17 |
|
double Hmat[3][3]; |
18 |
|
}; |
19 |
|
|
20 |
< |
strcut frameStruct* myFrames; |
20 |
> |
struct binStruct{ |
21 |
> |
double rmsd; |
22 |
> |
int nValues; |
23 |
> |
}; |
24 |
|
|
25 |
< |
void rmsd(double startTime, char* outPrefix ){ |
25 |
> |
struct binStruct rmsdCorr[RMSDBINS]; |
26 |
|
|
27 |
+ |
struct frameStruct* myFrames; |
28 |
+ |
|
29 |
+ |
void calcRMSDpair( int bin, int i, int j, enum atomNames rType ); |
30 |
+ |
|
31 |
+ |
void rmsd( enum atomNames rType, double startTime, char* outPrefix ){ |
32 |
+ |
|
33 |
|
// list of 'a priori' constants |
34 |
|
|
35 |
|
const int nLipAtoms = NL_ATOMS; |
41 |
|
// variables |
42 |
|
|
43 |
|
char outName[500]; |
44 |
+ |
|
45 |
|
FILE* outFile; |
46 |
+ |
|
47 |
|
int i, j, k; |
48 |
|
int startFrame, corrFrames, framesFinished; |
49 |
|
int startFound, percentComplete; |
50 |
< |
|
50 |
> |
int index; |
51 |
> |
int nCounts; |
52 |
> |
int bin; |
53 |
> |
|
54 |
|
double Hmat[3][3]; |
55 |
+ |
double diffTime; |
56 |
+ |
double rmsdDt; |
57 |
+ |
double timeOut, outVal; |
58 |
|
|
59 |
+ |
struct atomCoord* atoms; |
60 |
+ |
|
61 |
|
framesFinished = 0; |
62 |
|
|
63 |
|
startFound = 0; |
83 |
|
corrFrames = nFrames - startFrame; |
84 |
|
myFrames = (struct frameStruct*)calloc(corrFrames, |
85 |
|
sizeof(struct frameStruct)); |
86 |
+ |
|
87 |
+ |
index=0; |
88 |
+ |
for(i=startFrame;i<nFrames;i++){ |
89 |
+ |
|
90 |
+ |
if( index >= corrFrames ){ |
91 |
+ |
fprintf( stderr, |
92 |
+ |
"Error, number of frames, %d, exceeds corrFrames, %d.\n", |
93 |
+ |
index, |
94 |
+ |
corrFrames ); |
95 |
+ |
} |
96 |
+ |
|
97 |
+ |
// initialize the arrays |
98 |
+ |
|
99 |
+ |
atoms = myFrames[index].atoms; |
100 |
+ |
for(j=0;j<nLipids;j++){ |
101 |
+ |
|
102 |
+ |
atoms[nLipAtoms*j+0].type = HEAD; |
103 |
+ |
atoms[nLipAtoms*j+0].mass = 72; |
104 |
+ |
atoms[nLipAtoms*j+0].u[0] = 0.0; |
105 |
+ |
atoms[nLipAtoms*j+0].u[1] = 0.0; |
106 |
+ |
atoms[nLipAtoms*j+0].u[2] = 1.0; |
107 |
+ |
|
108 |
+ |
|
109 |
+ |
|
110 |
+ |
atoms[nLipAtoms*j+1].type = CH2; |
111 |
+ |
atoms[nLipAtoms*j+1].mass = 14.03; |
112 |
+ |
|
113 |
+ |
atoms[nLipAtoms*j+2].type = CH; |
114 |
+ |
atoms[nLipAtoms*j+2].mass = 13.02; |
115 |
+ |
|
116 |
+ |
