* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * 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 "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
{
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"
+const char* enumValueToString(PdbRecordType enumValue)
+{
+ static constexpr gmx::EnumerationArray<PdbRecordType, const char*> pdbRecordTypeName = {
+ "ATOM ", "HETATM", "ANISOU", "CRYST1", "COMPND", "MODEL",
+ "ENDMDL", "TER", "HEADER", "TITLE", "REMARK", "CONECT"
+ };
+ return pdbRecordTypeName[enumValue];
+}
void gmx_write_pdb_box(FILE* out, PbcType pbcType, const matrix box)
{
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
{
}
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
{
}
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
{
{
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
{
}
}
-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 */
int n = fprintf(fp,
"%-6s%5d %-4.4s%4.4s%c%4d %8.3f %8.3f %8.3f %6.2f %6.2f\n",
- pdbtp[record],
+ enumValueToString(record),
atom_seq_number,
atom_name,
res_name,
int nindex,
const int index[],
gmx_conect conect,
- bool usePqrFormat)
+ bool usePqrFormat,
+ bool standardCompliantMode)
{
- gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
- enum PDB_record type;
- char altloc;
- real occup, bfac;
- gmx_bool bOccup;
+ 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());
+ }
- 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, pbcType, box);
fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
- ResidueType rt;
+ // Collect last printed values for TER record
+ int lastAtomNumber = 0;
+ std::string lastResName;
+ int lastResNr = 0;
+
for (int ii = 0; ii < nindex; ii++)
{
int i = index[ii];
{
gmx_pdbinfo_init_default(&pdbinfo);
}
- type = static_cast<enum PDB_record>(pdbinfo.type);
+ type = pdbinfo.type;
altloc = pdbinfo.altloc;
if (!isalnum(altloc))
{
bfac,
atoms->atom[i].elem);
+ lastAtomNumber = i + 1;
+ lastResName = resnm;
+ lastResNr = resnr;
+
if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
{
fprintf(out,
}
}
- 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)
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)
{
int i, j, k, atomnr;
atomNumberSet = true;
}
}
- std::string buf;
+ 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;
- buf = aps->elementFromAtomNumber(atomnumber);
+ element = aps->elementFromAtomNumber(atomnumber);
if (debug)
{
fprintf(debug, "Atomnumber for atom '%s' is %d\n", anm, atomnumber);
}
}
- buf.resize(3);
- std::strncpy(atoms->atom[i].elem, buf.c_str(), 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)
+static int
+read_atom(t_symtab* symtab, const char line[], PdbRecordType type, int natom, t_atoms* atoms, rvec x[], int chainnum)
{
t_atom* atomn;
int j, k;
gmx_bool bCOMPND;
gmx_bool bConnWarn = FALSE;
char line[STRLEN + 1];
- int line_type;
char * c, *d;
int natom, chainnum;
gmx_bool bStop = FALSE;
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);
+ 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, pbcType, 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;
}
break;
- case epdbCOMPND:
+ case PdbRecordType::Compound:
if ((!std::strstr(line, ": ")) || (std::strstr(line + 6, "MOLECULE:")))
{
if (!(c = std::strstr(line + 6, "MOLECULE:")))
}
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);
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");
}
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,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff