00001 /*************************************************************************** 00002 *cr 00003 *cr (C) Copyright 1995-2019 The Board of Trustees of the 00004 *cr University of Illinois 00005 *cr All Rights Reserved 00006 *cr 00007 ***************************************************************************/ 00008 00009 /*************************************************************************** 00010 * RCS INFORMATION: 00011 * 00012 * $RCSfile: Atom.h,v $ 00013 * $Author: johns $ $Locker: $ $State: Exp $ 00014 * $Revision: 1.75 $ $Date: 2020年02月26日 03:51:30 $ 00015 * 00016 ***************************************************************************/ 00023 #ifndef ATOM_H 00024 #define ATOM_H 00025 00026 #include <string.h> 00027 #include <stdlib.h> 00028 #include "utilities.h" 00029 00030 // maximum number of bonds allowed to other atoms 00031 // XXX It may be desirable to finally get around 00032 // to reimplementing the bond storage using the same scheme that is used 00033 // for bond types and bond orders, which are each based on dynamically 00034 // allocated auxilliary arrays associated with string keywords. 00035 // There should be low impact on structure traversal performance except 00036 // for a minor increase in CPU TLB pressure due to traversal of multiple 00037 // arrays rather than just one, and the code would look almost the same. 00038 #if 0 00039 // Anyone can hack this macro for whatever max bond count they need to 00040 // support unusual models. 00041 #define MAXATOMBONDS 256L // example of a huge user-requested bond count 00042 #elif defined(ARCH_BLUEWATERS) || defined(ARCH_CRAY_XC) || defined(ARCH_CRAY_XK) 00043 #define MAXATOMBONDS 8L 00044 #else 00045 #define MAXATOMBONDS 12L 00046 #endif 00047 00048 // Atom type flags 00049 #define ATOMNORMAL 0 00050 #define ATOMPROTEINBACK 1 00051 #define ATOMNUCLEICBACK 2 00052 #define ATOMHYDROGEN 3 00053 00054 // Residue type flags 00055 #define RESNOTHING 0 00056 #define RESPROTEIN 1 00057 #define RESNUCLEIC 2 00058 #define RESWATERS 3 00059 00061 class MolAtom { 00062 public: 00063 // XXX contents of the Atom structure are ordered specifically so 00064 // that the compiler will pack it efficiently. 00065 00066 // items that make this particular atom unique and are absolutely 00067 // needed to link it up to the rest of the structure, or are speed-critical 00068 short nameindex; 00069 short typeindex; 00070 int uniq_resid; 00071 int bondTo[MAXATOMBONDS]; 00072 signed char bonds; 00073 signed char atomicnumber; 00074 signed char altlocindex; 00075 char insertionstr[2]; 00076 00077 // items which could potentially be moved into other data structures 00078 // to save memory, but are presently kept here for extra simplicity or speed 00079 short chainindex; 00080 short segnameindex; 00081 int resid; 00082 short resnameindex; 00083 00084 // ATOMNORMAL, ATOMPROTEINBACK, ATOMNUCLEICBACK, ATOMHYDROGEN 00085 // XXX this should be converted to an unsigned bit-field to save memory 00086 signed char atomType; 00087 00089 // RESNOTHING, RESPROTEIN, RESNUCLEIC, RESWATERS 00090 // XXX this should be converted to an unsigned bit-field to save memory 00091 signed char residueType; 00092 00093 00094 00095 void init(int n, int theresid, const char *insertion) { 00096 uniq_resid = 0; // don't know yet, found in BaseMolecule 00097 bonds = 0; 00098 resid = theresid; 00099 strncpy(insertionstr, insertion, 2); insertionstr[1] = '0円'; 00100 nameindex = typeindex = resnameindex = segnameindex = altlocindex = (-1); 00101 atomicnumber = (-1); 00102 00103 for (int i=0; i<MAXATOMBONDS; i++) { 00104 bondTo[i] = -1; 00105 } 00106 atomType = ATOMNORMAL; 00107 residueType = RESNOTHING; 00108 } 00109 00113 int add_bond(int a, int type) { 00114 if(bonds >= MAXATOMBONDS) // fail 00115 return -1; 00116 00117 bondTo[(int) bonds] = a; 00118 if (type == ATOMPROTEINBACK || type == ATOMNUCLEICBACK) 00119 atomType = type; 00120 bonds++; 00121 return 0; 00122 } 00123 00126 int bonded(int a) { 00127 for (int i=0; i < bonds; i++) { 00128 if (bondTo[i] == a) { 00129 return TRUE; 00130 } 00131 } 00132 00133 return FALSE; 00134 } 00135 00136 }; 00137 00138 #endif 00139