mirror of
https://github.com/arcan1s/moldyn.git
synced 2025-11-16 20:53:42 +00:00
Release envir-1.0.1
* edited shared library - deleted binary file and archive
This commit is contained in:
arcan1s
81
envir/src/1oct-1clb_clb1_150.pdb
Executable file
81
envir/src/1oct-1clb_clb1_150.pdb
Executable file
@ -0,0 +1,81 @@
|
||||
ATOM 1 CL MOL 1 -2.664 11.890 -17.525
|
||||
ATOM 2 CA MOL 1 -0.917 12.008 -17.545
|
||||
ATOM 3 CA MOL 1 -0.265 12.628 -16.449
|
||||
ATOM 4 CA MOL 1 1.141 12.679 -16.437
|
||||
ATOM 5 CA MOL 1 1.865 12.184 -17.521
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||||
ATOM 6 CA MOL 1 1.222 11.648 -18.663
|
||||
ATOM 7 CA MOL 1 -0.191 11.514 -18.640
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||||
ATOM 8 HC MOL 1 -0.936 12.995 -15.629
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||||
ATOM 9 HC MOL 1 1.720 13.106 -15.622
|
||||
ATOM 10 HC MOL 1 2.954 12.258 -17.471
|
||||
ATOM 11 HC MOL 1 1.854 11.343 -19.523
|
||||
ATOM 12 HC MOL 1 -0.575 11.044 -19.540
|
||||
ATOM 13 CL MOL 2 -6.134 15.323 -13.160
|
||||
ATOM 14 CA MOL 2 -6.616 14.489 -14.639
|
||||
ATOM 15 CA MOL 2 -5.740 13.483 -15.125
|
||||
ATOM 16 CA MOL 2 -6.152 12.814 -16.307
|
||||
ATOM 17 CA MOL 2 -7.335 13.116 -16.943
|
||||
ATOM 18 CA MOL 2 -8.190 14.137 -16.492
|
||||
ATOM 19 CA MOL 2 -7.807 14.850 -15.301
|
||||
ATOM 20 HC MOL 2 -4.814 13.230 -14.622
|
||||
ATOM 21 HC MOL 2 -5.487 12.040 -16.714
|
||||
ATOM 22 HC MOL 2 -7.577 12.578 -17.866
|
||||
ATOM 23 HC MOL 2 -9.151 14.499 -16.876
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||||
ATOM 24 HC MOL 2 -8.450 15.630 -14.941
|
||||
ATOM 25 CL MOL 3 -2.291 10.911 -13.849
|
||||
ATOM 26 CT MOL 3 -4.546 8.879 -13.092
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||||
ATOM 27 CA MOL 3 -3.302 8.337 -13.634
|
||||
ATOM 28 CA MOL 3 -3.217 6.974 -13.798
|
||||
ATOM 29 CA MOL 3 -2.019 6.430 -14.303
|
||||
ATOM 30 CA MOL 3 -0.898 7.214 -14.678
|
||||
ATOM 31 CA MOL 3 -1.007 8.608 -14.483
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||||
ATOM 32 CA MOL 3 -2.180 9.166 -13.977
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ATOM 33 HC MOL 3 -4.397 9.808 -12.580
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ATOM 34 HC MOL 3 -5.405 9.060 -13.843
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ATOM 35 HC MOL 3 -4.909 8.193 -12.354
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ATOM 36 HC MOL 3 -3.970 6.222 -13.557
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ATOM 37 HC MOL 3 -1.981 5.395 -14.406
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ATOM 38 HC MOL 3 -0.061 6.767 -15.059
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ATOM 39 HC MOL 3 -0.201 9.202 -14.754
|
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ATOM 40 CL MOL 4 2.265 8.067 -16.401
|
||||
ATOM 41 CT MOL 4 4.304 6.644 -14.331
|
||||
ATOM 42 CA MOL 4 4.338 6.294 -15.835
|
||||
ATOM 43 CA MOL 4 5.247 5.306 -16.251
|
||||
ATOM 44 CA MOL 4 5.322 4.933 -17.599
|
||||
ATOM 45 CA MOL 4 4.536 5.582 -18.550
|
||||
ATOM 46 CA MOL 4 3.626 6.566 -18.144
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ATOM 47 CA MOL 4 3.505 6.893 -16.799
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ATOM 48 HC MOL 4 4.424 5.830 -13.614
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ATOM 49 HC MOL 4 5.154 7.258 -14.121
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ATOM 50 HC MOL 4 3.454 7.240 -14.005
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ATOM 51 HC MOL 4 5.828 4.872 -15.488
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ATOM 52 HC MOL 4 5.986 4.115 -17.892
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ATOM 53 HC MOL 4 4.692 5.261 -19.616
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ATOM 54 HC MOL 4 2.976 7.091 -18.806
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ATOM 55 CL MOL 5 -2.477 15.433 -17.197
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ATOM 56 CA MOL 5 -3.971 16.235 -16.853
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ATOM 57 CA MOL 5 -4.072 17.013 -15.698
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ATOM 58 CA MOL 5 -5.276 17.755 -15.484
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ATOM 59 CA MOL 5 -6.309 17.673 -16.459
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ATOM 60 CA MOL 5 -6.182 16.896 -17.601
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||||
ATOM 61 CA MOL 5 -5.009 16.172 -17.784
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ATOM 62 HC MOL 5 -3.234 17.123 -14.977
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ATOM 63 HC MOL 5 -5.390 18.375 -14.614
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ATOM 64 HC MOL 5 -7.255 18.222 -16.363
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ATOM 65 HC MOL 5 -7.001 16.802 -18.354
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ATOM 66 HC MOL 5 -5.054 15.588 -18.738
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ATOM 67 CL MOL 6 4.729 13.255 -14.510
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ATOM 68 CT MOL 6 4.715 14.006 -11.534
|
||||
ATOM 69 CA MOL 6 3.736 12.879 -11.996
|
||||
ATOM 70 CA MOL 6 2.904 12.242 -11.010
|
||||
ATOM 71 CA MOL 6 2.037 11.182 -11.384
|
||||
ATOM 72 CA MOL 6 1.961 10.754 -12.723
|
||||
ATOM 73 CA MOL 6 2.804 11.402 -13.660
|
||||
ATOM 74 CA MOL 6 3.692 12.421 -13.322
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||||
ATOM 75 HC MOL 6 5.739 13.830 -11.938
|
||||
ATOM 76 HC MOL 6 4.503 15.011 -11.742
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||||
ATOM 77 HC MOL 6 4.934 14.104 -10.476
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||||
ATOM 78 HC MOL 6 2.865 12.507 -9.941
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||||
ATOM 79 HC MOL 6 1.422 10.678 -10.663
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||||
ATOM 80 HC MOL 6 1.383 9.975 -13.034
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||||
ATOM 81 HC MOL 6 2.733 11.097 -14.681
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61
envir/src/CMakeLists.txt
Normal file
61
envir/src/CMakeLists.txt
Normal file
@ -0,0 +1,61 @@
|
||||
set ("${PROJECT}_VERSION_MAJOR" 1)
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||||
set ("${PROJECT}_VERSION_MINOR" 0)
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set ("${PROJECT}_VERSION_PATCH" 1)
|
||||
set ("${PROJECT}_VERSION" ${${PROJECT}_VERSION_MAJOR}.${${PROJECT}_VERSION_MINOR}.${${PROJECT}_VERSION_PATCH})
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||||
message (STATUS ${${PROJECT}_VERSION})
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|
||||
## set files
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||||
# main files
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||||
set (MAIN_SOURCES main)
|
||||
# not public srcs
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||||
set (PRIVATE_CLASSES)
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||||
# headers only files
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SET (HEADERS_ONLY)
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||||
# public srcs
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set (PUBLIC_CLASSES add_main
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coords
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envir_search
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messages
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print_struct
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set_center)
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# public headers
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set (PUBLIC_HEADERS)
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# shared libraries
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if (CMAKE_COMPILER_IS_GNUCXX)
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set (ADDITIONAL_LIB m)
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||||
else ()
|
||||
set (ADDITIONAL_LIB)
|
||||
endif()
|
||||
set (SOURCES)
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||||
|
||||
# append list
|
||||
foreach (class ${PRIVATE_CLASSES})
|
||||
LIST (APPEND SOURCES ${class}.c)
|
||||
LIST (APPEND HEADERS ${class}.h)
|
||||
endforeach ()
|
||||
|
||||
foreach (class ${HEADERS_ONLY})
|
||||
LIST (APPEND HEADERS ${class}.h)
|
||||
endforeach ()
|
||||
|
||||
foreach (class ${PUBLIC_CLASSES})
|
||||
LIST (APPEND SOURCES ${class}.c)
|
||||
LIST (APPEND HEADERS ../include/${PROJECT}/${class}.h)
|
||||
LIST (APPEND PUBLIC_HEADERS ../include/${PROJECT}/${class}.h)
|
||||
endforeach ()
|
||||
|
||||
# message
|
||||
message (STATUS "SOURCES: ${SOURCES}")
|
||||
|
||||
# link libraries and compile
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||||
add_executable (${PROJECT} ${MAIN_SOURCES} ${SOURCES})
|
||||
target_link_libraries (${PROJECT} ${ADDITIONAL_LIB})
|
||||
|
||||
# install properties
|
||||
INSTALL (TARGETS ${PROJECT}
|
||||
DESTINATION bin)
|
||||
if (ADD_INCLUDE)
|
||||
INSTALL (FILES ${PUBLIC_HEADERS}
|
||||
DESTINATION include/${PROJECT})
|
||||
endif ()
|
||||
21
envir/src/Makefile
Normal file
21
envir/src/Makefile
Normal file
@ -0,0 +1,21 @@
|
||||
PROJECT=ENVIR
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||||
|
||||
CC=gcc
|
||||
CFLAGS=-c -Wall -fPIC
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||||
LDFLAGS=-lm
|
||||
SOURCES_DIR=src
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||||
SOURCES=main.c add_main.c coords.c envir_search.c messages.c print_struct.c set_center.c
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||||
OBJECTS=$(SOURCES:.c=.o)
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||||
EXECUTABLE=envir
|
||||
|
||||
$(PROJECT): $(SOURCES) $(EXECUTABLE)
|
||||
|
||||
$(EXECUTABLE): $(OBJECTS)
|
||||
$(CC) $(LDFLAGS) $(OBJECTS) -o $@
|
||||
|
||||
.c.o:
|
||||
$(CC) $(CFLAGS) $< -o $@
|
||||
|
||||
clean:
|
||||
rm -f *.o
|
||||
|
||||
49
envir/src/add_main.c
Normal file
49
envir/src/add_main.c
Normal file
@ -0,0 +1,49 @@
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||||
/* Additional library for main.c (envir)
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||||
*/
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||||
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||||
#include <stdio.h>
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||||
|
||||
// #include "messages.h"
|
||||
|
||||
|
||||
int error_checking (const float *cell, const char *input, const char *output)
|
||||
{
|
||||
if ((cell[0] == 0.0) || (cell[1] == 0.0) || (cell[2] == 0.0))
|
||||
return 11;
|
||||
if (input[0] == '#')
|
||||
return 12;
|
||||
if (output[0] == '#')
|
||||
return 13;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
int print_message (const int quiet, FILE *std_output, const int log, FILE *f_log,
|
||||
const int mode, const char *str)
|
||||
{
|
||||
if ((quiet != 1) && (std_output != stderr))
|
||||
message (0, mode, str, std_output);
|
||||
if (log == 1)
|
||||
message (1, mode, str, f_log);
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
int set_defaults (float *cell, char *input, int *log, int *num_of_mol, char *output,
|
||||
int *quiet, float *rad)
|
||||
{
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||||
int i;
|
||||
|
||||
for (i=0; i<3; i++)
|
||||
cell[i] = 0.0;
|
||||
input[0] = '#';
|
||||
*log = 0;
|
||||
*num_of_mol = 1;
|
||||
output[0] = '#';
|
||||
*quiet = 0;
|
||||
*rad = 6.0;
|
||||
|
||||
return 0;
|
||||
}
|
||||
313
envir/src/coords.c
Normal file
313
envir/src/coords.c
Normal file
@ -0,0 +1,313 @@
|
||||
/* Library for reading coordinates from input file
|
||||
*
|
||||
* Usage:
|
||||
* reading_coords (mode, filename, type_interaction, labels,
|
||||
* cell, &number_of_molecules, &number_of_atoms, true_label_molecule,
|
||||
* label_molecule, type_atoms, coords, char_type_atoms)
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
|
||||
int reading_coords (const int mode, const char *filename, const int type_inter,
|
||||
const int *label_atom, const float *cell, int *num_mol,
|
||||
int *num_atoms, int *true_label_mol, int *label_mol,
|
||||
int *type_atoms, float *coords, char *ch_type_atoms)
|
||||
/* filename - name of file with coordinates
|
||||
* type_inter - type interaction (number of molecules for interaction)
|
||||
* label_atom - types of atom for interaction
|
||||
* cell - cell dimension
|
||||
* num_mol - number of molecules for writing coordinates
|
||||
* num_atoms - number of atoms for writing coordinates
|
||||
* true_label_mol - massive of true numbers of molecule for atoms
|
||||
* label_mol - massive of numbers of molecule for atoms
|
||||
* type_atoms - massive of atom types for atoms
|
||||
* coords - massive of coordinates
|
||||
* ch_type_atoms - massive of char types for atoms
|
||||
*/
|
||||
{
|
||||
char at_symb[32], file_string[256];
|
||||
int atoms, cur_at_num, cur_at_type, cur_mol, i, j, tr_num_atoms, ref_mol, x, y;
|
||||
float cur_coords[3], *not_tr_coords, ref[3];
|
||||
FILE *inp;
|
||||
/* cur_*, at_symb - temp variables
|
||||
* file_string - temp string variable
|
||||
* atoms - total number of atoms in system
|
||||
* tr_num_atoms - number of translated atoms for writing coordinates (m.b. 8*num_atoms)
|
||||
* ref_mol - number of molecule for reference
|
||||
* not_tr_coords - not translated coordinates
|
||||
* ref - coordinates of reference molecule
|
||||
* inp - file with input data
|
||||
*/
|
||||
|
||||
*num_atoms = 0;
|
||||
*num_mol = 0;
|
||||
|
||||
// Reading file
|
||||
inp = fopen (filename, "r");
|
||||
if (inp == NULL)
|
||||
return 1;
|
||||
|
||||
ref_mol = -1;
|
||||
fscanf (inp, "%i", &atoms);
|
||||
not_tr_coords = (float *) malloc (3 * atoms * sizeof (float));
|
||||
fgets (file_string, 256, inp);
|
||||
for (i=0; i<atoms; i++)
|
||||
{
|
||||
fgets (file_string, 256, inp);
|
||||
sscanf (file_string, "%i%s%f%f%f%i%i", &cur_at_num, at_symb, &cur_coords[0],
|
||||
&cur_coords[1], &cur_coords[2], &cur_at_type, &cur_mol);
|
||||
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
// for statgen
|
||||
for (j=0; j<type_inter; j++)
|
||||
if (cur_at_type == label_atom[j])
|
||||
{
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
}
|
||||
break;
|
||||
case 1:
|
||||
// for envir
|
||||
not_tr_coords[3**num_atoms+0] = cur_coords[0];
|
||||
not_tr_coords[3**num_atoms+1] = cur_coords[1];
|
||||
not_tr_coords[3**num_atoms+2] = cur_coords[2];
|
||||
ch_type_atoms[2**num_atoms+0] = at_symb[0];
|
||||
ch_type_atoms[2**num_atoms+1] = at_symb[1];
|
||||
|
||||
if (ref_mol != cur_mol)
|
||||
{
|
||||
ref_mol = cur_mol;
|
||||
true_label_mol[*num_mol] = ref_mol;
|
||||
*num_mol = *num_mol + 1;
|
||||
}
|
||||
label_mol[*num_atoms] = *num_mol - 1;
|
||||
type_atoms[*num_atoms] = j;
|
||||
|
||||
*num_atoms = *num_atoms + 1;
|
||||
break;
|
||||
default: return 1;
|
||||
}
|
||||
}
|
||||
fclose (inp);
|
||||
|
||||
// Translation
|
||||
tr_num_atoms = *num_atoms;
|
||||
for (i=0; i<*num_atoms; i++)
|
||||
for (j=0; j<3; j++)
|
||||
coords[3*i+j] = not_tr_coords[3*i+j];
|
||||
|
||||
// Assign initial value to reference coordinates
|
||||
ref_mol = label_mol[0];
|
||||
for (i=0; i<3; i++)
|
||||
ref[i] = coords[3*0+i];
|
||||
|
||||
for (i=0; i<*num_atoms; i++)
|
||||
{
|
||||
if (label_mol[i] != ref_mol)
|
||||
{
|
||||
ref_mol = label_mol[i];
|
||||
for (j=0; j<3; j++)
|
||||
ref[j] = not_tr_coords[3*i+j];
|
||||
}
|
||||
|
||||
for (x=0; x<3; x++)
|
||||
{
|
||||
if (ref[x] >= 0.0)
|
||||
// if xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
else
|
||||
// if xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
for (x=0; x<3; x++)
|
||||
{
|
||||
for (y=x+1; y<3; y++)
|
||||
{
|
||||
if ((ref[x] >= 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz and xyz >= 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[x] < 0.0) && (ref[y] < 0.0))
|
||||
// if xyz and xyz < 0.0 A
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
if ((j == x) || (j == y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
else
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
for (y=0; y<3; y++)
|
||||
if ((ref[x] < 0.0) && (ref[y] >= 0.0))
|
||||
// if xyz OR xyz >= 0.0
|
||||
{
|
||||
for (j=0; j<3; j++)
|
||||
{
|
||||
if (j == x)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] + cell[j];
|
||||
if (j == y)
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j] - cell[j];
|
||||
if ((j != x) && (j != y))
|
||||
coords[3*tr_num_atoms+j] = not_tr_coords[3*i+j];
|
||||
}
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and y >= 0.0 A and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and z >= 0.0 A and y < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] >= 0.0))
|
||||
