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Copy pathPKINROTL.c
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PKINROTL.c
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/*3456789_123456789_123456789_123456789_123456789_123456789_123456789_12345678*/
/* PKINCOUT.c */
#include "PKIN.h"
/*#define ROTINFO*/
/*prototypes not defined in common*/
float findrotationangle(char tryatom[5][6]);
void findrotationaxis(int,int, char tryatom[5][6]);
void findrotationriders(int,int, char tryatom[5][6]);
int findatomnumber(char tryatom[6]);
int proteinmainchainname(char, char, char, char); /*040504*/
/****getresiduecode()********************************************************/
char getresiduecode(char u, char v, char w) /*returns 1-letter code*/
{
char creturn; /*local*/
if (u=='a' && v=='l' && w=='a') creturn='a';
else if(u=='c' && v=='y' && w=='s') creturn='c';
else if(u=='a' && v=='s' && w=='p') creturn='d';
else if(u=='g' && v=='l' && w=='u') creturn='e';
else if(u=='p' && v=='h' && w=='e') creturn='f';
else if(u=='g' && v=='l' && w=='y') creturn='g';
else if(u=='h' && v=='i' && w=='s') creturn='h';
else if(u=='i' && v=='l' && w=='e') creturn='i';
else if(u=='l' && v=='y' && w=='s') creturn='k';
else if(u=='l' && v=='e' && w=='u') creturn='l';
else if(u=='m' && v=='e' && w=='t') creturn='m';
else if(u=='m' && v=='s' && w=='e') creturn='M'; /*030605*/
else if(u=='a' && v=='s' && w=='n') creturn='n';
else if(u=='p' && v=='r' && w=='o') creturn='p';
else if(u=='g' && v=='l' && w=='n') creturn='q';
else if(u=='a' && v=='r' && w=='g') creturn='r';
else if(u=='s' && v=='e' && w=='r') creturn='s';
else if(u=='t' && v=='h' && w=='r') creturn='t';
else if(u=='v' && v=='a' && w=='l') creturn='v';
else if(u=='t' && v=='r' && w=='p') creturn='w';
else if(u=='t' && v=='y' && w=='r') creturn='y';
else if(u=='a' && v=='i' && w=='b') creturn='b';
else creturn='x';
return(creturn);
}
/*___getresiduecode()_______________________________________________________*/
/****getresiduerotations()****************************************************/
void getresiduerotations()
{
/*findrotationaxis() and findrotationriders() actually write to scratch*/
int i,nth,level;
char tryatom[5][6]; /*tryatom[][3,4] alternate possibilities for 4th char*/
/* index: 0,1,2,3 1st,2nd,3rd,4th char of atom name*/
/*int n1;*/
int n2,n3,n4;
double dihedral4pt(double,double,double,double,double,double
,double,double,double,double,double,double);
/*atom naming conventions are just wierd enough that it seemed*/
/*easier to set up a lot of special cases for the rotations.*/
/*base cases on what this residue is supposed to be*/
/*get into one letter code*/
i = rotoutl; /*rotoutl here is range number that defines rotated residue*/
rescode = getresiduecode(resid[i][0], resid[i][1], resid[i][2]);
/*reuse rotoutl now to flag number of rotatable bonds */
/*including hydrogens, and including branch rotations*/
rotoutl2 = 0;/*branch occurs at nth rotation (always the last for nat. aa)*/
/*global*/
branch = ' '; /*branch is at the nth (as a character) level of rotation*/
/*global*/
nth = 0; /*nth rotation being processed*/
level = 0; /*rotation level of axis under consideration*/
if(rescode=='g'||rescode=='x') /*proline needs rotations to show its rotatmers*/
{
rotoutl = 0; nth = 0; level = 0;
}
else if(rescode=='a') /*alanine */
{
rotoutl = 0; nth = 0; level = 0;
if( hyoutl)
{ rotoutl = 1; nth = 1; level = 1;
/* 01234 but sidechain already screened for alt conf*/
sprintf(tryatom[1]," n "); /*so fourth tryatom char used as extra */
sprintf(tryatom[2]," ca "); /*test for atom[j][3]*/
sprintf(tryatom[3]," cb "); /*historically, this allowed several */
sprintf(tryatom[4]," hb 1"); /*residues to be logically combined*/
/* h at index 1 of tryatom represents a hydrogen, isahydrogenname(atom) */
/* then can recognized if atoms match as elements 071222*/
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
findrotationriders(nth,level, tryatom); /*1HB_,2HB_,3HB_*/
/*newpdb: , HB1, HB2, HB3,*/
}
}
else if(rescode=='b')/*aib amino iso butaric acid: alanine with extra methyl */
{
rotoutl = 0; nth = 0; level = 0;
if( hyoutl)
{ rotoutl = 2; rotoutl2 = 2; branch = '1'; /*globals*/
nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb 1");
sprintf(tryatom[4]," hb 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
findrotationriders(nth,level, tryatom); /*1HB1,2HB1,3HB1*/
/*second axis:*/
nth = 2; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb22");
sprintf(tryatom[4]," hb22");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
findrotationriders(nth,level, tryatom); /*1HB2,2HB2,3HB2*/
}
}
else if(rescode=='c') /* cystine */
{ rotoutl = 1; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," sg 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if(!hyoutl)
{/*find S */
findrotationriders(nth,level, tryatom); /*_SG_*/
}
if( hyoutl)
{ rotoutl = 2;
/*has hydrogen riders on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_,2HB_*/
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," sg ");
sprintf(tryatom[4]," hg 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
/*final hydrogen is the only rider on second axis*/
findrotationriders(nth,level, tryatom); /*_HG_*/
}
}
else if(rescode=='s') /* serine */
{ rotoutl = 1; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," og 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if(!hyoutl)
{/*find O */
findrotationriders(nth,level, tryatom); /*_OG_*/
}
if( hyoutl)
{ rotoutl = 2;
/*has hydrogen riders on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_,2HB_*/
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," og ");
sprintf(tryatom[4]," hg 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
/*final hydrogen is the only rider on second axis*/
findrotationriders(nth,level, tryatom); /*_HG_*/
}
}
else if(rescode=='t') /* threonine */
{ rotoutl = 1; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," og 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( !hyoutl)
{/*need to get _OG1 and _CG2 */
findrotationriders(nth,level, tryatom); /*_OG1*/
sprintf(tryatom[4]," cg22");
findrotationriders(nth,level, tryatom); /*_CG2*/
}
if( hyoutl)
{ rotoutl = 3; rotoutl2 = 3; branch = '2'; /*globals*/
/*has hydrogen riders on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_,2HB_*/
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," og 1");
sprintf(tryatom[4]," hg 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
/*final hydrogen is the only rider on second axis*/
findrotationriders(nth,level, tryatom); /*_HG_*/
/*third, branch rotation:*/
nth = 3; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg22");
sprintf(tryatom[4],"1hg22");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
sprintf(tryatom[4]," hg22");
findrotationriders(nth,level, tryatom); /*1HG2,2HG2,3HG2*/
}
}
else if(rescode=='v') /* valine */
{ rotoutl = 1; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," cg 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if(!hyoutl)
{
sprintf(tryatom[4]," cg12");/*look for both 1&2 in char [3]*/
findrotationriders(nth,level, tryatom); /*_CG1,_CG2*/
}
if( hyoutl)
{ rotoutl = 3; rotoutl2 = 3; branch = '2'; /*globals*/
/*has hydrogen riders on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_*/
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg 1");
sprintf(tryatom[4]," hg 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
findrotationriders(nth,level, tryatom); /*1HG1,2HG1,3HG1*/
/*third, branch rotation:*/
nth = 3; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg22");
sprintf(tryatom[4],"1hg22");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
findrotationriders(nth,level, tryatom); /*1HG2,2HG2,3HG2*/
}
}
else if(rescode=='d'||rescode=='n') /* aspartate, asparagine */
{ rotoutl = 2; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," cg 1");/*4th char:alternate test for atom[j][3]*/
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_*/
}
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg ");
sprintf(tryatom[4]," od 1");/*both asp,asn have od */
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
findrotationriders(nth,level, tryatom); /*_OD1*/
if(rescode=='d')
{/*aspartic acid, find the other oxygen*/
sprintf(tryatom[4]," od22");
findrotationriders(nth,level, tryatom); /*_OD2*/
}
if(rescode=='n')
{/*asparagine, find the nitrogen*/
sprintf(tryatom[4]," nd22");
findrotationriders(nth,level, tryatom); /*_ND2*/
if(hyoutl)
{/*find hydrogens on the nitrogen*/
sprintf(tryatom[4]," hd22");
findrotationriders(nth,level, tryatom); /*1HD2,2HD2*/
}
}
}
else if(rescode=='f'||rescode=='h'||rescode=='w'||rescode=='y')/*aromatics*/
{ rotoutl = 2; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," cg 1");/*4th char:alternate test for atom[j][3]*/
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_,2HB_*/
}
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg ");
if(rescode=='h')
sprintf(tryatom[4]," nd 1");
else
sprintf(tryatom[4]," cd 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
/*lots of stuff rides on this second axis*/
sprintf(tryatom[4]," d "); /*permissive request: no element ID*/
findrotationriders(nth,level, tryatom); /*xxDx*/
sprintf(tryatom[4]," e ");
findrotationriders(nth,level, tryatom); /*xxEx*/
sprintf(tryatom[4]," z ");
findrotationriders(nth,level, tryatom); /*xxZx*/
if( hyoutl && rescode=='y')
{ rotoutl = 3; nth = 3; level = 3;
sprintf(tryatom[1]," ce 1");
sprintf(tryatom[2]," cz ");
sprintf(tryatom[3]," oh ");
sprintf(tryatom[4]," hh 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
/*the _HH_ is the only atom riding on 3rd tyr axis*/
findrotationriders(nth,level, tryatom); /*_HH_*/
}
else
{
sprintf(tryatom[4]," h ");
findrotationriders(nth,level, tryatom); /*xxHx*/
}
}
else if(rescode=='l'||rescode=='i') /* leucine, isoleucine */
{ rotoutl = 2; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," cg 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if(!hyoutl && rescode=='i')
{/*another carbon rides on first axis*/
sprintf(tryatom[4]," cg22");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
if( hyoutl)
{/*hydrogens ride on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg 1");
sprintf(tryatom[4]," cd 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if(!hyoutl)
{
findrotationriders(nth,level, tryatom); /*_CD1*/
if(rescode=='l')
{
/*another carbon rides on second axis*/
sprintf(tryatom[4]," cd22");
findrotationriders(nth,level, tryatom); /*_CD2*/
}
}
if( hyoutl)
{/*hydrogens ride on second axis*/
sprintf(tryatom[4]," hg 1");
findrotationriders(nth,level, tryatom); /*1HG_,(2HG_)*/
}
if( hyoutl)
{ rotoutl = 4;
/*third axis:*/
nth = 3; level = 3;
sprintf(tryatom[1]," cb ");
sprintf(tryatom[2]," cg 1");
sprintf(tryatom[3]," cd 1");
sprintf(tryatom[4]," hd 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on third axis*/
sprintf(tryatom[4]," hd 1");
findrotationriders(nth,level, tryatom); /*1HD1,2HD1,3HD1*/
}
/*fourth axis:*/
nth = 4; level = 4;
if(rescode=='l')/* leucine */
{ rotoutl2 = 4; branch = '3'; /*globals*/
sprintf(tryatom[1]," cb ");
sprintf(tryatom[2]," cg ");
sprintf(tryatom[3]," cd22");
sprintf(tryatom[4],"1hd22");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
findrotationriders(nth,level, tryatom); /*1HD2,2HD2,3HD2*/
}
if(rescode=='i')/* isoleucine */
{ rotoutl2 = 4; branch = '2'; /*globals*/
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg22");
sprintf(tryatom[4],"1hg22");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
findrotationriders(nth,level, tryatom); /*1HG2,2HG2,3HG2*/
}
}
}
else if(rescode=='e'||rescode=='q') /* glutamate, glutamine */
{ rotoutl = 3; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," cg 1");/*4th char:alternate test for atom[j][3]*/
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg ");
sprintf(tryatom[4]," cd 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on second axis*/
sprintf(tryatom[4]," hg 1");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
/*third axis:*/
nth = 3; level = 3;
sprintf(tryatom[1]," cb ");
sprintf(tryatom[2]," cg ");
sprintf(tryatom[3]," cd 1");
sprintf(tryatom[4]," oe 1");/*both glu,gln have oe */
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
findrotationriders(nth,level, tryatom); /*_OE1*/
if(rescode=='e')
{/*glutamic acid, find the other oxygen*/
sprintf(tryatom[4]," oe22");
findrotationriders(nth,level, tryatom); /*_OE2*/
}
if(rescode=='q')
{/*glutamine, find the nitrogen*/
sprintf(tryatom[4]," ne22");
findrotationriders(nth,level, tryatom); /*_NE2*/
if(hyoutl)
{/*find hydrogens on the nitrogen*/
sprintf(tryatom[4]," he22");
findrotationriders(nth,level, tryatom); /*1HD2,2HD2*/
}
}
}
else if(rescode=='m'||rescode=='M') /* methionine,selenoMet */
{ rotoutl = 3; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," cg 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg 1");
if(rescode=='m'){sprintf(tryatom[4]," sd 1");}
else {sprintf(tryatom[4],"sed 1");}
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on second axis*/
sprintf(tryatom[4]," hg 1");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
/*third axis:*/
nth = 3; level = 3;
sprintf(tryatom[1]," cb ");
sprintf(tryatom[2]," cg 1");
if(rescode=='m'){sprintf(tryatom[3]," sd 1");}
else {sprintf(tryatom[3],"sed 1");}
sprintf(tryatom[4]," ce 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if(!hyoutl)
{
findrotationriders(nth,level, tryatom); /*_CE_*/
}
if( hyoutl )
{ rotoutl = 4;
/*fourth axis:*/
nth = 4; level = 4;
sprintf(tryatom[1]," cg 1");
if(rescode=='m'){sprintf(tryatom[2]," sd 1");}
else {sprintf(tryatom[2],"sed 1");}
sprintf(tryatom[3]," ce 1");
sprintf(tryatom[4],"1he 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
{/*hydrogens ride on fourth axis*/
sprintf(tryatom[4]," he 1");
findrotationriders(nth,level, tryatom); /*1HE_,2HE_,3HE_*/
}
}
}
else if(rescode=='r') /* arginine*/
{ rotoutl = 4; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," cg 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg 1");
sprintf(tryatom[4]," cd 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on second axis*/
sprintf(tryatom[4]," hg 1");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
/*third axis:*/
nth = 3; level = 3;
sprintf(tryatom[1]," cb ");
sprintf(tryatom[2]," cg 1");
sprintf(tryatom[3]," cd 1");
sprintf(tryatom[4]," ne 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on third axis*/
sprintf(tryatom[4]," hd 1");
findrotationriders(nth,level, tryatom); /*1HD_,2HD_*/
}
/*fourth axis:*/
nth = 4; level = 4;
sprintf(tryatom[1]," cg 1");
sprintf(tryatom[2]," cd 1");
sprintf(tryatom[3]," ne 1");
sprintf(tryatom[4]," cz 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
/*guanidinium group rides on fourth axis*/
sprintf(tryatom[4]," cz 1");
findrotationriders(nth,level, tryatom); /*_CZ_*/
sprintf(tryatom[4]," nh 1");
findrotationriders(nth,level, tryatom); /*_NH1*/
sprintf(tryatom[4]," nh22");
findrotationriders(nth,level, tryatom); /*_NH2*/
if( hyoutl)
{/*hydrogens ride on fourth axis*/
sprintf(tryatom[4]," he 1");
findrotationriders(nth,level, tryatom); /*1HE_*/
sprintf(tryatom[4]," hh 1");
findrotationriders(nth,level, tryatom); /*1HH1,2HH1*/
sprintf(tryatom[4]," hh 2");
findrotationriders(nth,level, tryatom); /*1HH1,2HH1*/
}
}
else if(rescode=='k') /* lysine */
{ rotoutl = 4; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," cg 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg 1");
sprintf(tryatom[4]," cd 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on second axis*/
sprintf(tryatom[4]," hg 1");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
/*third axis:*/
nth = 3; level = 3;
sprintf(tryatom[1]," cb ");
sprintf(tryatom[2]," cg 1");
sprintf(tryatom[3]," cd 1");
sprintf(tryatom[4]," ce 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on third axis*/
sprintf(tryatom[4]," hd 1");
findrotationriders(nth,level, tryatom); /*1HD_,2HD_*/
}
/*fourth axis:*/
nth = 4; level = 4;
sprintf(tryatom[1]," cg 1");
sprintf(tryatom[2]," cd 1");
sprintf(tryatom[3]," ce 1");
sprintf(tryatom[4]," nz 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if(!hyoutl)
findrotationriders(nth,level, tryatom); /*_NZ_*/
if( hyoutl)
{/*hydrogens ride on fourth axis*/
sprintf(tryatom[4]," he 1");
findrotationriders(nth,level, tryatom); /*1HE_,2HE_*/
}
if( hyoutl )
{ rotoutl = 5;
/*fifth axis:*/
nth = 5; level = 5;
sprintf(tryatom[1]," cd 1");
sprintf(tryatom[2]," ce 1");
sprintf(tryatom[3]," nz 1");
sprintf(tryatom[4],"1hz 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
sprintf(tryatom[4]," hz 1");
findrotationriders(nth,level, tryatom); /*1HH_,2HH_,3HH_*/
}
}/*lys*/
else if(rescode=='p') /* proline */
{ rotoutl = 3; nth = 1; level = 1;
sprintf(tryatom[1]," n ");
sprintf(tryatom[2]," ca ");
sprintf(tryatom[3]," cb ");
sprintf(tryatom[4]," cg 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on first axis*/
sprintf(tryatom[4]," hb 1");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
/*second axis:*/
nth = 2; level = 2;
sprintf(tryatom[1]," ca ");
sprintf(tryatom[2]," cb ");
sprintf(tryatom[3]," cg 1");
sprintf(tryatom[4]," cd 1");
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
if( hyoutl)
{/*hydrogens ride on second axis*/
sprintf(tryatom[4]," hg 1");
findrotationriders(nth,level, tryatom); /*1HB_,(2HB_)*/
}
/*third axis:*/
nth = 3; level = 3;
sprintf(tryatom[1]," cb ");
sprintf(tryatom[2]," cg 1");
sprintf(tryatom[3]," cd 1");
sprintf(tryatom[4]," ne 1"); /*special proline dummy n atom*/
/*atoms are connected by distance, so to override the usual*/
/*base atom for CD which is N, the first atom close enough to*/
/*be connected, one must specify the base atom for CD and NE */
/*as special cases*/
/*n1 = findatomnumber(tryatom[1]);*/
n2 = findatomnumber(tryatom[2]);
n3 = findatomnumber(tryatom[3]);
n4 = findatomnumber(tryatom[4]);
base[n3] = n2;
base[n4] = n3;
bondangle[nth] = findrotationangle(tryatom);
findrotationaxis(nth,level, tryatom);
findrotationriders(nth,level, tryatom); /*_NE_*/
if( hyoutl)
{/*hydrogens ride on third axis*/
sprintf(tryatom[4]," hd 1");
findrotationriders(nth,level, tryatom); /*1HD_,2HD_*/
}
}/*pro*/
if(Ltestprint > 0)
{
sprintf(alertstr,CRLF"residue identified as: %c, with %d rotatable bonds"
CRLF,rescode,rotoutl);
pkintextinsert(alertstr); /*PKMCTEXT.C PKPCTEXT.C*/
adjusttext(2); /*PKMCTEXT.C PKPCTEXT.C*/
}
}
/*___getresiduerotations()___________________________________________________*/
/****findrotationangle()******************************************************/
float findrotationangle(char tryatom[5][6])
{
int i,icountatoms,j,LOK=1;
/* char tryatom[5][6];*/
double fxyz[3][5],dihedral4pt(double,double,double,double,double,double
,double,double,double,double,double,double);
char atomname[5][6];
float bondangle;
icountatoms = 0;
for(i=1;i<=4;i++) sprintf(atomname[i]," ");
/*find 4 linked atoms to define a dihedral rotation angle*/
for(i=1; i<=2; i++)
{/*atoms 1&&2: check char 1&&2 vs. (tryatom[1,2][1]&&tryatom[1,2][2])*/
for(j=1; j<=maxatm; j++)
{
/*if( atom[j][1] != 'h' && atom[j][1] != 'd' && atom[j][1] != 'q')*/
if( !isahydrogenname(atom[j]))
{/*atoms 1,2 cannot be hydrogens*/
if( ( atom[j][1]==tryatom[i][1]
&&atom[j][2]==tryatom[i][2] ) )
{
fxyz[0][i] = x[j];fxyz[1][i] = y[j];fxyz[2][i] = z[j];
icountatoms = icountatoms + 1;
sprintf(atomname[icountatoms],"%s",atom[j]);
break;
}
}
}
}
for(i=3; i<=4; i++)
{/*atoms 3&&4: check char2 vs. (tryatom[3,4][2])*/
/* also check char3 vs. (tryatom[3,4][3]||tryatom[3,4][4])*/
for(j=1; j<=maxatm; j++)
{
/*if( (i==3 &&atom[j][1] !='h'&&atom[j][1] !='d'&&atom[j][1] !='q'))*/
if( i==3 && (!isahydrogenname(atom[j]) ) )
{/*atom 3 cannot be hydrogen*/
if( (atom[j][2]==tryatom[i][2])
&&(atom[j][3]==tryatom[i][3] || atom[j][3]==tryatom[i][4]) )
{
fxyz[0][i] = x[j];fxyz[1][i] = y[j];fxyz[2][i] = z[j];
icountatoms = icountatoms + 1;
sprintf(atomname[icountatoms],"%s",atom[j]);
break;
}
}
else if(i==4)
{
LOK = 0;
if(tryatom[i][1]=='h')
{/*hydrogen as fourth atom*/
/*if(atom[j][1]=='h'||atom[j][1]=='d'||atom[j][1]=='q') LOK=1;*/
if(isahydrogenname(atom[j])) LOK=1;
}
else
{/*not looking for a hydrogen*/
if(atom[j][1]==tryatom[i][1]) LOK = 1;
}
if( LOK
&&(atom[j][2]==tryatom[i][2])
&&(atom[j][3]==tryatom[i][3] || atom[j][3]==tryatom[i][4]) )
{
fxyz[0][i] = x[j];fxyz[1][i] = y[j];fxyz[2][i] = z[j];
icountatoms = icountatoms + 1;
sprintf(atomname[icountatoms],"%s",atom[j]);
break;
}
}
}
}
if(icountatoms==4)
{
bondangle = (float)(dihedral4pt(
fxyz[0][1],fxyz[1][1],fxyz[2][1],
fxyz[0][2],fxyz[1][2],fxyz[2][2],
fxyz[0][3],fxyz[1][3],fxyz[2][3],
fxyz[0][4],fxyz[1][4],fxyz[2][4] ));
}
else bondangle = 0.0;
if(Ltestprint > 0)
{
sprintf(alertstr,CRLF"bondrot dihedral is %.1f from coords:"CRLF
"%.3f, %.3f, %.3f"CRLF
"%.3f, %.3f, %.3f"CRLF
"%.3f, %.3f, %.3f"CRLF
"%.3f, %.3f, %.3f"CRLF
,bondangle
,fxyz[0][1],fxyz[1][1],fxyz[2][1]
,fxyz[0][2],fxyz[1][2],fxyz[2][2]
,fxyz[0][3],fxyz[1][3],fxyz[2][3]
,fxyz[0][4],fxyz[1][4],fxyz[2][4]
);
pkintextinsert(alertstr); /*PKMCTEXT.C PKPCTEXT.C*/
adjusttext(6); /*PKMCTEXT.C PKPCTEXT.C*/
}
#ifdef ROTINFO
{
sprintf(alertstr,"%d atoms: %s, %s, %s, %s; angle==%.2f"CRLF
,icountatoms
,atomname[1],atomname[2],atomname[3],atomname[4]
,bondangle);
pkintextinsert(alertstr); /*PKMCTEXT.C PKPCTEXT.C*/
adjusttext(2); /*PKMCTEXT.C PKPCTEXT.C*/
}
#endif
return(bondangle);
}
/*___findrotationangle()_____________________________________________________*/
/****findrotationaxis()*******************************************************/
void findrotationaxis(int nthrot, int level, char tryatom[5][6])
{
static char cntl[] = " "; /* 4 blank characters */
char rds[16];
int j,k;
char status[16]; /*030605*/
/*||(tryatom[3][1]=='h'&&(atom[j][1]=='d'||atom[j][1]=='q')) )*/
level = level; /*avoids unused error message*/
for(j=1 ; j<=maxatm ; j++)
{/*scan over all atoms to find rotation axis*/
if(isc[j] > 0 ) /*only look at recognized sc, inc. alt conf. info.*/
{/*recognized sidechain atom*/ /*3rd atom of diheral & its base is axis*/
#ifdef OLDCODE
/*check explicitly for hydrogen*/
if( (atom[j][0] == tryatom[3][0])
&&( (atom[j][1] == tryatom[3][1])
||(isahydrogenname(tryatom[3])&&(isahydrogenname(atom[j]))) )
&&(atom[j][2] == tryatom[3][2])
&&(atom[j][3] == tryatom[3][3]||atom[j][3] == tryatom[3][4])
)
#endif
if( !isahydrogenname(atom[j]) /*hydrogen cannot be head of an axis*/
&& atom[j][1] == tryatom[3][1] /*element match */
&& atom[j][2] == tryatom[3][2] /*1st position match*/
&&(atom[j][3] == tryatom[3][3] || atom[j][3] == tryatom[3][4])
/*2nd position match*/
)
{/*e.g. _CB_ will have _CA_ as its base*/
k = base[j];
if(Latomradii)
{
if(atom[j][1]=='h')
{
if(atom[k][1]=='o'||atom[k][1]=='n')
{
sprintf(rds," r=%.2f ",polarHradius);
}
else
{
sprintf(rds," r=1.17 ");
}
}
else if(atom[j][1]=='o') sprintf(rds," r=1.4 ");
else if(atom[j][1]=='n') sprintf(rds," r=1.55 ");
else if(atom[j][1]=='c') sprintf(rds," r=1.75 ");
else if(atom[j][1]=='s') sprintf(rds," r=1.8 ");
else if(atom[j][1]=='p') sprintf(rds," r=1.8 ");
else rds[0] = '\0';
}
else
{
rds[0] = '\0';
}
if( res[j][0]=='p' &&res[j][1]=='r' &&res[j][2]=='o'
&&atom[j][1]=='n' &&atom[j][2]=='e')
{
sprintf(status," ghost"); /*Mage not to send atom ne to probe 030506*/
}
else if(atstyle[j] == 1)
{
sprintf(status," ghost"); /*Mage not to send extra atoms to probe 030920*/
}
else
{
status[0] = '\0'; /*no status flag*/
}
sprintf(cntl,"ro%1d ",nthrot); /*|ro#_|*/
/*make pointID fit PDB format spacing, 2char sub uses space 071222*/
/*format(a6,i5,1x,a5,a3,1x,a1,i4,a1,3x,3f8.3,2f6.2)*/
sprintf(temps,"%s{%5s%3s%2s%4d%1s} P %.3f, %.3f, %.3f "
"{%5s%3s%2s%4d%1s} L%s%s %.3f, %.3f, %.3f"EOLO
,cntl,atom[k],res[k],sub[k],num[k],rins[k],x[k],y[k],z[k]
,atom[j],res[j],sub[j],num[j],rins[j],rds,status
,x[j],y[j],z[j]);
putonetextblockline(&mainscratch,temps); /*PDB ptID*/
++countxyz;++pointcnt[typenow];countpoints(cntl,0); /*P point*/
++countxyz;++pointcnt[typenow];countpoints(cntl,0); /*L point*/
Listrot = rotoutl;
Listrot2 = rotoutl2;
if(hyoutl) Listhy = 1;
#ifdef ROTINFO
sprintf(alertstr,"rot_%1d(%d-->%d):%s{%5s%3s%2s%4d%1s} P %.3f, %.3f, %.3f "
"{%5s%3s%2s%4d%1s} L%s %.3f, %.3f, %.3f"CRLF
,nthrot,k,j,cntl,atom[k],res[k],sub[k],num[k],rins[k],x[k],y[k],z[k]
,atom[j],res[j],sub[j],num[j],rins[j],rds,x[j],y[j],z[j]);
pkintextinsert(alertstr); /*____TEXT.C*/
adjusttext(1); /*____TEXT.C*/
#endif
break; /*just find the first instance of this atom*/
}/*e.g. _CB_ will have _CA_ as its base*/
}/*recognized sidechain atom*/
}/*scan over all atoms to find rotation axis*/
}
/*___findrotationaxis()______________________________________________________*/
/****findatomnumber()*******************************************************/
int findatomnumber(char tryatom[6])
{
/*||(tryatom[1]=='h'&&(atom[j][1]=='d'||atom[j][1]=='q')))*/
int j=0,ireturn=-1;
for(j=1 ; j<=maxatm ; j++)
{/*scan over all atoms in residue to find atom number for this named atom*/
if( (atom[j][0] == tryatom[0]) /*so can get consistent hydrogen*/
&&( (atom[j][1] == tryatom[1])
||(isahydrogenname(tryatom)&&(isahydrogenname(atom[j]))) )
&&(atom[j][2] == tryatom[2])
&&(atom[j][3] == tryatom[3]||atom[j][3] == tryatom[4])
)
{
ireturn = j;
break; /*just find the first instance of this atom*/
}
}/*scan over all atoms to find rotation axis*/
return(ireturn);
}
/*___findatomnumber()______________________________________________________*/
/****findrotationriders()*****************************************************/
void findrotationriders(int nthrot, int level, char tryatom[5][6])
{
static char cntl[] = " "; /* 4 blank characters */
char rds[16];
char status[16]; /*030605*/
int j,k;
char greekchar = ' ';
char branchchar = ' ';
int match=0;
level = level; /*avoids unused error message*/
/*||( tryatom[4][1]=='h'&&(atom[j][1]=='d'||atom[j][1]=='q')))*/
/*4th atom of a dihedral defines the level of all the connected riding atoms*/
/*unfortunately the position-specific code of the oldpdb is broken... */
/*however, the third character of the oldcode or its equivalent is the level */
/*of heavy atoms that rides directly on the rotation axis */
/*while hydrogens are of the next level below */
/*tryatom is define here so that the third index is the old definition*/
/*Standardizing tryatom as idealized oldpdb simplifies the logic here */
/*element, greek, branch, Htwig */
/*oldpdb element[1], greek[2], branch[3], Htwig[0]*/
/*newpdb element[0,1], greek[1,2], branch[2,3], Htwig[3,] */