/* name: probe.h */ /* author: J. Michael Word */ /* date written: 2/26/96 */ /* modified: 10/18/96, 11/6/96 */ /* purpose: compute intersecton surfaces */ /*****************************************************************/ /* NOTICE: This is free software and the source code is freely */ /* available. You are free to redistribute or modify under the */ /* conditions that (1) this notice is not removed or modified */ /* in any way and (2) any modified versions of the program are */ /* also available for free. */ /* ** Absolutely no Warranty ** */ /* Copyright (C) 1999 J. Michael Word */ /*****************************************************************/ #ifndef PROBE_H #define PROBE_H 1 #include #include "utility.h" #include "dots.h" #include "abin.h" #include "readPDBrecs.h" #include "select.h" #include "atomprops.h" #include "stdconntable.h" #include "autobondrot.h" /* number of dot categories */ /*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 #define SET2 2 #define IGNORE_FLAG 4 /* mode types */ #define EXTERNALSURFACE 0 #define INTERSECTONCE 1 #define INTERSECTBOTHWAYS 2 #define SELFINTERSECT 3 #define DUMPATOMCOUNT 4 #define MCMCCHR 'M' /*dcr041017*/ #define SCSCCHR 'S' /*dcr041017*/ #define MCSCCHR 'P' /*dcr041017*/ #define OTHERCHR 'O' /*dcr041017*/ /* 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*/ 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 */ typedef struct { atom *ambigN[8]; /* first residue's ambiguous N in this chain [0-3]*/ /* along with the last residue's Ns [4-7] */ atom *ambigO[8]; /* last residue's ambiguous Os in this chain [0-7] */ int res_mc_oxy_cnt; /* how many mainchain Oxygens on last res? */ int first, last; /* where do the chain ids break? */ int Ntmarkers, Ctmarkers; /* where were N and C term markers observed? */ int hisNHcount[4]; } chainEndData_t; typedef struct { /* buffer to pass data to newMovingAtom */ int filenum; FILE *inf; int close; /* do we need to close the file */ pattern *srcPat; pattern *targPat; residue **reslstptr; residue *scratchRes; } movingAtomBuildInfo; typedef struct { /* buffer to pass data to movingDoCommand */ int firstPass; int keepUnselected; FILE *outf; int method; atom *allMainAtoms; atom *waterClones; atomBins *abins; pointSet *dots; float probeRad; float density; float spikelen; int countDots; int rawOutput; int drawSpike; int sayGroup; char* groupLabel; int argc; char **argv; char *message; } movingCommandInfo; int mainProbeProc(int argc, char **argv, FILE *outf); 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, int conFlag, char* rawname, double scoreBias, int drawSpike, int sayGroup, char* groupLabel, 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 **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); atomBins* binAtoms(atom* allAtoms, region *boundingBox, char serialNum, 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); int inRange(point3d *p, point3d *q, float lim); float gapSize(point3d *p, point3d *q, float qrad); void selectSource(atom *allAtoms, pattern *sp, int srcFlag, pattern *tp, int objFlag, pattern *ignorePat); 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, 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]); void markBonds(atom *src, atom *neighbors, int distcount, int max); int dotType(atom *src, atom *atomList, int recalcOnly); void genDotIntersect(atom *allMainAtoms, atomBins *abins, atom *allMovingAtoms, atomBins *bbins, pointSet dots[], float probeRad, float spikelen, int srcFlag, int targFlg, dotNode *results[][NODEWIDTH]); void genDotSurface(atom *allMainAtoms, atomBins *abins, atom *allMovingAtoms, atomBins *bbins, pointSet dots[], float probeRad, float spikelen, int srcFlag, dotNode *results[][NODEWIDTH]); void surfDots(atom *src, int type, atom *scratch, pointSet dots[], float probeRad, float spikelen, dotNode *results[][NODEWIDTH]); 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, 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,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, float density); void rawEnumerate(FILE *outf, char* groupname, dotNode *results[][NODEWIDTH], int method, int nsel, int spike, int outdots, int numSkinDots, float density, char *namestring, char *rawname, double scoreBias); int countSelected(atom *allAtoms, int srcFlag); int enumDotSkin(atom *allMainAtoms, atomBins *abins, atom *allMovingAtoms, atomBins *bbins, pointSet dots[], int srcFlag); int countSkin(atom *src, atom *scratch, pointSet dots[]); atom* updateHydrogenInfo(FILE *outf, atom *allMainAtoms, atomBins *abins, atom *allMovingAtoms, atomBins *bbins, int selectedFlag, int mustSaveMainWater); int dotClassIndex(int t, float mingap); void fixupLongBondChains(atom *src, atom *neighbors, int cutoff); float dot2bullsEye(point3d *dot, atom *src, atom *targ); float dot2srcCenter(point3d *dot, atom *src, atom *targ); float kissEdge2bullsEye(float ra, float rb, float rp); char* assignGapColorForKin(float gap, int class); char* assignGapColorForO(float gap, int class); char* assignGapColorForXV(float gap, int class); char* convertKinColorToO(char* incolor); char* convertKinColorToXV(char* incolor); atom * newMovingAtom(char *rec, void* userdata); void deleteMovingAtom(atom *a, void*); void movingAtomListProcessing(atom *atomlst, void *userdata); void movingDoCommand(char* name, double scoreBias, atom *allMovingAtoms, void* userdata); void initEndData(chainEndData_t *ed); void hisNHcheck(chainEndData_t *ed, atom *atomlist, int rescnt); void resCheck(chainEndData_t *ed, atom *atomlist, int rescnt); void CtermCheck(chainEndData_t *ed, int rescnt, int isChainEnd); void noticedNt(chainEndData_t *ed, int rescnt); void noticedCt(chainEndData_t *ed, int rescnt); void NtermCheck(chainEndData_t *ed, int rescnt, int isChainEnd); void ProcessResInfo(chainEndData_t *ed, atom *a); ringInfo * newRingInfo(ringInfo **head, point3d* ctr, point3d* norm); void deleteRingInfoList(ringInfo *ri); residue * newResidueData(); void deleteResidueData(residue *r); void disposeListOfResidues(residue *theRes); void deleteAtom(atom *a); void disposeListOfAtoms(atom *theAtom); int resDiffersFromPrev(residue *r1, residue *r2); void dumpRes(residue *theRes); void dump_changes(FILE *outf); void countsummary(FILE *outf, char* modestr, int Lines, int Pass); /*dcr041101*/ #endif