0.2
#define METALIC_ATOM_FLAG (1 << 0) /*atomProp AtomTbl flags: element features*/
#define IONIC_ATOM_FLAG (1 << 1) /*dcr041007 partial, now on halides*/
#ifdef INIT_ATOM_TABLE
/* For non-metals, explicit VDW radii from */
/* Gavezzotti, J. Am. Chem. Soc. (1983) 105, 5220-5225. */
/* or, if unavailable, */
/* Bondi, J. Phys. Chem. (1964), V68, N3, 441-451. */
/* Covalent and ionic radii from */
/* Advanced Inorganic Chemistry, Cotton & Wilkinson, 1962, p93. */
/* from above: struct atomProp, NUMATOMTYPES from enum of atomIdentifiers*/
/*type; atom identifier */
/*atno; atomic number */
/*name; atom name */
/*eRad; (explicit H) ecloud VDW radius */
/*eRad_nuc; (explicit H) nuclear VDW radius */ //jjh 130307
/*iRad; (implicit H) VDW radius */
/*covRad; covalent radius */
/*color; dot color */
/*flags; element features */
atomProp AtomTbl[NUMATOMTYPES] = { /* noAtom must be first */
{noAtom, 0, "?", 1.05, 1.05, 0.00, 0.00, "magenta", 0},
{ignoreAtom, 0, ".", 0.00, 0.00, 0.00, 0.00, "grey", 0},
{atomH, 1, "H", 1.22, 1.17, 0.00, 0.30, "grey", 0},
{atomHarom, 1, "Har", 1.05, 1.00, 0.00, 0.30, "grey", 0},
{atomHpolar, 1, "Hpol", 1.05, 1.00, 0.00, 0.30, "grey", 0},
{atomHOd, 1, "HOd", 1.05, 1.00, 0.00, 0.30, "grey", 0},/*hb-only-dummy*/
{atomC, 6, "C", 1.70, 1.70, 1.90, 0.77, "white", 0},
{atomCarom, 6, "Car", 1.75, 1.75, 1.90, 0.77, "white", 0},
{atomN, 7, "N", 1.55, 1.55, 1.70, 0.70, "sky", 0},
{atomO, 8, "O", 1.40, 1.40, 1.50, 0.66, "red", 0},
{atomP, 15, "P", 1.80, 1.80, 1.80, 1.10, "pink", 0},
{atomS, 16, "S", 1.80, 1.80, 1.90, 1.04, "yellow", 0},
{atomAs, 33, "As", 2.00, 2.00, 2.10, 1.21, "grey", 0},
{atomSe, 34, "Se", 1.90, 1.90, 2.00, 1.17, "green", 0},
/*dcr041007 halides given IONIC_ATOM_FLAG*/
{atomF, 9, "F", 1.30, 1.30, 1.30, 0.58, "green", IONIC_ATOM_FLAG},
{atomCl, 17, "Cl", 1.77, 1.77, 1.77, 0.99, "green", IONIC_ATOM_FLAG},
{atomBr, 35, "Br", 1.95, 1.95, 1.95, 1.14, "brown", IONIC_ATOM_FLAG},
{atomI, 53, "I", 2.10, 2.10, 2.10, 1.33, "brown", IONIC_ATOM_FLAG},
/* for most common metals we use Pauling's ionic radii */
/* "covalent radii" = ionic + 0.74 (i.e., oxygenVDW(1.4) - oxygenCov(0.66)) */
/* because the ionic radii are usually calculated from Oxygen-Metal distance */
{atomLi, 3, "Li", 0.60, 0.60, 0.60, 1.34, "grey", METALIC_ATOM_FLAG},
{atomNa, 11, "Na", 0.95, 0.95, 0.95, 1.69, "grey", METALIC_ATOM_FLAG},
{atomAl, 13, "Al", 0.50, 0.50, 0.50, 1.24, "grey", METALIC_ATOM_FLAG},
{atomK, 19, "K", 1.33, 1.33, 1.33, 2.07, "grey", METALIC_ATOM_FLAG},
{atomMg, 12, "Mg", 0.65, 0.65, 0.65, 1.39, "grey", METALIC_ATOM_FLAG},
{atomCa, 20, "Ca", 0.99, 0.99, 0.99, 1.73, "grey", METALIC_ATOM_FLAG},
{atomMn, 25, "Mn", 0.80, 0.80, 0.80, 1.54, "grey", METALIC_ATOM_FLAG},
{atomFe, 26, "Fe", 0.74, 0.74, 0.74, 1.48, "grey", METALIC_ATOM_FLAG},
{atomCo, 27, "Co", 0.70, 0.70, 0.70, 1.44, "blue", METALIC_ATOM_FLAG},
{atomNi, 28, "Ni", 0.66, 0.66, 0.66, 1.40, "grey", METALIC_ATOM_FLAG},
{atomCu, 29, "Cu", 0.72, 0.72, 0.72, 1.46,"orange",METALIC_ATOM_FLAG},
{atomZn, 30, "Zn", 0.71, 0.71, 0.71, 1.45, "grey", METALIC_ATOM_FLAG},
{atomRb, 37, "Rb", 1.48, 1.48, 1.48, 2.22, "grey", METALIC_ATOM_FLAG},
{atomSr, 38, "Sr", 1.10, 1.10, 1.10, 1.84, "grey", METALIC_ATOM_FLAG},
{atomMo, 42, "Mo", 0.93, 0.93, 0.93, 1.67, "grey", METALIC_ATOM_FLAG},
{atomAg, 47, "Ag", 1.26, 1.26, 1.26, 2.00, "white",METALIC_ATOM_FLAG},
{atomCd, 48, "Cd", 0.91, 0.91, 0.91, 1.65, "grey", METALIC_ATOM_FLAG},
{atomIn, 49, "In", 0.81, 0.81, 0.81, 1.55, "grey", METALIC_ATOM_FLAG},
{atomCs, 55, "Cs", 1.69, 1.69, 1.69, 2.43, "grey", METALIC_ATOM_FLAG},
{atomBa, 56, "Ba", 1.29, 1.29, 1.29, 2.03, "grey", METALIC_ATOM_FLAG},
{atomAu, 79, "Au", 1.10, 1.10, 1.10, 1.84, "gold", METALIC_ATOM_FLAG},
{atomHg, 80, "Hg", 1.00, 1.00, 1.00, 1.74, "grey", METALIC_ATOM_FLAG},
{atomTl, 81, "Tl", 1.44, 1.44, 1.44, 2.18, "grey", METALIC_ATOM_FLAG},
{atomPb, 82, "Pb", 0.84, 0.84, 0.84, 1.58, "grey", METALIC_ATOM_FLAG},
/* for other metals we use Shannon's ionic radii */
/* Acta Crystallogr. (1975) A32, pg751. */
{atomV, 23, "V", 0.79, 0.79, 0.79, 1.53, "grey", METALIC_ATOM_FLAG},
{atomCr, 24, "Cr", 0.73, 0.73, 0.73, 1.47, "grey", METALIC_ATOM_FLAG},
{atomTe, 52, "Te", 0.97, 0.97, 0.97, 1.71, "grey", METALIC_ATOM_FLAG},
{atomSm, 62, "Sm", 1.08, 1.08, 1.08, 1.82, "grey", METALIC_ATOM_FLAG},
{atomGd, 64, "Gd", 1.05, 1.05, 1.05, 1.79, "grey", METALIC_ATOM_FLAG},
{atomYb, 70, "Yb", 1.14, 1.14, 1.14, 1.88, "grey", METALIC_ATOM_FLAG},
{atomW, 74, "W", 0.66, 0.66, 0.66, 1.40, "grey", METALIC_ATOM_FLAG},
{atomPt, 78, "Pt", 0.63, 0.63, 0.63, 1.37, "grey", METALIC_ATOM_FLAG},
{atomU, 92, "U", 1.03, 1.03, 1.03, 1.77, "grey", METALIC_ATOM_FLAG},
/* Cotton & Wilkinson and also- */
/* L.E. Sutton (ed.) in Table of interatomic distances and configuration in molecules */