// if y and z >= 0.0 A and x < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] >= 0.0))
|
||||
// if x and y < 0.0 A and z >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] - cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] >= 0.0) && (ref[2] < 0.0))
|
||||
// if x and z < 0.0 A and y >= 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] - cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] >= 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x >= 0.0 A and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] - cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
|
||||
if ((ref[0] < 0.0) && (ref[1] < 0.0) && (ref[2] < 0.0))
|
||||
// if x and y and z < 0.0 A
|
||||
{
|
||||
coords[3*tr_num_atoms+0] = not_tr_coords[3*i+0] + cell[0];
|
||||
coords[3*tr_num_atoms+1] = not_tr_coords[3*i+1] + cell[1];
|
||||
coords[3*tr_num_atoms+2] = not_tr_coords[3*i+2] + cell[2];
|
||||
|
||||
label_mol[tr_num_atoms] = label_mol[i];
|
||||
type_atoms[tr_num_atoms] = type_atoms[i];
|
||||
tr_num_atoms++;
|
||||
}
|
||||
}
|
||||
|
||||
// free memory
|
||||
free (not_tr_coords);
|
||||
|
||||
return 0;
|
||||
}
|
||||
40
envir/src/envir_search.c
Normal file
40
envir/src/envir_search.c
Normal file
@ -0,0 +1,40 @@
|
||||
/* Library for search environment
|
||||
*
|
||||
* Usage:
|
||||
* search_envir (number_of_molecule, num_mol, centr_coords, rad, needed_mol,
|
||||
* &num_needed_mol)
|
||||
*/
|
||||
|
||||
#include <math.h>
|
||||
|
||||
|
||||
int search_envir (const int num_of_mol, const int num_mol, const float *centr_coords,
|
||||
const double rad, int *needed_mol, int *num_needed_mol)
|
||||
/* num_of_mol - number of molecule for search
|
||||
* num_mol - number of molecules for writing coordinates
|
||||
* centr_coords - massive of centered coordinates
|
||||
* rad - criterion
|
||||
* needed_mol - massive of needed molecules
|
||||
* num_needed_mol - number of needed molecules
|
||||
*/
|
||||
{
|
||||
float r;
|
||||
int i;
|
||||
/* r - radius
|
||||
*/
|
||||
*num_needed_mol = 0;
|
||||
|
||||
for (i=0; i<8*num_mol; i++)
|
||||
{
|
||||
r = sqrt (pow ((centr_coords[3*i+0]-centr_coords[3*8*(num_of_mol-1)+0]), 2) +
|
||||
pow ((centr_coords[3*i+1]-centr_coords[3*8*(num_of_mol-1)+1]), 2) +
|
||||
pow ((centr_coords[3*i+2]-centr_coords[3*8*(num_of_mol-1)+2]), 2));
|
||||
if (r < rad)
|
||||
{
|
||||
needed_mol[*num_needed_mol] = i;
|
||||
*num_needed_mol = *num_needed_mol + 1;
|
||||
}
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
220
envir/src/main.c
Normal file
220
envir/src/main.c
Normal file
@ -0,0 +1,220 @@
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
|
||||
// #include "add_main.h"
|
||||
// #include "coords.h"
|
||||
// #include "envir_search.h"
|
||||
// #include "messages.h"
|
||||
// #include "print_struct.h"
|
||||
// #include "set_center.h"
|
||||
|
||||
|
||||
int main(int argc, char *argv[])
|
||||
{
|
||||
char tmp_str[2048];
|
||||
int error, i, j, *tmp_int;
|
||||
FILE *f_inp, *f_log;
|
||||
|
||||
char *ch_type_atoms, input[256], logfile[256], output[256];
|
||||
float cell[3], *centr_coords, *coords, rad;
|
||||
int *label_mol, log, num_atoms, num_mol, num_needed_mol, num_of_mol,
|
||||
*needed_mol, quiet, *true_label_mol;
|
||||
/* ch_type_atoms - massive of char types for atoms
|
||||
* input - input file name
|
||||
* logfile - log file name
|
||||
* output - output file name
|
||||
*
|
||||
* cell - cell dimension
|
||||
* centr_coords - massive of coordinates of center molecules
|
||||
* coords - massive of coordinates
|
||||
* rad - criterion
|
||||
*
|
||||
* label_mol - massive of numbers of molecule for atoms
|
||||
* log - status of log-mode
|
||||
* num_atoms - number of atoms for writing coordinates
|
||||
* num_mol - number of molecules for writing coordinates
|
||||
* num_needed_mol - number of needed molecules
|
||||
* num_of_mol - number of molecule for search
|
||||
* needed_mol - massive of needed molecules
|
||||
* quiet - status of quiet-mode
|
||||
* true_label_mol - massive of true numbers of molecule for atoms
|
||||
*/
|
||||
|
||||
set_defaults (cell, input, &log, &num_of_mol, output, &quiet, &rad);
|
||||
|
||||
for (i=1; i<argc; i++)
|
||||
{
|
||||
if ((argv[i][0] == '-') && (argv[i][1] == 'h'))
|
||||
{
|
||||
sprintf (tmp_str, " envir\n");
|
||||
sprintf (tmp_str, "%sProgram for search environment for chosen molecule by geometric criterion\n", tmp_str);
|
||||
sprintf (tmp_str, "%sVersion : 1.0.1 License : GPL\n", tmp_str);
|
||||
sprintf (tmp_str, "%s Evgeniy Alekseev aka arcanis\n", tmp_str);
|
||||
sprintf (tmp_str, "%s E-mail : esalexeev@gmail.com\n\n", tmp_str);
|
||||
sprintf (tmp_str, "%sUsage:\n", tmp_str);
|
||||
sprintf (tmp_str, "%senvir -i FILENAME -c X,Y,Z -o FILEMANE [ -n NUM_OF_MOLECULE ] [ -r RADIUS ] [ -l LOGFILE] [ -q ] [ -h ]\n\n", tmp_str);
|
||||
sprintf (tmp_str, "%sParametrs:\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -i - input file with coordinates\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -c - cell size (float), A\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -o - output file with coordinates\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -n - number of molecule for search (integer). Default is 1\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -r - radius of environment (float). Default is 6.0\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -l - log enable\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -q - quiet enable\n", tmp_str);
|
||||
sprintf (tmp_str, "%s -h - show this help and exit\n", tmp_str);
|
||||
fputs (tmp_str, stdout);
|
||||
return 0;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'i'))
|
||||
// input file
|
||||
{
|
||||
strcpy (input, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'c'))
|
||||
// cell size
|
||||
{
|
||||
sscanf (argv[i+1], "%f,%f,%f", &cell[0], &cell[1], &cell[2]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'o'))
|
||||
// output file
|
||||
{
|
||||
strcpy (output, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'n'))
|
||||
// number of molecule
|
||||
{
|
||||
sscanf (argv[i+1], "%i", &num_of_mol);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'r'))
|
||||
// radius of environment
|
||||
{
|
||||
sscanf (argv[i+1], "%f", &rad);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'l'))
|
||||
// log mode
|
||||
{
|
||||
log = 1;
|
||||
strcpy (logfile, argv[i+1]);
|
||||
i++;
|
||||
}
|
||||
else if ((argv[i][0] == '-') && (argv[i][1] == 'q'))
|
||||
// quiet mode
|
||||
{
|
||||
quiet = 1;
|
||||
}
|
||||
}
|
||||
|
||||
if (log == 1)
|
||||
f_log = fopen (logfile, "w");
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 0, argv[0]);
|
||||
print_message (quiet, stdout, log, f_log, 1, argv[0]);
|
||||
|
||||
// error check
|
||||
error = error_checking (cell, input, output);
|
||||
if (error != 0)
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 17, argv[0]);
|
||||
return 1;
|
||||
}
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 2, argv[0]);
|
||||
|
||||
// processing
|
||||
// initial variables
|
||||
print_message (quiet, stdout, log, f_log, 3, input);
|
||||
f_inp = fopen (input, "r");
|
||||
if (f_inp == NULL)
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 18, input);
|
||||
return 1;
|
||||
}
|
||||
fscanf (f_inp, "%i", &num_atoms);
|
||||
fclose (f_inp);
|
||||
ch_type_atoms = (char *) malloc (2 * num_atoms * sizeof (char));
|
||||
coords = (float *) malloc (3 * 8 * num_atoms * sizeof (float));
|
||||
label_mol = (int *) malloc (8 * num_atoms * sizeof (int));
|
||||
tmp_int = (int *) malloc (8 * num_atoms * sizeof (int));
|
||||
true_label_mol = (int *) malloc (num_atoms * sizeof (int));
|
||||
// error checking
|
||||
if ((ch_type_atoms == NULL) ||
|
||||
(coords == NULL) ||
|
||||
(label_mol == NULL) ||
|
||||
(tmp_int == NULL) ||
|
||||
(true_label_mol == NULL))
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
||||
return 17;
|
||||
}
|
||||
sprintf (tmp_str, "%6cInput file: '%s';\n%6cOutput file: '%s';\n%6cLog: %i;\n\
|
||||
%6cQuiet: %i;\n%6cCell size: %.4f, %.4f, %.4f;\n%6cSelect molecule: %i;\n\
|
||||
%6cCriterion: %.1f\n", ' ', input, ' ', output, ' ', log, ' ', quiet, ' ', cell[0],
|
||||
cell[1], cell[2], ' ' , num_of_mol, ' ', rad);
|
||||
print_message (quiet, stdout, log, f_log, 5, tmp_str);
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 6, argv[0]);
|
||||
|
||||
// reading coordinates
|
||||
print_message (quiet, stdout, log, f_log, 7, input);
|
||||
error = reading_coords (1, input, tmp_int, tmp_int, cell, &num_mol, &num_atoms,
|
||||
true_label_mol, label_mol, tmp_int, coords, ch_type_atoms);
|
||||
centr_coords = (float *) malloc (3 * 8 * num_mol * sizeof (float));
|
||||
needed_mol = (int *) malloc (num_mol * sizeof (int));
|
||||
if (error == 0)
|
||||
{
|
||||
sprintf (tmp_str, "%6cNumber of molecules: %i; %6cNumber of atoms: %i\n",
|
||||
' ', num_mol, ' ', num_atoms);
|
||||
print_message (quiet, stdout, log, f_log, 8, tmp_str);
|
||||
}
|
||||
// error checking
|
||||
if ((centr_coords == NULL) ||
|
||||
(needed_mol == NULL))
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 19, argv[0]);
|
||||
return 17;
|
||||
}
|
||||
|
||||
// analyze
|
||||
if (error == 0)
|
||||
{
|
||||
error = set_center (num_atoms, num_mol, label_mol, coords, centr_coords);
|
||||
if (error == 0)
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 20, argv[0]);
|
||||
error = search_envir (num_of_mol, num_mol, centr_coords, rad, needed_mol,
|
||||
&num_needed_mol);
|
||||
if (error == 0)
|
||||
{
|
||||
print_message (quiet, stderr, log, f_log, 21, argv[0]);
|
||||
error = print_structure (output, num_needed_mol, needed_mol, num_atoms,
|
||||
label_mol, ch_type_atoms, coords);
|
||||
print_message (quiet, stderr, log, f_log, 12, output);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 13, argv[0]);
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 15, argv[0]);
|
||||
// free memory
|
||||
free (ch_type_atoms);
|
||||
free (centr_coords);
|
||||
free (coords);
|
||||
free (label_mol);
|
||||
free (needed_mol);
|
||||
free (tmp_int);
|
||||
free (true_label_mol);
|
||||
|
||||
print_message (quiet, stdout, log, f_log, 16, argv[0]);
|
||||
|
||||
if (log == 1)
|
||||
fclose (f_log);
|
||||
return 0;
|
||||
}
|
||||
99
envir/src/messages.c
Normal file
99
envir/src/messages.c
Normal file
@ -0,0 +1,99 @@
|
||||
/* Library for printing messages at output
|
||||
*
|
||||
* Usage:
|
||||
* message (log, mode, text, output)
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
#include <time.h>
|
||||
|
||||
|
||||
int message (const int log, const int mode, const char *text, FILE *output)
|
||||
/* mode - number of message
|
||||
* text - additional text
|
||||
*/
|
||||
{
|
||||
char out[4096];
|
||||
|
||||
if (log == 1)
|
||||
{
|
||||
char time_str[256];
|
||||
time_t t = time (NULL);
|
||||
struct tm* aTm = localtime (&t);
|
||||
sprintf (time_str, "[%04d-%02d-%02d %02d:%02d:%02d] [%2i]: ", aTm->tm_year+1900,
|
||||
aTm->tm_mon+1, aTm->tm_mday, aTm->tm_hour, aTm->tm_min, aTm->tm_sec, mode);
|
||||
fputs (time_str, output);
|
||||
}
|
||||
|
||||
switch (mode)
|
||||
{
|
||||
case 0:
|
||||
sprintf (out, "Starting program: '%s'\n", text);
|
||||
break;
|
||||
case 1:
|
||||
sprintf (out, "Checking errors\n");
|
||||
break;
|
||||
case 2:
|
||||
sprintf (out, "Errors are not detected\n");
|
||||
break;
|
||||
case 3:
|
||||
sprintf (out, "Initialization of variables from file '%s'\n", text);
|
||||
break;
|
||||
case 4:
|
||||
break;
|
||||
case 5:
|
||||
sprintf (out, "Initial parametrs: \n%s", text);
|
||||
break;
|
||||
case 6:
|
||||
sprintf (out, "Processing\n");
|
||||
break;
|
||||
case 7:
|
||||
sprintf (out, "Open file: '%s'\n", text);
|
||||
break;
|
||||
case 8:
|
||||
sprintf (out, "%s", text);
|
||||
break;
|
||||
case 9:
|
||||
sprintf (out, "%6cSize of variables was changed successfully\n", ' ');
|
||||
break;
|
||||
case 10:
|
||||
sprintf (out, "%6cConnectivity matrix was created successfully\n", ' ');
|
||||
break;
|
||||
case 11:
|
||||
sprintf (out, "%6cConnectivity matrix was processed successfully\n", ' ');
|
||||
break;
|
||||
case 12:
|
||||
sprintf (out, "%6cResult was printed to file '%s' successfully\n", ' ', text);
|
||||
break;
|
||||
case 13:
|
||||
sprintf (out, "End of processing\n");
|
||||
break;
|
||||
case 14:
|
||||
sprintf (out, "Printing summary statistic to file '%s'\n", text);
|
||||
break;
|
||||
case 15:
|
||||
sprintf (out, "Free memory\n");
|
||||
break;
|
||||
case 16:
|
||||
sprintf (out, "Exiting without errors\n");
|
||||
break;
|
||||
case 17:
|
||||
sprintf (out, "Something wrong!\nSee '%s -h' for more details\n", text);
|
||||
break;
|
||||
case 18:
|
||||
sprintf (out, "File '%s' not found\nError\n", text);
|
||||
break;
|
||||
case 19:
|
||||
sprintf (out, "Memory error\n");
|
||||
break;
|
||||
case 20:
|
||||
sprintf (out, "%6cCenter of molecules was set successfully\n", ' ');
|
||||
break;
|
||||
case 21:
|
||||
sprintf (out, "%6cEnvironment was selected successfully\n", ' ');
|
||||
break;
|
||||
}
|
||||
|
||||
fputs (out, output);
|
||||
return 0;
|
||||
}
|
||||
3376
envir/src/oct-clb.150
Executable file
3376
envir/src/oct-clb.150
Executable file
File diff suppressed because it is too large
Load Diff
58
envir/src/print_struct.c
Normal file
58
envir/src/print_struct.c
Normal file
@ -0,0 +1,58 @@
|
||||
/* Library for printing structure to pdb file
|
||||
*
|
||||
* Usage:
|
||||
* print_structure (output, num_needed_mol, needed_mol, num_atoms,
|
||||
* label_mol, char_type_atoms, coords)
|
||||
*/
|
||||
|
||||
#include <stdio.h>
|
||||
|
||||
|
||||
int print_structure (const char *output, const int num_needed_mol, const int *needed_mol,
|
||||
const int num_atoms, const int *label_mol, const char *ch_type_atoms,
|
||||
const float *coords)
|
||||
/* output - output file name
|
||||
* num_needed_mol - number of needed molecules
|
||||
* needed_mol - massive of needed molecules
|
||||
* num_atoms - number of atoms
|
||||
* label_mol - massive of numbers of molecule for atoms
|
||||
* ch_type_atoms - massive of char types for atoms
|
||||
* coords - massive of coordinates
|
||||
*/
|
||||
{
|
||||
int cur_atom, cur_atom_num, cur_mol, i, j;
|
||||
FILE *f_out;
|
||||
/* cur_atom - current atom
|
||||
* cur_atom_num - true atom number
|
||||
* cur_mol - current molecule
|
||||
*/
|
||||
|
||||
cur_atom = 1;
|
||||
f_out = fopen (output, "w");
|
||||
|
||||
for (i=0; i<num_needed_mol; i++)
|
||||
for (j=0; j<8*num_atoms; j++)
|
||||
{
|
||||
if (j < num_atoms)
|
||||
{
|
||||
cur_mol = 0;
|
||||
cur_atom_num = j;
|
||||
}
|
||||
else
|
||||
{
|
||||
cur_mol = ((j - num_atoms) % 7) + 1;
|
||||
cur_atom_num = (j - num_atoms) / 7;
|
||||
}
|
||||
if (needed_mol[i] == (8*label_mol[j]+cur_mol))
|
||||
{
|
||||
fprintf(f_out, "ATOM %5i %c%c MOL %4i %8.3f%8.3f%8.3f\n", cur_atom,
|
||||
ch_type_atoms[2*cur_atom_num+0], ch_type_atoms[2*cur_atom_num+1],
|
||||
i+1, coords[3*j+0], coords[3*j+1], coords[3*j+2]);
|
||||
cur_atom++;
|
||||
}
|
||||
}
|
||||
|
||||
fclose (f_out);
|
||||
|
||||
return 0;
|
||||
}
|
||||
52
envir/src/set_center.c
Normal file
52
envir/src/set_center.c
Normal file
@ -0,0 +1,52 @@
|
||||
/* Library for search center mass of molecules
|
||||
*
|
||||
* Usage:
|
||||
* set_center (num_of_atoms, num_of_molecules, label_molecules, coords,
|
||||
* centr_coords)
|
||||
*/
|
||||
|
||||
|
||||
int set_center (const int num_atoms, const int num_mol, const int *label_mol,
|
||||
const float *coords, float *centr_coords)
|
||||
/* num_atoms - number of atoms for writing coordinates
|
||||
* num_mol - number of molecules for writing coordinates
|
||||
* label_mol - massive of numbers of molecule for atoms
|
||||
* coords - massive of coordinates
|
||||
* coords - massive of coordinates of center molecules
|
||||
*/
|
||||
{
|
||||
int at_in_mol, cur_mol, i, j, k;
|
||||
/* at_int_mol - number of atoms in molecule
|
||||
* cur_mol - current molecule
|
||||
*/
|
||||
|
||||
for (i=0; i<8*num_mol; i++)
|
||||
for (j=0; j<3; j++)
|
||||
centr_coords[i*3+j] = 0.0;
|
||||
|
||||
for (i=0; i<8*num_atoms; i++)
|
||||
{
|
||||
if (i < num_atoms)
|
||||
cur_mol = 0;
|
||||
else
|
||||
cur_mol = ((i - num_atoms) % 7) + 1;
|
||||
for (j=0; j<3; j++)
|
||||
centr_coords[3*(8*label_mol[i]+cur_mol)+j] += coords[3*i+j];
|
||||
}
|
||||
|
||||
at_in_mol = 0;
|
||||
cur_mol = 0;
|
||||
for (i=0; i<num_atoms; i++)
|
||||
if (cur_mol != label_mol[i])
|
||||
{
|
||||
for (j=0; j<8; j++)
|
||||
for (k=0; k<3; k++)
|
||||
centr_coords[3*(8*cur_mol+j)+k] = centr_coords[3*(8*cur_mol+j)+k] / at_in_mol;
|
||||
at_in_mol = 0;
|
||||
cur_mol = label_mol[i];
|
||||
}
|
||||
else
|
||||
at_in_mol++;
|
||||
|
||||
return 0;
|
||||
}
|
||||
Reference in New Issue
Block a user