biod.pnpi.spb.ru
/
alexxy
/
gromacs.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'master' into pygromacs
[alexxy/gromacs.git]
/
src
/
gromacs
/
gmxana
/
gmx_confrms.cpp
diff --git
a/src/gromacs/gmxana/gmx_confrms.c
b/src/gromacs/gmxana/gmx_confrms.cpp
similarity index 97%
rename from
src/gromacs/gmxana/gmx_confrms.c
rename to
src/gromacs/gmxana/gmx_confrms.cpp
index 26add192a6f9ad1c628a5b2578557dfa24160305..4bd9cdb19e9370db4ef71b4af0adf4c0c4de0919 100644
(file)
--- a/
src/gromacs/gmxana/gmx_confrms.c
+++ b/
src/gromacs/gmxana/gmx_confrms.cpp
@@
-36,8
+36,10
@@
*/
#include "gmxpre.h"
*/
#include "gmxpre.h"
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
+
+#include <algorithm>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
@@
-119,7
+121,7
@@
int debug_strcmp(char s1[], char s2[])
{
fprintf(debug, " %s-%s", s1, s2);
}
{
fprintf(debug, " %s-%s", s1, s2);
}
- return strcmp(s1, s2);
+ return st
d::st
rcmp(s1, s2);
}
int find_next_match_atoms_in_res(int *i1, atom_id index1[],
}
int find_next_match_atoms_in_res(int *i1, atom_id index1[],
@@
-130,10
+132,9
@@
int find_next_match_atoms_in_res(int *i1, atom_id index1[],
int dx, dy, dmax, cmp;
gmx_bool bFW = FALSE;
int dx, dy, dmax, cmp;
gmx_bool bFW = FALSE;
- dx = dy = 0;
cmp = NOTSET;
cmp = NOTSET;
- dmax = max(m1-*i1, m2-*i2);
- for (dx = 0; dx < dmax && cmp != 0; dx++)
+ dmax =
std::
max(m1-*i1, m2-*i2);
+ for (dx = 0
, dy = 0
; dx < dmax && cmp != 0; dx++)
{
for (dy = dx; dy < dmax && cmp != 0; dy++)
{
{
for (dy = dx; dy < dmax && cmp != 0; dy++)
{
@@
-198,7
+199,6
@@
static int find_next_match_res(int *rnr1, int isize1,
int dx, dy, dmax, cmp, rr1, rr2;
gmx_bool bFW = FALSE, bFF = FALSE;
int dx, dy, dmax, cmp, rr1, rr2;
gmx_bool bFW = FALSE, bFF = FALSE;
- dx = dy = 0;
rr1 = 0;
while (rr1 < isize1 && *rnr1 != index1[rr1])
{
rr1 = 0;
while (rr1 < isize1 && *rnr1 != index1[rr1])
{
@@
-211,7
+211,7
@@
static int find_next_match_res(int *rnr1, int isize1,
}
cmp = NOTSET;
}
cmp = NOTSET;
- dmax = max(isize1-rr1, isize2-rr2);
+ dmax =
std::
max(isize1-rr1, isize2-rr2);
if (debug)
{
fprintf(debug, " R:%d-%d:%d-%d:%d ",
if (debug)
{
fprintf(debug, " R:%d-%d:%d-%d:%d ",
@@
-329,12
+329,11
@@
int find_first_atom_in_res(int rnr, int isize, atom_id index[], t_atom atom[])
void find_matching_names(int *isize1, atom_id index1[], t_atoms *atoms1,
int *isize2, atom_id index2[], t_atoms *atoms2)
{
void find_matching_names(int *isize1, atom_id index1[], t_atoms *atoms1,
int *isize2, atom_id index2[], t_atoms *atoms2)
{
- int i
, i
1, i2, ii1, ii2, m1, m2;
+ int i1, i2, ii1, ii2, m1, m2;
int atcmp, rescmp;
int atcmp, rescmp;
- int r
, r
nr1, rnr2, prnr1, prnr2;
+ int rnr1, rnr2, prnr1, prnr2;
int rsize1, rsize2;
int *rindex1, *rindex2;
int rsize1, rsize2;
int *rindex1, *rindex2;
- char *resnm1, *resnm2, *atnm1, *atnm2;
char ***atnms1, ***atnms2;
t_resinfo *resinfo1, *resinfo2;
char ***atnms1, ***atnms2;
t_resinfo *resinfo1, *resinfo2;
@@
-370,7
+369,7
@@
void find_matching_names(int *isize1, atom_id index1[], t_atoms *atoms1,
fprintf(debug, "R: %s%d %s%d\n",
*resinfo1[rnr1].name, rnr1, *resinfo2[rnr2].name, rnr2);
}
fprintf(debug, "R: %s%d %s%d\n",
*resinfo1[rnr1].name, rnr1, *resinfo2[rnr2].name, rnr2);
}
- rescmp = strcmp(*resinfo1[rnr1].name, *resinfo2[rnr2].name);
+ rescmp = st
d::st
rcmp(*resinfo1[rnr1].name, *resinfo2[rnr2].name);
}
if (debug)
{
}
if (debug)
{
@@
-538,10
+537,9
@@
int gmx_confrms(int argc, char *argv[])
output_env_t oenv;
/* counters */
output_env_t oenv;
/* counters */
- int i,
j,
m;
+ int i, m;
/* center of mass calculation */
/* center of mass calculation */
- real tmas1, tmas2;
rvec xcm1, xcm2;
/* variables for fit */
rvec xcm1, xcm2;
/* variables for fit */
@@
-632,7
+630,7
@@
int gmx_confrms(int argc, char *argv[])
{
name1 = *atoms1->atomname[index1[i]];
name2 = *atoms2->atomname[index2[i]];
{
name1 = *atoms1->atomname[index1[i]];
name2 = *atoms2->atomname[index2[i]];
- if (strcmp(name1, name2))
+ if (st
d::st
rcmp(name1, name2))
{
if (warn < 20)
{
{
if (warn < 20)
{
@@
-696,11
+694,11
@@
int gmx_confrms(int argc, char *argv[])
rms += msd*mass;
msds[at] += msd;
}
rms += msd*mass;
msds[at] += msd;
}
- maxmsd = max(maxmsd, msds[at]);
- minmsd = min(minmsd, msds[at]);
+ maxmsd =
std::
max(maxmsd, msds[at]);
+ minmsd =
std::
min(minmsd, msds[at]);
totmass += mass;
}
totmass += mass;
}
- rms = sqrt(rms/totmass);
+ rms = s
td::s
qrt(rms/totmass);
printf("Root mean square deviation after lsq fit = %g nm\n", rms);
if (bBfac)
printf("Root mean square deviation after lsq fit = %g nm\n", rms);
if (bBfac)