/* and ions, Supplement 1956-1959, Special publication No. 18, Chemical Society, */
/* London, UK, 1965 (as listed in web-elements by Mark Winter) */
/* http://www.shef.ac.uk/chemistry/web-elements */
{atomHe, 2, "He", 1.60, 1.60, 1.60, 0.00, "sky", 0},
{atomBe, 4, "Be", 0.31, 0.31, 0.31, 0.90, "grey", METALIC_ATOM_FLAG},
{atomB, 5, "B", 0.20, 0.20, 0.20, 0.86, "grey", 0},
{atomNe, 10, "Ne", 1.60, 1.60, 1.60, 0.00, "pink", 0},
{atomSi, 14, "Si", 2.10, 2.10, 2.10, 1.17, "grey", METALIC_ATOM_FLAG},
{atomAr, 18, "Ar", 1.89, 1.89, 1.89, 0.00, "orange", 0},
{atomSc, 21, "Sc", 0.68, 0.68, 0.68, 0.44, "grey", METALIC_ATOM_FLAG},
{atomTi, 22, "Ti", 0.75, 0.75, 0.75, 1.49, "grey", METALIC_ATOM_FLAG},
{atomGa, 31, "Ga", 0.53, 0.53, 0.53, 1.27, "grey", METALIC_ATOM_FLAG},
{atomGe, 32, "Ge", 0.60, 0.60, 0.60, 1.34, "grey", METALIC_ATOM_FLAG},
{atomKr, 36, "Kr", 2.01, 2.01, 2.01, 1.15, "greentint", 0},
{atomY, 39, "Y", 0.90, 0.90, 0.90, 1.64, "grey", METALIC_ATOM_FLAG},
{atomZr, 40, "Zr", 0.77, 0.77, 0.77, 1.51, "grey", METALIC_ATOM_FLAG},
{atomSn, 50, "Sn", 0.71, 0.71, 0.71, 1.45, "grey", METALIC_ATOM_FLAG},
{atomSb, 51, "Sb", 2.20, 2.20, 2.20, 1.41, "grey", METALIC_ATOM_FLAG},
{atomXe, 54, "Xe", 2.18, 2.18, 2.18, 1.28, "magenta", 0},
{atomLa, 57, "La", 1.03, 1.03, 1.03, 1.77, "grey", METALIC_ATOM_FLAG},
{atomCe, 58, "Ce", 0.87, 0.87, 0.87, 1.61, "grey", METALIC_ATOM_FLAG},
{atomFr, 87, "Fr", 1.94, 1.94, 1.94, 2.68, "grey", METALIC_ATOM_FLAG},
{atomRa, 88, "Ra", 1.62, 1.62, 1.62, 2.36, "grey", METALIC_ATOM_FLAG},
{atomTh, 90, "Th", 1.08, 1.08, 1.08, 1.82, "grey", METALIC_ATOM_FLAG},
/* finally, we have a set of elements where the radii are unknown */
/* so we use estimates and extrapolations based on web-elements data */
{atomNb, 41, "Nb", 0.86, 0.86, 0.86, 1.40, "grey", METALIC_ATOM_FLAG},
{atomTc, 43, "Tc", 0.71, 0.71, 0.71, 1.25, "grey", METALIC_ATOM_FLAG},
{atomRu, 44, "Ru", 0.82, 0.82, 0.82, 1.36, "grey", METALIC_ATOM_FLAG},
{atomRh, 45, "Rh", 0.76, 0.76, 1.76, 1.30, "grey", METALIC_ATOM_FLAG},
{atomPd, 46, "Pd", 1.05, 1.05, 1.05, 1.59, "grey", METALIC_ATOM_FLAG},
{atomPr, 59, "Pr", 1.11, 1.11, 1.11, 1.65, "grey", METALIC_ATOM_FLAG},
{atomNd, 60, "Nd", 1.10, 1.10, 1.10, 1.64, "grey", METALIC_ATOM_FLAG},
{atomPm, 61, "Pm", 1.15, 1.15, 1.15, 1.89, "grey", METALIC_ATOM_FLAG},
{atomEu, 63, "Eu", 1.31, 1.31, 1.31, 1.85, "grey", METALIC_ATOM_FLAG},
{atomTb, 65, "Tb", 1.05, 1.05, 1.05, 1.59, "grey", METALIC_ATOM_FLAG},
{atomDy, 66, "Dy", 1.05, 1.05, 1.05, 1.59, "grey", METALIC_ATOM_FLAG},
{atomHo, 67, "Ho", 1.04, 1.04, 1.04, 1.58, "grey", METALIC_ATOM_FLAG},
{atomEr, 68, "Er", 1.03, 1.03, 1.03, 1.57, "grey", METALIC_ATOM_FLAG},
{atomTm, 69, "Tm", 1.02, 1.02, 1.02, 1.56, "grey", METALIC_ATOM_FLAG},
{atomLu, 71, "Lu", 1.02, 1.02, 1.02, 1.56, "grey", METALIC_ATOM_FLAG},
{atomHf, 72, "Hf", 0.85, 0.85, 0.85, 1.46, "grey", METALIC_ATOM_FLAG},
{atomTa, 73, "Ta", 0.86, 0.86, 0.86, 1.40, "grey", METALIC_ATOM_FLAG},
{atomRe, 75, "Re", 0.77, 0.77, 0.77, 1.31, "grey", METALIC_ATOM_FLAG},
{atomOs, 76, "Os", 0.78, 0.78, 0.78, 1.32, "grey", METALIC_ATOM_FLAG},
{atomIr, 77, "Ir", 0.80, 0.80, 0.80, 1.34, "grey", METALIC_ATOM_FLAG},
{atomBi, 83, "Bi", 1.17, 1.17, 1.17, 1.71, "grey", METALIC_ATOM_FLAG},
{atomPo, 84, "Po", 0.99, 0.99, 0.99, 1.53, "grey", METALIC_ATOM_FLAG},
{atomAt, 85, "At", 0.91, 0.91, 0.91, 1.45, "grey", METALIC_ATOM_FLAG},
{atomRn, 86, "Rn", 2.50, 2.50, 2.50, 1.25, "pinktint", 0},
{atomAc, 89, "Ac", 1.30, 1.30, 1.30, 2.00, "grey", METALIC_ATOM_FLAG},
{atomPa, 91, "Pa", 1.10, 1.10, 1.10, 1.85, "grey", METALIC_ATOM_FLAG},
{atomNp, 93, "Np", 1.00, 1.00, 1.00, 1.72, "grey", METALIC_ATOM_FLAG},
{atomPu, 94, "Pu", 1.00, 1.00, 1.00, 1.67, "grey", METALIC_ATOM_FLAG},
{atomAm, 95, "Am", 1.00, 1.00, 1.00, 1.63, "grey", METALIC_ATOM_FLAG},
{atomCm, 96, "Cm", 1.00, 1.00, 1.00, 1.60, "grey", METALIC_ATOM_FLAG},
{atomBk, 97, "Bk", 1.00, 1.00, 1.00, 1.58, "grey", METALIC_ATOM_FLAG},
{atomCf, 98, "Cf", 1.00, 1.00, 1.00, 1.57, "grey", METALIC_ATOM_FLAG},
{atomEs, 99, "Es", 1.00, 1.00, 1.00, 1.56, "grey", METALIC_ATOM_FLAG},
{atomFm, 100,"Fm", 1.00, 1.00, 1.00, 1.55, "grey", METALIC_ATOM_FLAG},
{atomMd, 101,"Md", 1.00, 1.00, 1.00, 1.55, "grey", METALIC_ATOM_FLAG},
{atomNo, 102,"No", 1.00, 1.00, 1.00, 1.55, "grey", METALIC_ATOM_FLAG},
/* base identifiers are used in color hack (see note in enum above) */
{baseA, 0, "a", 0.00, 0.00, 0.00, 0.00, "pink", 0},
{baseC, 0, "c", 0.00, 0.00, 0.00, 0.00, "yellow", 0},
{baseTU, 0, "t/u", 0.00, 0.00, 0.00, 0.00, "sky", 0},
{baseG, 0, "g", 0.00, 0.00, 0.00, 0.00, "sea", 0},
{baseOther, 0,"other na",0.00, 0.00, 0.00, 0.00, "white", 0},
{nonBase, 0, "nonbase",0.00, 0.00, 0.00, 0.00, "grey", 0}
};
#endif
#endif
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