/* 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*/ /* Explicit vdW radius of carbonyl (C=O, atomC) entry. */ #define ATOMC_EXPLICIT_VDW (1.70) #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", ATOMC_EXPLICIT_VDW, ATOMC_EXPLICIT_VDW, 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