--- /dev/null
+ ACADEMIC LICENSE AGREEMENT
+ for the program
+ IUPred
+
+A nonexclusive, nontransferable right to use the IUPred executable, source
+code and related documentation ("Licensed Material") is granted
+by Zsuzsanna Dosztanyi ("Author") to
+
+
+ ....................................
+
+in exchange of the following commitments:
+
+I hereby certify and accept that
+
+ 1. I am an academic user at an academic research institution. In using the
+ Licensed Material, I will respect the interests of the Author and the
+ Institute of Enzymology.
+
+ 2. All rights, title, and interest in and to the Licensed Material shall at
+ all times remain with the Author.
+
+ 3. I may, for internal use only, execute, enhance, modify, or expand the
+ Licensed Material, may merge it into other material, and may use the
+ Licensed Material as modified. All such modifications shall include the
+ Author copyright notice.
+
+ 4. There is no warranty or other guarantee of fitness of the Licensed
+ Material. It is provided solely "as is". The Author disclaims all res-
+ ponsibility and liability with respect to this software's usage or its
+ effect upon hardware or computer systems. The Author has no obligation
+ to provide support or maintenance services for the Licensed Material.
+
+ 5. I will not use the software in commercial activities. Incorporation of
+ the Software into a commercial Web site or other fee paying service is
+ not allowed.
+
+ 6. The program shall not be made available to users outside the recipient's
+ laboratory. I will suggest to other interested research groups to
+ contact the authors directly.
+
+ 7. I will not alter or suppress the run-time copyright message.
+
+ 8. I will acknowledge the program authors on any publication of scientific
+ results based in part on use of the program and cite the article in
+ which the program was described:
+
+The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates
+between Folded and Intrinsically Unstructured Proteins
+Zsuzsanna Dosztanyi, Veronika Csizmok, Peter Tompa and Istvan Simon
+J. Mol. Biol. (2005) 347, 827-839.
+
+ 9. I will report evidence of program bugs to the Author.
+
+Purpose of research:
+
+
+Full name and institutional address:
+
+
+
+Internet email address:
+
+Date: Signature:
+
+
+
+
+Mail of fax the signed form to:
+
+Dr Zsuzsanna Dosztanyi
+Institute of Enzymology
+Biological Research Center
+Hungarian Academy of Sciences
+H-1518 Budapest PO Box 7
+Fax: +36-1 466-5465
--- /dev/null
+CFLAGS = -O3 -funroll-loops -Winline
+LDLIBS = -lm
+
+OBJ = .o
+EXE =
+
+RM = rm -f
+CP = cp
+
+GPP = cc
+LD = $(GPP) $(CFLAGS)
+CPP = $(GPP) -c $(CFLAGS)
+
+
+all: iupred
+
+CPPSRC = $(sort $(wildcard *.c))
+CPPOBJ = $(subst .c,.o,$(CPPSRC))
+
+$(CPPOBJ): %.o: %.c
+ $(CPP) $< -o $@
+
+iupred: $(CPPOBJ)
+ $(LD) -o iupred $(CPPOBJ) $(LDLIBS)
+ strip iupred
--- /dev/null
+ IUPred RELEASE NOTES
+ ====================
+
+IUPred Version 1.0
+
+by Zsuzsanna Dosztanyi
+
+
+IUPred is supplied in source code form along with the required data files. The
+program is written in ANSI C and the code should compile on any ANSI C compiler
+e.g. the GNU C compiler. To be able to run outside the source directory, the
+IUPred_PATH environment variable has to be set to the location of the source
+files.
+
+TO COMPILE:
+
+cc iupred.c -o iupred
+
+TO RUN IUPred:
+
+iupred seqfile type
+
+ where seqfile is the name of the sequence file
+
+ type is any of the option of
+
+ long
+ short
+ glob
+
+ for prediction of long disorder, short disorder ( e.g. missing residues in
+ X-ray structures) or predicting globular domains.
+
+
+INPUT FILE: sequence_file in fasta format. One sequence per file.
+
+EXAMPLE RUN:
+
+iupred P53_HUMAN.seq long
+
+
+INTERPRETATION OF THE OUTPUT:
+
+In the case of long and short types of disorder the output gives the
+likelihood of disorder for each residue, i.e. it is a value between 0 and 1,
+and higher values indicate higher probability of disorder. Residues with values
+above 0.5 can be regarded as disordered, and at this cutoff 5% of globular
+proteins is expected to be predicted to disordered (false positives).
+
+For the prediction type of globular domains it gives the number of globular
+domains and list their start and end position in the sequence. This is followed
+by the submitted sequence with residues of globular domains indicated by
+uppercase letters.
+
+
+Please see the LICENSE file for the license terms for the software. It is
+basically free for academic users, but a license fee applies to commercial
+users.
+
+THE PUBLICATION OF RESEARCH USING IUPred MUST INCLUDE AN APPROPRIATE
+CITATION TO THE METHOD:
+
+The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates
+between Folded and Intrinsically Unstructured Proteins
+Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon
+J. Mol. Biol. (2005) 347, 827-839.
+
+
+SHORT SUMMARY OF THE METHOD
+
+Intrinsically unstructured/disordered proteins have no single well-defined
+tertiary structure in their native, functional state. Our server recognizes
+such regions from the amino acid sequence based on the estimated pairwise
+energy content. The underlying assumption is that globular proteins make a
+large number of interresidue interactions, providing the stabilizing energy to
+overcome the entropy loss during folding. In contrast, IUPs have special
+sequences that do not have the capacity to form sufficient interresidue
+interactions. Taking a set of globular proteins with known structure, we have
+developed a simple formalism that allows the estimation of the pairwise
+interaction energies of these proteins. It uses a quadratic expression in the
+amino acid composition, which takes into account that the contribution of an
+amino acid to order/disorder depends not only its own chemical type, but also
+on its sequential environment, including its potential interaction partners.
+Applying this calculation for IUP sequences, their estimated energies are
+clearly shifted towards less favorable energies compared to globular proteins,
+enabling the predicion of protein disorder on this ground.
--- /dev/null
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+ 931 3.5100 0.000000 0.999970 0.000030
+ 932 3.5150 0.000000 0.999970 0.000030
+ 933 3.5200 0.000429 0.999974 0.000026
+ 934 3.5250 0.000000 0.999974 0.000026
+ 935 3.5300 0.000000 0.999974 0.000026
+ 936 3.5350 0.000000 0.999974 0.000026
+ 937 3.5400 0.000000 0.999974 0.000026
+ 938 3.5450 0.000000 0.999974 0.000026
+ 939 3.5500 0.000000 0.999974 0.000026
+ 940 3.5550 0.000000 0.999974 0.000026
+ 941 3.5600 0.000000 0.999974 0.000026
+ 942 3.5650 0.000000 0.999974 0.000026
+ 943 3.5700 0.000000 0.999974 0.000026
+ 944 3.5750 0.000000 0.999974 0.000026
+ 945 3.5800 0.000000 0.999974 0.000026
+ 946 3.5850 0.000000 0.999974 0.000026
+ 947 3.5900 0.000000 0.999974 0.000026
+ 948 3.5950 0.000000 0.999974 0.000026
+ 949 3.6000 0.000000 0.999974 0.000026
+ 950 3.6050 0.000000 0.999974 0.000026
+ 951 3.6100 0.000000 0.999974 0.000026
+ 952 3.6150 0.000429 0.999979 0.000021
+ 953 3.6200 0.000000 0.999979 0.000021
+ 954 3.6250 0.000429 0.999983 0.000017
+ 955 3.6300 0.000000 0.999983 0.000017
+ 956 3.6350 0.000000 0.999983 0.000017
+ 957 3.6400 0.000000 0.999983 0.000017
+ 958 3.6450 0.000000 0.999983 0.000017
+ 959 3.6500 0.000000 0.999983 0.000017
+ 960 3.6550 0.000000 0.999983 0.000017
+ 961 3.6600 0.000000 0.999983 0.000017
+ 962 3.6650 0.000000 0.999983 0.000017
+ 963 3.6700 0.000000 0.999983 0.000017
+ 964 3.6750 0.000000 0.999983 0.000017
+ 965 3.6800 0.000000 0.999983 0.000017
+ 966 3.6850 0.000000 0.999983 0.000017
+ 967 3.6900 0.000000 0.999983 0.000017
+ 968 3.6950 0.000000 0.999983 0.000017
+ 969 3.7000 0.000000 0.999983 0.000017
+ 970 3.7050 0.000000 0.999983 0.000017
+ 971 3.7100 0.000000 0.999983 0.000017
+ 972 3.7150 0.000000 0.999983 0.000017
+ 973 3.7200 0.000000 0.999983 0.000017
+ 974 3.7250 0.000000 0.999983 0.000017
+ 975 3.7300 0.000000 0.999983 0.000017
+ 976 3.7350 0.000000 0.999983 0.000017
+ 977 3.7400 0.000000 0.999983 0.000017
+ 978 3.7450 0.000000 0.999983 0.000017
+ 979 3.7500 0.000429 0.999987 0.000013
+ 980 3.7550 0.000429 0.999991 0.000009
+ 981 3.7600 0.000000 0.999991 0.000009
+ 982 3.7650 0.000000 0.999991 0.000009
+ 983 3.7700 0.000000 0.999991 0.000009
+ 984 3.7750 0.000000 0.999991 0.000009
+ 985 3.7800 0.000000 0.999991 0.000009
+ 986 3.7850 0.000000 0.999991 0.000009
+ 987 3.7900 0.000000 0.999991 0.000009
+ 988 3.7950 0.000000 0.999991 0.000009
+ 989 3.8000 0.000000 0.999991 0.000009
+ 990 3.8050 0.000000 0.999991 0.000009
+ 991 3.8100 0.000000 0.999991 0.000009
+ 992 3.8150 0.000000 0.999991 0.000009
+ 993 3.8200 0.000000 0.999991 0.000009
+ 994 3.8250 0.000000 0.999991 0.000009
+ 995 3.8300 0.000000 0.999991 0.000009
+ 996 3.8350 0.000000 0.999991 0.000009
+ 997 3.8400 0.000000 0.999991 0.000009
+ 998 3.8450 0.000000 0.999991 0.000009
+ 999 3.8500 0.000000 0.999991 0.000009
+ 1000 3.8550 0.000000 0.999991 0.000009
+ 1001 3.8600 0.000000 0.999991 0.000009
+ 1002 3.8650 0.000000 0.999991 0.000009
+ 1003 3.8700 0.000000 0.999991 0.000009
+ 1004 3.8750 0.000000 0.999991 0.000009
+ 1005 3.8800 0.000000 0.999991 0.000009
+ 1006 3.8850 0.000000 0.999991 0.000009
+ 1007 3.8900 0.000000 0.999991 0.000009
+ 1008 3.8950 0.000000 0.999991 0.000009
+ 1009 3.9000 0.000000 0.999991 0.000009
+ 1010 3.9050 0.000000 0.999991 0.000009
+ 1011 3.9100 0.000000 0.999991 0.000009
+ 1012 3.9150 0.000000 0.999991 0.000009
+ 1013 3.9200 0.000000 0.999991 0.000009
+ 1014 3.9250 0.000000 0.999991 0.000009
+ 1015 3.9300 0.000000 0.999991 0.000009
+ 1016 3.9350 0.000000 0.999991 0.000009
+ 1017 3.9400 0.000000 0.999991 0.000009
+ 1018 3.9450 0.000000 0.999991 0.000009
+ 1019 3.9500 0.000000 0.999991 0.000009
+ 1020 3.9550 0.000000 0.999991 0.000009
+ 1021 3.9600 0.000000 0.999991 0.000009
+ 1022 3.9650 0.000000 0.999991 0.000009
+ 1023 3.9700 0.000000 0.999991 0.000009
+ 1024 3.9750 0.000000 0.999991 0.000009
+ 1025 3.9800 0.000000 0.999991 0.000009
+ 1026 3.9850 0.000000 0.999991 0.000009
+ 1027 3.9900 0.000000 0.999991 0.000009
+ 1028 3.9950 0.000000 0.999991 0.000009
+ 1029 4.0000 0.000000 0.999991 0.000009
+ 1030 4.0050 0.000000 0.999991 0.000009
+ 1031 4.0100 0.000000 0.999991 0.000009
+ 1032 4.0150 0.000000 0.999991 0.000009
+ 1033 4.0200 0.000000 0.999991 0.000009
+ 1034 4.0250 0.000000 0.999991 0.000009
+ 1035 4.0300 0.000000 0.999991 0.000009
+ 1036 4.0350 0.000000 0.999991 0.000009
+ 1037 4.0400 0.000000 0.999991 0.000009
+ 1038 4.0450 0.000000 0.999991 0.000009
+ 1039 4.0500 0.000000 0.999991 0.000009
+ 1040 4.0550 0.000000 0.999991 0.000009
+ 1041 4.0600 0.000000 0.999991 0.000009
+ 1042 4.0650 0.000000 0.999991 0.000009
+ 1043 4.0700 0.000000 0.999991 0.000009
+ 1044 4.0750 0.000000 0.999991 0.000009
+ 1045 4.0800 0.000000 0.999991 0.000009
+ 1046 4.0850 0.000000 0.999991 0.000009
+ 1047 4.0900 0.000000 0.999991 0.000009
+ 1048 4.0950 0.000000 0.999991 0.000009
+ 1049 4.1000 0.000000 0.999991 0.000009
+ 1050 4.1050 0.000000 0.999991 0.000009
+ 1051 4.1100 0.000000 0.999991 0.000009
+ 1052 4.1150 0.000000 0.999991 0.000009
+ 1053 4.1200 0.000000 0.999991 0.000009
+ 1054 4.1250 0.000000 0.999991 0.000009
+ 1055 4.1300 0.000000 0.999991 0.000009
+ 1056 4.1350 0.000000 0.999991 0.000009
+ 1057 4.1400 0.000000 0.999991 0.000009
+ 1058 4.1450 0.000000 0.999991 0.000009
+ 1059 4.1500 0.000000 0.999991 0.000009
+ 1060 4.1550 0.000000 0.999991 0.000009
+ 1061 4.1600 0.000000 0.999991 0.000009
+ 1062 4.1650 0.000000 0.999991 0.000009
+ 1063 4.1700 0.000000 0.999991 0.000009
+ 1064 4.1750 0.000000 0.999991 0.000009
+ 1065 4.1800 0.000000 0.999991 0.000009
+ 1066 4.1850 0.000000 0.999991 0.000009
+ 1067 4.1900 0.000429 0.999996 0.000004
+ 1068 4.1950 0.000000 0.999996 0.000004
+ 1069 4.2000 0.000429 1.000000 0.000000
+ 1070 4.2050 0.000000 1.000000 0.000000
--- /dev/null
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include <math.h>
+
+
+
+#define AA "GAVLIFPSTCMWYNQDEKRH"
+#define AAN 20
+#define MSL 40000
+#define ML 1000
+
+#define DLC 1
+#define DUC 100
+#define DWS 10
+#define DMin_Ene 0.3
+#define DJOIN 45
+#define DDEL 35
+
+
+#define MAX(a,b) ((a)>(b)?(a):(b))
+#define MIN(a,b) ((a)<(b)?(a):(b))
+
+
+typedef struct
+{
+ char name[1000];
+ int le;
+ char *seq;
+ double expscore;
+ double *eprof;
+ double *smp;
+ double *en;
+ int ngr;
+ int **gr;
+} SEQ_STR;
+
+
+typedef struct
+{
+ double **CC;
+ double *distro;
+ double min, max;
+ double step;
+ double cutoff;
+ int nb;
+} P_STR;
+
+
+void read_mat(char *path, char *fn, double **MAT, double *matave);
+int getargs(char *line,char *args[],int max);
+void read_ref(char *path, char *fn, double **REF);
+void Get_Histo( P_STR *P, char *path, char *);
+double **DMatrix(int n_rows, int n_cols);
+void *my_malloc(size_t size);
+void IUPred(SEQ_STR *SEQ, P_STR *P);
+void getRegions(SEQ_STR *SEQ );
+void Get_Seq(char *fn, SEQ_STR *SEQ);
+
+
+int LC, UC, WS;
+double Min_Ene;
+int JOIN, DEL;
+int Flag_EP;
+double EP;
+
+
+int main(int argc, char **argv)
+{
+ P_STR *P;
+ SEQ_STR *SEQ;
+ int i,j;
+ int type;
+ char *path;
+
+
+
+ if (argc!=3) {
+ printf(" Usage: %s seqfile type \n",argv[0]);
+ printf(" where type stands for one of the options of \n");
+ printf(" \"long\", \"short\" or \"glob\"\n");
+ exit(1);
+ }
+ if ((path=getenv("IUPred_PATH"))==NULL) {
+ fprintf(stderr,"IUPred_PATH environment variable is not set\n");
+ path="./";
+ }
+
+ printf("# IUPred \n");
+ printf("# Copyright (c) Zsuzsanna Dosztanyi, 2005\n");
+ printf("#\n");
+ printf("# Z. Dosztanyi, V. Csizmok, P. Tompa and I. Simon\n");
+ printf("# J. Mol. Biol. (2005) 347, 827-839. \n");
+ printf("#\n");
+ printf("#\n");
+
+
+
+
+ if ((strncmp(argv[2],"long",4))==0) {
+ type=0;
+ }
+ else if ((strncmp(argv[2],"short",5))==0) {
+ type=1;
+ }
+ else if ((strncmp(argv[2],"glob",4))==0) {
+ type=2;
+ }
+ else {
+ printf("Wrong argument\n");exit(1);
+ }
+
+
+ SEQ=malloc(sizeof(SEQ_STR));
+ Get_Seq(argv[1],SEQ);
+ if (SEQ->le==0) {printf(" Sequence length 0\n");exit(1);}
+
+#ifdef DEBUG
+ printf("%s %d\n%s\n",SEQ->name,SEQ->le,SEQ->seq);
+#endif
+
+
+ P=malloc(sizeof(P_STR));
+ P->CC= DMatrix(AAN,AAN);
+
+ if (type==0) {
+
+ LC=1;
+ UC=100;
+ WS=10;
+ Flag_EP=0;
+
+ read_ref(path,"ss",P->CC);
+ Get_Histo(P, path, "histo");
+
+
+ IUPred(SEQ,P);
+
+ printf("# Prediction output \n");
+ printf("# %s\n",SEQ->name);
+ for (i=0;i<SEQ->le;i++)
+ printf("%5d %c %10.4f\n",i+1,SEQ->seq[i],SEQ->en[i]);
+ }
+ if (type==1) {
+ LC=1;
+ UC=25;
+ WS=10;
+ Flag_EP=1;
+ EP=-1.26;
+
+ read_ref(path,"ss_casp",P->CC);
+ Get_Histo(P, path, "histo_casp");
+
+ IUPred(SEQ,P);
+
+ printf("# Prediction output \n");
+ printf("# %s\n",SEQ->name);
+ for (i=0;i<SEQ->le;i++)
+ printf("%5d %c %10.4f\n",i+1,SEQ->seq[i],SEQ->en[i]);
+ }
+ if (type==2) {
+ char *globseq;
+
+ LC=1;
+ UC=100;
+ WS=15;
+ Flag_EP=0;
+
+
+
+ read_ref(path,"ss",P->CC);
+ Get_Histo(P,path,"histo");
+
+ IUPred(SEQ,P);
+
+ Min_Ene=DMin_Ene;
+ JOIN=DJOIN;
+ DEL=DDEL;
+
+ getRegions(SEQ);
+ globseq=malloc((SEQ->le+1)*sizeof(char));
+ for (i=0;i<SEQ->le;i++) globseq[i]=tolower(SEQ->seq[i]);
+
+ printf("# Prediction output \n");
+ printf("# %s\n",SEQ->name);
+ printf("Number of globular domains: %5d \n",SEQ->ngr);
+ for (i=0;i<SEQ->ngr;i++) {
+ printf(" globular domain %5d. %d - %d \n",
+ i+1,SEQ->gr[i][0]+1,SEQ->gr[i][1]+1);
+ for (j=SEQ->gr[i][0];j<SEQ->gr[i][1]+1;j++) {
+ globseq[j]=toupper(globseq[j]);
+ }
+ }
+ printf(">%s\n",SEQ->name);
+ for (i=0;i<SEQ->le;i++) {
+ if ((i>0)&&(i%60==0)) printf("\n");
+ else if ((i>0)&&(i%10==0)) printf(" ");
+ printf("%c",globseq[i]);
+ }
+ printf("\n");
+ free(globseq);
+
+
+#ifdef DEBUG
+ for (i=0;i<SEQ->le;i++)
+ printf("%5d %c %10.4f\n",i,SEQ->seq[i],SEQ->en[i]);
+#endif
+ }
+
+ free(SEQ->seq);
+ free(SEQ->eprof);free(SEQ->en);free(SEQ->smp);
+ free(SEQ);
+
+
+ return 0;
+}
+
+
+void IUPred(SEQ_STR *SEQ, P_STR *P)
+{
+ int i,j, a1, a2, p;
+ int naa;
+ double n2;
+ double min, max, step;
+
+ naa=SEQ->le;
+ min=P->min; max=P->max;step=P->step;
+
+ SEQ->eprof=malloc(naa*sizeof(double));
+ for (i=0;i<naa;i++) SEQ->eprof[i]=0;
+ SEQ->en=malloc(naa*sizeof(double));
+ for (i=0;i<naa;i++) SEQ->en[i]=0;
+ SEQ->smp=malloc(naa*sizeof(double));
+ for (i=0;i<naa;i++) SEQ->smp[i]=0;
+
+
+ SEQ->expscore=0;
+ for (i=0;i<naa;i++) {
+ a1=strchr(AA,((toupper(SEQ->seq[i]))))-AA;
+ if ((a1<0) || (a1>=AAN)) continue;
+ n2=0;
+ for (j=0;j<naa;j++) if (((abs(i-j))>LC)&&((abs(i-j))<UC)) {
+ a2=strchr(AA,((toupper(SEQ->seq[j]))))-AA;
+ if ((a2<0) || (a2>=AAN)) continue;
+ SEQ->eprof[i]+=P->CC[a1][a2];
+ n2++;
+ }
+ SEQ->expscore+=SEQ->eprof[i]/(naa*n2);
+ SEQ->eprof[i]/=n2;
+
+ }
+
+ if (Flag_EP==0) {
+ for (i=0;i<naa;i++) {
+ n2=0;
+ for (j=MAX(0,i-WS);j<=MIN(naa,i+WS+1);j++) {
+ SEQ->smp[i]+=SEQ->eprof[j];
+ n2++;
+ }
+ SEQ->smp[i]/=n2;
+ }
+ } else {
+ for (i=0;i<naa;i++) {
+ n2=0;
+ for (j=i-WS;j<i+WS;j++) {
+ if ((j<0)||(j>=naa)) SEQ->smp[i]+=EP;
+ else SEQ->smp[i]+=SEQ->eprof[j];
+
+ n2++;
+ }
+ SEQ->smp[i]/=n2;
+ }
+ }
+
+ for (i=0;i<naa;i++) {
+
+ if (SEQ->smp[i]<=min+2*step) SEQ->en[i]=1;
+ if (SEQ->smp[i]>=max-2*step) SEQ->en[i]=0;
+ if ((SEQ->smp[i]>min+2*step)&&(SEQ->smp[i]<max-2*step)) {
+ p=(int)((SEQ->smp[i]-min)*(1.0/step));
+ SEQ->en[i]=P->distro[p];
+ }
+
+#ifdef DEBUG
+ printf("%5d %10.4f %10.4f %10.4f\n",
+ i,SEQ->eprof[i], SEQ->smp[i],SEQ->en[i]);
+
+#endif
+
+ }
+
+}
+
+
+
+void getRegions(SEQ_STR *SEQ )
+{
+ int naa;
+ int i, k,kk;
+ int **GR, **mGR;
+ int in_GR;
+ int nr, mnr;
+ int beg_GR, end_GR;
+ int beg,end;
+
+
+ naa=SEQ->le;
+
+
+ GR=NULL;
+ nr=0;
+ in_GR=0;
+ beg_GR=end_GR=0;
+
+
+ for (i=0;i<naa;i++) {
+
+ if ((in_GR==1)&&(SEQ->smp[i]<=Min_Ene)) {
+ GR=realloc(GR,(nr+1)*sizeof(int *));
+ GR[nr]=malloc(2*sizeof(int));
+ GR[nr][0]=beg_GR;
+ GR[nr][1]=end_GR;
+ in_GR=0;
+ nr++;
+ }
+ else if (in_GR==1)
+ end_GR++;
+ if ((SEQ->smp[i]>Min_Ene)&&(in_GR==0)) {
+ beg_GR=i;
+ end_GR=i;
+ in_GR=1;
+ }
+ }
+ if (in_GR==1) {
+ GR=realloc(GR,(nr+1)*sizeof(int *));
+ GR[nr]=malloc(2*sizeof(int));
+ GR[nr][0]=beg_GR;
+ GR[nr][1]=end_GR;
+ in_GR=0;
+ nr++;
+ }
+
+
+ mnr=0;
+ k=0;mGR=NULL;
+ kk=k+1;
+ if (nr>0) {
+ beg=GR[0][0];end=GR[0][1];
+ }
+ while (k<nr) {
+ if ((kk<nr)&&(GR[kk][0]-end)<JOIN) {
+ beg=GR[k][0];
+ end=GR[kk][1];
+ kk++;
+ }
+ else if ((end-beg+1)<DEL) {
+ k++;
+ if (k<nr) {
+ beg=GR[k][0];
+ end=GR[k][1];
+ }
+ }
+ else {
+ mGR=realloc(mGR,(mnr+1)*sizeof(int*));
+ mGR[mnr]=malloc(2*sizeof(int));
+ mGR[mnr][0]=beg;
+ mGR[mnr][1]=end;
+ mnr++;
+ k=kk;
+ kk++;
+ if (k<nr) {
+ beg=GR[k][0];
+ end=GR[k][1];
+ }
+ }
+ }
+
+
+ for (i=0;i<nr;i++) free(GR[i]);
+ free(GR);
+
+ SEQ->ngr=mnr;
+ SEQ->gr=mGR;
+
+
+
+}
+
+
+void Get_Histo(P_STR *P, char *path, char *fn)
+{
+ FILE *f;
+ char ln[ML];
+ int i,nb, set;
+ double v, min, max, cutoff, c;
+ char *fullfn;
+ int sl;
+
+ sl=strlen(path)+strlen(fn)+2;
+ fullfn=malloc(sl*sizeof(char));
+ sprintf(fullfn,"%s/%s",path,fn);
+
+ if ((f=fopen(fullfn,"r"))==NULL) {
+ printf("Could not open %s\n",fullfn);
+ exit(1);
+ }
+
+
+
+ fscanf(f,"%*s %lf %lf %d\n",&min, &max, &nb);
+
+ P->distro=malloc(nb*sizeof(double ));
+ for (i=0;i<nb;i++) P->distro[i]=0;
+
+
+ for (i=0,set=0;i<nb;i++) {
+ fgets(ln,ML,f);
+ if (feof(f)) break;
+ if (ln[0]=='#') continue;
+
+ sscanf(ln,"%*s %lf %*s %*s %lf\n", &c,&v);
+ if ((set==0)&&(v<=0.5)) {set=1;cutoff=c;}
+ P->distro[i]=v;
+ }
+
+ fclose(f);
+ P->max=max;
+ P->min=min;
+ P->nb=nb;
+ P->cutoff=cutoff;
+
+
+
+ P->step=(max-min)/nb;
+ P->cutoff-=P->step;
+
+}
+
+
+void read_ref(char *path, char *fn, double **REF)
+{
+
+ FILE *f;
+ int p1,p2;
+ double v;
+ char line[1000],s[20];
+ int i,j;
+ char *fullfn;
+ int sl;
+
+ sl=strlen(path)+strlen(fn)+2;
+ fullfn=malloc(sl*sizeof(char));
+ sprintf(fullfn,"%s/%s",path,fn);
+
+ if ((f=fopen(fullfn,"r"))==NULL) {
+ printf("Could not open %s\n",fullfn);
+ exit(1);
+ }
+
+
+ while (!feof(f)) {
+ fgets(line,1000,f);
+
+ sscanf(line,"%d",&p1);
+ sscanf(&line[8],"%d",&p2);
+ sscanf(&line[17],"%s",s);
+ v=atof(s);
+ REF[p1][p2]=v;
+
+ }
+
+
+ if (REF[9][9]<0) {
+ for (i=0;i<AAN;i++) for (j=0;j<AAN;j++)
+ REF[i][j]*=-1;
+ }
+
+
+ fclose(f);
+
+}
+
+
+
+void read_mat(char *path, char *fn, double **MAT, double *matave)
+{
+ FILE *f;
+ char ln[ML];
+ int numargs;
+ char *args[AAN+2], AAL[AAN],a1,a2;
+ int i,j,k ,p, q;
+ double val;
+ int sl;
+ char *fullfn;
+
+ sl=strlen(path)+strlen(fn)+2;
+ fullfn=malloc(sl*sizeof(char));
+ sprintf(fullfn,"%s/%s",path,fn);
+
+ if ((f=fopen(fullfn,"r"))==NULL) {
+ printf("Could not open %s\n",fullfn);
+ exit(1);
+ }
+
+
+ fgets(ln,ML,f);
+ sprintf(AAL,"%s",ln);
+ i=0;
+ while (!feof(f)) {
+ fgets(ln,ML,f);
+ k=0;j=0;
+ if (feof(f)) break;
+
+
+ if (ln[0] == '\n') continue;
+ if (ln[0] == '#') continue;
+ numargs = getargs(ln,args,AAN+2);
+
+
+
+ for (j=0;j<numargs;j++) {
+ val=atof(args[j]);
+ a1=AAL[i];
+ a2=AAL[j];
+ p=strchr(AA,a1)-AA;
+ q=strchr(AA,a2)-AA;
+
+ MAT[p][q]=val;
+
+ }
+ i++;
+
+ }
+
+ *matave=0;
+ for (i=0;i<AAN;i++) for (j=0;j<AAN;j++) *matave+=MAT[i][j];
+ *matave/=(AAN*AAN);
+
+
+ fclose(f);
+
+
+}
+
+
+int getargs(char *line,char *args[],int max)
+{
+ char *inptr;
+ int i;
+
+ inptr=line;
+ for (i=0;i<max;i++) {
+ if ((args[i]=strtok(inptr," \t\n"))==NULL)
+ break;
+ inptr=NULL;
+
+ }
+
+ return(i);
+
+}
+
+void *my_malloc(size_t size)
+{
+
+ void *new_mem;
+
+ if (size == 0)
+ return NULL;
+ new_mem = malloc(size);
+ if (new_mem == NULL) {
+ fprintf(stderr, "can't allocate enough memory: %d bytes\n", size);
+ }
+ return new_mem;
+}
+
+
+
+double **DMatrix(int n_rows, int n_cols)
+{
+ double **matrix;
+ int i,j;
+
+ matrix = (double **) my_malloc(n_rows*sizeof(double *));
+ matrix[0] = (double *) my_malloc(n_rows*n_cols*sizeof(double));
+
+ for (i = 1; i < n_rows; i++)
+ matrix[i] = matrix[i-1] + n_cols;
+ for (i=0;i<n_rows;i++) for (j=0;j<n_cols;j++) matrix[i][j]=0;
+
+ return matrix;
+
+}
+
+
+void Get_Seq(char *fn, SEQ_STR *SEQ)
+{
+ char line[ML];
+ char c=0;
+ int j;
+ FILE *f;
+
+ if ((fn==NULL)||(strlen(fn)==0)) {
+ printf("No sequence filename\n"),exit(1);
+ }
+
+ if ((f=fopen(fn,"r"))==NULL) {
+ printf("Could not open %s\n",fn),exit(1);
+ }
+
+
+ SEQ->seq=calloc(MSL,sizeof(char));
+
+ fgets(line,ML,f);
+ sscanf(&line[1],"%s",SEQ->name);
+
+
+ j=0;
+ while ((c!='>') && (!feof(f))) {
+ c=fgetc(f);
+ if (isalpha((int)(c))) {
+ SEQ->seq[j]=c;
+ j++;
+ if ((j>0)&&(j%MSL==0)) {
+ SEQ->seq=realloc(SEQ->seq,(j+MSL)*sizeof(char));
+ }
+ }
+ }
+ SEQ->le=j;
+
+#ifdef DEBUG
+ printf("%s %5d\n%s\n",SEQ->name,SEQ->le,SEQ->seq);
+#endif
+
+
+}
+
+
--- /dev/null
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+ 0 G 1 A -0.40578783
+ 0 G 2 V -0.37910502
+ 0 G 3 L -0.54873266
+ 0 G 4 I -0.65126784
+ 0 G 5 F 0.35032415
+ 0 G 6 P 2.25263848
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+ 0 G 12 Y -1.90348864
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--- /dev/null
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git://source.jalview.org / jabaws.git / commitdiff