[med-svn] [Git][med-team/king-probe][master] 8 commits: Imported Upstream version 2.13.110909
Andreas Tille
gitlab at salsa.debian.org
Mon Jul 16 08:11:31 BST 2018
Andreas Tille pushed to branch master at Debian Med / king-probe
Commits:
1d994832 by Malihe Asemani at 2015-08-18T06:09:37+00:00
Imported Upstream version 2.13.110909
- - - - -
3e8d58d1 by Andreas Tille at 2018-07-16T09:06:51+02:00
Use git mode in watch file
- - - - -
20a3bbc0 by Andreas Tille at 2018-07-16T09:07:30+02:00
New upstream version 2.16.160404+git20180613.a09b012
- - - - -
b99a47a8 by Andreas Tille at 2018-07-16T09:07:31+02:00
Update upstream source from tag 'upstream/2.16.160404+git20180613.a09b012'
Update to upstream version '2.16.160404+git20180613.a09b012'
with Debian dir c9f5489f654e41cc81dfb1230c5645f3dd51d264
- - - - -
856d0ca9 by Andreas Tille at 2018-07-16T09:08:27+02:00
debhelper 11
- - - - -
254e4121 by Andreas Tille at 2018-07-16T09:08:29+02:00
Point Vcs fields to salsa.debian.org
- - - - -
a4babbab by Andreas Tille at 2018-07-16T09:08:29+02:00
Standards-Version: 4.1.5
- - - - -
44f543a4 by Andreas Tille at 2018-07-16T09:09:27+02:00
Upload to unstable
- - - - -
20 changed files:
- .gitignore
- Makefile
- Makefile.macOSX
- README.probe.txt
- abin.h
- atomprops.c
- atomprops.h
- command_line/probe.launch
- debian/changelog
- debian/compat
- debian/control
- debian/watch
- parse.c
- parse.h
- probe.c
- probe.h
- readPDBrecs.c
- select.c
- select.h
- stdconntable.c
Changes:
=====================================
.gitignore
=====================================
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,2 @@
*~
-*.o
-.pc
\ No newline at end of file
+*.o
\ No newline at end of file
=====================================
Makefile
=====================================
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
MACHINEFLAGS =
CFLAGS = $(MACHINEFLAGS)
-LFLAGS = -static -lm $(MACHINEFLAGS)
+LFLAGS = -lm $(MACHINEFLAGS)
OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \
parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o
=====================================
Makefile.macOSX
=====================================
--- a/Makefile.macOSX
+++ b/Makefile.macOSX
@@ -1,29 +1,20 @@
-# This Makefile for Probe was adopted from the gcc makefile, it will
-# generate a MACH-O file containing any mixture of MacOSX 32 bit
-# ( -arch i386 or -arch ppc) or MacOSX 64 bit ( -arch x86_64 or -arch ppc64 )
-# executables. It is up to the user of the makefile to choose which flags
-# are appropriate; but as a reminder, 10.7 is only intel 64 bit, 10.6 is only
-# intel.
-# When using a compiler from a later OS to compile against an earlier SDK,
-# minimum OS flag will need to be added after the arch flag(s). So for
-# compilation of a Snow Leopard ( 10.6 ) executable on a Lion ( 10.7 ) OS
-# computer, one should use the MacOSX10.6.sdk, the arch flag(s) i386 and/or
-# x86_64, AND a "MINOS = -mmacosx-version-min=10.6"
-
-
-ARCHFLAGi32 = -arch i386
-ARCHFLAGi64 = -arch x86_64
-ARCHFLAGp31 = -arch ppc
-ARCHFLAGp64 = -arch ppc64
-MINOS =
-# MINOS = -mmacosx-version-min=10.5
-# MINOS = -mmacosx-version-min=10.6
-
-CFLAGS = -isysroot /Developer/SDKs/MacOSX10.7.sdk $(ARCHFLAGi64) $(MINOS)
-LFLAGS = -lm -Wl,-syslibroot,/Developer/SDKs/MacOSX10.7.sdk $(ARCHFLAGi64) $(MINOS)
-
-OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \
- parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o
+# Probe Makefile for Mac OS X 10.8.x (Mountain Lion).
+# Uses 10.8 SDK with compiler flag declaring exec to be backward compatible
+# to Mac OS X 10.6 (Snow Leopard); -mmacosx-version-min=10.6
+# Either (or both) Intel architecture flags can be used: -arch i386 to create
+# a 32bit MACH-O exec, -arch x86_64 to create a 64bit MACH-O exec.
+
+# Either copy the Makefile.macOSX to Makefile to run the standard make command;
+# or use 'make -f Makefile.macOSX'.
+
+MIN_OS = -mmacosx-version-min=10.6
+SDK_HOME = /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk
+MACHINEFLAGS = -arch x86_64
+CFLAGS = -isysroot $(SDK_HOME) $(MACHINEFLAGS) $(MIN_OS)
+LFLAGS = -lm -Wl,-syslibroot,$(SDK_HOME) $(MACHINEFLAGS) $(MIN_OS)
+OBJLIST = dots.o select.o readPDBrecs.o geom3d.o stdconntable.o \
+ abin.o parse.o atomprops.o utility.o autobondrot.o \
+ hybrid_36_c.o
.c.o:
cc -c $*.c $(CFLAGS)
@@ -35,26 +26,26 @@ clean:
@rm -f *.o *.ckp
install: probe
- mv probe /local/bin
+ mv probe /usr/local/bin
installtest: probe
- mv probe /local/bin/probeTest
+ mv probe /usr/local/bin/probeTest
# DO NOT DELETE THIS LINE -- make depend uses it
-abin.o: abin.h geom3d.h utility.h abin.c
-atomprops.o: atomprops.h atomprops.c
-autobondrot.o: abin.h autobondrot.h geom3d.h readPDBrecs.h \
- utility.h autobondrot.c
-dots.o: dots.h geom3d.h dots.c
-geom3d.o: geom3d.h geom3d.c
-parse.o: parse.h utility.h parse.c
-probe.o: abin.h atomprops.h autobondrot.h dots.h geom3d.h \
- parse.h probe.h readPDBrecs.h select.h \
- stdconntable.h utility.h probe.c
-readPDBrecs.o: geom3d.h readPDBrecs.h utility.h readPDBrecs.c
-select.o: abin.h atomprops.h geom3d.h parse.h select.h \
- stdconntable.h utility.h select.c
-stdconntable.o: stdconntable.h stdconntable.c
+abin.o: ./abin.h ./geom3d.h ./utility.h abin.c
+atomprops.o: ./atomprops.h atomprops.c
+autobondrot.o: ./abin.h ./autobondrot.h ./geom3d.h ./readPDBrecs.h \
+ ./utility.h autobondrot.c
+dots.o: ./dots.h ./geom3d.h dots.c
+geom3d.o: ./geom3d.h geom3d.c
+parse.o: ./parse.h ./utility.h parse.c
+probe.o: ./abin.h ./atomprops.h ./autobondrot.h ./dots.h ./geom3d.h \
+ ./parse.h ./probe.h ./readPDBrecs.h ./select.h \
+ ./stdconntable.h ./utility.h probe.c
+readPDBrecs.o: ./geom3d.h ./readPDBrecs.h ./utility.h readPDBrecs.c
+select.o: ./abin.h ./atomprops.h ./geom3d.h ./parse.h ./select.h \
+ ./stdconntable.h ./utility.h select.c
+stdconntable.o: ./stdconntable.h stdconntable.c
utility.o: utility.c
-hybrid_36_c.o: hybrid_36_c.h hybrid_36_c.c
+hybrid_36_c.o: ./hybrid_36_c.h hybrid_36_c.c
# DO NOT DELETE THIS 2nd LINE -- make depend uses it
=====================================
README.probe.txt
=====================================
--- a/README.probe.txt
+++ b/README.probe.txt
@@ -43,6 +43,11 @@ v2.5 (7/25/01) - Selections can now refer to negative residue numbers.
space to prevent the selection from being treated as
a command line option.)
+v2.6 (10/28/2011) - Introduced the -condense flag, which when used with the -u option
+ will give one line per source atom - target atom pair. Also it will give
+ the number of dots in that interaction, as an additional column.
