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basic function structure for mmcif established
1 parent 54fa970 commit 1394751

16 files changed

Lines changed: 298 additions & 198 deletions

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‎ChangeLog‎

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,11 +3,17 @@
33
## Adaptation to R-compatible output and FunPDBe starts at version 2.0
44
## Development of Shiny App starts at version 3.0
55
## Docker image released at version 3.1
6+
## Added mmcif capability at version 3.4
67
#===============================================================================
78

9+
#_______________________________________________________________________________
10+
http://popscomp.org
11+
12+
#_______________________________________________________________________________
13+
814
- 3.4
915
Fri 20 Feb 11:18:33 GMT 2026
10-
Added mmcif capability.
16+
Added mmcif capability using the 'gemmi' cif reader.
1117

1218
- 3.3
1319
Thu 29 Feb 08:39:24 GMT 2024

‎POPSC/autom4te.cache/requests‎

Lines changed: 139 additions & 139 deletions
Large diffs are not rendered by default.

‎POPSC/config.log‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -12,9 +12,9 @@ generated by GNU Autoconf 2.71. Invocation command line was
1212

1313
hostname = ac
1414
uname -m = x86_64
15-
uname -r = 6.8.0-100-generic
15+
uname -r = 6.8.0-111-generic
1616
uname -s = Linux
17-
uname -v = #100-Ubuntu SMP PREEMPT_DYNAMIC Tue Jan 13 16:40:06 UTC 2026
17+
uname -v = #111-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 11 23:16:02 UTC 2026
1818

1919
/usr/bin/uname -p = x86_64
2020
/bin/uname -X = unknown
@@ -472,6 +472,7 @@ config.status:879: creating src/config.h
472472
config.status:1060: src/config.h is unchanged
473473
config.status:1108: executing depfiles commands
474474
config.status:1185: cd src && sed -e '/# am--include-marker/d' Makefile | make -f - am--depfiles
475+
make: Nothing to be done for 'am--depfiles'.
475476
config.status:1190: $? = 0
476477

477478
## ---------------- ##

‎POPSC/src/Makefile‎

Lines changed: 27 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -109,12 +109,12 @@ am__installdirs = "$(DESTDIR)$(bindir)"
109109
PROGRAMS = $(bin_PROGRAMS)
110110
am__dirstamp = $(am__leading_dot)dirstamp
111111
am_pops_OBJECTS = arg.$(OBJEXT) atomgroup.$(OBJEXT) cJSON.$(OBJEXT) \
112-
error.$(OBJEXT) fs.$(OBJEXT) getpdb.$(OBJEXT) \
113-
getpdbml.$(OBJEXT) gettraj.$(OBJEXT) json.$(OBJEXT) \
114-
matrix.$(OBJEXT) modstring.$(OBJEXT) pattern.$(OBJEXT) \
115-
pops.$(OBJEXT) putsasa.$(OBJEXT) putbsasa.$(OBJEXT) \
116-
putsigma.$(OBJEXT) safe.$(OBJEXT) sasa.$(OBJEXT) \
117-
sigma.$(OBJEXT) topol.$(OBJEXT) type.$(OBJEXT) \
112+
error.$(OBJEXT) fs.$(OBJEXT) getmmcif.$(OBJEXT) \
113+
getpdb.$(OBJEXT) getpdbml.$(OBJEXT) gettraj.$(OBJEXT) \
114+
json.$(OBJEXT) matrix.$(OBJEXT) modstring.$(OBJEXT) \
115+
pattern.$(OBJEXT) pops.$(OBJEXT) putsasa.$(OBJEXT) \
116+
putbsasa.$(OBJEXT) putsigma.$(OBJEXT) safe.$(OBJEXT) \
117+
sasa.$(OBJEXT) sigma.$(OBJEXT) topol.$(OBJEXT) type.$(OBJEXT) \
118118
vector.$(OBJEXT) cif_reader.$(OBJEXT) \
119119
../gemmi/src/mmcif.$(OBJEXT) ../gemmi/src/symmetry.$(OBJEXT) \
120120
../gemmi/src/polyheur.$(OBJEXT) ../gemmi/src/resinfo.$(OBJEXT)
@@ -142,14 +142,15 @@ am__depfiles_remade = ../gemmi/src/$(DEPDIR)/mmcif.Po \
142142
../gemmi/src/$(DEPDIR)/symmetry.Po ./$(DEPDIR)/arg.Po \
143143
./$(DEPDIR)/atomgroup.Po ./$(DEPDIR)/cJSON.Po \
144144
./$(DEPDIR)/cif_reader.Po ./$(DEPDIR)/error.Po \
145-
./$(DEPDIR)/fs.Po ./$(DEPDIR)/getpdb.Po \
146-
./$(DEPDIR)/getpdbml.Po ./$(DEPDIR)/gettraj.Po \
147-
./$(DEPDIR)/json.Po ./$(DEPDIR)/matrix.Po \
148-
./$(DEPDIR)/modstring.Po ./$(DEPDIR)/pattern.Po \
149-
./$(DEPDIR)/pops.Po ./$(DEPDIR)/putbsasa.Po \
150-
./$(DEPDIR)/putsasa.Po ./$(DEPDIR)/putsigma.Po \
151-
./$(DEPDIR)/safe.Po ./$(DEPDIR)/sasa.Po ./$(DEPDIR)/sigma.Po \
152-
./$(DEPDIR)/topol.Po ./$(DEPDIR)/type.Po ./$(DEPDIR)/vector.Po
145+
./$(DEPDIR)/fs.Po ./$(DEPDIR)/getmmcif.Po \
146+
./$(DEPDIR)/getpdb.Po ./$(DEPDIR)/getpdbml.Po \
147+
./$(DEPDIR)/gettraj.Po ./$(DEPDIR)/json.Po \
148+
./$(DEPDIR)/matrix.Po ./$(DEPDIR)/modstring.Po \
149+
./$(DEPDIR)/pattern.Po ./$(DEPDIR)/pops.Po \
150+
./$(DEPDIR)/putbsasa.Po ./$(DEPDIR)/putsasa.Po \
151+
./$(DEPDIR)/putsigma.Po ./$(DEPDIR)/safe.Po \
152+
./$(DEPDIR)/sasa.Po ./$(DEPDIR)/sigma.Po ./$(DEPDIR)/topol.Po \
153+
./$(DEPDIR)/type.Po ./$(DEPDIR)/vector.Po
153154
am__mv = mv -f
154155
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
155156
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
@@ -319,15 +320,15 @@ AM_CPPFLAGS = $(INTI_CFLAGS) $(XML_CFLAGS) $(ZLIB_CFLAGS) \
319320
AM_CFLAGS = -Wall -D_FORTIFY_SOURCE=2
320321
AM_CXXFLAGS = -Wall
321322
pops_SOURCES = arg.c arg.h argpdb.h atomgroup.c atomgroup.h \
322-
atomgroup_data.h cJSON.c cJSON.h error.c error.h fs.c fs.h \
323-
getpdb.c getpdb.h getpdbml.c getpdbml.h gettraj.c gettraj.h \
324-
json.c json.h matrix.c matrix.h modstring.c modstring.h \
325-
pattern.c pattern.h pdb_structure.h pops.c pops.h putsasa.c \
326-
putsasa.h putbsasa.c putbsasa.h putsigma.c putsigma.h safe.c \
327-
safe.h sasa.c sasa.h sasa_const.h sasa_data.h seq.h sigma.c \
328-
sigma.h sigma_const.h sigma_data.h topol.c topol.h type.c \
329-
type.h vector.c vector.h cif_reader.cpp cif_reader.h \
330-
../gemmi/src/mmcif.cpp ../gemmi/src/symmetry.cpp \
323+
atomgroup_data.h cif_header.h cJSON.c cJSON.h error.c error.h \
324+
fs.c fs.h getmmcif.c getmmcif.h getpdb.c getpdb.h getpdbml.c \
325+
getpdbml.h gettraj.c gettraj.h json.c json.h matrix.c matrix.h \
326+
modstring.c modstring.h pattern.c pattern.h pdb_structure.h \
327+
pops.c pops.h putsasa.c putsasa.h putbsasa.c putbsasa.h \
328+
putsigma.c putsigma.h safe.c safe.h sasa.c sasa.h sasa_const.h \
329+
sasa_data.h seq.h sigma.c sigma.h sigma_const.h sigma_data.h \
330+
topol.c topol.h type.c type.h vector.c vector.h cif_reader.cpp \
331+
cif_reader.h ../gemmi/src/mmcif.cpp ../gemmi/src/symmetry.cpp \
331332
../gemmi/src/polyheur.cpp ../gemmi/src/resinfo.cpp
332333

333334
# Force link with the C++ linker if any C++ objects are present
@@ -463,6 +464,7 @@ include ./$(DEPDIR)/cJSON.Po # am--include-marker
463464
include ./$(DEPDIR)/cif_reader.Po # am--include-marker
464465
include ./$(DEPDIR)/error.Po # am--include-marker
465466
include ./$(DEPDIR)/fs.Po # am--include-marker
467+
include ./$(DEPDIR)/getmmcif.Po # am--include-marker
466468
include ./$(DEPDIR)/getpdb.Po # am--include-marker
467469
include ./$(DEPDIR)/getpdbml.Po # am--include-marker
468470
include ./$(DEPDIR)/gettraj.Po # am--include-marker
@@ -659,6 +661,7 @@ distclean: distclean-am
659661
-rm -f ./$(DEPDIR)/cif_reader.Po
660662
-rm -f ./$(DEPDIR)/error.Po
661663
-rm -f ./$(DEPDIR)/fs.Po
664+
-rm -f ./$(DEPDIR)/getmmcif.Po
662665
-rm -f ./$(DEPDIR)/getpdb.Po
663666
-rm -f ./$(DEPDIR)/getpdbml.Po
664667
-rm -f ./$(DEPDIR)/gettraj.Po
@@ -731,6 +734,7 @@ maintainer-clean: maintainer-clean-am
731734
-rm -f ./$(DEPDIR)/cif_reader.Po
732735
-rm -f ./$(DEPDIR)/error.Po
733736
-rm -f ./$(DEPDIR)/fs.Po
737+
-rm -f ./$(DEPDIR)/getmmcif.Po
734738
-rm -f ./$(DEPDIR)/getpdb.Po
735739
-rm -f ./$(DEPDIR)/getpdbml.Po
736740
-rm -f ./$(DEPDIR)/gettraj.Po

‎POPSC/src/Makefile.am‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,9 +14,11 @@ AM_CXXFLAGS = -Wall
1414

1515
pops_SOURCES = \
1616
arg.c arg.h argpdb.h atomgroup.c atomgroup.h atomgroup_data.h \
17+
cif_header.h \
1718
cJSON.c cJSON.h \
1819
error.c error.h fs.c fs.h \
19-
getpdb.c getpdb.h getpdbml.c getpdbml.h gettraj.c gettraj.h \
20+
getmmcif.c getmmcif.h getpdb.c getpdb.h getpdbml.c getpdbml.h \
21+
gettraj.c gettraj.h \
2022
json.c json.h \
2123
matrix.c matrix.h modstring.c modstring.h \
2224
pattern.c pattern.h pdb_structure.h pops.c pops.h \

‎POPSC/src/Makefile.in‎

Lines changed: 27 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -109,12 +109,12 @@ am__installdirs = "$(DESTDIR)$(bindir)"
109109
PROGRAMS = $(bin_PROGRAMS)
110110
am__dirstamp = $(am__leading_dot)dirstamp
111111
am_pops_OBJECTS = arg.$(OBJEXT) atomgroup.$(OBJEXT) cJSON.$(OBJEXT) \
112-
error.$(OBJEXT) fs.$(OBJEXT) getpdb.$(OBJEXT) \
113-
getpdbml.$(OBJEXT) gettraj.$(OBJEXT) json.$(OBJEXT) \
114-
matrix.$(OBJEXT) modstring.$(OBJEXT) pattern.$(OBJEXT) \
115-
pops.$(OBJEXT) putsasa.$(OBJEXT) putbsasa.$(OBJEXT) \
116-
putsigma.$(OBJEXT) safe.$(OBJEXT) sasa.$(OBJEXT) \
117-
sigma.$(OBJEXT) topol.$(OBJEXT) type.$(OBJEXT) \
112+
error.$(OBJEXT) fs.$(OBJEXT) getmmcif.$(OBJEXT) \
113+
getpdb.$(OBJEXT) getpdbml.$(OBJEXT) gettraj.$(OBJEXT) \
114+
json.$(OBJEXT) matrix.$(OBJEXT) modstring.$(OBJEXT) \
115+
pattern.$(OBJEXT) pops.$(OBJEXT) putsasa.$(OBJEXT) \
116+
putbsasa.$(OBJEXT) putsigma.$(OBJEXT) safe.$(OBJEXT) \
117+
sasa.$(OBJEXT) sigma.$(OBJEXT) topol.$(OBJEXT) type.$(OBJEXT) \
118118
vector.$(OBJEXT) cif_reader.$(OBJEXT) \
119119
../gemmi/src/mmcif.$(OBJEXT) ../gemmi/src/symmetry.$(OBJEXT) \
120120
../gemmi/src/polyheur.$(OBJEXT) ../gemmi/src/resinfo.$(OBJEXT)
@@ -142,14 +142,15 @@ am__depfiles_remade = ../gemmi/src/$(DEPDIR)/mmcif.Po \
142142
../gemmi/src/$(DEPDIR)/symmetry.Po ./$(DEPDIR)/arg.Po \
143143
./$(DEPDIR)/atomgroup.Po ./$(DEPDIR)/cJSON.Po \
144144
./$(DEPDIR)/cif_reader.Po ./$(DEPDIR)/error.Po \
145-
./$(DEPDIR)/fs.Po ./$(DEPDIR)/getpdb.Po \
146-
./$(DEPDIR)/getpdbml.Po ./$(DEPDIR)/gettraj.Po \
147-
./$(DEPDIR)/json.Po ./$(DEPDIR)/matrix.Po \
148-
./$(DEPDIR)/modstring.Po ./$(DEPDIR)/pattern.Po \
149-
./$(DEPDIR)/pops.Po ./$(DEPDIR)/putbsasa.Po \
150-
./$(DEPDIR)/putsasa.Po ./$(DEPDIR)/putsigma.Po \
151-
./$(DEPDIR)/safe.Po ./$(DEPDIR)/sasa.Po ./$(DEPDIR)/sigma.Po \
152-
./$(DEPDIR)/topol.Po ./$(DEPDIR)/type.Po ./$(DEPDIR)/vector.Po
145+
./$(DEPDIR)/fs.Po ./$(DEPDIR)/getmmcif.Po \
146+
./$(DEPDIR)/getpdb.Po ./$(DEPDIR)/getpdbml.Po \
147+
./$(DEPDIR)/gettraj.Po ./$(DEPDIR)/json.Po \
148+
./$(DEPDIR)/matrix.Po ./$(DEPDIR)/modstring.Po \
149+
./$(DEPDIR)/pattern.Po ./$(DEPDIR)/pops.Po \
150+
./$(DEPDIR)/putbsasa.Po ./$(DEPDIR)/putsasa.Po \
151+
./$(DEPDIR)/putsigma.Po ./$(DEPDIR)/safe.Po \
152+
./$(DEPDIR)/sasa.Po ./$(DEPDIR)/sigma.Po ./$(DEPDIR)/topol.Po \
153+
./$(DEPDIR)/type.Po ./$(DEPDIR)/vector.Po
153154
am__mv = mv -f
154155
COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \
155156
$(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS)
@@ -319,15 +320,15 @@ AM_CPPFLAGS = $(INTI_CFLAGS) $(XML_CFLAGS) $(ZLIB_CFLAGS) \
319320
AM_CFLAGS = -Wall -D_FORTIFY_SOURCE=2
320321
AM_CXXFLAGS = -Wall
321322
pops_SOURCES = arg.c arg.h argpdb.h atomgroup.c atomgroup.h \
322-
atomgroup_data.h cJSON.c cJSON.h error.c error.h fs.c fs.h \
323-
getpdb.c getpdb.h getpdbml.c getpdbml.h gettraj.c gettraj.h \
324-
json.c json.h matrix.c matrix.h modstring.c modstring.h \
325-
pattern.c pattern.h pdb_structure.h pops.c pops.h putsasa.c \
326-
putsasa.h putbsasa.c putbsasa.h putsigma.c putsigma.h safe.c \
327-
safe.h sasa.c sasa.h sasa_const.h sasa_data.h seq.h sigma.c \
328-
sigma.h sigma_const.h sigma_data.h topol.c topol.h type.c \
329-
type.h vector.c vector.h cif_reader.cpp cif_reader.h \
330-
../gemmi/src/mmcif.cpp ../gemmi/src/symmetry.cpp \
323+
atomgroup_data.h cif_header.h cJSON.c cJSON.h error.c error.h \
324+
fs.c fs.h getmmcif.c getmmcif.h getpdb.c getpdb.h getpdbml.c \
325+
getpdbml.h gettraj.c gettraj.h json.c json.h matrix.c matrix.h \
326+
modstring.c modstring.h pattern.c pattern.h pdb_structure.h \
327+
pops.c pops.h putsasa.c putsasa.h putbsasa.c putbsasa.h \
328+
putsigma.c putsigma.h safe.c safe.h sasa.c sasa.h sasa_const.h \
329+
sasa_data.h seq.h sigma.c sigma.h sigma_const.h sigma_data.h \
330+
topol.c topol.h type.c type.h vector.c vector.h cif_reader.cpp \
331+
cif_reader.h ../gemmi/src/mmcif.cpp ../gemmi/src/symmetry.cpp \
331332
../gemmi/src/polyheur.cpp ../gemmi/src/resinfo.cpp
332333

333334
# Force link with the C++ linker if any C++ objects are present
@@ -463,6 +464,7 @@ distclean-compile:
463464
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/cif_reader.Po@am__quote@ # am--include-marker
464465
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/error.Po@am__quote@ # am--include-marker
465466
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/fs.Po@am__quote@ # am--include-marker
467+
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/getmmcif.Po@am__quote@ # am--include-marker
466468
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/getpdb.Po@am__quote@ # am--include-marker
467469
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/getpdbml.Po@am__quote@ # am--include-marker
468470
@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/gettraj.Po@am__quote@ # am--include-marker
@@ -659,6 +661,7 @@ distclean: distclean-am
659661
-rm -f ./$(DEPDIR)/cif_reader.Po
660662
-rm -f ./$(DEPDIR)/error.Po
661663
-rm -f ./$(DEPDIR)/fs.Po
664+
-rm -f ./$(DEPDIR)/getmmcif.Po
662665
-rm -f ./$(DEPDIR)/getpdb.Po
663666
-rm -f ./$(DEPDIR)/getpdbml.Po
664667
-rm -f ./$(DEPDIR)/gettraj.Po
@@ -731,6 +734,7 @@ maintainer-clean: maintainer-clean-am
731734
-rm -f ./$(DEPDIR)/cif_reader.Po
732735
-rm -f ./$(DEPDIR)/error.Po
733736
-rm -f ./$(DEPDIR)/fs.Po
737+
-rm -f ./$(DEPDIR)/getmmcif.Po
734738
-rm -f ./$(DEPDIR)/getpdb.Po
735739
-rm -f ./$(DEPDIR)/getpdbml.Po
736740
-rm -f ./$(DEPDIR)/gettraj.Po

‎POPSC/src/arg.c‎

Lines changed: 17 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -73,8 +73,11 @@ static void print_citation()
7373
/** set defaults */
7474
static void set_defaults(Arg *arg, Argpdb *argpdb)
7575
{
76+
arg->mmcifInFileName = "";
7677
arg->pdbInFileName = "";
7778
arg->pdbmlInFileName = "";
79+
arg->mmcif = 0;
80+
arg->pdb = 0;
7881
arg->pdbml = 0;
7982
arg->zipped = 0;
8083
arg->trajInFileName = 0; /* trajectory input file */
@@ -118,9 +121,12 @@ static void set_defaults(Arg *arg, Argpdb *argpdb)
118121
/** check input */
119122
static void check_input(Arg *arg, Argpdb *argpdb)
120123
{
121-
if ((strlen(arg->pdbInFileName) == 0) &&
124+
if ((strlen(arg->mmcifInFileName) == 0) &&
125+
(strlen(arg->pdbInFileName) == 0) &&
122126
(strlen(arg->pdbmlInFileName) == 0))
123127
Error("Invalid PDB file name");
128+
assert(arg->mmcif == 0 || arg->mmcif == 1);
129+
assert(arg->pdb == 0 || arg->pdb == 1);
124130
assert(arg->pdbml == 0 || arg->pdbml == 1);
125131
assert(arg->zipped == 0 || arg->zipped == 1);
126132
assert(argpdb->coarse == 0 || argpdb->coarse == 1);
@@ -162,7 +168,8 @@ static void print_args(Arg *arg, Argpdb *argpdb)
162168
time(&now);
163169

164170
if (! arg->silent) fprintf(stdout, "date: %s", ctime(&now));
165-
fprintf(stdout, "%s%s\n",
171+
fprintf(stdout, "%s%s%s\n",
172+
arg->mmcifInFileName,
166173
arg->pdbInFileName, arg->pdbmlInFileName);
167174
if (! arg->silent) fprintf(stdout, \
168175
"zipped: %d\n"
@@ -185,6 +192,7 @@ int parse_args(int argc, char **argv, Arg *arg, Argpdb *argpdb)
185192
const char usage[] = "\npops [--pdb ... | --pdbml ...] [OPTIONS ...]\n\
186193
INPUT OPTIONS\n\
187194
Input syntax is either '--pdb <name>.pdb[.gz]' or '--pdbml <name>.xml[.gz]'.\n\
195+
--mmcif <PDB input>\t\t(type: char , default: void)\n\
188196
--pdb <PDB input>\t\t(type: char , default: void)\n\
189197
--pdbml <PDBML input>\t(type: char , default: void)\n\
190198
--traj <trajectory input>\t(type: char , default: void)\n\
@@ -267,14 +275,15 @@ int parse_args(int argc, char **argv, Arg *arg, Argpdb *argpdb)
267275
{"pdbml", required_argument, 0, 30},
268276
{"zipped", no_argument, 0, 31},
269277
{"outDirName", required_argument, 0, 32},
278+
{"mmcif", required_argument, 0, 33},
270279
{"cite", no_argument, 0, 40},
271280
{"version", no_argument, 0, 41},
272281
{"help", no_argument, 0, 42},
273282
{0, 0, 0, 0}
274283
};
275284

276285
/** assign parameters to long options */
277-
while ((c = getopt_long(argc, argv, "1:2:3 4 5:6:7:8:9:10:11:12 13 14 15 16 17 18 19 20 21 22 23 24 25 26:27 28 29 30:31 32:40 41", long_options, NULL)) != -1) {
286+
while ((c = getopt_long(argc, argv, "1:2:3 4 5:6:7:8:9:10:11:12 13 14 15 16 17 18 19 20 21 22 23 24 25 26:27 28 29 30:31 32:33:40 41", long_options, NULL)) != -1) {
278287
switch(c) {
279288
case 1:
280289
arg->pdbInFileName = optarg;
@@ -374,6 +383,11 @@ int parse_args(int argc, char **argv, Arg *arg, Argpdb *argpdb)
374383
case 32:
375384
arg->outDirName = optarg;
376385
break;
386+
case 33:
387+
arg->mmcifInFileName = optarg;
388+
arg->pdbIn = basename(optarg);
389+
arg->mmcif = 1;
390+
break;
377391
case 40:
378392
print_citation();
379393
exit(0);

‎POPSC/src/arg.h‎

Lines changed: 3 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -25,9 +25,12 @@ Read the COPYING file for license information.
2525
typedef struct
2626
{
2727
FILE *pdbInFile;
28+
char *mmcifInFileName;
2829
char *pdbInFileName;
2930
char *pdbmlInFileName;
3031
char *pdbIn;
32+
int mmcif;
33+
int pdb;
3134
int pdbml;
3235
int zipped;
3336
FILE *trajInFile;

‎POPSC/src/cif_reader.cpp‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
/*==============================================================================
22
cif_reader.cpp : C++ code to process mmcif structures
3+
34
Copyright (C) 2026 Jens Kleinjung
45
Read the COPYING file for license information.
56
==============================================================================*/

‎POPSC/src/cif_reader.h‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
/*==============================================================================
2-
cif_header.h : wrapper header to use C++ functions from 'gemma'
2+
cif_reader.h : wrapper header to use C++ functions from 'gemmi'
3+
The 'gemmi' library provides functions for the now default mmcif format.
34
Copyright (C) 2026 Jens Kleinjung
45
Read the COPYING file for license information.
56
==============================================================================*/

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