atoms[nLipAtoms*j+3].type = CH2; |
117 |
+ |
atoms[nLipAtoms*j+3].mass = 14.03; |
118 |
+ |
|
119 |
+ |
atoms[nLipAtoms*j+4].type = CH2; |
120 |
+ |
atoms[nLipAtoms*j+4].mass = 14.03; |
121 |
+ |
|
122 |
+ |
atoms[nLipAtoms*j+5].type = CH2; |
123 |
+ |
atoms[nLipAtoms*j+5].mass = 14.03; |
124 |
+ |
|
125 |
+ |
atoms[nLipAtoms*j+6].type = CH2; |
126 |
+ |
atoms[nLipAtoms*j+6].mass = 14.03; |
127 |
+ |
|
128 |
+ |
atoms[nLipAtoms*j+7].type = CH2; |
129 |
+ |
atoms[nLipAtoms*j+7].mass = 14.03; |
130 |
+ |
|
131 |
+ |
atoms[nLipAtoms*j+8].type = CH2; |
132 |
+ |
atoms[nLipAtoms*j+8].mass = 14.03; |
133 |
+ |
|
134 |
+ |
atoms[nLipAtoms*j+9].type = CH2; |
135 |
+ |
atoms[nLipAtoms*j+9].mass = 14.03; |
136 |
+ |
|
137 |
+ |
atoms[nLipAtoms*j+10].type = CH3; |
138 |
+ |
atoms[nLipAtoms*j+10].mass = 15.04; |
139 |
+ |
|
140 |
+ |
atoms[nLipAtoms*j+11].type = CH2; |
141 |
+ |
atoms[nLipAtoms*j+11].mass = 14.03; |
142 |
+ |
|
143 |
+ |
atoms[nLipAtoms*j+12].type = CH2; |
144 |
+ |
atoms[nLipAtoms*j+12].mass = 14.03; |
145 |
+ |
|
146 |
+ |
atoms[nLipAtoms*j+13].type = CH2; |
147 |
+ |
atoms[nLipAtoms*j+13].mass = 14.03; |
148 |
+ |
|
149 |
+ |
atoms[nLipAtoms*j+14].type = CH2; |
150 |
+ |
atoms[nLipAtoms*j+14].mass = 14.03; |
151 |
+ |
|
152 |
+ |
atoms[nLipAtoms*j+15].type = CH2; |
153 |
+ |
atoms[nLipAtoms*j+15].mass = 14.03; |
154 |
+ |
|
155 |
+ |
atoms[nLipAtoms*j+16].type = CH2; |
156 |
+ |
atoms[nLipAtoms*j+16].mass = 14.03; |
157 |
+ |
|
158 |
+ |
atoms[nLipAtoms*j+17].type = CH2; |
159 |
+ |
atoms[nLipAtoms*j+17].mass = 14.03; |
160 |
+ |
|
161 |
+ |
atoms[nLipAtoms*j+18].type = CH3; |
162 |
+ |
atoms[nLipAtoms*j+18].mass = 15.04; |
163 |
+ |
} |
164 |
+ |
|
165 |
+ |
for(j=(nLipAtoms*nLipids);j<nAtoms;j++){ |
166 |
+ |
atoms[j].type = SSD; |
167 |
+ |
atoms[j].mass = 18.03; |
168 |
+ |
atoms[j].u[0] = 0.0; |
169 |
+ |
atoms[j].u[1] = 0.0; |
170 |
+ |
atoms[j].u[2] = 1.0; |
171 |
+ |
} |
172 |
+ |
myFrames[index].time = frameTimes[i]; |
173 |
+ |
readFrame(i, atoms, myFrames[index].Hmat ); |
174 |
+ |
} |
175 |
+ |
|
176 |
+ |
// initialize the counts and the correlation |
177 |
+ |
|
178 |
+ |
nCounts = 0; |
179 |
+ |
for(i=0;i<(corrFrames-1);i++) |
180 |
+ |
for(j=i+1;j<corrFrames;j++) |
181 |
+ |
nCounts++; |
182 |
+ |
|
183 |
+ |
for(i=0;i<RMSDBINS;i++){ |
184 |
+ |
rmsdCorr[i].rmsd = 0.0; |
185 |
+ |
rmsdCorr[i].nValues = 0; |
186 |
+ |
} |
187 |
+ |
|
188 |
+ |
rmsdDt = (myFrames[corrFrames-1].time - myFrames[0].time) / RMSDBINS; |
189 |
+ |
|
190 |
+ |
// perform the calculation |
191 |
+ |
|
192 |
+ |
index = 0; |
193 |
+ |
for(i=0;i<(corrFrames-1);i++){ |
194 |
+ |
for(j=i+1;j<corrFrames;j++){ |
195 |
+ |
|
196 |
+ |
diffTime = myFrames[j].time - myFrames[i].time; |
197 |
+ |
if( diffTime > 0.0 ){ |
198 |
+ |
|
199 |
+ |
percentComplete = |
200 |
+ |
(int)( 100.0 * (double)index / (double) nCounts ); |
201 |
+ |
|
202 |
+ |
fprintf( stdout, |
203 |
+ |
"\rRMSD corr %3d%% complete.", |
204 |
+ |
percentComplete ); |
205 |
+ |
fflush( stdout ); |
206 |
+ |
|
207 |
+ |
bin = (int)(diffTime / rmsdDt); |
208 |
+ |
if( bin < RMSDBINS) |
209 |
+ |
calcRMSDpair( bin, i, j, rType ); |
210 |
+ |
} |
211 |
+ |
|
212 |
+ |
index++; |
213 |
+ |
} |
214 |
+ |
} |
215 |
+ |
|
216 |
+ |
// print out the correlation |
217 |
+ |
|
218 |
+ |
sprintf( outName, "%s.rmsd", outPrefix ); |
219 |
+ |
outFile = fopen( outName, "w" ); |
220 |
+ |
|
221 |
+ |
fprintf( outFile, |
222 |
+ |
"#time\trmsd\n"); |
223 |
+ |
|
224 |
+ |
for(i=0;i<RMSDBINS;i++){ |
225 |
+ |
|
226 |
+ |
if(rmsdCorr[i].nValues){ |
227 |
+ |
|
228 |
+ |
timeOut = (2.0*(double)i+1.0)*rmsdDt*0.5; |
229 |
+ |
outVal = rmsdCorr[i].rmsd / (double)rmsdCorr[i].nValues; |
230 |
+ |
|
231 |
+ |
fprintf( outFile, |
232 |
+ |
"%6G\t%6G\n", |
233 |
+ |
timeOut, outVal ); |
234 |
+ |
} |
235 |
+ |
} |
236 |
+ |
|
237 |
+ |
fflush(outFile); |
238 |
+ |
fclose(outFile); |
239 |
+ |
|
240 |
+ |
percentComplete = |
241 |
+ |
(int)( 100.0 * (double)index / (double) nCounts ); |
242 |
+ |
|
243 |
+ |
fprintf( stdout, |
244 |
+ |
"\rRMSD corr %3d%% complete.", |
245 |
+ |
percentComplete ); |
246 |
+ |
fflush( stdout ); |
247 |
+ |
|
248 |
+ |
free( myFrames ); |
249 |
+ |
myFrames = NULL; |
250 |
+ |
} |
251 |
+ |
|
252 |
+ |
|
253 |
+ |
void calcRMSDpair( int bin, int frameI, int frameJ, enum atomNames rType ){ |
254 |
+ |
|
255 |
+ |
struct atomCoord* atomsI; |
256 |
+ |
struct atomCoord* atomsJ; |
257 |
+ |
|
258 |
+ |
int i,j,k,l,m,n; |
259 |
+ |
int nAccums; |
260 |
+ |
|
261 |
+ |
double d[3]; |
262 |
+ |
double dSqr; |
263 |
+ |
double comI[3]; |
264 |
+ |
double comJ[3]; |
265 |
+ |
double totMass; |
266 |
+ |
double accum; |
267 |
+ |
|
268 |
+ |
|
269 |
+ |
|
270 |
+ |
// list of 'a priori' constants |
271 |
+ |
|
272 |
+ |
const int nLipAtoms = NL_ATOMS; |
273 |
+ |
const int nBonds = NBONDS; |
274 |
+ |
const int nLipids = NLIPIDS; |
275 |
+ |
const int nSSD = NSSD; |
276 |
+ |
const int nAtoms = nLipAtoms * nLipids + nSSD; |
277 |
+ |
|
278 |
+ |
|
279 |
+ |
atomsI = myFrames[frameI].atoms; |
280 |
+ |
atomsJ = myFrames[frameJ].atoms; |
281 |
+ |
|
282 |
+ |
if( rType != COM ){ |
283 |
+ |
|
284 |
+ |
nAccums = 0; |
285 |
+ |
for(i=0;i<nAtoms;i++){ |
286 |
+ |
|
287 |
+ |
if (atomsI[i].type == rType){ |
288 |
+ |
|
289 |
+ |
for(j=0;j<3;j++) |
290 |
+ |
d[j] = atomsJ[i].pos[j] - atomsI[i].pos[j]; |
291 |
+ |
|
292 |
+ |
dSqr = 0.0; |
293 |
+ |
for(j=0;j<3;j++) |
294 |
+ |
dSqr += d[j] * d[j]; |
295 |
+ |
|
296 |
+ |
accum += sqrt(dSqr); |
297 |
+ |
nAccums++; |
298 |
+ |
} |
299 |
+ |
} |
300 |
+ |
} |
301 |
+ |
else{ |
302 |
+ |
|
303 |
+ |
nAccums = 0; |
304 |
+ |
for(i=0;i<nLipids;i++){ |
305 |
+ |
|
306 |
+ |
k = i*nLipAtoms; |
307 |
+ |
|
308 |
+ |
// com calc |
309 |
+ |
|
310 |
+ |
totMass = 0.0; |
311 |
+ |
for(m=0;m<3;m++){ |
312 |
+ |
comI[m] = 0.0; |
313 |
+ |
comJ[m] = 0.0; |
314 |
+ |
} |
315 |
+ |
for(j=0;j<nLipAtoms;j++){ |
316 |
+ |
l=k+j; |
317 |
+ |
|
318 |
+ |
for(m=0;m<3;m++){ |
319 |
+ |
comI[m] += atomsI[l].mass * atomsI[l].pos[m]; |
320 |
+ |
comJ[m] += atomsJ[l].mass * atomsJ[l].pos[m]; |
321 |
+ |
|
322 |
+ |
totMass += atomsI[l].mass; |
323 |
+ |
} |
324 |
+ |
for(m=0;m<3;m++){ |
325 |
+ |
comI[m] /= totMass; |
326 |
+ |
comJ[m] /= totMass; |
327 |
+ |
} |
328 |
+ |
} |
329 |
+ |
|
330 |
+ |
for(j=0;j<3;j++) |
331 |
+ |
d[j] = comJ[j] - comI[j]; |
332 |
+ |
|
333 |
+ |
dSqr = 0.0; |
334 |
+ |
for(j=0;j<3;j++) |
335 |
+ |
dSqr += d[j] * d[j]; |
336 |
+ |
|
337 |
+ |
accum += sqrt(dSqr); |
338 |
+ |
nAccums++; |
339 |
+ |
} |
340 |
+ |
} |
341 |
+ |
|
342 |
+ |
accum /= (double)nAccums; |
343 |
+ |
rmsdCorr[bin].rmsd += accum; |
344 |
+ |
rmsdCorr[bin].nValues++; |
345 |
+ |
} |
346 |
+ |
|
347 |
+ |
|
348 |
+ |
|