+ (Changes made by Swati Jain)
+
USAGE:
Probe was designed for UNIX and the commands described below follow the
UNIX conventions. For a brief description of probe features, run "probe"
@@ -116,6 +121,10 @@ Even more dot information for each dot can be tabulated with -unformated
probe -unformated -self "all" mypdbH > rawinfo.table
+If you need just one line/sot per source atom - target atom pair, use -condense
+
+ probe -unformated -condense -self -mc MC mypdbH > reducedinfo.table
+
You can create surface dots
probe -out all 1filH.pdb >> surfacedots.kin
=====================================
abin.h
=====================================
--- a/abin.h
+++ b/abin.h
@@ -88,7 +88,7 @@ typedef struct residue_t {
char resname[5]; /* residue name */
char resInsCode; /* insertion code */
- char chain[3]; /* peptide chain code */
+ char chain[5]; /* peptide chain code */
} residue, *residuePtr;
typedef struct {
=====================================
atomprops.c
=====================================
--- a/atomprops.c
+++ b/atomprops.c
@@ -22,10 +22,12 @@ static atomProp* AtomTblIndex[NUMATOMTYPES];
static float ExplMaxRad = 0.0;
static float ImplMaxRad = 0.0;
+extern int NuclearRadii; /* defined in probe.c JJH */
+
void initalizeAtomTbl() {
int i;
atomProp *ap;
-
+
ExplMaxRad = 0.0;
ImplMaxRad = 0.0;
for(i=0; i < NUMATOMTYPES; i++) { /* default to noAtom */
@@ -36,14 +38,32 @@ void initalizeAtomTbl() {
ap = &(AtomTbl[i]);
AtomTblIndex[ap->type] = ap;
- if (ap->iRad > ImplMaxRad){ ImplMaxRad = ap->iRad; }
- if (ap->eRad > ExplMaxRad){ ExplMaxRad = ap->eRad; }
+ if (ap->iRad > ImplMaxRad){ ImplMaxRad = ap->iRad; }
+ if (!NuclearRadii) {
+ if (ap->eRad > ExplMaxRad){ ExplMaxRad = ap->eRad; }
+ }
+ else {
+ if (ap->eRad_nuc > ExplMaxRad){ ExplMaxRad = ap->eRad_nuc; }
+ }
}
}
int getAtno(int a) { return AtomTblIndex[a]->atno; }
char* getAtomName(int a) { return AtomTblIndex[a]->name; }
-float getExplRad(int a) { return AtomTblIndex[a]->eRad; }
+float getExplRad(int a) {
+ if (NuclearRadii) {
+ /*if ( (strcmp(AtomTblIndex[a]->name, "H") == 0) ||
+ (strcmp(AtomTblIndex[a]->name, "Har") == 0) ||
+ (strcmp(AtomTblIndex[a]->name, "Hpol") == 0) ||
+ (strcmp(AtomTblIndex[a]->name, "HOd") == 0) ) {
+ return ( (AtomTblIndex[a]->eRad - 0.05) );
+ }*/
+ return AtomTblIndex[a]->eRad_nuc;
+ }
+ else {
+ return AtomTblIndex[a]->eRad;
+ }
+}
float getImplRad(int a) { return AtomTblIndex[a]->iRad; }
float getCovRad(int a) { return AtomTblIndex[a]->covRad; }
char* getColor(int a) { return AtomTblIndex[a]->color; }
@@ -61,7 +81,7 @@ int fixAtomName(const char* atomname, char resname[], int position) { /* no bool
sprintf(resn, ":%-3.3s:", resname);
for (i = 0; i < 4; i++) { /* uppercase the input */
if (atomname[i] == '\0') { break; }
- name[i] = toupper(atomname[i]);
+ name[i] = toupper(atomname[i]);
}
name[i] = '\0';
switch(name[position]) {
@@ -72,7 +92,7 @@ int fixAtomName(const char* atomname, char resname[], int position) { /* no bool
case 'S': if (strstr(HS_RESNAMES, resn) != NULL) { return 1; }
default: break;
}
- return 0;
+ return 0;
}
int identifyAtom(char* name, char resname[], int Verbose) { /*dcr041007 allow warning choice*/
@@ -95,7 +115,7 @@ int identifyAtom(char* name, char resname[], int Verbose) { /*dcr041007 allow w
case 'F': n = atomF; break;
case 'H':
switch(name[2]) {
- case 'E': n = fixAtomName(name,resname,2) ? atomHe : atomH; break;
+ case 'E': n = fixAtomName(name,resname,2) ? atomHe : atomH; break;
case 'F': n = fixAtomName(name,resname,2) ? atomHf : atomH; break;
case 'G': n = fixAtomName(name,resname,2) ? atomHg : atomH; break;
case 'O': n = fixAtomName(name,resname,2) ? atomHo : atomH; break;
@@ -108,8 +128,8 @@ int identifyAtom(char* name, char resname[], int Verbose) { /*dcr041007 allow w
case 'O': n = atomO; break;
case 'P': n = atomP; break;
/*case 'S': n = atomS; break;*/
- case 'S':
- if(name[0] == ' ' && name[2] == 'E')
+ case 'S':
+ if(name[0] == ' ' && name[2] == 'E')
{/*_SE likely refmac,cns missplaced Selenium atom name dcr041007*/
n = atomSe; emitWarning = 1; break;
}
@@ -142,7 +162,7 @@ int identifyAtom(char* name, char resname[], int Verbose) { /*dcr041007 allow w
case 'K': n = atomBk; break;
case 'R': n = atomBr; break;
} break;
- case 'C':
+ case 'C':
switch(name[1]) {
case 'A': n = atomCa; break;
case 'C': n = atomC; emitWarning = 1;break;
=====================================
atomprops.h
=====================================
--- a/atomprops.h
+++ b/atomprops.h
@@ -31,14 +31,15 @@
"currently there are none RMI 070711"
typedef struct atomProp_t {
- int type; /* atom identifier */
- int atno; /* atomic number */
- char* name; /* atom name */
- float eRad; /* (explicit H) VDW radius */
- float iRad; /* (implicit H) VDW radius */
- float covRad;/* covalent radius */
- char* color; /* dot color */
- int flags; /* element features */
+ int type; /* atom identifier */
+ int atno; /* atomic number */
+ char* name; /* atom name */
+ float eRad; /* (explicit H) ecloud VDW radius */
+ float eRad_nuc; /* (explicit H) nuclear VDW radius */
+ float iRad; /* (implicit H) VDW radius */
+ float covRad; /* covalent radius */
+ char* color; /* dot color */
+ int flags; /* element features */
} atomProp;
void initalizeAtomTbl(void);
@@ -60,7 +61,7 @@ int atomHasProp(int a, int f);
enum atomIdentifiers {
noAtom=0, ignoreAtom,
atomH, atomHarom, atomHpolar, atomHOd,
- atomC, atomN, atomO, atomF, atomS, atomP,
+ atomC, atomCarom, atomN, atomO, atomF, atomS, atomP,
atomAc, atomAg, atomAl, atomAm, atomAr, atomAs, atomAt, atomAu,
atomB, atomBa, atomBe, atomBi, atomBk, atomBr, atomCa, atomCd,
@@ -84,6 +85,7 @@ enum atomIdentifiers {
};
#define isHatom(atype) (getAtno(atype) == 1)
+#define isCatom(atype) (getAtno(atype) == 6)
#define NUMATOMTYPES endAtomTypes
#define COVRADFUDGE 0.2
@@ -100,76 +102,78 @@ enum atomIdentifiers {
/* Advanced Inorganic Chemistry, Cotton & Wilkinson, 1962, p93. */
/* from above: struct atomProp, NUMATOMTYPES from enum of atomIdentifiers*/
- /*type; atom identifier */
- /*atno; atomic number */
- /*name; atom name */
