*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "pdbio.h"
+#include "gromacs/fileio/pdbio.h"
+#include <algorithm>
#include <cctype>
#include <cmath>
#include <cstdlib>
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/math/units.h"
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/ifunc.h"
-#include "gromacs/topology/residuetypes.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/coolstuff.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
+#include "gromacs/utility/stringtoenumvalueconverter.h"
-typedef struct {
+typedef struct
+{
int ai, aj;
} gmx_conection_t;
-typedef struct gmx_conect_t {
+typedef struct gmx_conect_t
+{
int nconect;
gmx_bool bSorted;
- gmx_conection_t *conect;
+ gmx_conection_t* conect;
} gmx_conect_t;
-static const char *pdbtp[epdbNR] = {
- "ATOM ", "HETATM", "ANISOU", "CRYST1",
- "COMPND", "MODEL", "ENDMDL", "TER", "HEADER", "TITLE", "REMARK",
- "CONECT"
-};
-
-
-#define REMARK_SIM_BOX "REMARK THIS IS A SIMULATION BOX"
-
-static void xlate_atomname_pdb2gmx(char *name)
+const char* enumValueToString(PdbRecordType enumValue)
{
- int i, length;
- char temp;
-
- length = std::strlen(name);
- if (length > 3 && std::isdigit(name[0]))
- {
- temp = name[0];
- for (i = 1; i < length; i++)
- {
- name[i-1] = name[i];
- }
- name[length-1] = temp;
- }
+ static constexpr gmx::EnumerationArray<PdbRecordType, const char*> pdbRecordTypeName = {
+ "ATOM ", "HETATM", "ANISOU", "CRYST1", "COMPND", "MODEL",
+ "ENDMDL", "TER", "HEADER", "TITLE", "REMARK", "CONECT"
+ };
+ return pdbRecordTypeName[enumValue];
}
-static void xlate_atomname_gmx2pdb(char *name)
-{
- int i, length;
- char temp;
-
- length = std::strlen(name);
- if (length > 3 && std::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, const matrix box)
+void gmx_write_pdb_box(FILE* out, PbcType pbcType, const matrix box)
{
real alpha, beta, gamma;
- if (ePBC == -1)
+ if (pbcType == PbcType::Unset)
{
- ePBC = guess_ePBC(box);
+ pbcType = guessPbcType(box);
}
- if (ePBC == epbcNONE)
+ if (pbcType == PbcType::No)
{
return;
}
- if (norm2(box[YY])*norm2(box[ZZ]) != 0)
+ if (norm2(box[YY]) * norm2(box[ZZ]) != 0)
{
- alpha = RAD2DEG*gmx_angle(box[YY], box[ZZ]);
+ alpha = gmx::c_rad2Deg * gmx_angle(box[YY], box[ZZ]);
}
else
{
alpha = 90;
}
- if (norm2(box[XX])*norm2(box[ZZ]) != 0)
+ if (norm2(box[XX]) * norm2(box[ZZ]) != 0)
{
- beta = RAD2DEG*gmx_angle(box[XX], box[ZZ]);
+ beta = gmx::c_rad2Deg * gmx_angle(box[XX], box[ZZ]);
}
else
{
- beta = 90;
+ beta = 90;
}
- if (norm2(box[XX])*norm2(box[YY]) != 0)
+ if (norm2(box[XX]) * norm2(box[YY]) != 0)
{
- gamma = RAD2DEG*gmx_angle(box[XX], box[YY]);
+ gamma = gmx::c_rad2Deg * gmx_angle(box[XX], box[YY]);
}
else
{
gamma = 90;
}
fprintf(out, "REMARK THIS IS A SIMULATION BOX\n");
- if (ePBC != epbcSCREW)
+ if (pbcType != PbcType::Screw)
{
- 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);
+ 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);
-
+ 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, PbcType* pbcType, 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;
+ 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;
+ PbcType pbcTypeFile;
sscanf(line, "%*s%s%s%s%lf%lf%lf", sa, sb, sc, &alpha, &beta, &gamma);
- ePBC_file = -1;
+ pbcTypeFile = PbcType::Unset;
if (strlen(line) >= 55)
{
- strncpy(sg, line+55, SG_SIZE);
+ 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)
+ if (ident == 'P' && syma == 1 && symb <= 1 && symc <= 1)
{
- fc = strtod(sc, nullptr)*0.1;
- ePBC_file = (fc > 0 ? epbcXYZ : epbcXY);
+ fc = strtod(sc, nullptr) * 0.1;
+ pbcTypeFile = (fc > 0 ? PbcType::Xyz : PbcType::XY);
}
if (ident == 'P' && syma == 21 && symb == 1 && symc == 1)
{
- ePBC_file = epbcSCREW;
+ pbcTypeFile = PbcType::Screw;
}
}
- if (ePBC)
+ if (pbcType)
{
- *ePBC = ePBC_file;
+ *pbcType = pbcTypeFile;
}
if (box)
{
- fa = strtod(sa, nullptr)*0.1;
- fb = strtod(sb, nullptr)*0.1;
- fc = strtod(sc, nullptr)*0.1;
- if (ePBC_file == epbcSCREW)
+ fa = strtod(sa, nullptr) * 0.1;
+ fb = strtod(sb, nullptr) * 0.1;
+ fc = strtod(sc, nullptr) * 0.1;
+ if (pbcTypeFile == PbcType::Screw)
{
fa *= 0.5;
}
{
if (alpha != 90.0)
{
- cosa = std::cos(alpha*DEG2RAD);
+ cosa = std::cos(alpha * gmx::c_deg2Rad);
}
else
{
}
if (beta != 90.0)
{
- cosb = std::cos(beta*DEG2RAD);
+ cosb = std::cos(beta * gmx::c_deg2Rad);
}
else
{
}
if (gamma != 90.0)
{
- cosg = std::cos(gamma*DEG2RAD);
- sing = std::sin(gamma*DEG2RAD);
+ cosg = std::cos(gamma * gmx::c_deg2Rad);
+ sing = std::sin(gamma * gmx::c_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] = std::sqrt(fc*fc
- - box[ZZ][XX]*box[ZZ][XX] - box[ZZ][YY]*box[ZZ][YY]);
+ 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] = std::sqrt(fc * fc - box[ZZ][XX] * box[ZZ][XX] - box[ZZ][YY] * box[ZZ][YY]);
}
else
{
}
}
-static int
-gmx_fprintf_pqr_atomline(FILE * fp,
- enum PDB_record record,
- int atom_seq_number,
- const char * atom_name,
- const char * res_name,
- char chain_id,
- int res_seq_number,
- real x,
- real y,
- real z,
- real occupancy,
- real b_factor)
+static int gmx_fprintf_pqr_atomline(FILE* fp,
+ PdbRecordType record,
+ int atom_seq_number,
+ const char* atom_name,
+ const char* res_name,
+ char chain_id,
+ int res_seq_number,
+ real x,
+ real y,
+ real z,
+ real occupancy,
+ real b_factor)
{
- GMX_RELEASE_ASSERT(record == epdbATOM || record == epdbHETATM,
+ GMX_RELEASE_ASSERT(record == PdbRecordType::Atom || record == PdbRecordType::Hetatm,
"Can only print PQR atom lines as ATOM or HETATM records");
/* Check atom name */
- GMX_RELEASE_ASSERT(atom_name != nullptr,
- "Need atom information to print pqr");
+ GMX_RELEASE_ASSERT(atom_name != nullptr, "Need atom information to print pqr");
/* Check residue name */
- GMX_RELEASE_ASSERT(res_name != nullptr,
- "Need residue information to print pqr");
+ GMX_RELEASE_ASSERT(res_name != nullptr, "Need residue information to print pqr");
/* Truncate integers so they fit */
atom_seq_number = atom_seq_number % 100000;
res_seq_number = res_seq_number % 10000;
int n = fprintf(fp,
- "%s %d %s %s %c %d %8.3f %8.3f %8.3f %6.2f %6.2f\n",
- pdbtp[record],
+ "%-6s%5d %-4.4s%4.4s%c%4d %8.3f %8.3f %8.3f %6.2f %6.2f\n",
+ enumValueToString(record),
atom_seq_number,
atom_name,
res_name,
chain_id,
res_seq_number,
- x, y, z,
+ x,
+ y,
+ z,
occupancy,
b_factor);
return n;
}
-void write_pdbfile_indexed(FILE *out, const char *title,
- const t_atoms *atoms, const rvec x[],
- int ePBC, const matrix box, char chainid,
- int model_nr, int nindex, const int index[],
- gmx_conect conect, gmx_bool bTerSepChains,
- bool usePqrFormat)
+void write_pdbfile_indexed(FILE* out,
+ const char* title,
+ const t_atoms* atoms,
+ const rvec x[],
+ PbcType pbcType,
+ const matrix box,
+ char chainid,
+ int model_nr,
+ int nindex,
+ const int index[],
+ gmx_conect conect,
+ bool usePqrFormat,
+ bool standardCompliantMode)
{
- gmx_conect_t *gc = static_cast<gmx_conect_t *>(conect);
- char resnm[6], nm[6];
- int i, ii;
- int resind, resnr;
- enum PDB_record type;
- unsigned char resic, ch;
- char altloc;
- real occup, bfac;
- gmx_bool bOccup;
- int chainnum, lastchainnum;
- gmx_residuetype_t*rt;
- const char *p_restype;
- const char *p_lastrestype;
-
- gmx_residuetype_init(&rt);
-
- fprintf(out, "TITLE %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
- if (box && ( (norm2(box[XX]) != 0.0f) || (norm2(box[YY]) != 0.0f) || (norm2(box[ZZ]) != 0.0f) ) )
+ gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
+ PdbRecordType type;
+ char altloc;
+ real occup, bfac;
+ gmx_bool bOccup;
+
+ if (standardCompliantMode)
+ {
+ fprintf(out, "HEADER GROMACS SIMULATION BOX 01-JAN-00 0000\n");
+ fprintf(out,
+ "TITLE Gromacs simulation box\n"
+ "COMPND MOL_ID: 1; \n"
+ "COMPND 2 MOLECULE: GROMACS SIMULATION BOX; \n"
+ "COMPND 3 CHAIN: A; \n"
+ "SOURCE MOL_ID: 1;\n"
+ "SOURCE 2 SYNTHETIC\n"
+ "KEYWDS GROMACS\n"
+ "EXPDTA PURE PRODUCT OF COMPUTER SIMULATION\n"
+ "AUTHOR GROMACS\n"
+ "REVDAT 1 01-JAN-00 0000 0\n");
+ }
+ else
+ {
+ fprintf(out, "TITLE %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
+ }
+
+
+ if (box && ((norm2(box[XX]) != 0.0F) || (norm2(box[YY]) != 0.0F) || (norm2(box[ZZ]) != 0.0F)))
{
- gmx_write_pdb_box(out, ePBC, box);
+ gmx_write_pdb_box(out, pbcType, box);
}
if (atoms->havePdbInfo)
{
* otherwise set them all to one
*/
bOccup = TRUE;
- for (ii = 0; (ii < nindex) && bOccup; ii++)
+ for (int ii = 0; (ii < nindex) && bOccup; ii++)
{
- i = index[ii];
+ int i = index[ii];
bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
}
}
fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
- lastchainnum = -1;
- p_restype = nullptr;
+ // Collect last printed values for TER record
+ int lastAtomNumber = 0;
+ std::string lastResName;
+ int lastResNr = 0;
- for (ii = 0; ii < nindex; ii++)
+ for (int ii = 0; ii < nindex; ii++)
{
- i = index[ii];
- 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;
- }
-
- strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
- resnm[sizeof(resnm)-1] = 0;
- strncpy(nm, *atoms->atomname[i], sizeof(nm)-1);
- nm[sizeof(nm)-1] = 0;
-
- /* rename HG12 to 2HG1, etc. */
- xlate_atomname_gmx2pdb(nm);
- resnr = atoms->resinfo[resind].nr;
- resic = atoms->resinfo[resind].ic;
+ int i = index[ii];
+ int resind = atoms->atom[i].resind;
+ std::string resnm = *atoms->resinfo[resind].name;
+ std::string nm = *atoms->atomname[i];
+
+ int resnr = atoms->resinfo[resind].nr;
+ unsigned char resic = atoms->resinfo[resind].ic;
+ unsigned char ch;
if (chainid != ' ')
{
ch = chainid;
{
gmx_pdbinfo_init_default(&pdbinfo);
}
- type = static_cast<enum PDB_record>(pdbinfo.type);
+ type = pdbinfo.type;
altloc = pdbinfo.altloc;
if (!isalnum(altloc))
{
{
gmx_fprintf_pdb_atomline(out,
type,
- i+1,
- nm,
+ i + 1,
+ nm.c_str(),
altloc,
- resnm,
+ resnm.c_str(),
ch,
resnr,
resic,
- 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ],
+ 10 * x[i][XX],
+ 10 * x[i][YY],
+ 10 * x[i][ZZ],
occup,
bfac,
atoms->atom[i].elem);
+ lastAtomNumber = i + 1;
+ lastResName = resnm;
+ lastResNr = resnr;
+
if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
{
- fprintf(out, "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n",
- (i+1)%100000, nm, resnm, ch, resnr,
+ fprintf(out,
+ "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n",
+ (i + 1) % 100000,
+ nm.c_str(),
+ resnm.c_str(),
+ 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]);
+ 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
{
gmx_fprintf_pqr_atomline(out,
type,
- i+1,
- nm,
- resnm,
+ i + 1,
+ nm.c_str(),
+ resnm.c_str(),
ch,
resnr,
- 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ],
+ 10 * x[i][XX],
+ 10 * x[i][YY],
+ 10 * x[i][ZZ],
occup,
bfac);
}
}
- fprintf(out, "TER\n");
+ if (standardCompliantMode)
+ {
+ fprintf(out, "TER %5d %4.4s%c%4d\n", lastAtomNumber, lastResName.c_str(), chainid, lastResNr);
+ }
+ else
+ {
+ fprintf(out, "TER\n");
+ }
+
fprintf(out, "ENDMDL\n");
if (nullptr != gc)
{
/* Write conect records */
- for (i = 0; (i < gc->nconect); i++)
+ for (int i = 0; (i < gc->nconect); i++)
{
- fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai+1, gc->conect[i].aj+1);
+ fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai + 1, gc->conect[i].aj + 1);
}
}
-
- gmx_residuetype_destroy(rt);
}
-void write_pdbfile(FILE *out, const char *title, const t_atoms *atoms, const rvec x[],
- int ePBC, const matrix box, char chainid, int model_nr, gmx_conect conect, gmx_bool bTerSepChains)
+void write_pdbfile(FILE* out,
+ const char* title,
+ const t_atoms* atoms,
+ const rvec x[],
+ PbcType pbcType,
+ const matrix box,
+ char chainid,
+ int model_nr,
+ gmx_conect conect)
{
int i, *index;
{
index[i] = i;
}
- write_pdbfile_indexed(out, title, atoms, x, ePBC, box, chainid, model_nr,
- atoms->nr, index, conect, bTerSepChains, false);
+ write_pdbfile_indexed(
+ out, title, atoms, x, pbcType, box, chainid, model_nr, atoms->nr, index, conect, false);
sfree(index);
}
-static int line2type(const 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 (std::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';
/* Search backwards for number and name only */
atomnr = std::strtol(anr, nullptr, 10);
- for (i = natom-1; (i >= 0); i--)
+ for (i = natom - 1; (i >= 0); i--)
{
- if ((std::strcmp(anm, *(atoms->atomname[i])) == 0) &&
- (atomnr == atoms->pdbinfo[i].atomnr))
+ if ((std::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);
+ 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])
+ 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;
}
}
-void get_pdb_atomnumber(const t_atoms *atoms, gmx_atomprop_t aps)
+void get_pdb_atomnumber(const t_atoms* atoms, AtomProperties* aps)
{
int i, atomnumber, len;
size_t k;
- char anm[6], anm_copy[6], *ptr;
+ char anm[6], anm_copy[6];
char nc = '\0';
real eval;
std::strcpy(anm, atoms->pdbinfo[i].atomnm);
std::strcpy(anm_copy, atoms->pdbinfo[i].atomnm);
bool atomNumberSet = false;
- len = strlen(anm);
+ len = strlen(anm);
if ((anm[0] != ' ') && ((len <= 2) || !std::isdigit(anm[2])))
{
anm_copy[2] = nc;
- if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
{
- atomnumber = std::round(eval);
+ atomnumber = gmx::roundToInt(eval);
atomNumberSet = true;
}
else
{
anm_copy[1] = nc;
- if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
{
- atomnumber = std::round(eval);
+ atomnumber = gmx::roundToInt(eval);
atomNumberSet = true;
}
}
}
anm_copy[0] = anm[k];
anm_copy[1] = nc;
- if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
{
- atomnumber = std::round(eval);
+ atomnumber = gmx::roundToInt(eval);
atomNumberSet = true;
}
}
+ static constexpr size_t sc_maxElementNameLength = 3;
+ static_assert(sizeof(atoms->atom[i].elem) >= sc_maxElementNameLength + 1);
+ std::string element;
if (atomNumberSet)
{
atoms->atom[i].atomnumber = atomnumber;
- ptr = gmx_atomprop_element(aps, atomnumber);
+ element = aps->elementFromAtomNumber(atomnumber);
if (debug)
{
- fprintf(debug, "Atomnumber for atom '%s' is %d\n",
- anm, atomnumber);
+ fprintf(debug, "Atomnumber for atom '%s' is %d\n", anm, atomnumber);
}
}
- else
- {
- ptr = nullptr;
- }
- std::strncpy(atoms->atom[i].elem, ptr == nullptr ? "" : ptr, 4);
+ element.resize(sc_maxElementNameLength);
+ std::strcpy(atoms->atom[i].elem, element.c_str());
}
}
-static int read_atom(t_symtab *symtab,
- const char line[], int type, int natom,
- t_atoms *atoms, rvec x[], int chainnum, gmx_bool bChange)
+static int
+read_atom(t_symtab* symtab, const char line[], PdbRecordType type, int natom, t_atoms* atoms, rvec x[], int chainnum)
{
- t_atom *atomn;
+ t_atom* atomn;
int j, k;
char nc = '\0';
char anr[12], anm[12], anm_copy[12], altloc, resnm[12], rnr[12], elem[3];
if (natom >= atoms->nr)
{
- gmx_fatal(FARGS, "\nFound more atoms (%d) in pdb file than expected (%d)",
- natom+1, atoms->nr);
+ gmx_fatal(FARGS, "\nFound more atoms (%d) in pdb file than expected (%d)", natom + 1, atoms->nr);
}
/* Skip over type */
trim(rnr);
resnr = std::strtol(rnr, nullptr, 10);
resic = line[j];
- j += 4;
+ j += 4;
/* X,Y,Z Coordinate */
for (k = 0; (k < 8); k++, j++)
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) || 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)
{
}
else
{
- atomn->resind = atoms->atom[natom-1].resind + 1;
+ 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);
+ atomn->resind = atoms->atom[natom - 1].resind;
}
atoms->atomname[natom] = put_symtab(symtab, anm);
atomn->m = 0.0;
atomn->atomnumber = atomnumber;
strncpy(atomn->elem, elem, 4);
}
- x[natom][XX] = strtod(xc, nullptr)*0.1;
- x[natom][YY] = strtod(yc, nullptr)*0.1;
- x[natom][ZZ] = strtod(zc, nullptr)*0.1;
+ x[natom][XX] = strtod(xc, nullptr) * 0.1;
+ x[natom][YY] = strtod(yc, nullptr) * 0.1;
+ x[natom][ZZ] = strtod(zc, nullptr) * 0.1;
if (atoms->pdbinfo)
{
atoms->pdbinfo[natom].type = type;
return natom;
}
-gmx_bool is_hydrogen(const char *nm)
+gmx_bool is_hydrogen(const char* nm)
{
char buf[30];
std::strcpy(buf, nm);
trim(buf);
- if (buf[0] == 'H')
- {
- return TRUE;
- }
- else if ((std::isdigit(buf[0])) && (buf[1] == 'H'))
- {
- return TRUE;
- }
- return FALSE;
+ return ((buf[0] == 'H') || ((std::isdigit(buf[0]) != 0) && (buf[1] == 'H')));
}
-gmx_bool is_dummymass(const char *nm)
+gmx_bool is_dummymass(const char* nm)
{
char buf[30];
std::strcpy(buf, nm);
trim(buf);
- return (buf[0] == 'M') && (std::isdigit(buf[strlen(buf)-1]) != 0);
+ return (buf[0] == 'M') && (std::isdigit(buf[strlen(buf) - 1]) != 0);
}
-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];
+ int n, ai, aj;
- sprintf(form2, "%%*s");
- sprintf(format, "%s%%d", form2);
- if (sscanf(line, format, &ai) == 1)
+ std::string form2 = "%*s";
+ std::string format = form2 + "%d";
+ if (sscanf(line, format.c_str(), &ai) == 1)
{
do
{
- std::strcat(form2, "%*s");
- sprintf(format, "%s%%d", form2);
- n = sscanf(line, format, &aj);
+ form2 += "%*s";
+ format = form2 + "%d";
+ n = sscanf(line, format.c_str(), &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;
+ gmx_conect_add(con, ai - 1, aj - 1); /* to prevent duplicated records */
}
- }
- while (n == 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 = static_cast<gmx_conect_t *>(conect);
+ gmx_conect_t* gc = static_cast<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);
+ 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;
+ gmx_conect_t* gc;
snew(gc, 1);
void gmx_conect_done(gmx_conect conect)
{
- gmx_conect_t *gc = conect;
+ gmx_conect_t* gc = conect;
sfree(gc->conect);
}
gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj)
{
- gmx_conect_t *gc = conect;
+ gmx_conect_t* gc = conect;
int i;
/* if (!gc->bSorted)
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)))
+ if (((gc->conect[i].ai == ai) && (gc->conect[i].aj == aj))
+ || ((gc->conect[i].aj == ai) && (gc->conect[i].ai == aj)))
{
return TRUE;
}
void gmx_conect_add(gmx_conect conect, int ai, int aj)
{
- gmx_conect_t *gc = static_cast<gmx_conect_t *>(conect);
+ gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
/* 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;
+ 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, t_symtab *symtab, 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,
+ t_symtab* symtab,
+ rvec x[],
+ PbcType* pbcType,
+ matrix box,
+ gmx_conect conect)
{
- gmx_conect_t *gc = conect;
+ gmx_conect_t* gc = conect;
gmx_bool bCOMPND;
gmx_bool bConnWarn = FALSE;
- char line[STRLEN+1];
- int line_type;
- char *c, *d;
+ char line[STRLEN + 1];
+ char * c, *d;
int natom, chainnum;
- gmx_bool bStop = FALSE;
+ gmx_bool bStop = FALSE;
- if (ePBC)
+ if (pbcType)
{
/* Only assume pbc when there is a CRYST1 entry */
- *ePBC = epbcNONE;
+ *pbcType = PbcType::No;
}
if (box != nullptr)
{
title[0] = '\0';
natom = 0;
chainnum = 0;
+ static const gmx::StringToEnumValueConverter<PdbRecordType, enumValueToString, gmx::StringCompareType::Exact, gmx::StripStrings::Yes>
+ sc_pdbRecordTypeIdentifier;
while (!bStop && (fgets2(line, STRLEN, in) != nullptr))
{
- line_type = line2type(line);
+ // Convert line to a null-terminated string, then take a substring of at most 6 chars
+ std::string lineAsString(line);
+ std::optional<PdbRecordType> line_type =
+ sc_pdbRecordTypeIdentifier.valueFrom(lineAsString.substr(0, 6));
+ if (!line_type)
+ {
+ // Skip this line because it does not start with a
+ // recognized leading string describing a PDB record type.
+ continue;
+ }
- switch (line_type)
+ switch (line_type.value())
{
- case epdbATOM:
- case epdbHETATM:
- natom = read_atom(symtab, line, line_type, natom, atoms, x, chainnum, bChange);
+ case PdbRecordType::Atom:
+ case PdbRecordType::Hetatm:
+ natom = read_atom(symtab, line, line_type.value(), natom, atoms, x, chainnum);
break;
- case epdbANISOU:
+ case PdbRecordType::Anisou:
if (atoms->havePdbInfo)
{
read_anisou(line, natom, atoms);
}
break;
- case epdbCRYST1:
- read_cryst1(line, ePBC, box);
- break;
+ case PdbRecordType::Cryst1: read_cryst1(line, pbcType, box); break;
- case epdbTITLE:
- case epdbHEADER:
+ case PdbRecordType::Title:
+ case PdbRecordType::Header:
if (std::strlen(line) > 6)
{
- c = line+6;
+ c = line + 6;
/* skip HEADER or TITLE and spaces */
while (c[0] != ' ')
{
}
break;
- case epdbCOMPND:
- if ((!std::strstr(line, ": ")) || (std::strstr(line+6, "MOLECULE:")))
+ case PdbRecordType::Compound:
+ if ((!std::strstr(line, ": ")) || (std::strstr(line + 6, "MOLECULE:")))
{
- if (!(c = std::strstr(line+6, "MOLECULE:")) )
+ if (!(c = std::strstr(line + 6, "MOLECULE:")))
{
c = line;
}
d = strstr(c, " ");
if (d)
{
- while ( (d[-1] == ';') && d > c)
+ while ((d[-1] == ';') && d > c)
{
d--;
}
}
break;
- case epdbTER:
- chainnum++;
- break;
+ case PdbRecordType::Ter: chainnum++; break;
- case epdbMODEL:
+ case PdbRecordType::Model:
if (model_nr)
{
sscanf(line, "%*s%d", model_nr);
}
break;
- case epdbENDMDL:
- bStop = TRUE;
- break;
- case epdbCONECT:
+ case PdbRecordType::EndModel: bStop = TRUE; break;
+ case PdbRecordType::Conect:
if (gc)
{
gmx_conect_addline(gc, line);
}
break;
- default:
- break;
+ default: break;
}
}
return natom;
}
-void get_pdb_coordnum(FILE *in, int *natoms)
+void get_pdb_coordnum(FILE* in, int* natoms)
{
char line[STRLEN];
}
}
-void gmx_pdb_read_conf(const char *infile,
- t_symtab *symtab, char **name, t_atoms *atoms,
- rvec x[], int *ePBC, matrix box)
+void gmx_pdb_read_conf(const char* infile, t_symtab* symtab, char** name, t_atoms* atoms, rvec x[], PbcType* pbcType, matrix box)
{
- FILE *in = gmx_fio_fopen(infile, "r");
+ FILE* in = gmx_fio_fopen(infile, "r");
char title[STRLEN];
- read_pdbfile(in, title, nullptr, atoms, symtab, x, ePBC, box, TRUE, nullptr);
+ read_pdbfile(in, title, nullptr, atoms, symtab, x, pbcType, box, nullptr);
if (name != nullptr)
{
*name = gmx_strdup(title);
gmx_fio_fclose(in);
}
-gmx_conect gmx_conect_generate(const t_topology *top)
+gmx_conect gmx_conect_generate(const t_topology* top)
{
int f, i;
gmx_conect gc;
/* Fill the conect records */
- gc = gmx_conect_init();
+ 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)
+ 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]);
+ gmx_conect_add(gc, top->idef.il[f].iatoms[i + 1], top->idef.il[f].iatoms[i + 2]);
}
}
}
return gc;
}
-int
-gmx_fprintf_pdb_atomline(FILE * fp,
- enum PDB_record record,
- int atom_seq_number,
- const char * atom_name,
- char alternate_location,
- const char * res_name,
- char chain_id,
- int res_seq_number,
- char res_insertion_code,
- real x,
- real y,
- real z,
- real occupancy,
- real b_factor,
- const char * element)
+int gmx_fprintf_pdb_atomline(FILE* fp,
+ PdbRecordType record,
+ int atom_seq_number,
+ const char* atom_name,
+ char alternate_location,
+ const char* res_name,
+ char chain_id,
+ int res_seq_number,
+ char res_insertion_code,
+ real x,
+ real y,
+ real z,
+ real occupancy,
+ real b_factor,
+ const char* element)
{
char tmp_atomname[6], tmp_resname[6];
gmx_bool start_name_in_col13;
int n;
- if (record != epdbATOM && record != epdbHETATM)
+ if (record != PdbRecordType::Atom && record != PdbRecordType::Hetatm)
{
gmx_fatal(FARGS, "Can only print PDB atom lines as ATOM or HETATM records");
}
/* If the atom name is an element name with two chars, it should start already in column 13.
* Otherwise it should start in column 14, unless the name length is 4 chars.
*/
- if ( (element != nullptr) && (std::strlen(element) >= 2) && (gmx_strncasecmp(atom_name, element, 2) == 0) )
+ if ((element != nullptr) && (std::strlen(element) >= 2)
+ && (gmx_strncasecmp(atom_name, element, 2) == 0))
{
start_name_in_col13 = TRUE;
}
n = fprintf(fp,
"%-6s%5d %-4.4s%c%4.4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %2s\n",
- pdbtp[record],
+ enumValueToString(record),
atom_seq_number,
tmp_atomname,
alternate_location,
chain_id,
res_seq_number,
res_insertion_code,
- x, y, z,
+ x,
+ y,
+ z,
occupancy,
b_factor,
(element != nullptr) ? element : "");
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff