Andreas Tille pushed to branch upstream at Debian Med / king-probe
Commits: 873d4f7b by Andreas Tille at 2022-05-02T13:48:14+02:00 New upstream version 02.23 - - - - - 2 changed files: - probe.c - select.c Changes: ===================================== probe.c ===================================== @@ -51,8 +51,8 @@ #define INLINE_FOR_SPEED 1 -static char* versionString = "probe: version 2.21.211221, Copyright 1996-2016, J. Michael Word; 2021 Richardson Lab"; -static char* shortVersionStr = "probe.2.21.211221"; +static char* versionString = "probe: version 2.23.040422, Copyright 1996-2016, J. Michael Word; 2021-2022 Richardson Lab"; +static char* shortVersionStr = "probe.2.23.040422"; static char *referenceString = "Word, et. al. (1999) J. Mol. Biol. 285, 1711-1733."; static char *electronicReference = "http://kinemage.biochem.duke.edu/";; @@ -204,7 +204,7 @@ int mainProbeProc(int argc, char **argv, FILE *outf) int method; int keepUnselected; region boundingBoxA; - atom *allMainAtoms = NULL; + atom *a, *allMainAtoms = NULL; atomBins *abins = NULL; pointSet dots[NUMATOMTYPES]; char *srcArg=NULL, *targArg=NULL, *extraArg=NULL, *ignoreArg=NULL; /* extraArg dcr 111022*/ @@ -215,6 +215,7 @@ int mainProbeProc(int argc, char **argv, FILE *outf) char message[200]; movingAtomBuildInfo mabis; residue *resLst = NULL; + FILE* dumpFile = NULL; /*mabis moving atom build info structure */ /*buffer to pass data to newMovingAtom for autobondrot*/ @@ -401,9 +402,8 @@ int mainProbeProc(int argc, char **argv, FILE *outf) /* Dump the atom information if we've been asked to. */ if (dumpFileName) { - FILE* dumpFile = 0; dumpFile = fopen(dumpFileName, "wb"); - for (atom* a = allMainAtoms; a; a = a->next) { + for (a = allMainAtoms; a; a = a->next) { /* Don't dump Phantom Hydrogen information. */ if (a->elem != atomHOd) { fprintf(dumpFile, "%s %s %3d %-4s %c %7.3f %7.3f %7.3f %5.2f %s %s %s\n", @@ -5219,6 +5219,7 @@ void writeOutput(FILE *outf, char* groupname, dotNode *results[][NODEWIDTH], int {/*kinemage point or point-line for each node in (ij)th dot-node list*/ a = node->a; /*owner of dot*/ t = node->t; /*cause of dot, use for OneDotEach 111013dcr*/ + /* Slow way to determine integer truncation of k/5 with a maximum of 9. */ for(k=0; k<10; k++){if(a->bval < k*5) {break;}} /*2:10A,3:15B,4:20C,5:25D,6:30E,8:40F,10:50G*/ if(k<=2){ptm[0] = 'A';} @@ -5226,8 +5227,8 @@ void writeOutput(FILE *outf, char* groupname, dotNode *results[][NODEWIDTH], int else if(k<=4){ptm[0] = 'C';} else if(k<=5){ptm[0] = 'D';} else if(k<=6){ptm[0] = 'E';} - else if(k<=2){ptm[0] = 'F';} - else if(k<=2){ptm[0] = 'G';} + else if(k<=7){ptm[0] = 'F';} + else if(k<=8){ptm[0] = 'G';} else{ptm[0] = 'H';} /*Note first nemdstr char of inputfilename 20120120dcr*/ fprintf(outf,"{%6s %s%c%s%s%c%s:O=%4.2f, B=%6.2f; %s%c%s%s%c%s:O=%4.2f, B=%6.2f; GAP %6.3f}'%s' %8.3f, %8.3f , %8.3f\n", @@ -6509,11 +6510,14 @@ fprintf(outf,"2.15.130427 version number change for merged code! \n"); fprintf(outf,"2.16.130509 jjh added support for segid instead of chaind\n"); fprintf(outf,"2.16.130520 jjh fixed bug in segid handling\n"); fprintf(outf,"04/16/2015 - SJ added the -sepworse flag, if true will seperate the overlaps of >= 0.4 and overlaps of >=0.5. This is default by false. Had to change NODEWIDTH value (see probe.h)\n One can change the 0.5 cutoff for worse overlap by specifying the flag DIVWorse\n"); -fprintf(outf,"09/24/2021 - RMT Version 2.17 Fixed crash when finding ambiguous Oxygens\n"); -fprintf(outf,"10/05/2021 - RMT Version 2.18 Makes default C=O radius scale depend on table value\n"); -fprintf(outf,"12/09/2021 - RMT Version 2.19 Adds commend-line argument to dump atom info\n"); -fprintf(outf,"12/21/2021 - RMT Version 2.20 Dumps atom information after hydrogens have been updated.\n"); -fprintf(outf,"12/21/2021 - RMT Version 2.21 Does not dump Phantom Hydrogen information.\n"); +fprintf(outf,"09/24/2021 - RMT Version 2.17 fixed crash when finding ambiguous Oxygens\n"); +fprintf(outf,"10/05/2021 - RMT Version 2.18 makes default C=O radius scale depend on table value\n"); +fprintf(outf,"12/09/2021 - RMT Version 2.19 adds commend-line argument to dump atom info\n"); +fprintf(outf,"12/21/2021 - RMT Version 2.20 dumps atom information after hydrogens have been updated.\n"); +fprintf(outf,"12/21/2021 - RMT Version 2.21 does not dump Phantom Hydrogen information.\n"); +fprintf(outf,"03/31/2022 - RMT Version 2.22 does not mark Nitrogens in the HIS ring or atoms in the\n"); +fprintf(outf," TRP 5-membered ring as acceptors. Too many side contacts are made to these rings.\n"); +fprintf(outf,"04/04/2022 - RMT Version 2.22 fixes copy/paste bug to allow F and G pointmasters.\n"); exit(0); ===================================== select.c ===================================== @@ -63,7 +63,11 @@ static ResidueAndAtomPair AromaticAtomsTbl[] = { ":PHE:", ": CG : CD1: CD2: CE1: CE2: CZ :", TEST_ACCEPT_ANGLE_PROP, ":HIS:", ": ND1: CD2: CE1: NE2: CG :", 0, ":TYR:", ": CG : CD1: CD2: CE1: CE2: CZ :", TEST_ACCEPT_ANGLE_PROP, -":TRP:", ": CG : CD1: CD2: NE1: CE2: CE3: CZ2: CZ3: CH2:", TEST_ACCEPT_ANGLE_PROP, +// The 5-membered ring is not treated as an aromatic acceptor face, but the 6-membered +// ring is. +//":TRP:", ": CG : CD1: CD2: NE1: CE2: CE3: CZ2: CZ3: CH2:", TEST_ACCEPT_ANGLE_PROP, +":TRP:", ": CG : CD1: NE1:", 0, +":TRP:", ": CD2: CE2: CE3: CZ2: CZ3: CH2:", TEST_ACCEPT_ANGLE_PROP, ": U:URA:UTP:UDP:UMP:PSU: UR:", ": N1 : C2 : N3 : C4 : C5 : C6 :", TEST_ACCEPT_ANGLE_PROP, ": T:THY:TTP:TDP:TMP:5MU: DT: TR:", @@ -269,7 +273,10 @@ static ResidueAndAtomPair DonorAcceptorAtomTbl[] = { : DE :1DH1:2DH1:1DH2:2DH2:DH11:DH12:DH21:DH22:", DONOR_PROP, -":HIS:", ": ND1: NE2:", DONOR_PROP|ACCEPTOR_PROP, +// The Nitrogens on Histidine's ring are not marked as acceptors just because of their +// status as being on the ring. +//":HIS:", ": ND1: NE2:", DONOR_PROP | ACCEPTOR_PROP, +":HIS:", ": ND1: NE2:", DONOR_PROP, ":HIS:", ": HD1: HE2: DD1: DE2:", DONOR_PROP, ":HIS:", ": HD2: HE1: DD2: DE1:", DONOR_PROP|CH_DONOR_PROP, ":SER:", ": OG :", DONOR_PROP|ACCEPTOR_PROP, View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/commit/873d4f7b0ae9cf9a5142245eb8d7b244d1be54e0 -- View it on GitLab: https://salsa.debian.org/med-team/king-probe/-/commit/873d4f7b0ae9cf9a5142245eb8d7b244d1be54e0 You're receiving this email because of your account on salsa.debian.org.
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