- /*eRad; (explicit H) VDW radius */
- /*iRad; (implicit H) VDW radius */
- /*covRad; covalent radius */
- /*color; dot color */
- /*flags; element features */
+ /*type; atom identifier */
+ /*atno; atomic number */
+ /*name; atom name */
+ /*eRad; (explicit H) ecloud VDW radius */
+ /*eRad_nuc; (explicit H) nuclear VDW radius */ //jjh 130307
+ /*iRad; (implicit H) VDW radius */
+ /*covRad; covalent radius */
+ /*color; dot color */
+ /*flags; element features */
atomProp AtomTbl[NUMATOMTYPES] = { /* noAtom must be first */
- {noAtom, 0, "?", 1.00, 0.00, 0.00, "magenta", 0},
- {ignoreAtom, 0, ".", 0.00, 0.00, 0.00, "grey", 0},
-
- {atomH, 1, "H", 1.17, 0.00, 0.30, "grey", 0},
- {atomHarom, 1, "Har", 1.00, 0.00, 0.30, "grey", 0},
- {atomHpolar, 1, "Hpol", 1.00, 0.00, 0.30, "grey", 0},
- {atomHOd, 1, "HOd", 1.00, 0.00, 0.30, "grey", 0},/*hb-only-dummy*/
- {atomC, 6, "C", 1.75, 1.90, 0.77, "white", 0},
- {atomN, 7, "N", 1.55, 1.70, 0.70, "sky", 0},
- {atomO, 8, "O", 1.40, 1.50, 0.66, "red", 0},
- {atomP, 15, "P", 1.80, 1.80, 1.10, "pink", 0},
- {atomS, 16, "S", 1.80, 1.90, 1.04, "yellow", 0},
- {atomAs, 33, "As", 2.00, 2.10, 1.21, "grey", 0},
- {atomSe, 34, "Se", 1.90, 2.00, 1.17, "green", 0},
+ {noAtom, 0, "?", 1.05, 1.05, 0.00, 0.00, "magenta", 0},
+ {ignoreAtom, 0, ".", 0.00, 0.00, 0.00, 0.00, "grey", 0},
+
+ {atomH, 1, "H", 1.22, 1.17, 0.00, 0.30, "grey", 0},
+ {atomHarom, 1, "Har", 1.05, 1.00, 0.00, 0.30, "grey", 0},
+ {atomHpolar, 1, "Hpol", 1.05, 1.00, 0.00, 0.30, "grey", 0},
+ {atomHOd, 1, "HOd", 1.05, 1.00, 0.00, 0.30, "grey", 0},/*hb-only-dummy*/
+ {atomC, 6, "C", 1.70, 1.70, 1.90, 0.77, "white", 0},
+ {atomCarom, 6, "Car", 1.75, 1.75, 1.90, 0.77, "white", 0},
+ {atomN, 7, "N", 1.55, 1.55, 1.70, 0.70, "sky", 0},
+ {atomO, 8, "O", 1.40, 1.40, 1.50, 0.66, "red", 0},
+ {atomP, 15, "P", 1.80, 1.80, 1.80, 1.10, "pink", 0},
+ {atomS, 16, "S", 1.80, 1.80, 1.90, 1.04, "yellow", 0},
+ {atomAs, 33, "As", 2.00, 2.00, 2.10, 1.21, "grey", 0},
+ {atomSe, 34, "Se", 1.90, 1.90, 2.00, 1.17, "green", 0},
/*dcr041007 halides given IONIC_ATOM_FLAG*/
- {atomF, 9, "F", 1.30, 1.30, 0.58, "green", IONIC_ATOM_FLAG},
- {atomCl, 17, "Cl", 1.77, 1.77, 0.99, "green", IONIC_ATOM_FLAG},
- {atomBr, 35, "Br", 1.95, 1.95, 1.14, "brown", IONIC_ATOM_FLAG},
- {atomI, 53, "I", 2.10, 2.10, 1.33, "brown", IONIC_ATOM_FLAG},
+ {atomF, 9, "F", 1.30, 1.30, 1.30, 0.58, "green", IONIC_ATOM_FLAG},
+ {atomCl, 17, "Cl", 1.77, 1.77, 1.77, 0.99, "green", IONIC_ATOM_FLAG},
+ {atomBr, 35, "Br", 1.95, 1.95, 1.95, 1.14, "brown", IONIC_ATOM_FLAG},
+ {atomI, 53, "I", 2.10, 2.10, 2.10, 1.33, "brown", IONIC_ATOM_FLAG},
/* for most common metals we use Pauling's ionic radii */
/* "covalent radii" = ionic + 0.74 (i.e., oxygenVDW(1.4) - oxygenCov(0.66)) */
/* because the ionic radii are usually calculated from Oxygen-Metal distance */
- {atomLi, 3, "Li", 0.60, 0.60, 1.34, "grey", METALIC_ATOM_FLAG},
- {atomNa, 11, "Na", 0.95, 0.95, 1.69, "grey", METALIC_ATOM_FLAG},
- {atomAl, 13, "Al", 0.50, 0.50, 1.24, "grey", METALIC_ATOM_FLAG},
- {atomK, 19, "K", 1.33, 1.33, 2.07, "grey", METALIC_ATOM_FLAG},
- {atomMg, 12, "Mg", 0.65, 0.65, 1.39, "grey", METALIC_ATOM_FLAG},
- {atomCa, 20, "Ca", 0.99, 0.99, 1.73, "grey", METALIC_ATOM_FLAG},
- {atomMn, 25, "Mn", 0.80, 0.80, 1.54, "grey", METALIC_ATOM_FLAG},
- {atomFe, 26, "Fe", 0.74, 0.74, 1.48, "grey", METALIC_ATOM_FLAG},
- {atomCo, 27, "Co", 0.70, 0.70, 1.44, "blue", METALIC_ATOM_FLAG},
- {atomNi, 28, "Ni", 0.66, 0.66, 1.40, "grey", METALIC_ATOM_FLAG},
- {atomCu, 29, "Cu", 0.72, 0.72, 1.46,"orange",METALIC_ATOM_FLAG},
- {atomZn, 30, "Zn", 0.71, 0.71, 1.45, "grey", METALIC_ATOM_FLAG},
- {atomRb, 37, "Rb", 1.48, 1.48, 2.22, "grey", METALIC_ATOM_FLAG},
- {atomSr, 38, "Sr", 1.10, 1.10, 1.84, "grey", METALIC_ATOM_FLAG},
- {atomMo, 42, "Mo", 0.93, 0.93, 1.67, "grey", METALIC_ATOM_FLAG},
- {atomAg, 47, "Ag", 1.26, 1.26, 2.00, "white",METALIC_ATOM_FLAG},
- {atomCd, 48, "Cd", 0.91, 0.91, 1.65, "grey", METALIC_ATOM_FLAG},
- {atomIn, 49, "In", 0.81, 0.81, 1.55, "grey", METALIC_ATOM_FLAG},
- {atomCs, 55, "Cs", 1.69, 1.69, 2.43, "grey", METALIC_ATOM_FLAG},
- {atomBa, 56, "Ba", 1.29, 1.29, 2.03, "grey", METALIC_ATOM_FLAG},
- {atomAu, 79, "Au", 1.10, 1.10, 1.84, "gold", METALIC_ATOM_FLAG},
- {atomHg, 80, "Hg", 1.00, 1.00, 1.74, "grey", METALIC_ATOM_FLAG},
- {atomTl, 81, "Tl", 1.44, 1.44, 2.18, "grey", METALIC_ATOM_FLAG},
- {atomPb, 82, "Pb", 0.84, 0.84, 1.58, "grey", METALIC_ATOM_FLAG},
+ {atomLi, 3, "Li", 0.60, 0.60, 0.60, 1.34, "grey", METALIC_ATOM_FLAG},
+ {atomNa, 11, "Na", 0.95, 0.95, 0.95, 1.69, "grey", METALIC_ATOM_FLAG},
+ {atomAl, 13, "Al", 0.50, 0.50, 0.50, 1.24, "grey", METALIC_ATOM_FLAG},
+ {atomK, 19, "K", 1.33, 1.33, 1.33, 2.07, "grey", METALIC_ATOM_FLAG},
+ {atomMg, 12, "Mg", 0.65, 0.65, 0.65, 1.39, "grey", METALIC_ATOM_FLAG},
+ {atomCa, 20, "Ca", 0.99, 0.99, 0.99, 1.73, "grey", METALIC_ATOM_FLAG},
+ {atomMn, 25, "Mn", 0.80, 0.80, 0.80, 1.54, "grey", METALIC_ATOM_FLAG},
+ {atomFe, 26, "Fe", 0.74, 0.74, 0.74, 1.48, "grey", METALIC_ATOM_FLAG},
+ {atomCo, 27, "Co", 0.70, 0.70, 0.70, 1.44, "blue", METALIC_ATOM_FLAG},
+ {atomNi, 28, "Ni", 0.66, 0.66, 0.66, 1.40, "grey", METALIC_ATOM_FLAG},
+ {atomCu, 29, "Cu", 0.72, 0.72, 0.72, 1.46,"orange",METALIC_ATOM_FLAG},
+ {atomZn, 30, "Zn", 0.71, 0.71, 0.71, 1.45, "grey", METALIC_ATOM_FLAG},
+ {atomRb, 37, "Rb", 1.48, 1.48, 1.48, 2.22, "grey", METALIC_ATOM_FLAG},
+ {atomSr, 38, "Sr", 1.10, 1.10, 1.10, 1.84, "grey", METALIC_ATOM_FLAG},
+ {atomMo, 42, "Mo", 0.93, 0.93, 0.93, 1.67, "grey", METALIC_ATOM_FLAG},
+ {atomAg, 47, "Ag", 1.26, 1.26, 1.26, 2.00, "white",METALIC_ATOM_FLAG},
+ {atomCd, 48, "Cd", 0.91, 0.91, 0.91, 1.65, "grey", METALIC_ATOM_FLAG},
+ {atomIn, 49, "In", 0.81, 0.81, 0.81, 1.55, "grey", METALIC_ATOM_FLAG},
+ {atomCs, 55, "Cs", 1.69, 1.69, 1.69, 2.43, "grey", METALIC_ATOM_FLAG},
+ {atomBa, 56, "Ba", 1.29, 1.29, 1.29, 2.03, "grey", METALIC_ATOM_FLAG},
+ {atomAu, 79, "Au", 1.10, 1.10, 1.10, 1.84, "gold", METALIC_ATOM_FLAG},
+ {atomHg, 80, "Hg", 1.00, 1.00, 1.00, 1.74, "grey", METALIC_ATOM_FLAG},
+ {atomTl, 81, "Tl", 1.44, 1.44, 1.44, 2.18, "grey", METALIC_ATOM_FLAG},
+ {atomPb, 82, "Pb", 0.84, 0.84, 0.84, 1.58, "grey", METALIC_ATOM_FLAG},
/* for other metals we use Shannon's ionic radii */
/* Acta Crystallogr. (1975) A32, pg751. */
- {atomV, 23, "V", 0.79, 0.79, 1.53, "grey", METALIC_ATOM_FLAG},
- {atomCr, 24, "Cr", 0.73, 0.73, 1.47, "grey", METALIC_ATOM_FLAG},
- {atomTe, 52, "Te", 0.97, 0.97, 1.71, "grey", METALIC_ATOM_FLAG},
- {atomSm, 62, "Sm", 1.08, 1.08, 1.82, "grey", METALIC_ATOM_FLAG},
- {atomGd, 64, "Gd", 1.05, 1.05, 1.79, "grey", METALIC_ATOM_FLAG},
- {atomYb, 70, "Yb", 1.14, 1.14, 1.88, "grey", METALIC_ATOM_FLAG},
- {atomW, 74, "W", 0.66, 0.66, 1.40, "grey", METALIC_ATOM_FLAG},
- {atomPt, 78, "Pt", 0.63, 0.63, 1.37, "grey", METALIC_ATOM_FLAG},
- {atomU, 92, "U", 1.03, 1.03, 1.77, "grey", METALIC_ATOM_FLAG},
+ {atomV, 23, "V", 0.79, 0.79, 0.79, 1.53, "grey", METALIC_ATOM_FLAG},
+ {atomCr, 24, "Cr", 0.73, 0.73, 0.73, 1.47, "grey", METALIC_ATOM_FLAG},
+ {atomTe, 52, "Te", 0.97, 0.97, 0.97, 1.71, "grey", METALIC_ATOM_FLAG},
+ {atomSm, 62, "Sm", 1.08, 1.08, 1.08, 1.82, "grey", METALIC_ATOM_FLAG},
+ {atomGd, 64, "Gd", 1.05, 1.05, 1.05, 1.79, "grey", METALIC_ATOM_FLAG},
+ {atomYb, 70, "Yb", 1.14, 1.14, 1.14, 1.88, "grey", METALIC_ATOM_FLAG},
+ {atomW, 74, "W", 0.66, 0.66, 0.66, 1.40, "grey", METALIC_ATOM_FLAG},
+ {atomPt, 78, "Pt", 0.63, 0.63, 0.63, 1.37, "grey", METALIC_ATOM_FLAG},
+ {atomU, 92, "U", 1.03, 1.03, 1.03, 1.77, "grey", METALIC_ATOM_FLAG},
/* Cotton & Wilkinson and also- */
/* L.E. Sutton (ed.) in Table of interatomic distances and configuration in molecules */
@@ -177,74 +181,74 @@ atomProp AtomTbl[NUMATOMTYPES] = { /* noAtom must be first */
/* London, UK, 1965 (as listed in web-elements by Mark Winter) */
/* http://www.shef.ac.uk/chemistry/web-elements */
- {atomHe, 2, "He", 1.60, 1.60, 0.00, "sky", 0},
- {atomBe, 4, "Be", 0.31, 0.31, 0.90, "grey", METALIC_ATOM_FLAG},
- {atomB, 5, "B", 0.20, 0.20, 0.86, "grey", 0},
- {atomNe, 10, "Ne", 1.60, 1.60, 0.00, "pink", 0},
- {atomSi, 14, "Si", 2.10, 2.10, 1.17, "grey", METALIC_ATOM_FLAG},
- {atomAr, 18, "Ar", 1.89, 1.89, 0.00, "orange", 0},
- {atomSc, 21, "Sc", 0.68, 0.68, 0.44, "grey", METALIC_ATOM_FLAG},
- {atomTi, 22, "Ti", 0.75, 0.75, 1.49, "grey", METALIC_ATOM_FLAG},
- {atomGa, 31, "Ga", 0.53, 0.53, 1.27, "grey", METALIC_ATOM_FLAG},
- {atomGe, 32, "Ge", 0.60, 0.60, 1.34, "grey", METALIC_ATOM_FLAG},
- {atomKr, 36, "Kr", 2.01, 2.01, 1.15, "greentint", 0},
- {atomY, 39, "Y", 0.90, 0.90, 1.64, "grey", METALIC_ATOM_FLAG},
- {atomZr, 40, "Zr", 0.77, 0.77, 1.51, "grey", METALIC_ATOM_FLAG},
- {atomSn, 50, "Sn", 0.71, 0.71, 1.45, "grey", METALIC_ATOM_FLAG},
- {atomSb, 51, "Sb", 2.20, 2.20, 1.41, "grey", METALIC_ATOM_FLAG},
- {atomXe, 54, "Xe", 2.18, 2.18, 1.28, "magenta", 0},
- {atomLa, 57, "La", 1.03, 1.03, 1.77, "grey", METALIC_ATOM_FLAG},
- {atomCe, 58, "Ce", 0.87, 0.87, 1.61, "grey", METALIC_ATOM_FLAG},
- {atomFr, 87, "Fr", 1.94, 1.94, 2.68, "grey", METALIC_ATOM_FLAG},
- {atomRa, 88, "Ra", 1.62, 1.62, 2.36, "grey", METALIC_ATOM_FLAG},
- {atomTh, 90, "Th", 1.08, 1.08, 1.82, "grey", METALIC_ATOM_FLAG},
+ {atomHe, 2, "He", 1.60, 1.60, 1.60, 0.00, "sky", 0},
+ {atomBe, 4, "Be", 0.31, 0.31, 0.31, 0.90, "grey", METALIC_ATOM_FLAG},
+ {atomB, 5, "B", 0.20, 0.20, 0.20, 0.86, "grey", 0},
+ {atomNe, 10, "Ne", 1.60, 1.60, 1.60, 0.00, "pink", 0},
+ {atomSi, 14, "Si", 2.10, 2.10, 2.10, 1.17, "grey", METALIC_ATOM_FLAG},
+ {atomAr, 18, "Ar", 1.89, 1.89, 1.89, 0.00, "orange", 0},
+ {atomSc, 21, "Sc", 0.68, 0.68, 0.68, 0.44, "grey", METALIC_ATOM_FLAG},
+ {atomTi, 22, "Ti", 0.75, 0.75, 0.75, 1.49, "grey", METALIC_ATOM_FLAG},
+ {atomGa, 31, "Ga", 0.53, 0.53, 0.53, 1.27, "grey", METALIC_ATOM_FLAG},
+ {atomGe, 32, "Ge", 0.60, 0.60, 0.60, 1.34, "grey", METALIC_ATOM_FLAG},
+ {atomKr, 36, "Kr", 2.01, 2.01, 2.01, 1.15, "greentint", 0},
+ {atomY, 39, "Y", 0.90, 0.90, 0.90, 1.64, "grey", METALIC_ATOM_FLAG},
+ {atomZr, 40, "Zr", 0.77, 0.77, 0.77, 1.51, "grey", METALIC_ATOM_FLAG},
+ {atomSn, 50, "Sn", 0.71, 0.71, 0.71, 1.45, "grey", METALIC_ATOM_FLAG},
+ {atomSb, 51, "Sb", 2.20, 2.20, 2.20, 1.41, "grey", METALIC_ATOM_FLAG},
+ {atomXe, 54, "Xe", 2.18, 2.18, 2.18, 1.28, "magenta", 0},
+ {atomLa, 57, "La", 1.03, 1.03, 1.03, 1.77, "grey", METALIC_ATOM_FLAG},
+ {atomCe, 58, "Ce", 0.87, 0.87, 0.87, 1.61, "grey", METALIC_ATOM_FLAG},
+ {atomFr, 87, "Fr", 1.94, 1.94, 1.94, 2.68, "grey", METALIC_ATOM_FLAG},
+ {atomRa, 88, "Ra", 1.62, 1.62, 1.62, 2.36, "grey", METALIC_ATOM_FLAG},
+ {atomTh, 90, "Th", 1.08, 1.08, 1.08, 1.82, "grey", METALIC_ATOM_FLAG},
/* finally, we have a set of elements where the radii are unknown */
/* so we use estimates and extrapolations based on web-elements data */
- {atomNb, 41, "Nb", 0.86, 0.86, 1.40, "grey", METALIC_ATOM_FLAG},
- {atomTc, 43, "Tc", 0.71, 0.71, 1.25, "grey", METALIC_ATOM_FLAG},
- {atomRu, 44, "Ru", 0.82, 0.82, 1.36, "grey", METALIC_ATOM_FLAG},
- {atomRh, 45, "Rh", 0.76, 1.76, 1.30, "grey", METALIC_ATOM_FLAG},
- {atomPd, 46, "Pd", 1.05, 1.05, 1.59, "grey", METALIC_ATOM_FLAG},
- {atomPr, 59, "Pr", 1.11, 1.11, 1.65, "grey", METALIC_ATOM_FLAG},
- {atomNd, 60, "Nd", 1.10, 1.10, 1.64, "grey", METALIC_ATOM_FLAG},
- {atomPm, 61, "Pm", 1.15, 1.15, 1.89, "grey", METALIC_ATOM_FLAG},
- {atomEu, 63, "Eu", 1.31, 1.31, 1.85, "grey", METALIC_ATOM_FLAG},
- {atomTb, 65, "Tb", 1.05, 1.05, 1.59, "grey", METALIC_ATOM_FLAG},
- {atomDy, 66, "Dy", 1.05, 1.05, 1.59, "grey", METALIC_ATOM_FLAG},
- {atomHo, 67, "Ho", 1.04, 1.04, 1.58, "grey", METALIC_ATOM_FLAG},
- {atomEr, 68, "Er", 1.03, 1.03, 1.57, "grey", METALIC_ATOM_FLAG},
- {atomTm, 69, "Tm", 1.02, 1.02, 1.56, "grey", METALIC_ATOM_FLAG},
- {atomLu, 71, "Lu", 1.02, 1.02, 1.56, "grey", METALIC_ATOM_FLAG},
- {atomHf, 72, "Hf", 0.85, 0.85, 1.46, "grey", METALIC_ATOM_FLAG},
- {atomTa, 73, "Ta", 0.86, 0.86, 1.40, "grey", METALIC_ATOM_FLAG},
- {atomRe, 75, "Re", 0.77, 0.77, 1.31, "grey", METALIC_ATOM_FLAG},
- {atomOs, 76, "Os", 0.78, 0.78, 1.32, "grey", METALIC_ATOM_FLAG},
- {atomIr, 77, "Ir", 0.80, 0.80, 1.34, "grey", METALIC_ATOM_FLAG},
- {atomBi, 83, "Bi", 1.17, 1.17, 1.71, "grey", METALIC_ATOM_FLAG},
- {atomPo, 84, "Po", 0.99, 0.99, 1.53, "grey", METALIC_ATOM_FLAG},
- {atomAt, 85, "At", 0.91, 0.91, 1.45, "grey", METALIC_ATOM_FLAG},
- {atomRn, 86, "Rn", 2.50, 2.50, 1.25, "pinktint", 0},
- {atomAc, 89, "Ac", 1.30, 1.30, 2.00, "grey", METALIC_ATOM_FLAG},
- {atomPa, 91, "Pa", 1.10, 1.10, 1.85, "grey", METALIC_ATOM_FLAG},
- {atomNp, 93, "Np", 1.00, 1.00, 1.72, "grey", METALIC_ATOM_FLAG},
- {atomPu, 94, "Pu", 1.00, 1.00, 1.67, "grey", METALIC_ATOM_FLAG},
- {atomAm, 95, "Am", 1.00, 1.00, 1.63, "grey", METALIC_ATOM_FLAG},
- {atomCm, 96, "Cm", 1.00, 1.00, 1.60, "grey", METALIC_ATOM_FLAG},
- {atomBk, 97, "Bk", 1.00, 1.00, 1.58, "grey", METALIC_ATOM_FLAG},
- {atomCf, 98, "Cf", 1.00, 1.00, 1.57, "grey", METALIC_ATOM_FLAG},
- {atomEs, 99, "Es", 1.00, 1.00, 1.56, "grey", METALIC_ATOM_FLAG},
- {atomFm, 100,"Fm", 1.00, 1.00, 1.55, "grey", METALIC_ATOM_FLAG},
- {atomMd, 101,"Md", 1.00, 1.00, 1.55, "grey", METALIC_ATOM_FLAG},
- {atomNo, 102,"No", 1.00, 1.00, 1.55, "grey", METALIC_ATOM_FLAG},
-
+ {atomNb, 41, "Nb", 0.86, 0.86, 0.86, 1.40, "grey", METALIC_ATOM_FLAG},
+ {atomTc, 43, "Tc", 0.71, 0.71, 0.71, 1.25, "grey", METALIC_ATOM_FLAG},
+ {atomRu, 44, "Ru", 0.82, 0.82, 0.82, 1.36, "grey", METALIC_ATOM_FLAG},
+ {atomRh, 45, "Rh", 0.76, 0.76, 1.76, 1.30, "grey", METALIC_ATOM_FLAG},
+ {atomPd, 46, "Pd", 1.05, 1.05, 1.05, 1.59, "grey", METALIC_ATOM_FLAG},
+ {atomPr, 59, "Pr", 1.11, 1.11, 1.11, 1.65, "grey", METALIC_ATOM_FLAG},
+ {atomNd, 60, "Nd", 1.10, 1.10, 1.10, 1.64, "grey", METALIC_ATOM_FLAG},
+ {atomPm, 61, "Pm", 1.15, 1.15, 1.15, 1.89, "grey", METALIC_ATOM_FLAG},
+ {atomEu, 63, "Eu", 1.31, 1.31, 1.31, 1.85, "grey", METALIC_ATOM_FLAG},
+ {atomTb, 65, "Tb", 1.05, 1.05, 1.05, 1.59, "grey", METALIC_ATOM_FLAG},
+ {atomDy, 66, "Dy", 1.05, 1.05, 1.05, 1.59, "grey", METALIC_ATOM_FLAG},
+ {atomHo, 67, "Ho", 1.04, 1.04, 1.04, 1.58, "grey", METALIC_ATOM_FLAG},
+ {atomEr, 68, "Er", 1.03, 1.03, 1.03, 1.57, "grey", METALIC_ATOM_FLAG},
+ {atomTm, 69, "Tm", 1.02, 1.02, 1.02, 1.56, "grey", METALIC_ATOM_FLAG},
+ {atomLu, 71, "Lu", 1.02, 1.02, 1.02, 1.56, "grey", METALIC_ATOM_FLAG},
+ {atomHf, 72, "Hf", 0.85, 0.85, 0.85, 1.46, "grey", METALIC_ATOM_FLAG},
+ {atomTa, 73, "Ta", 0.86, 0.86, 0.86, 1.40, "grey", METALIC_ATOM_FLAG},
+ {atomRe, 75, "Re", 0.77, 0.77, 0.77, 1.31, "grey", METALIC_ATOM_FLAG},
+ {atomOs, 76, "Os", 0.78, 0.78, 0.78, 1.32, "grey", METALIC_ATOM_FLAG},
+ {atomIr, 77, "Ir", 0.80, 0.80, 0.80, 1.34, "grey", METALIC_ATOM_FLAG},
+ {atomBi, 83, "Bi", 1.17, 1.17, 1.17, 1.71, "grey", METALIC_ATOM_FLAG},
+ {atomPo, 84, "Po", 0.99, 0.99, 0.99, 1.53, "grey", METALIC_ATOM_FLAG},
+ {atomAt, 85, "At", 0.91, 0.91, 0.91, 1.45, "grey", METALIC_ATOM_FLAG},
+ {atomRn, 86, "Rn", 2.50, 2.50, 2.50, 1.25, "pinktint", 0},
+ {atomAc, 89, "Ac", 1.30, 1.30, 1.30, 2.00, "grey", METALIC_ATOM_FLAG},
+ {atomPa, 91, "Pa", 1.10, 1.10, 1.10, 1.85, "grey", METALIC_ATOM_FLAG},
+ {atomNp, 93, "Np", 1.00, 1.00, 1.00, 1.72, "grey", METALIC_ATOM_FLAG},
+ {atomPu, 94, "Pu", 1.00, 1.00, 1.00, 1.67, "grey", METALIC_ATOM_FLAG},
+ {atomAm, 95, "Am", 1.00, 1.00, 1.00, 1.63, "grey", METALIC_ATOM_FLAG},
+ {atomCm, 96, "Cm", 1.00, 1.00, 1.00, 1.60, "grey", METALIC_ATOM_FLAG},
+ {atomBk, 97, "Bk", 1.00, 1.00, 1.00, 1.58, "grey", METALIC_ATOM_FLAG},
+ {atomCf, 98, "Cf", 1.00, 1.00, 1.00, 1.57, "grey", METALIC_ATOM_FLAG},
+ {atomEs, 99, "Es", 1.00, 1.00, 1.00, 1.56, "grey", METALIC_ATOM_FLAG},
+ {atomFm, 100,"Fm", 1.00, 1.00, 1.00, 1.55, "grey", METALIC_ATOM_FLAG},
+ {atomMd, 101,"Md", 1.00, 1.00, 1.00, 1.55, "grey", METALIC_ATOM_FLAG},
+ {atomNo, 102,"No", 1.00, 1.00, 1.00, 1.55, "grey", METALIC_ATOM_FLAG},
+
/* base identifiers are used in color hack (see note in enum above) */
- {baseA, 0, "a", 0.00, 0.00, 0.00, "pink", 0},
- {baseC, 0, "c", 0.00, 0.00, 0.00, "yellow", 0},
- {baseTU, 0, "t/u", 0.00, 0.00, 0.00, "sky", 0},
- {baseG, 0, "g", 0.00, 0.00, 0.00, "sea", 0},
- {baseOther, 0,"other na",0.00, 0.00, 0.00, "white", 0},
- {nonBase, 0, "nonbase",0.00, 0.00, 0.00, "grey", 0}
+ {baseA, 0, "a", 0.00, 0.00, 0.00, 0.00, "pink", 0},
+ {baseC, 0, "c", 0.00, 0.00, 0.00, 0.00, "yellow", 0},
+ {baseTU, 0, "t/u", 0.00, 0.00, 0.00, 0.00, "sky", 0},
+ {baseG, 0, "g", 0.00, 0.00, 0.00, 0.00, "sea", 0},
+ {baseOther, 0,"other na",0.00, 0.00, 0.00, 0.00, "white", 0},
+ {nonBase, 0, "nonbase",0.00, 0.00, 0.00, 0.00, "grey", 0}
};
#endif
=====================================
command_line/probe.launch
=====================================
--- a/command_line/probe.launch
+++ b/command_line/probe.launch
@@ -1,2 +1,3 @@
# LIBTBX_SET_DISPATCHER_NAME phenix.probe
+# LIBTBX_SET_DISPATCHER_NAME molprobity.probe
# LIBTBX_LAUNCH_EXE
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+king-probe (2.16.160404+git20180613.a09b012-1) unstable; urgency=medium
+
+ * Use git mode in watch file
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.1.5
+
+ -- Andreas Tille <tille at debian.org> Mon, 16 Jul 2018 09:08:29 +0200
+
king-probe (2.13.110909-2) unstable; urgency=medium
* Fix watch file
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -5,10 +5,10 @@ Uploaders: Malihe Asemani <ml.asemani at gmail.com>,
Michael Prisant <michael.prisant at gmail.com>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/king-probe.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/king-probe.git
+Build-Depends: debhelper (>= 11~)
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/king-probe
+Vcs-Git: https://salsa.debian.org/med-team/king-probe.git
Homepage: http://kinemage.biochem.duke.edu/software/probe.php
Package: king-probe
=====================================
debian/watch
=====================================
--- a/debian/watch
+++ b/debian/watch
@@ -1,7 +1,7 @@
-version=3
+version=4
-http://kinemage.biochem.duke.edu/software/probe.php .*/downloads/software/probe/probe.([\d.]+)\.src\.zip
+opts="mode=git,pretty=2.16.160404+git%cd.%h" \
+ https://github.com/rlabduke/probe.git HEAD
-# if there would be release tags ...
-# https://github.com/rlabduke/probe/releases .*/archive/#PREFIX#(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
-# asked for this in https://github.com/rlabduke/probe/issues/4
+# asked for release tags in
+# https://github.com/rlabduke/probe/issues/4
=====================================
parse.c
=====================================
--- a/parse.c
+++ b/parse.c
@@ -296,7 +296,10 @@ pattern* idItem() {
else if (strcmp(s, "METAL") == 0) {
type = PROP_NODE; val = METAL_PROP;
}
- else if (strcmp(s, "METHYL") == 0) {
+ else if (strcmp(s, "METHYLENE") == 0) {
+ type = PROP_NODE; val = METHYLENE_PROP;
+ }/*longer name first*/
+ else if (strcmp(s, "METHYL") == 0) {
type = PROP_NODE; val = METHYL_PROP;
}
else if (strcmp(s, "DONOR") == 0) {
@@ -851,6 +854,7 @@ void recPrint(FILE *outf, pattern *pat) {
case DNA_PROP: fprintf(outf,"dna/rna"); break;
case METAL_PROP: fprintf(outf,"metal"); break;
case METHYL_PROP: fprintf(outf,"methyl"); break;
+ case METHYLENE_PROP: fprintf(outf,"methylene"); break; /*20111210dcr*/
case DONOR_PROP: fprintf(outf,"donor"); break;
case ACCEPTOR_PROP: fprintf(outf,"acceptor"); break;
case RHPHOBIC_PROP:
=====================================
parse.h
=====================================
--- a/parse.h
+++ b/parse.h
@@ -84,7 +84,7 @@
#define CHECK_ENDS_PROP (1 << 27)
#define AMBIGWATER_PROP (1 << 28)
#define ION_PROP (1 << 29) /*re atomprops.h IONIC_ATOM_FLAG dcr041007*/
-
+#define METHYLENE_PROP (1 << 30) /*re atomprops.h dcr20111210 */
typedef struct patternType {
struct patternType *lhs; /* link to sub-pattern */
struct patternType *rhs; /* ditto */
=====================================
probe.c
=====================================
The diff for this file was not included because it is too large.
=====================================
probe.h
=====================================
--- a/probe.h
+++ b/probe.h
@@ -28,7 +28,11 @@
#include "autobondrot.h"
/* number of dot categories */
-#define NODEWIDTH 5
+/*0 wide contact,1 close contact,2 small overlap,3 bad overlap,4 H-bonds - original, changed by SJ see below*/
+/*0 wide contact,1 close contact,2 weak H bonds, 3 small overlap,4 bad overlap (0.4-0.5),5 worse overlap (>= 0.5), 6 H-bonds*/ /*04/08/2015 SJ moved weak H bonds catergory with the contacts, and separated bad overlap into bad and worse*/
+/*#define NODEWIDTH 6*/ /*20111215dcr change 5 to 6 for optional weak H bonds*/
+#define NODEWIDTH 7 /*04/08/2015 SJ adding category for worse overlap*/
+/* the new numbers are: 0 wide contact, 1 close contact, 2 weak H-bond, 3 small overlap, 4 bad overlap, 5 worse overlap, 6 H-bonds - weak H bonds and worse overlaps only separated when LweakHbonds and LworseOverlaps is true. This is false by default*/
/* selection identifiers */
#define SET1 1
@@ -49,14 +53,16 @@
/* before output, dots are stored in dotNodes */
typedef struct dotNode_t {
- struct dotNode_t *next; /* link to next dot */
- atom *a; /* dot's owner */
- atom *t; /* dot's cause */
- point3d loc; /* dot position */
- point3d spike; /* end of spike */
- int type; /* -1 bump, 0 touch, +1 H bond */
- float gap; /* vdw-vdw distance */
- char ptmaster; /* point master, kinemage output, (M for mc) dcr041009*/
+ struct dotNode_t *next; /* link to next dot */
+ atom *a; /* dot's owner */
+ atom *t; /* dot's cause */
+ point3d loc; /* dot position */
+ point3d spike; /* end of spike */
+ int type; /* -1 bump, 0 touch, +1 H bond */
+ float gap; /* vdw-vdw distance */
+ char ptmaster; /* point master, kinemage output, (M for mc) dcr041009*/
+ int dotCount; /*added by SJ -10/07/2011 for keeping count of number of dots in the interaction, used only in writeRaw and Condense functions*/
+ float angle; /*dcr20120120 angle: dot's: parent, self, cause, esp for H */
} dotNode;
/* data structure used to determine if N and O are at chain ends */
@@ -107,24 +113,24 @@ void doCommand(FILE *outf, int method,
atom *allMainAtoms, atomBins *abins,
atom *allMovingAtoms, atomBins *bbins,
pointSet dots[], float probeRad, float density, float spikelen,
- int countDots, int rawOutput, char* rawname, double scoreBias,
+ int countDots, int rawOutput, int conFlag, char* rawname, double scoreBias,
int drawSpike, int sayGroup, char* groupLabel,
- int argc, char **argv, char message[]);
+ int argc, char **argv, char message[]);//conFlag added by SJ 10/07/2011
void descrCommand(FILE *fp, char* hdr1, char* hdr2, int argc, char **argv);
void loadDotSpheres(pointSet dots[], float density);
void unloadDotSpheres(pointSet dots[]);
atom* processCommandline(int argc, char **argv, int *method, region *bboxA,
- float *density, float *probeRad,
- int *drawSpike, float *spikelen, int *countDots,
- int *keepUnselected,
- char **srcArg, char **targArg, char **ignoreArg,
- char **groupLabel, int *rawOutput, int *sayGroup,
- int *addKinToFile, movingAtomBuildInfo *mabip,
- residue **reslstptr);
+ float *density, float *probeRad,
+ int *drawSpike, float *spikelen, int *countDots,
+ int *keepUnselected,
+ char **srcArg, char **targArg, char **extraArg, char **ignoreArg,
+ char **groupLabel, int *rawOutput, int * conFlag, int *sayGroup,
+ int *addKinToFile, movingAtomBuildInfo *mabip,
+ residue **reslstptr);//conFlag added by SJ - 01/07/2011
atom* loadAtoms(FILE *fp, atom *atomlist, region *boundingBox, int file,
- residue **resDataLst);
+ residue **resDataLst);
atomBins* binAtoms(atom* allAtoms, region *boundingBox, char serialNum,
- float probeRad, int keepUnselected, int selflags);
+ float probeRad, int keepUnselected, int selflags);
float getRadius(int at, int useCOScale);
atom * newAtom(char *rec, int file, int model, residue* resDataBlk);
int atomsClose(atom *a, atom *b, float probeRad);
@@ -135,9 +141,13 @@ void selectSource(atom *allAtoms, pattern *sp, int srcFlag,
atom* findTouchingAtoms(atom *src, atom *head, atomBins *bins, float probeRad, int flag,int *ok);
void saveDot(atom *src, atom *targ, int type, point3d *loc, point3d *spike,
- dotNode *results[][NODEWIDTH], int ovrlaptype, float mingap, char ptmaster);/*dcr041009*/
-dotNode * newDot(atom *src,atom *targ, point3d *loc, point3d *spike, int ovrlaptype, float gap, char ptmaster);/*dcr041009*/
+ dotNode *results[][NODEWIDTH], int ovrlaptype, float mingap, char ptmaster, float XHTangle);/*dcr041009,XHTangle dcr20120120 */
+ dotNode * newDot(atom *src,atom *targ, point3d *loc, point3d *spike, int ovrlaptype, float gap, char ptmaster, float angle);/*dcr041009*/ /*XHTangle dcr20120120*/
+void examineOneDotEach(atom *src, int type, atom *scratch,
+ pointSet dots[], float probeRad, float spikelen,
+ int objFlag, dotNode *results[][NODEWIDTH], atom *allMainAtoms);
+ /*allMainAtoms20120120*/
void examineDots(atom *src, int type, atom *scratch,
pointSet dots[], float probeRad, float spikelen,
int objFlag, dotNode *results[][NODEWIDTH]);
