/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* GROningen Mixture of Alchemy and Childrens' Stories
*/
#include "gmxfio.h"
typedef struct {
- int ai,aj;
+ int ai, aj;
} gmx_conection_t;
typedef struct gmx_conect_t {
- int nconect;
- gmx_bool bSorted;
- gmx_conection_t *conect;
+ int nconect;
+ gmx_bool bSorted;
+ gmx_conection_t *conect;
} gmx_conect_t;
-static const char *pdbtp[epdbNR]={
- "ATOM ","HETATM", "ANISOU", "CRYST1",
- "COMPND", "MODEL", "ENDMDL", "TER", "HEADER", "TITLE", "REMARK",
- "CONECT"
+static const char *pdbtp[epdbNR] = {
+ "ATOM ", "HETATM", "ANISOU", "CRYST1",
+ "COMPND", "MODEL", "ENDMDL", "TER", "HEADER", "TITLE", "REMARK",
+ "CONECT"
};
-/* this is not very good,
+/* this is not very good,
but these are only used in gmx_trjconv and gmx_editconv */
-static gmx_bool bWideFormat=FALSE;
+static gmx_bool bWideFormat = FALSE;
#define REMARK_SIM_BOX "REMARK THIS IS A SIMULATION BOX"
void set_pdb_wide_format(gmx_bool bSet)
{
- bWideFormat = bSet;
+ bWideFormat = bSet;
}
static void xlate_atomname_pdb2gmx(char *name)
{
- int i,length;
- char temp;
-
- length=strlen(name);
- if (length>3 && isdigit(name[0])) {
- temp=name[0];
- for(i=1; i<length; i++)
- name[i-1]=name[i];
- name[length-1]=temp;
- }
+ int i, length;
+ char temp;
+
+ length = strlen(name);
+ if (length > 3 && isdigit(name[0]))
+ {
+ temp = name[0];
+ for (i = 1; i < length; i++)
+ {
+ name[i-1] = name[i];
+ }
+ name[length-1] = temp;
+ }
}
static void xlate_atomname_gmx2pdb(char *name)
{
- int i,length;
- char temp;
-
- length=strlen(name);
- if (length>3 && isdigit(name[length-1])) {
- temp=name[length-1];
- for(i=length-1; i>0; --i)
- name[i]=name[i-1];
- name[0]=temp;
- }
+ int i, length;
+ char temp;
+
+ length = strlen(name);
+ if (length > 3 && isdigit(name[length-1]))
+ {
+ temp = name[length-1];
+ for (i = length-1; i > 0; --i)
+ {
+ name[i] = name[i-1];
+ }
+ name[0] = temp;
+ }
}
-void gmx_write_pdb_box(FILE *out,int ePBC,matrix box)
+void gmx_write_pdb_box(FILE *out, int ePBC, matrix box)
{
- real alpha,beta,gamma;
-
- if (ePBC == -1)
- ePBC = guess_ePBC(box);
-
- if (ePBC == epbcNONE)
- return;
-
- if (norm2(box[YY])*norm2(box[ZZ])!=0)
- alpha = RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ]));
- else
- alpha = 90;
- if (norm2(box[XX])*norm2(box[ZZ])!=0)
- beta = RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ]));
- else
- beta = 90;
- if (norm2(box[XX])*norm2(box[YY])!=0)
- gamma = RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY]));
- else
- gamma = 90;
- fprintf(out,"REMARK THIS IS A SIMULATION BOX\n");
- if (ePBC != epbcSCREW) {
- fprintf(out,"CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
- 10*norm(box[XX]),10*norm(box[YY]),10*norm(box[ZZ]),
- alpha,beta,gamma,"P 1",1);
- } else {
- /* Double the a-vector length and write the correct space group */
- fprintf(out,"CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
- 20*norm(box[XX]),10*norm(box[YY]),10*norm(box[ZZ]),
- alpha,beta,gamma,"P 21 1 1",1);
-
- }
+ real alpha, beta, gamma;
+
+ if (ePBC == -1)
+ {
+ ePBC = guess_ePBC(box);
+ }
+
+ if (ePBC == epbcNONE)
+ {
+ return;
+ }
+
+ if (norm2(box[YY])*norm2(box[ZZ]) != 0)
+ {
+ alpha = RAD2DEG*acos(cos_angle_no_table(box[YY], box[ZZ]));
+ }
+ else
+ {
+ alpha = 90;
+ }
+ if (norm2(box[XX])*norm2(box[ZZ]) != 0)
+ {
+ beta = RAD2DEG*acos(cos_angle_no_table(box[XX], box[ZZ]));
+ }
+ else
+ {
+ beta = 90;
+ }
+ if (norm2(box[XX])*norm2(box[YY]) != 0)
+ {
+ gamma = RAD2DEG*acos(cos_angle_no_table(box[XX], box[YY]));
+ }
+ else
+ {
+ gamma = 90;
+ }
+ fprintf(out, "REMARK THIS IS A SIMULATION BOX\n");
+ if (ePBC != epbcSCREW)
+ {
+ fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
+ 10*norm(box[XX]), 10*norm(box[YY]), 10*norm(box[ZZ]),
+ alpha, beta, gamma, "P 1", 1);
+ }
+ else
+ {
+ /* Double the a-vector length and write the correct space group */
+ fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
+ 20*norm(box[XX]), 10*norm(box[YY]), 10*norm(box[ZZ]),
+ alpha, beta, gamma, "P 21 1 1", 1);
+
+ }
}
-static void read_cryst1(char *line,int *ePBC,matrix box)
+static void read_cryst1(char *line, int *ePBC, matrix box)
{
#define SG_SIZE 11
- char sa[12],sb[12],sc[12],sg[SG_SIZE+1],ident;
- double fa,fb,fc,alpha,beta,gamma,cosa,cosb,cosg,sing;
- int syma,symb,symc;
- int ePBC_file;
-
- sscanf(line,"%*s%s%s%s%lf%lf%lf",sa,sb,sc,&alpha,&beta,&gamma);
-
- ePBC_file = -1;
- if (strlen(line) >= 55) {
- strncpy(sg,line+55,SG_SIZE);
- sg[SG_SIZE] = '\0';
- ident = ' ';
- syma = 0;
- symb = 0;
- symc = 0;
- sscanf(sg,"%c %d %d %d",&ident,&syma,&symb,&symc);
- if (ident == 'P' && syma == 1 && symb <= 1 && symc <= 1) {
- fc = strtod(sc,NULL)*0.1;
- ePBC_file = (fc > 0 ? epbcXYZ : epbcXY);
- }
- if (ident == 'P' && syma == 21 && symb == 1 && symc == 1) {
- ePBC_file = epbcSCREW;
- }
- }
- if (ePBC) {
- *ePBC = ePBC_file;
- }
-
- if (box) {
- fa = strtod(sa,NULL)*0.1;
- fb = strtod(sb,NULL)*0.1;
- fc = strtod(sc,NULL)*0.1;
- if (ePBC_file == epbcSCREW) {
- fa *= 0.5;
- }
- clear_mat(box);
- box[XX][XX] = fa;
- if ((alpha!=90.0) || (beta!=90.0) || (gamma!=90.0)) {
- if (alpha != 90.0) {
- cosa = cos(alpha*DEG2RAD);
- } else {
- cosa = 0;
- }
- if (beta != 90.0) {
- cosb = cos(beta*DEG2RAD);
- } else {
- cosb = 0;
- }
- if (gamma != 90.0) {
- cosg = cos(gamma*DEG2RAD);
- sing = sin(gamma*DEG2RAD);
- } else {
- cosg = 0;
- sing = 1;
- }
- box[YY][XX] = fb*cosg;
- box[YY][YY] = fb*sing;
- box[ZZ][XX] = fc*cosb;
- box[ZZ][YY] = fc*(cosa - cosb*cosg)/sing;
- box[ZZ][ZZ] = sqrt(fc*fc
- - box[ZZ][XX]*box[ZZ][XX] - box[ZZ][YY]*box[ZZ][YY]);
- } else {
- box[YY][YY] = fb;
- box[ZZ][ZZ] = fc;
- }
- }
+ char sa[12], sb[12], sc[12], sg[SG_SIZE+1], ident;
+ double fa, fb, fc, alpha, beta, gamma, cosa, cosb, cosg, sing;
+ int syma, symb, symc;
+ int ePBC_file;
+
+ sscanf(line, "%*s%s%s%s%lf%lf%lf", sa, sb, sc, &alpha, &beta, &gamma);
+
+ ePBC_file = -1;
+ if (strlen(line) >= 55)
+ {
+ strncpy(sg, line+55, SG_SIZE);
+ sg[SG_SIZE] = '\0';
+ ident = ' ';
+ syma = 0;
+ symb = 0;
+ symc = 0;
+ sscanf(sg, "%c %d %d %d", &ident, &syma, &symb, &symc);
+ if (ident == 'P' && syma == 1 && symb <= 1 && symc <= 1)
+ {
+ fc = strtod(sc, NULL)*0.1;
+ ePBC_file = (fc > 0 ? epbcXYZ : epbcXY);
+ }
+ if (ident == 'P' && syma == 21 && symb == 1 && symc == 1)
+ {
+ ePBC_file = epbcSCREW;
+ }
+ }
+ if (ePBC)
+ {
+ *ePBC = ePBC_file;
+ }
+
+ if (box)
+ {
+ fa = strtod(sa, NULL)*0.1;
+ fb = strtod(sb, NULL)*0.1;
+ fc = strtod(sc, NULL)*0.1;
+ if (ePBC_file == epbcSCREW)
+ {
+ fa *= 0.5;
+ }
+ clear_mat(box);
+ box[XX][XX] = fa;
+ if ((alpha != 90.0) || (beta != 90.0) || (gamma != 90.0))
+ {
+ if (alpha != 90.0)
+ {
+ cosa = cos(alpha*DEG2RAD);
+ }
+ else
+ {
+ cosa = 0;
+ }
+ if (beta != 90.0)
+ {
+ cosb = cos(beta*DEG2RAD);
+ }
+ else
+ {
+ cosb = 0;
+ }
+ if (gamma != 90.0)
+ {
+ cosg = cos(gamma*DEG2RAD);
+ sing = sin(gamma*DEG2RAD);
+ }
+ else
+ {
+ cosg = 0;
+ sing = 1;
+ }
+ box[YY][XX] = fb*cosg;
+ box[YY][YY] = fb*sing;
+ box[ZZ][XX] = fc*cosb;
+ box[ZZ][YY] = fc*(cosa - cosb*cosg)/sing;
+ box[ZZ][ZZ] = sqrt(fc*fc
+ - box[ZZ][XX]*box[ZZ][XX] - box[ZZ][YY]*box[ZZ][YY]);
+ }
+ else
+ {
+ box[YY][YY] = fb;
+ box[ZZ][ZZ] = fc;
+ }
+ }
}
-
-void write_pdbfile_indexed(FILE *out,const char *title,
- t_atoms *atoms,rvec x[],
- int ePBC,matrix box,char chainid,
- int model_nr, atom_id nindex, const atom_id index[],
- gmx_conect conect, gmx_bool bTerSepChains)
+
+void write_pdbfile_indexed(FILE *out, const char *title,
+ t_atoms *atoms, rvec x[],
+ int ePBC, matrix box, char chainid,
+ int model_nr, atom_id nindex, const atom_id index[],
+ gmx_conect conect, gmx_bool bTerSepChains)
{
- gmx_conect_t *gc = (gmx_conect_t *)conect;
- char resnm[6],nm[6],pdbform[128],pukestring[100];
- atom_id i,ii;
- int resind,resnr,type;
- unsigned char resic,ch;
- real occup,bfac;
- gmx_bool bOccup;
- int nlongname=0;
- int chainnum,lastchainnum;
- int lastresind,lastchainresind;
- gmx_residuetype_t rt;
- const char *p_restype;
- const char *p_lastrestype;
-
- gmx_residuetype_init(&rt);
-
- bromacs(pukestring,99);
- fprintf(out,"TITLE %s\n",(title && title[0])?title:pukestring);
- if (bWideFormat) {
- fprintf(out,"REMARK This file does not adhere to the PDB standard\n");
- fprintf(out,"REMARK As a result of, some programs may not like it\n");
- }
- if (box && ( norm2(box[XX]) || norm2(box[YY]) || norm2(box[ZZ]) ) ) {
- gmx_write_pdb_box(out,ePBC,box);
- }
- if (atoms->pdbinfo) {
- /* Check whether any occupancies are set, in that case leave it as is,
- * otherwise set them all to one
- */
- bOccup = TRUE;
- for (ii=0; (ii<nindex) && bOccup; ii++) {
- i = index[ii];
- bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
- }
- }
- else
- bOccup = FALSE;
-
- fprintf(out,"MODEL %8d\n",model_nr>0 ? model_nr : 1);
-
- lastchainresind = -1;
- lastchainnum = -1;
- resind = -1;
- p_restype = NULL;
-
- for (ii=0; ii<nindex; ii++) {
- i=index[ii];
- lastresind = resind;
- resind = atoms->atom[i].resind;
- chainnum = atoms->resinfo[resind].chainnum;
- p_lastrestype = p_restype;
- gmx_residuetype_get_type(rt,*atoms->resinfo[resind].name,&p_restype);
-
- /* Add a TER record if we changed chain, and if either the previous or this chain is protein/DNA/RNA. */
- if( bTerSepChains && ii>0 && chainnum != lastchainnum)
- {
- /* Only add TER if the previous chain contained protein/DNA/RNA. */
- if(gmx_residuetype_is_protein(rt,p_lastrestype) || gmx_residuetype_is_dna(rt,p_lastrestype) || gmx_residuetype_is_rna(rt,p_lastrestype))
- {
- fprintf(out,"TER\n");
- }
- lastchainnum = chainnum;
- lastchainresind = lastresind;
- }
-
- strncpy(resnm,*atoms->resinfo[resind].name,sizeof(resnm)-1);
- strncpy(nm,*atoms->atomname[i],sizeof(nm)-1);
- /* rename HG12 to 2HG1, etc. */
- xlate_atomname_gmx2pdb(nm);
- resnr = atoms->resinfo[resind].nr;
- resic = atoms->resinfo[resind].ic;
- if (chainid!=' ')
- {
- ch = chainid;
+ gmx_conect_t *gc = (gmx_conect_t *)conect;
+ char resnm[6], nm[6], pdbform[128], pukestring[100];
+ atom_id i, ii;
+ int resind, resnr, type;
+ unsigned char resic, ch;
+ real occup, bfac;
+ gmx_bool bOccup;
+ int nlongname = 0;
+ int chainnum, lastchainnum;
+ int lastresind, lastchainresind;
+ gmx_residuetype_t rt;
+ const char *p_restype;
+ const char *p_lastrestype;
+
+ gmx_residuetype_init(&rt);
+
+ bromacs(pukestring, 99);
+ fprintf(out, "TITLE %s\n", (title && title[0]) ? title : pukestring);
+ if (bWideFormat)
+ {
+ fprintf(out, "REMARK This file does not adhere to the PDB standard\n");
+ fprintf(out, "REMARK As a result of, some programs may not like it\n");
+ }
+ if (box && ( norm2(box[XX]) || norm2(box[YY]) || norm2(box[ZZ]) ) )
+ {
+ gmx_write_pdb_box(out, ePBC, box);
+ }
+ if (atoms->pdbinfo)
+ {
+ /* Check whether any occupancies are set, in that case leave it as is,
+ * otherwise set them all to one
+ */
+ bOccup = TRUE;
+ for (ii = 0; (ii < nindex) && bOccup; ii++)
+ {
+ i = index[ii];
+ bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
+ }
}
else
{
- ch = atoms->resinfo[resind].chainid;
-
- if (ch == 0)
- {
- ch = ' ';
- }
+ bOccup = FALSE;
}
- if (resnr>=10000)
- resnr = resnr % 10000;
- if (atoms->pdbinfo) {
- type = atoms->pdbinfo[i].type;
- occup = bOccup ? 1.0 : atoms->pdbinfo[i].occup;
- bfac = atoms->pdbinfo[i].bfac;
+
+ fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
+
+ lastchainresind = -1;
+ lastchainnum = -1;
+ resind = -1;
+ p_restype = NULL;
+
+ for (ii = 0; ii < nindex; ii++)
+ {
+ i = index[ii];
+ lastresind = resind;
+ resind = atoms->atom[i].resind;
+ chainnum = atoms->resinfo[resind].chainnum;
+ p_lastrestype = p_restype;
+ gmx_residuetype_get_type(rt, *atoms->resinfo[resind].name, &p_restype);
+
+ /* Add a TER record if we changed chain, and if either the previous or this chain is protein/DNA/RNA. */
+ if (bTerSepChains && ii > 0 && chainnum != lastchainnum)
+ {
+ /* Only add TER if the previous chain contained protein/DNA/RNA. */
+ if (gmx_residuetype_is_protein(rt, p_lastrestype) || gmx_residuetype_is_dna(rt, p_lastrestype) || gmx_residuetype_is_rna(rt, p_lastrestype))
+ {
+ fprintf(out, "TER\n");
+ }
+ lastchainnum = chainnum;
+ lastchainresind = lastresind;
+ }
+
+ strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
+ strncpy(nm, *atoms->atomname[i], sizeof(nm)-1);
+ /* rename HG12 to 2HG1, etc. */
+ xlate_atomname_gmx2pdb(nm);
+ resnr = atoms->resinfo[resind].nr;
+ resic = atoms->resinfo[resind].ic;
+ if (chainid != ' ')
+ {
+ ch = chainid;
+ }
+ else
+ {
+ ch = atoms->resinfo[resind].chainid;
+
+ if (ch == 0)
+ {
+ ch = ' ';
+ }
+ }
+ if (resnr >= 10000)
+ {
+ resnr = resnr % 10000;
+ }
+ if (atoms->pdbinfo)
+ {
+ type = atoms->pdbinfo[i].type;
+ occup = bOccup ? 1.0 : atoms->pdbinfo[i].occup;
+ bfac = atoms->pdbinfo[i].bfac;
+ }
+ else
+ {
+ type = 0;
+ occup = 1.0;
+ bfac = 0.0;
+ }
+ if (bWideFormat)
+ {
+ strcpy(pdbform,
+ "%-6s%5u %-4.4s %3.3s %c%4d%c %10.5f%10.5f%10.5f%8.4f%8.4f %2s\n");
+ }
+ else
+ {
+ /* Check whether atomname is an element name */
+ if ((strlen(nm) < 4) && (gmx_strcasecmp(nm, atoms->atom[i].elem) != 0))
+ {
+ strcpy(pdbform, get_pdbformat());
+ }
+ else
+ {
+ strcpy(pdbform, get_pdbformat4());
+ if (strlen(nm) > 4)
+ {
+ int maxwln = 20;
+ if (nlongname < maxwln)
+ {
+ fprintf(stderr, "WARNING: Writing out atom name (%s) longer than 4 characters to .pdb file\n", nm);
+ }
+ else if (nlongname == maxwln)
+ {
+ fprintf(stderr, "WARNING: More than %d long atom names, will not write more warnings\n", maxwln);
+ }
+ nlongname++;
+ }
+ }
+ strcat(pdbform, "%6.2f%6.2f %2s\n");
+ }
+ fprintf(out, pdbform, pdbtp[type], (i+1)%100000, nm, resnm, ch, resnr,
+ (resic == '\0') ? ' ' : resic,
+ 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], occup, bfac, atoms->atom[i].elem);
+ if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
+ {
+ fprintf(out, "ANISOU%5u %-4.4s%3.3s %c%4d%c %7d%7d%7d%7d%7d%7d\n",
+ (i+1)%100000, nm, resnm, ch, resnr,
+ (resic == '\0') ? ' ' : resic,
+ atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1],
+ atoms->pdbinfo[i].uij[2], atoms->pdbinfo[i].uij[3],
+ atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
+ }
}
- else {
- type = 0;
- occup = 1.0;
- bfac = 0.0;
+
+ fprintf(out, "TER\n");
+ fprintf(out, "ENDMDL\n");
+
+ if (NULL != gc)
+ {
+ /* Write conect records */
+ for (i = 0; (i < gc->nconect); i++)
+ {
+ fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai+1, gc->conect[i].aj+1);
+ }
}
- if (bWideFormat)
- strcpy(pdbform,
- "%-6s%5u %-4.4s %3.3s %c%4d%c %10.5f%10.5f%10.5f%8.4f%8.4f %2s\n");
- else {
- /* Check whether atomname is an element name */
- if ((strlen(nm)<4) && (gmx_strcasecmp(nm,atoms->atom[i].elem) != 0))
- strcpy(pdbform,get_pdbformat());
- else {
- strcpy(pdbform,get_pdbformat4());
- if (strlen(nm) > 4) {
- int maxwln=20;
- if (nlongname < maxwln) {
- fprintf(stderr,"WARNING: Writing out atom name (%s) longer than 4 characters to .pdb file\n",nm);
- } else if (nlongname == maxwln) {
- fprintf(stderr,"WARNING: More than %d long atom names, will not write more warnings\n",maxwln);
- }
- nlongname++;
- }
- }
- strcat(pdbform,"%6.2f%6.2f %2s\n");
- }
- fprintf(out,pdbform,pdbtp[type],(i+1)%100000,nm,resnm,ch,resnr,
- (resic == '\0') ? ' ' : resic,
- 10*x[i][XX],10*x[i][YY],10*x[i][ZZ],occup,bfac,atoms->atom[i].elem);
- if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic) {
- fprintf(out,"ANISOU%5u %-4.4s%3.3s %c%4d%c %7d%7d%7d%7d%7d%7d\n",
- (i+1)%100000,nm,resnm,ch,resnr,
- (resic == '\0') ? ' ' : resic,
- atoms->pdbinfo[i].uij[0],atoms->pdbinfo[i].uij[1],
- atoms->pdbinfo[i].uij[2],atoms->pdbinfo[i].uij[3],
- atoms->pdbinfo[i].uij[4],atoms->pdbinfo[i].uij[5]);
- }
- }
-
- fprintf(out,"TER\n");
- fprintf(out,"ENDMDL\n");
-
- if (NULL != gc) {
- /* Write conect records */
- for(i=0; (i<gc->nconect); i++) {
- fprintf(out,"CONECT%5d%5d\n",gc->conect[i].ai+1,gc->conect[i].aj+1);
- }
- }
-
- gmx_residuetype_destroy(rt);
+
+ gmx_residuetype_destroy(rt);
}
-void write_pdbfile(FILE *out,const char *title, t_atoms *atoms,rvec x[],
- int ePBC,matrix box,char chainid,int model_nr,gmx_conect conect,gmx_bool bTerSepChains)
+void write_pdbfile(FILE *out, const char *title, t_atoms *atoms, rvec x[],
+ int ePBC, matrix box, char chainid, int model_nr, gmx_conect conect, gmx_bool bTerSepChains)
{
- atom_id i,*index;
-
- snew(index,atoms->nr);
- for(i=0; i<atoms->nr; i++)
- index[i]=i;
- write_pdbfile_indexed(out,title,atoms,x,ePBC,box,chainid,model_nr,
- atoms->nr,index,conect,bTerSepChains);
- sfree(index);
+ atom_id i, *index;
+
+ snew(index, atoms->nr);
+ for (i = 0; i < atoms->nr; i++)
+ {
+ index[i] = i;
+ }
+ write_pdbfile_indexed(out, title, atoms, x, ePBC, box, chainid, model_nr,
+ atoms->nr, index, conect, bTerSepChains);
+ sfree(index);
}
int line2type(char *line)
{
- int k;
- char type[8];
-
- for(k=0; (k<6); k++)
- type[k]=line[k];
- type[k]='\0';
-
- for(k=0; (k<epdbNR); k++)
- if (strncmp(type,pdbtp[k],strlen(pdbtp[k])) == 0)
- break;
-
- return k;
+ int k;
+ char type[8];
+
+ for (k = 0; (k < 6); k++)
+ {
+ type[k] = line[k];
+ }
+ type[k] = '\0';
+
+ for (k = 0; (k < epdbNR); k++)
+ {
+ if (strncmp(type, pdbtp[k], strlen(pdbtp[k])) == 0)
+ {
+ break;
+ }
+ }
+
+ return k;
}
-static void read_anisou(char line[],int natom,t_atoms *atoms)
+static void read_anisou(char line[], int natom, t_atoms *atoms)
{
- int i,j,k,atomnr;
- char nc='\0';
- char anr[12],anm[12];
-
- /* Skip over type */
- j=6;
- for(k=0; (k<5); k++,j++) anr[k]=line[j];
- anr[k]=nc;
- j++;
- for(k=0; (k<4); k++,j++) anm[k]=line[j];
- anm[k]=nc;
- j++;
-
- /* Strip off spaces */
- trim(anm);
-
- /* Search backwards for number and name only */
- atomnr = strtol(anr, NULL, 10);
- for(i=natom-1; (i>=0); i--)
- if ((strcmp(anm,*(atoms->atomname[i])) == 0) &&
- (atomnr == atoms->pdbinfo[i].atomnr))
- break;
- if (i < 0)
- fprintf(stderr,"Skipping ANISOU record (atom %s %d not found)\n",
- anm,atomnr);
- else {
- if (sscanf(line+29,"%d%d%d%d%d%d",
- &atoms->pdbinfo[i].uij[U11],&atoms->pdbinfo[i].uij[U22],
- &atoms->pdbinfo[i].uij[U33],&atoms->pdbinfo[i].uij[U12],
- &atoms->pdbinfo[i].uij[U13],&atoms->pdbinfo[i].uij[U23])
- == 6) {
- atoms->pdbinfo[i].bAnisotropic = TRUE;
- }
- else {
- fprintf(stderr,"Invalid ANISOU record for atom %d\n",i);
- atoms->pdbinfo[i].bAnisotropic = FALSE;
- }
- }
+ int i, j, k, atomnr;
+ char nc = '\0';
+ char anr[12], anm[12];
+
+ /* Skip over type */
+ j = 6;
+ for (k = 0; (k < 5); k++, j++)
+ {
+ anr[k] = line[j];
+ }
+ anr[k] = nc;
+ j++;
+ for (k = 0; (k < 4); k++, j++)
+ {
+ anm[k] = line[j];
+ }
+ anm[k] = nc;
+ j++;
+
+ /* Strip off spaces */
+ trim(anm);
+
+ /* Search backwards for number and name only */
+ atomnr = strtol(anr, NULL, 10);
+ for (i = natom-1; (i >= 0); i--)
+ {
+ if ((strcmp(anm, *(atoms->atomname[i])) == 0) &&
+ (atomnr == atoms->pdbinfo[i].atomnr))
+ {
+ break;
+ }
+ }
+ if (i < 0)
+ {
+ fprintf(stderr, "Skipping ANISOU record (atom %s %d not found)\n",
+ anm, atomnr);
+ }
+ else
+ {
+ if (sscanf(line+29, "%d%d%d%d%d%d",
+ &atoms->pdbinfo[i].uij[U11], &atoms->pdbinfo[i].uij[U22],
+ &atoms->pdbinfo[i].uij[U33], &atoms->pdbinfo[i].uij[U12],
+ &atoms->pdbinfo[i].uij[U13], &atoms->pdbinfo[i].uij[U23])
+ == 6)
+ {
+ atoms->pdbinfo[i].bAnisotropic = TRUE;
+ }
+ else
+ {
+ fprintf(stderr, "Invalid ANISOU record for atom %d\n", i);
+ atoms->pdbinfo[i].bAnisotropic = FALSE;
+ }
+ }
}
-void get_pdb_atomnumber(t_atoms *atoms,gmx_atomprop_t aps)
+void get_pdb_atomnumber(t_atoms *atoms, gmx_atomprop_t aps)
{
- int i,atomnumber,len;
- size_t k;
- char anm[6],anm_copy[6],*ptr;
- char nc='\0';
- real eval;
-
- if (!atoms->pdbinfo) {
- gmx_incons("Trying to deduce atomnumbers when no pdb information is present");
- }
- for(i=0; (i<atoms->nr); i++) {
- strcpy(anm,atoms->pdbinfo[i].atomnm);
- strcpy(anm_copy,atoms->pdbinfo[i].atomnm);
- len = strlen(anm);
- atomnumber = NOTSET;
- if ((anm[0] != ' ') && ((len <=2) || ((len > 2) && !isdigit(anm[2])))) {
- anm_copy[2] = nc;
- if (gmx_atomprop_query(aps,epropElement,"???",anm_copy,&eval))
- atomnumber = gmx_nint(eval);
- else {
- anm_copy[1] = nc;
- if (gmx_atomprop_query(aps,epropElement,"???",anm_copy,&eval))
- atomnumber = gmx_nint(eval);
- }
- }
- if (atomnumber == NOTSET) {
- k=0;
- while ((k < strlen(anm)) && (isspace(anm[k]) || isdigit(anm[k])))
- k++;
- anm_copy[0] = anm[k];
- anm_copy[1] = nc;
- if (gmx_atomprop_query(aps,epropElement,"???",anm_copy,&eval))
- atomnumber = gmx_nint(eval);
- }
- atoms->atom[i].atomnumber = atomnumber;
- ptr = gmx_atomprop_element(aps,atomnumber);
- strncpy(atoms->atom[i].elem,ptr==NULL ? "" : ptr,4);
- if (debug)
- fprintf(debug,"Atomnumber for atom '%s' is %d\n",anm,atomnumber);
- }
+ int i, atomnumber, len;
+ size_t k;
+ char anm[6], anm_copy[6], *ptr;
+ char nc = '\0';
+ real eval;
+
+ if (!atoms->pdbinfo)
+ {
+ gmx_incons("Trying to deduce atomnumbers when no pdb information is present");
+ }
+ for (i = 0; (i < atoms->nr); i++)
+ {
+ strcpy(anm, atoms->pdbinfo[i].atomnm);
+ strcpy(anm_copy, atoms->pdbinfo[i].atomnm);
+ len = strlen(anm);
+ atomnumber = NOTSET;
+ if ((anm[0] != ' ') && ((len <= 2) || ((len > 2) && !isdigit(anm[2]))))
+ {
+ anm_copy[2] = nc;
+ if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ {
+ atomnumber = gmx_nint(eval);
+ }
+ else
+ {
+ anm_copy[1] = nc;
+ if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ {
+ atomnumber = gmx_nint(eval);
+ }
+ }
+ }
+ if (atomnumber == NOTSET)
+ {
+ k = 0;
+ while ((k < strlen(anm)) && (isspace(anm[k]) || isdigit(anm[k])))
+ {
+ k++;
+ }
+ anm_copy[0] = anm[k];
+ anm_copy[1] = nc;
+ if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ {
+ atomnumber = gmx_nint(eval);
+ }
+ }
+ atoms->atom[i].atomnumber = atomnumber;
+ ptr = gmx_atomprop_element(aps, atomnumber);
+ strncpy(atoms->atom[i].elem, ptr == NULL ? "" : ptr, 4);
+ if (debug)
+ {
+ fprintf(debug, "Atomnumber for atom '%s' is %d\n", anm, atomnumber);
+ }
+ }
}
static int read_atom(t_symtab *symtab,
- char line[],int type,int natom,
- t_atoms *atoms,rvec x[],int chainnum,gmx_bool bChange)
+ char line[], int type, int natom,
+ t_atoms *atoms, rvec x[], int chainnum, gmx_bool bChange)
{
- t_atom *atomn;
- int j,k;
- char nc='\0';
- char anr[12],anm[12],anm_copy[12],altloc,resnm[12],rnr[12];
- char xc[12],yc[12],zc[12],occup[12],bfac[12];
- unsigned char resic;
- char chainid;
- int resnr,atomnumber;
-
- if (natom>=atoms->nr)
- gmx_fatal(FARGS,"\nFound more atoms (%d) in pdb file than expected (%d)",
- natom+1,atoms->nr);
-
- /* Skip over type */
- j=6;
- for(k=0; (k<5); k++,j++) anr[k]=line[j];
- anr[k]=nc;
- trim(anr);
- j++;
- for(k=0; (k<4); k++,j++) anm[k]=line[j];
- anm[k]=nc;
- strcpy(anm_copy,anm);
- rtrim(anm_copy);
- atomnumber = NOTSET;
- trim(anm);
- altloc=line[j];
- j++;
- for(k=0; (k<4); k++,j++)
- resnm[k]=line[j];
- resnm[k]=nc;
- trim(resnm);
-
- chainid = line[j];
- j++;
-
- for(k=0; (k<4); k++,j++) {
- rnr[k] = line[j];
- }
- rnr[k] = nc;
- trim(rnr);
- resnr = strtol(rnr, NULL, 10);
- resic = line[j];
- j+=4;
-
- /* X,Y,Z Coordinate */
- for(k=0; (k<8); k++,j++) xc[k]=line[j];
- xc[k]=nc;
- for(k=0; (k<8); k++,j++) yc[k]=line[j];
- yc[k]=nc;
- for(k=0; (k<8); k++,j++) zc[k]=line[j];
- zc[k]=nc;
-
- /* Weight */
- for(k=0; (k<6); k++,j++) occup[k]=line[j];
- occup[k]=nc;
-
- /* B-Factor */
- for(k=0; (k<7); k++,j++) bfac[k]=line[j];
- bfac[k]=nc;
-
- if (atoms->atom) {
- atomn=&(atoms->atom[natom]);
- if ((natom==0) ||
- atoms->resinfo[atoms->atom[natom-1].resind].nr != resnr ||
- atoms->resinfo[atoms->atom[natom-1].resind].ic != resic ||
- (strcmp(*atoms->resinfo[atoms->atom[natom-1].resind].name,resnm) != 0))
- {
- if (natom == 0) {
- atomn->resind = 0;
- } else {
- atomn->resind = atoms->atom[natom-1].resind + 1;
- }
- atoms->nres = atomn->resind + 1;
- t_atoms_set_resinfo(atoms,natom,symtab,resnm,resnr,resic,chainnum,chainid);
+ t_atom *atomn;
+ int j, k;
+ char nc = '\0';
+ char anr[12], anm[12], anm_copy[12], altloc, resnm[12], rnr[12];
+ char xc[12], yc[12], zc[12], occup[12], bfac[12];
+ unsigned char resic;
+ char chainid;
+ int resnr, atomnumber;
+
+ if (natom >= atoms->nr)
+ {
+ gmx_fatal(FARGS, "\nFound more atoms (%d) in pdb file than expected (%d)",
+ natom+1, atoms->nr);
}
- else
+
+ /* Skip over type */
+ j = 6;
+ for (k = 0; (k < 5); k++, j++)
+ {
+ anr[k] = line[j];
+ }
+ anr[k] = nc;
+ trim(anr);
+ j++;
+ for (k = 0; (k < 4); k++, j++)
+ {
+ anm[k] = line[j];
+ }
+ anm[k] = nc;
+ strcpy(anm_copy, anm);
+ rtrim(anm_copy);
+ atomnumber = NOTSET;
+ trim(anm);
+ altloc = line[j];
+ j++;
+ for (k = 0; (k < 4); k++, j++)
+ {
+ resnm[k] = line[j];
+ }
+ resnm[k] = nc;
+ trim(resnm);
+
+ chainid = line[j];
+ j++;
+
+ for (k = 0; (k < 4); k++, j++)
{
- atomn->resind = atoms->atom[natom-1].resind;
- }
- if (bChange) {
- xlate_atomname_pdb2gmx(anm);
- }
- atoms->atomname[natom]=put_symtab(symtab,anm);
- atomn->m = 0.0;
- atomn->q = 0.0;
- atomn->atomnumber = atomnumber;
- atomn->elem[0] = '\0';
- }
- x[natom][XX]=strtod(xc,NULL)*0.1;
- x[natom][YY]=strtod(yc,NULL)*0.1;
- x[natom][ZZ]=strtod(zc,NULL)*0.1;
- if (atoms->pdbinfo) {
- atoms->pdbinfo[natom].type=type;
- atoms->pdbinfo[natom].atomnr=strtol(anr, NULL, 10);
- atoms->pdbinfo[natom].altloc=altloc;
- strcpy(atoms->pdbinfo[natom].atomnm,anm_copy);
- atoms->pdbinfo[natom].bfac=strtod(bfac,NULL);
- atoms->pdbinfo[natom].occup=strtod(occup,NULL);
- }
- natom++;
-
- return natom;
+ rnr[k] = line[j];
+ }
+ rnr[k] = nc;
+ trim(rnr);
+ resnr = strtol(rnr, NULL, 10);
+ resic = line[j];
+ j += 4;
+
+ /* X,Y,Z Coordinate */
+ for (k = 0; (k < 8); k++, j++)
+ {
+ xc[k] = line[j];
+ }
+ xc[k] = nc;
+ for (k = 0; (k < 8); k++, j++)
+ {
+ yc[k] = line[j];
+ }
+ yc[k] = nc;
+ for (k = 0; (k < 8); k++, j++)
+ {
+ zc[k] = line[j];
+ }
+ zc[k] = nc;
+
+ /* Weight */
+ for (k = 0; (k < 6); k++, j++)
+ {
+ occup[k] = line[j];
+ }
+ occup[k] = nc;
+
+ /* B-Factor */
+ for (k = 0; (k < 7); k++, j++)
+ {
+ bfac[k] = line[j];
+ }
+ bfac[k] = nc;
+
+ if (atoms->atom)
+ {
+ atomn = &(atoms->atom[natom]);
+ if ((natom == 0) ||
+ atoms->resinfo[atoms->atom[natom-1].resind].nr != resnr ||
+ atoms->resinfo[atoms->atom[natom-1].resind].ic != resic ||
+ (strcmp(*atoms->resinfo[atoms->atom[natom-1].resind].name, resnm) != 0))
+ {
+ if (natom == 0)
+ {
+ atomn->resind = 0;
+ }
+ else
+ {
+ atomn->resind = atoms->atom[natom-1].resind + 1;
+ }
+ atoms->nres = atomn->resind + 1;
+ t_atoms_set_resinfo(atoms, natom, symtab, resnm, resnr, resic, chainnum, chainid);
+ }
+ else
+ {
+ atomn->resind = atoms->atom[natom-1].resind;
+ }
+ if (bChange)
+ {
+ xlate_atomname_pdb2gmx(anm);
+ }
+ atoms->atomname[natom] = put_symtab(symtab, anm);
+ atomn->m = 0.0;
+ atomn->q = 0.0;
+ atomn->atomnumber = atomnumber;
+ atomn->elem[0] = '\0';
+ }
+ x[natom][XX] = strtod(xc, NULL)*0.1;
+ x[natom][YY] = strtod(yc, NULL)*0.1;
+ x[natom][ZZ] = strtod(zc, NULL)*0.1;
+ if (atoms->pdbinfo)
+ {
+ atoms->pdbinfo[natom].type = type;
+ atoms->pdbinfo[natom].atomnr = strtol(anr, NULL, 10);
+ atoms->pdbinfo[natom].altloc = altloc;
+ strcpy(atoms->pdbinfo[natom].atomnm, anm_copy);
+ atoms->pdbinfo[natom].bfac = strtod(bfac, NULL);
+ atoms->pdbinfo[natom].occup = strtod(occup, NULL);
+ }
+ natom++;
+
+ return natom;
}
gmx_bool is_hydrogen(const char *nm)
{
- char buf[30];
-
- strcpy(buf,nm);
- trim(buf);
-
- if (buf[0] == 'H')
- return TRUE;
- else if ((isdigit(buf[0])) && (buf[1] == 'H'))
- return TRUE;
- return FALSE;
+ char buf[30];
+
+ strcpy(buf, nm);
+ trim(buf);
+
+ if (buf[0] == 'H')
+ {
+ return TRUE;
+ }
+ else if ((isdigit(buf[0])) && (buf[1] == 'H'))
+ {
+ return TRUE;
+ }
+ return FALSE;
}
gmx_bool is_dummymass(const char *nm)
{
- char buf[30];
-
- strcpy(buf,nm);
- trim(buf);
-
- if ((buf[0] == 'M') && isdigit(buf[strlen(buf)-1]))
- return TRUE;
-
- return FALSE;
+ char buf[30];
+
+ strcpy(buf, nm);
+ trim(buf);
+
+ if ((buf[0] == 'M') && isdigit(buf[strlen(buf)-1]))
+ {
+ return TRUE;
+ }
+
+ return FALSE;
}
-static void gmx_conect_addline(gmx_conect_t *con,char *line)
+static void gmx_conect_addline(gmx_conect_t *con, char *line)
{
- int n,ai,aj;
- char format[32],form2[32];
-
- sprintf(form2,"%%*s");
- sprintf(format,"%s%%d",form2);
- if (sscanf(line,format,&ai) == 1) {
- do {
- strcat(form2,"%*s");
- sprintf(format,"%s%%d",form2);
- n = sscanf(line,format,&aj);
- if (n == 1) {
- srenew(con->conect,++con->nconect);
- con->conect[con->nconect-1].ai = ai-1;
- con->conect[con->nconect-1].aj = aj-1;
- }
- } while (n == 1);
- }
+ int n, ai, aj;
+ char format[32], form2[32];
+
+ sprintf(form2, "%%*s");
+ sprintf(format, "%s%%d", form2);
+ if (sscanf(line, format, &ai) == 1)
+ {
+ do
+ {
+ strcat(form2, "%*s");
+ sprintf(format, "%s%%d", form2);
+ n = sscanf(line, format, &aj);
+ if (n == 1)
+ {
+ srenew(con->conect, ++con->nconect);
+ con->conect[con->nconect-1].ai = ai-1;
+ con->conect[con->nconect-1].aj = aj-1;
+ }
+ }
+ while (n == 1);
+ }
}
-void gmx_conect_dump(FILE *fp,gmx_conect conect)
+void gmx_conect_dump(FILE *fp, gmx_conect conect)
{
- gmx_conect_t *gc = (gmx_conect_t *)conect;
- int i;
-
- for(i=0; (i<gc->nconect); i++)
- fprintf(fp,"%6s%5d%5d\n","CONECT",
- gc->conect[i].ai+1,gc->conect[i].aj+1);
+ gmx_conect_t *gc = (gmx_conect_t *)conect;
+ int i;
+
+ for (i = 0; (i < gc->nconect); i++)
+ {
+ fprintf(fp, "%6s%5d%5d\n", "CONECT",
+ gc->conect[i].ai+1, gc->conect[i].aj+1);
+ }
}
gmx_conect gmx_conect_init()
{
- gmx_conect_t *gc;
-
- snew(gc,1);
-
- return (gmx_conect) gc;
+ gmx_conect_t *gc;
+
+ snew(gc, 1);
+
+ return (gmx_conect) gc;
}
void gmx_conect_done(gmx_conect conect)
{
- gmx_conect_t *gc = (gmx_conect_t *)conect;
-
- sfree(gc->conect);
+ gmx_conect_t *gc = (gmx_conect_t *)conect;
+
+ sfree(gc->conect);
}
-gmx_bool gmx_conect_exist(gmx_conect conect,int ai,int aj)
+gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj)
{
- gmx_conect_t *gc = (gmx_conect_t *)conect;
- int i;
-
- /* if (!gc->bSorted)
- sort_conect(gc);*/
-
- for(i=0; (i<gc->nconect); i++)
- if (((gc->conect[i].ai == ai) &&
- (gc->conect[i].aj == aj)) ||
- ((gc->conect[i].aj == ai) &&
- (gc->conect[i].ai == aj)))
- return TRUE;
- return FALSE;
+ gmx_conect_t *gc = (gmx_conect_t *)conect;
+ int i;
+
+ /* if (!gc->bSorted)
+ sort_conect(gc);*/
+
+ for (i = 0; (i < gc->nconect); i++)
+ {
+ if (((gc->conect[i].ai == ai) &&
+ (gc->conect[i].aj == aj)) ||
+ ((gc->conect[i].aj == ai) &&
+ (gc->conect[i].ai == aj)))
+ {
+ return TRUE;
+ }
+ }
+ return FALSE;
}
-void gmx_conect_add(gmx_conect conect,int ai,int aj)
+void gmx_conect_add(gmx_conect conect, int ai, int aj)
{
- gmx_conect_t *gc = (gmx_conect_t *)conect;
- int i;
-
- /* if (!gc->bSorted)
- sort_conect(gc);*/
-
- if (!gmx_conect_exist(conect,ai,aj)) {
- srenew(gc->conect,++gc->nconect);
- gc->conect[gc->nconect-1].ai = ai;
- gc->conect[gc->nconect-1].aj = aj;
- }
+ gmx_conect_t *gc = (gmx_conect_t *)conect;
+ int i;
+
+ /* if (!gc->bSorted)
+ sort_conect(gc);*/
+
+ if (!gmx_conect_exist(conect, ai, aj))
+ {
+ srenew(gc->conect, ++gc->nconect);
+ gc->conect[gc->nconect-1].ai = ai;
+ gc->conect[gc->nconect-1].aj = aj;
+ }
}
-int read_pdbfile(FILE *in,char *title,int *model_nr,
- t_atoms *atoms,rvec x[],int *ePBC,matrix box,gmx_bool bChange,
- gmx_conect conect)
+int read_pdbfile(FILE *in, char *title, int *model_nr,
+ t_atoms *atoms, rvec x[], int *ePBC, matrix box, gmx_bool bChange,
+ gmx_conect conect)
{
gmx_conect_t *gc = (gmx_conect_t *)conect;
- t_symtab symtab;
- gmx_bool bCOMPND;
- gmx_bool bConnWarn = FALSE;
- char line[STRLEN+1];
- int line_type;
- char *c,*d;
- int natom,chainnum,nres_ter_prev=0;
- char chidmax=' ';
- gmx_bool bStop=FALSE;
-
- if (ePBC)
+ t_symtab symtab;
+ gmx_bool bCOMPND;
+ gmx_bool bConnWarn = FALSE;
+ char line[STRLEN+1];
+ int line_type;
+ char *c, *d;
+ int natom, chainnum, nres_ter_prev = 0;
+ char chidmax = ' ';
+ gmx_bool bStop = FALSE;
+
+ if (ePBC)
{
/* Only assume pbc when there is a CRYST1 entry */
*ePBC = epbcNONE;
}
- if (box != NULL)
+ if (box != NULL)
{
clear_mat(box);
}
-
+
open_symtab(&symtab);
- bCOMPND=FALSE;
- title[0]='\0';
- natom=0;
- chainnum=0;
- while (!bStop && (fgets2(line,STRLEN,in) != NULL))
+ bCOMPND = FALSE;
+ title[0] = '\0';
+ natom = 0;
+ chainnum = 0;
+ while (!bStop && (fgets2(line, STRLEN, in) != NULL))
{
line_type = line2type(line);
-
- switch(line_type)
+
+ switch (line_type)
{
case epdbATOM:
case epdbHETATM:
- natom = read_atom(&symtab,line,line_type,natom,atoms,x,chainnum,bChange);
+ natom = read_atom(&symtab, line, line_type, natom, atoms, x, chainnum, bChange);
break;
-
+
case epdbANISOU:
if (atoms->pdbinfo)
{
- read_anisou(line,natom,atoms);
+ read_anisou(line, natom, atoms);
}
break;
-
+
case epdbCRYST1:
- read_cryst1(line,ePBC,box);
+ read_cryst1(line, ePBC, box);
break;
-
+
case epdbTITLE:
case epdbHEADER:
- if (strlen(line) > 6)
+ if (strlen(line) > 6)
{
- c=line+6;
+ c = line+6;
/* skip HEADER or TITLE and spaces */
- while (c[0]!=' ') c++;
- while (c[0]==' ') c++;
+ while (c[0] != ' ')
+ {
+ c++;
+ }
+ while (c[0] == ' ')
+ {
+ c++;
+ }
/* truncate after title */
- d=strstr(c," ");
- if (d)
+ d = strstr(c, " ");
+ if (d)
{
- d[0]='\0';
+ d[0] = '\0';
}
- if (strlen(c)>0)
+ if (strlen(c) > 0)
{
- strcpy(title,c);
+ strcpy(title, c);
}
}
break;
-
+
case epdbCOMPND:
- if ((!strstr(line,": ")) || (strstr(line+6,"MOLECULE:")))
+ if ((!strstr(line, ": ")) || (strstr(line+6, "MOLECULE:")))
{
- if ( !(c=strstr(line+6,"MOLECULE:")) )
+ if (!(c = strstr(line+6, "MOLECULE:")) )
{
- c=line;
+ c = line;
}
/* skip 'MOLECULE:' and spaces */
- while (c[0]!=' ') c++;
- while (c[0]==' ') c++;
+ while (c[0] != ' ')
+ {
+ c++;
+ }
+ while (c[0] == ' ')
+ {
+ c++;
+ }
/* truncate after title */
- d=strstr(c," ");
- if (d)
+ d = strstr(c, " ");
+ if (d)
{
- while ( (d[-1]==';') && d>c) d--;
- d[0]='\0';
+ while ( (d[-1] == ';') && d > c)
+ {
+ d--;
+ }
+ d[0] = '\0';
}
if (strlen(c) > 0)
{
- if (bCOMPND)
+ if (bCOMPND)
{
- strcat(title,"; ");
- strcat(title,c);
- }
+ strcat(title, "; ");
+ strcat(title, c);
+ }
else
{
- strcpy(title,c);
+ strcpy(title, c);
}
}
- bCOMPND=TRUE;
+ bCOMPND = TRUE;
}
break;
-
+
case epdbTER:
chainnum++;
break;
-
+
case epdbMODEL:
- if(model_nr)
+ if (model_nr)
{
- sscanf(line,"%*s%d",model_nr);
+ sscanf(line, "%*s%d", model_nr);
}
break;
case epdbENDMDL:
- bStop=TRUE;
+ bStop = TRUE;
break;
case epdbCONECT:
- if (gc)
+ if (gc)
{
- gmx_conect_addline(gc,line);
+ gmx_conect_addline(gc, line);
}
else if (!bConnWarn)
{
- fprintf(stderr,"WARNING: all CONECT records are ignored\n");
+ fprintf(stderr, "WARNING: all CONECT records are ignored\n");
bConnWarn = TRUE;
}
break;
-
+
default:
break;
}
return natom;
}
-void get_pdb_coordnum(FILE *in,int *natoms)
+void get_pdb_coordnum(FILE *in, int *natoms)
{
char line[STRLEN];
-
- *natoms=0;
- while (fgets2(line,STRLEN,in))
+
+ *natoms = 0;
+ while (fgets2(line, STRLEN, in))
{
- if ( strncmp(line,"ENDMDL",6) == 0 )
+ if (strncmp(line, "ENDMDL", 6) == 0)
{
break;
}
- if ((strncmp(line,"ATOM ",6) == 0) || (strncmp(line,"HETATM",6) == 0))
+ if ((strncmp(line, "ATOM ", 6) == 0) || (strncmp(line, "HETATM", 6) == 0))
{
(*natoms)++;
}
}
}
-void read_pdb_conf(const char *infile,char *title,
- t_atoms *atoms,rvec x[],int *ePBC,matrix box,gmx_bool bChange,
- gmx_conect conect)
+void read_pdb_conf(const char *infile, char *title,
+ t_atoms *atoms, rvec x[], int *ePBC, matrix box, gmx_bool bChange,
+ gmx_conect conect)
{
- FILE *in;
-
- in = gmx_fio_fopen(infile,"r");
- read_pdbfile(in,title,NULL,atoms,x,ePBC,box,bChange,conect);
- gmx_fio_fclose(in);
+ FILE *in;
+
+ in = gmx_fio_fopen(infile, "r");
+ read_pdbfile(in, title, NULL, atoms, x, ePBC, box, bChange, conect);
+ gmx_fio_fclose(in);
}
gmx_conect gmx_conect_generate(t_topology *top)
{
- int f,i;
- gmx_conect gc;
-
- /* Fill the conect records */
- gc = gmx_conect_init();
-
- for(f=0; (f<F_NRE); f++) {
- if (IS_CHEMBOND(f))
- for(i=0; (i<top->idef.il[f].nr); i+=interaction_function[f].nratoms+1) {
- gmx_conect_add(gc,top->idef.il[f].iatoms[i+1],
- top->idef.il[f].iatoms[i+2]);
- }
- }
- return gc;
+ int f, i;
+ gmx_conect gc;
+
+ /* Fill the conect records */
+ gc = gmx_conect_init();
+
+ for (f = 0; (f < F_NRE); f++)
+ {
+ if (IS_CHEMBOND(f))
+ {
+ for (i = 0; (i < top->idef.il[f].nr); i += interaction_function[f].nratoms+1)
+ {
+ gmx_conect_add(gc, top->idef.il[f].iatoms[i+1],
+ top->idef.il[f].iatoms[i+2]);
+ }
+ }
+ }
+ return gc;
}
const char* get_pdbformat()
{
- static const char *pdbformat ="%-6s%5u %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f";
+ static const char *pdbformat = "%-6s%5u %-4.4s%3.3s %c%4d%c %8.3f%8.3f%8.3f";
return pdbformat;
}
const char* get_pdbformat4()
{
- static const char *pdbformat4="%-6s%5u %-4.4s %3.3s %c%4d%c %8.3f%8.3f%8.3f";
+ static const char *pdbformat4 = "%-6s%5u %-4.4s %3.3s %c%4d%c %8.3f%8.3f%8.3f";
return pdbformat4;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff