diff --git a/atomprops.h b/atomprops.h index 2e40612..dd11562 100644 --- a/atomprops.h +++ b/atomprops.h @@ -93,6 +93,9 @@ enum atomIdentifiers { #define METALIC_ATOM_FLAG (1 << 0) /*atomProp AtomTbl flags: element features*/ #define IONIC_ATOM_FLAG (1 << 1) /*dcr041007 partial, now on halides*/ +/* Explicit vdW radius of carbonyl (C=O, atomC) entry. */ +#define ATOMC_EXPLICIT_VDW (1.70) + #ifdef INIT_ATOM_TABLE /* For non-metals, explicit VDW radii from */ /* Gavezzotti, J. Am. Chem. Soc. (1983) 105, 5220-5225. */ @@ -120,7 +123,7 @@ atomProp AtomTbl[NUMATOMTYPES] = { /* noAtom must be first */ {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}, + {atomC, 6, "C", ATOMC_EXPLICIT_VDW, ATOMC_EXPLICIT_VDW, 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}, diff --git a/probe.c b/probe.c index 6cad2f1..b10db7e 100644 --- a/probe.c +++ b/probe.c @@ -51,7 +51,7 @@ #define INLINE_FOR_SPEED 1 -static char* versionString = "probe: version 2.17.210924, Copyright 1996-2016, J. Michael Word; 2021 Richardson Lab"; +static char* versionString = "probe: version 2.18.211005, Copyright 1996-2016, J. Michael Word; 2021 Richardson Lab"; /*static char *versionString = "probe: version 2.16.160404, Copyright 1996-2016, J. Michael Word";*/ /*static char *versionString = "probe: version 2.16.130520, Copyright 1996-2013, J. Michael Word";*/ /*"probe: version 2.15.130427, merged probeVector, Copyright 1996-2013, J. Michael Word";*/ @@ -71,7 +71,7 @@ static char* versionString = "probe: version 2.17.210924, Copyright 1996-2016, J /*"probe: version 2.10.031014dcr041101, Copyright 1996-2004, J. Michael Word";*/ /*"probe: version 2.10 10/14/2003, Copyright 1996-2003, J. Michael Word";*/ /*jmw & dcr agreement on version name and maintenance by dcr 041110*/ -static char* shortVersionStr = "probe.2.17.210924"; +static char* shortVersionStr = "probe.2.18.211005"; /*static char *shortVersionStr = "probe.2.16.160404";*/ /*static char *shortVersionStr = "probe.2.16.130520";*/ /*static char *shortVersionStr = "probe.2.15.130427";*/ @@ -151,7 +151,7 @@ static float Min_regular_hb_cutoff=0.6; /* globals controling hbond cutoff */ static float Min_charged_hb_cutoff=0.8; /* defaults set in processCommandline() */ static float RadScaleFactor =1.0; /* global VDW radius scale Factor r*f */ static float RadScaleOffset =0.0; /* global VDW radius scale Offset r+o */ -static float CORadScale =(1.65/1.75); /* global VDW radius scale Factor for C=O */ +static float CORadScale =(1.65/ATOMC_EXPLICIT_VDW); /* global VDW radius scale Factor for C=O */ static float GAPweight =0.25;/* global raw GAP score weight */ static float BUMPweight =10.0;/* global raw BUMP score scale Factor */ static float HBweight = 4.0;/* global raw HBond score scale Factor */ @@ -299,7 +299,7 @@ int mainProbeProc(int argc, char **argv, FILE *outf) note(message); } sprintf(message, "C=O carbon VDW scaled by %.3f to a radius of %g A", - CORadScale, CORadScale*1.75); + CORadScale, CORadScale* ATOMC_EXPLICIT_VDW); note(message); if (rawOutput || countDots) { sprintf(message, "Score Weights: gapWt=%g, bumpWt=%g, HBWt=%g", @@ -6519,6 +6519,7 @@ 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"); exit(0);