@@ -159,16 +169,18 @@ void surfDots(atom *src, int type, atom *scratch,
void initResults(dotNode *results[][NODEWIDTH]);
void freeResults(dotNode *results[][NODEWIDTH]);
void writeOutput(FILE *outf, char *groupname, dotNode *results[][NODEWIDTH],
- int drawSpike, int method, char *extramastername);
+ int drawSpike, int method, char *extramastername, float probeRad);
/*041020 method for better kinemage keywords*/
/*060129 extra master name controls original vs fitted dots*/
+ /*probeRad added 20111220dcr*/
void writeAltFmtO(FILE *outf, int showBegin, int showEnd,
char* groupname, dotNode *results[][NODEWIDTH], int drawSpike);
void writeAltFmtXV(FILE *outf, int showBegin, int showEnd,
char* groupname, dotNode *results[][NODEWIDTH], int drawSpike);
void writeRaw(FILE *outf, char *groupname, dotNode *results[][NODEWIDTH],
- float rp, char*s, float);
+ float rp, char*s, float,int conFlag);
+dotNode * Condense(dotNode * head,int conFlag); //added 10/04/11 - SJ for condensing the rawOutput
void enumerate(FILE *outf, char* groupname, dotNode *results[][NODEWIDTH],
float probeRad, int method,
int nsel, int spike, int outdots, int numSkinDots,
=====================================
readPDBrecs.c
=====================================
--- a/readPDBrecs.c
+++ b/readPDBrecs.c
@@ -121,41 +121,41 @@ int isModel(char *line) {
}
int parseModel(char *line) {
-
+
return parseInteger(line, 6, 8);
}
/*
int parseAtomNumber(char *line) {
-
+
return parseInteger(line, 6, 5);
}
int parseResidueNumber(char *line) {
-
+
return parseInteger(line, 22, 4);
}
*/
int parseAtomNumber(char *line) {
- int atomno;
+ int atomno;
const char* errmsg = hy36decode(5, &line[6], 5, &atomno);
-/* if (errmsg) throw std::runtime_error(errmsg);
+/* if (errmsg) throw std::runtime_error(errmsg);
fprintf(stderr, "ATOM NUMBER %d\n", atomno); */
return atomno;
}
int parseResidueNumber(char *line) {
- int resid;
+ int resid;
const char* errmsg = hy36decode(4, &line[22], 4, &resid);
-/* if (errmsg) throw std::runtime_error(errmsg);
+/* if (errmsg) throw std::runtime_error(errmsg);
fprintf(stderr, "RESIDUE NUMBER %d\n", resid); */
return resid;
}
-void parseResidueHy36Num(char *line, char Hy36resno[]) {
+void parseResidueHy36Num(char *line, char Hy36resno[]) {
Hy36resno[0] = line[22];
Hy36resno[1] = line[23];
Hy36resno[2] = line[24];
@@ -171,7 +171,7 @@ void parseChain(char *line, char chain[]) {
/* Now using two character chain ids
char parseChain(char *line) {
-
+
return line[21];
}
*/
@@ -182,33 +182,33 @@ float parseOccupancy(char *line) {
}
float parseTempFactor(char *line) {
-
+
return nonblankrange(line, 60, 6) ? parseReal(line, 60, 6) : 0.0;
}
char parseResidueInsertionCode(char *line) {
-
+
return line[26];
}
char parseAltLocCode(char *line) {
-
+
return line[16];
}
void parseResidueName(char *line, char name[]) {
- name[0] = line[17];
- name[1] = line[18];
- name[2] = line[19];
- name[3] = '\0';
+ name[0] = line[17];
+ name[1] = line[18];
+ name[2] = line[19];
+ name[3] = '\0';
}
void parseAtomName(char *line, char name[]) {
- name[0] = line[12];
- name[1] = line[13];
- name[2] = line[14];
- name[3] = line[15];
- name[4] = '\0';
+ name[0] = line[12];
+ name[1] = line[13];
+ name[2] = line[14];
+ name[3] = line[15];
+ name[4] = '\0';
}
void parseXYZ(char *line, point3d *loc) {
@@ -224,5 +224,5 @@ void parseSegID(char *line, char id[]) {
id[1] = (reclen >= 74) ? line[73] : ' ';
id[2] = (reclen >= 75) ? line[74] : ' ';
id[3] = (reclen >= 76) ? line[75] : ' ';
- id[4] = '\0';
+ id[4] = '\0';
}
=====================================
select.c
=====================================
--- a/select.c
+++ b/select.c
@@ -26,24 +26,24 @@
/*{{{getPat() ****************************************************************/
/*select.h includes parse.h, so why is getPat here instead of in parse.c ? */
-pattern* getPat(char *line, char *which, int verbose)
+pattern* getPat(char *line, char *which, int verbose)
{
pattern *pat;
if (!line) return NULL;
-
+
pat = parseArg(line); /* parse.c/parseArg() */
if (verbose && pat) {
fprintf(stderr, "%s: ", which);
printPattern(stderr, pat); /* parse.c/printPattern() */
}
-
+
return pat;
}
/*}}}getPat() _______________________________________________________________*/
-/*{{{declarations ... globals */
+/*{{{declarations ... global AA and Atom properties */
/*{{{AromaticAtomsTbl[] ***/
static ResidueAndAtomPair AromaticAtomsTbl[] = {
@@ -80,7 +80,7 @@ static ResidueAndAtomPair AromaticAtomsTbl[] = {
":HEM:", ": N C: C1C: C2C: C3C: C4C: N D: C1D: C2D: C3D: C4D:", TEST_ACCEPT_ANGLE_PROP,
0, 0, 0};
-/*061018 not allow HIS to accept H-bonds as as aromatic ring system
+/*061018 not allow HIS to accept H-bonds as aromatic ring system
":HIS:", ": ND1: CD2: CE1: NE2: CG :", TEST_ACCEPT_ANGLE_PROP, */
/*}}}AromaticAtomsTbl[] ___________________________________________*/
@@ -142,7 +142,7 @@ static ResidueAndAtomPair MethylAtomsTbl[] = { /* including xplor names */
: CD1:1HD1:2HD1:3HD1:HD11:HD12:HD13:", 0,
": T:", ": C5M:1H5M:2H5M:3H5M:H5M1:H5M2:H5M3:", 0,
":THY:", ": C5A:1H5 :2H5 :3H5 : H51: H52: H53:", 0,
-": DT:", ": C7 : H71: H72: H73:", 0,
+": DT:", ": C7 : H71: H72: H73:", 0,
":AIB:", ": CB1:1HB1:2HB1:3HB1:HB11:HB12:HB13:\
: CB2:1HB2:2HB2:3HB2:HB21:HB22:HB23:", 0,
":ABU:", ": CG :1HG :2HG :3HG : HG1: HG2: HG3:", 0,
@@ -170,6 +170,34 @@ static ResidueAndAtomPair MethylAtomsTbl[] = { /* including xplor names */
":T6A:", ": C15:1H15:2H15:3H15:H152:H152:H153:", 0,
0, 0, 0};
/*}}}MethylAtomsTbl[] */
+
+/*{{{MethyleneResList, protein only ***/
+/* for identifying methylene groups on which to find methylene H 20111211dcr*/
+static char *MethyleneResList =
+":LYS:ILE:ARG:PRO:GLN:GLU:MET:CIS:SER:ASN:ASP:PHE:TYR:TRP:LEU:";
+ /*}}}MethyleneResList */
+
+/*{{{MethyleneAtomsTbl[] ***/
+static ResidueAndAtomPair MethyleneAtomsTbl[] = {
+":LYS:", ": HE2: HE3: HD2: HD3: HG2: HG3: HB2: HB3:", 0,
+":ILE:", ":HG12:HG13:", 0,
+":PRO:", ": HD2: HD3: HG2: HG3: HB2: HB3:", 0,
+":ARG:", ": HD2: HD3: HG2: HG3: HB2: HB3:", 0,
+":GLN:", ": HG2: HG3: HB2: HB3:", 0,
+":GLU:", ": HG2: HG3: HB2: HB3:", 0,
+":MET:", ": HG2: HG3: HB2: HB3:", 0,
+":CIS:", ": HB2: HB3:", 0,
+":SER:", ": HB2: HB3:", 0,
+":ASN:", ": HB2: HB3:", 0,
+":ASP:", ": HB2: HB3:", 0,
+":PHE:", ": HB2: HB3:", 0,
+":TYR:", ": HB2: HB3:", 0,
+":HIS:", ": HB2: HB3:", 0,
+":TRP:", ": HB2: HB3:", 0,
+":LEU:", ": HB2: HB3:", 0,
+0, 0, 0};
+/*}}}MethyleneAtomsTbl[] */
+
/*{{{ChargedAAList ***/
/* for computing charge state (currently treating HIS as charged) */
static char *ChargedAAList = ":ASP:GLU:LYS:ARG:HIS:HEM:";
@@ -203,7 +231,7 @@ static char *ChargedNucAcidAtomsList = ": P : O1P: O2P:\
S1G:";
/*}}}ChargedNucAcidAtomsList */
/*{{{WaterList ***/
-static char *WaterList = ":HOH:DOD:H2O:D2O:WAT:TIP:SOL:MTO:";
+static char *WaterList = ":HOH:DOD:H2O:WAT:TIP:SOL:MTO:";
/*}}}WaterList */
/*{{{DonorAcceptorAtomTbl[] ***/
static ResidueAndAtomPair DonorAcceptorAtomTbl[] = {
@@ -313,8 +341,8 @@ static ResidueAndAtomPair DonorAcceptorAtomTbl[] = {
": G:GUA:GTP:GDP:GMP:GSP:OMG:1MG:2MG:M2G:7MG: YG: DG: GR:", ": H8 :", DONOR_PROP|CH_DONOR_PROP,
#ifdef EXPLICIT_WATER_ATOM_NAMES
-":HOH:DOD:H2O:D2O:WAT:TIP:SOL:MTO:", ": O : OH2: OD2: OW :", DONOR_PROP|ACCEPTOR_PROP,
-":HOH:DOD:H2O:D2O:WAT:TIP:SOL:MTO:",
+":HOH:DOD:H2O:WAT:TIP:SOL:MTO:", ": O : OH2: OD2: OW :", DONOR_PROP|ACCEPTOR_PROP,
+":HOH:DOD:H2O:WAT:TIP:SOL:MTO:",
": H : H1 : H2 :1H :2H : D : D1 : D2 :1D :2D : H? :", DONOR_PROP,
#endif
@@ -349,6 +377,7 @@ int naBaseCategory(atom *a) {
/*{{{setAromaticProp() *******************************************************/
/* hunt for aromatic atoms and set AROMATIC property & atomHarom */
+/* also find aromatic carbon atoms and set atomCarom */
void setAromaticProp(atom *a) {
ResidueAndAtomPair *pair;
@@ -361,6 +390,7 @@ void setAromaticProp(atom *a) {
a->props |= AROMATIC_PROP;
a->props |= pair->bits; /* selectively set TEST_ACCEPT_ANGLE prop */
if(isHatom(a->elem)) { a->elem = atomHarom; }
+ if(isCatom(a->elem)) { a->elem = atomCarom; }
break;
}
}
@@ -386,6 +416,24 @@ void setMethylProp(atom *a) {
}
/*}}}setMethylProp()_________________________________________________________*/
+/*{{{setMethyleneProp() ******************************************************/
+/* hunt for Methyene atoms and set METHYLENE property */
+
+void setMethyleneProp(atom *a) {
+ ResidueAndAtomPair *pair;
+
+ if(strstr(MethyleneResList, a->r->resname)) {
+ for(pair = MethyleneAtomsTbl; pair->rlist && pair->alist; pair++) {
+ if( (strstr(pair->rlist, a->r->resname))
+ && (strstr(pair->alist, a->atomname)) ) {
+ a->props |= METHYLENE_PROP;
+ break;
+ }
+ }
+ }
+}
+/*}}}setMethyleneProp()______________________________________________________*/
+
/*{{{isCarbonylAtom() ********************************************************/
int isCarbonylAtom(atom *a) { /* limitation: this will not handle het groups properly */
return (strstr(AAList, a->r->resname) && (!strcmp(a->atomname, " C ")))
@@ -417,6 +465,7 @@ void setProperties(atom *a, int hetflag, int hb2aromaticFace, int chohb) {
setAromaticProp(a);
setMethylProp(a);
+ setMethyleneProp(a); /*20111211dcr*/
if (strstr(WaterList, a->r->resname)) {
a->props |= WATER_PROP;
@@ -434,7 +483,7 @@ void setProperties(atom *a, int hetflag, int hb2aromaticFace, int chohb) {
if(strstr(HphobicAAList, a->r->resname)){a->props |= RHPHOBIC_PROP;}
else if(strstr(HphilicAAList, a->r->resname)){a->props |= RHPHILIC_PROP;}
else if(strstr(ChargedAAList, a->r->resname)){a->props |= RCHARGED_PROP;}
- s = a->atomname;
+ s = a->atomname;
if (a->elem == atomC || isHatom(a->elem)) {
if (s[2] == 'A') {
if (!strcmp(s, "2HA ")){ a->props |= ALPHA_PROP; }
@@ -574,13 +623,13 @@ void setProperties(atom *a, int hetflag, int hb2aromaticFace, int chohb) {
/*{{{matchPat() ************* only called from probe.c/selectSource() ********/
/* recursive at OR,AND,NOT nodes; TRUE,FALSE nodes allow those logic choices*/
-int matchPat(atom *a, pattern *pat)
+int matchPat(atom *a, pattern *pat)
{
int lp, rc = FALSE;
- if (pat)
+ if (pat)
{
- switch(pat->type)
+ switch(pat->type)
{
case OR_NODE: rc = matchPat(a, pat->lhs) ?
TRUE : matchPat(a, pat->rhs); break;
@@ -590,7 +639,7 @@ int matchPat(atom *a, pattern *pat)
case FILE_NODE: rc = (a->r->file == pat->val); break;
case MODEL_NODE: rc = (a->r->model == pat->val); break;
case CHAIN_NODE: lp = strlen(lexString(pat->val));
- rc = (strncmp(lexString(pat->val), a->r->chain, lp)
+ rc = (strncmp(lexString(pat->val), a->r->chain, lp)
== 0); break;
case ALT_NODE: rc = (a->altConf == ' ' || a->altConf == pat->val); break;
case RES_NODE: rc = (a->r->resid == pat->val); break;
@@ -614,7 +663,7 @@ int matchPat(atom *a, pattern *pat)
case B_LT_NODE: rc = (a->bval < pat->val); break;
case B_GT_NODE: rc = (a->bval > pat->val); break;
case INS_NODE: rc = (a->r->resInsCode == pat->val); break;
-
+
/* ignores the insertion code */
case INS_RANGE_NODE: rc = (((pat->lhs->val == AND_NODE)
? pat->lhs->lhs->val
=====================================
select.h
=====================================
--- a/select.h
+++ b/select.h
@@ -26,6 +26,7 @@ void setProperties(atom *a, int hetflag, int hb2aromaticFace, int chohb);
int matchPat(atom *a, pattern *pat);
void setAromaticProp(atom *a);
void setMethylProp(atom *a);
+void setMethyleneProp(atom *a); /*20111211dcr*/
int isCarbonylAtom(atom *a);
int atomWithinDistance(atom *a, float *fvec);
char * setHydrogenParentName(char *rname, char *aname);
=====================================
stdconntable.c
=====================================
--- a/stdconntable.c
+++ b/stdconntable.c
@@ -2640,7 +2640,7 @@ void initStdConnTable() {
/* searchForStdBondingPartner() - given a residue name and atom name find the bonded atom */
char * searchForStdBondingPartner(char *resname, char *atomname, int isAhydrogen) {
char querystring[10], *p;
-
+
/* a large part of this routine is devoted to converting residue names */
/* and atom names into a search pattern. This pattern is 8 chars long */
/* and all uppercase. It has a colon as the forth character, separating*/
@@ -2716,8 +2716,8 @@ char * searchForStdBondingPartner(char *resname, char *atomname, int isAhydrogen
querystring[0] = querystring[1] = ' '; /* i.e., blank-blank-[GACUT] */
/* put the string back together */
- querystring[3] = ':';
-
+ querystring[3] = ':';
+
p = SearchStdResConnTable(querystring); /* second time is a charm */
}
}
@@ -2734,7 +2734,7 @@ int HashInStdResTbl(char *s) {
for (h = 0; *s != '\0'; s++) {
h = (h<<4) + *s;
- if (g = h & 0xf0000000) {
+ if ( (g = h & 0xf0000000) ) {
h ^= g >> 24;
h ^= g;
}
@@ -2746,7 +2746,7 @@ int HashInStdResTbl(char *s) {
int InsertInStdResConnTable(StdResConnTableEntry_t *elem) {
int r = 0, h = 0, rc = 1;
StdResConnTableEntry_t *t = NULL;
-
+
h = HashInStdResTbl(elem->key);
t = StdResTblBucket[h];
@@ -2786,9 +2786,9 @@ int InsertInStdResConnTable(StdResConnTableEntry_t *elem) {
char *SearchStdResConnTable(char *key) {
int r = 0;
StdResConnTableEntry_t *t;
-
+
t = StdResTblBucket[HashInStdResTbl(key)];
-
+
while (t && (r = strcmp(key, t->key)) > 0) {
t = t->next;
}
@@ -2800,7 +2800,7 @@ char *SearchStdResConnTable(char *key) {
void dumpStdConnTable(FILE * outf) {
int h;
StdResConnTableEntry_t *t;
-
+
for (h = 0; h < M; h++) {
fprintf(outf, "%5d] ", h);
for (t = StdResTblBucket[h]; t; t = t->next) {
View it on GitLab: https://salsa.debian.org/med-team/king-probe/compare/e7c42da5f14a878bef74ac8952579ecd6b941e5c...44f543a410ef06e2cec818c7356b8d97d28a5324
--
View it on GitLab: https://salsa.debian.org/med-team/king-probe/compare/e7c42da5f14a878bef74ac8952579ecd6b941e5c...44f543a410ef06e2cec818c7356b8d97d28a5324
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