#include <cstdio>
#include <cstring>
+#include <algorithm>
+
#include "gromacs/compat/make_unique.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/utilities.h"
NOTFOUND = -4, WILDCARD, WILDPROT, PROTEIN
};
+//! Basic entries in AtomProperty.
+struct BaseEntry {
+ //! Default constructor.
+ BaseEntry(const std::string &aName, const std::string &rName)
+ : atomName(aName), residueName(rName), isAvailable(false), value(0.0)
+ {}
+ //! Name for atom.
+ std::string atomName;
+ //! Name for residue.
+ std::string residueName;
+ //! Is property available.
+ bool isAvailable;
+ //! Value set for property.
+ real value;
+};
+
//! Conglomeration of atom property entries.
struct AtomProperty {
//! Has property been set.
- bool isSet = false;
- //! Number of properties.
- int nprop = 0;
- //! Max number of properties.
- int maxprop = 0;
+ bool isSet = false;
//! Database the property is coming from.
- char *db = nullptr;
+ std::string db;
//! Default value for property.
- double def = 0.0;
- //! Array of names for atoms.
- char **atomName = nullptr;
- //! Array of names for residues.
- char **residueName = nullptr;
- //! Array of flags if property is available.
- bool *isAvailable = nullptr;
- //! Array of values for property.
- real *value = nullptr;
+ double def = 0.0;
+ //! Basic entries for properties.
+ std::vector<BaseEntry> entry;
};
//! Implementation detail type for Atomproperties.
* \param[in] database Name of the database entry to compare to.
* \returns Number of matching characters or NOTFOUND.
*/
-static int findNumberOfMatches(const char *search, const char *database)
+static int compareToDatabase(const std::string &search, const std::string &database)
{
- int i = 0;
- while (search[i] && database[i] && (search[i] == database[i]) )
+ if (database.length() > search.length())
{
- i++;
+ return NOTFOUND;
}
-
- if (database[i])
+ size_t matches = 0;
+ for (size_t i = 0; i < database.length(); i++)
+ {
+ if (search[i] == database[i])
+ {
+ matches++;
+ }
+ }
+ if (matches == database.length())
+ {
+ return matches;
+ }
+ else
{
- i = NOTFOUND;
+ return NOTFOUND;
}
- return i;
}
/*! \brief
* \returns The index for the property.
*/
static int findPropertyIndex(AtomProperty *ap, gmx_residuetype_t *restype,
- char *residueName, char *atomName,
+ const std::string &residueName, const std::string &atomName,
gmx_bool *bExact)
{
int j = NOTFOUND;
- bool bProtein = gmx_residuetype_is_protein(restype, residueName);
- bool bProtWild = (strcmp(residueName, "AAA") == 0);
+ bool bProtein = gmx_residuetype_is_protein(restype, residueName.c_str());
+ bool bProtWild = residueName == "AAA";
int malen = NOTFOUND;
int mrlen = NOTFOUND;
- for (int i = 0; (i < ap->nprop); i++)
+ for (size_t i = 0; (i < ap->entry.size()); i++)
{
- int rlen = findNumberOfMatches(residueName, ap->residueName[i]);
+ int rlen = compareToDatabase(residueName, ap->entry[i].residueName);
if (rlen == NOTFOUND)
{
- if ( (strcmp(ap->residueName[i], "*") == 0) ||
- (strcmp(ap->residueName[i], "???") == 0) )
+ if ( (ap->entry[i].residueName == "*") ||
+ (ap->entry[i].residueName == "???") )
{
rlen = WILDCARD;
}
- else if (strcmp(ap->residueName[i], "AAA") == 0)
+ else if (ap->entry[i].residueName == "AAA")
{
rlen = WILDPROT;
}
}
- int alen = findNumberOfMatches(atomName, ap->atomName[i]);
+ int alen = compareToDatabase(atomName, ap->entry[i].atomName);
if ( (alen > NOTFOUND) && (rlen > NOTFOUND))
{
if ( ( (alen > malen) && (rlen >= mrlen)) ||
}
}
- *bExact = ((malen == static_cast<long int>(strlen(atomName))) &&
- ((mrlen == static_cast<long int>(strlen(residueName))) ||
+ *bExact = ((malen == static_cast<long int>(atomName.length())) &&
+ ((mrlen == static_cast<long int>(residueName.length())) ||
((mrlen == WILDPROT) && bProtWild) ||
((mrlen == WILDCARD) && !bProtein && !bProtWild)));
if (debug)
{
- fprintf(debug, "searching residue: %4s atom: %4s\n", residueName, atomName);
+ fprintf(debug, "searching residue: %4s atom: %4s\n", residueName.c_str(),
+ atomName.c_str());
if (j == NOTFOUND)
{
fprintf(debug, " not successful\n");
}
else
{
- fprintf(debug, " match: %4s %4s\n", ap->residueName[j], ap->atomName[j]);
+ fprintf(debug, " match: %4s %4s\n",
+ ap->entry[j].residueName.c_str(), ap->entry[j].atomName.c_str());
}
}
return j;
* \param[in] line Where to add property.
*/
static void addProperty(AtomProperty *ap, gmx_residuetype_t *restype,
- char *residueName, char *atomName,
+ const std::string &residueName, const std::string &atomName,
real propValue, int line)
{
bool bExact;
if (!bExact)
{
- if (ap->nprop >= ap->maxprop)
- {
- ap->maxprop += 10;
- srenew(ap->residueName, ap->maxprop);
- srenew(ap->atomName, ap->maxprop);
- srenew(ap->value, ap->maxprop);
- srenew(ap->isAvailable, ap->maxprop);
- for (int i = ap->nprop; (i < ap->maxprop); i++)
- {
- ap->atomName[i] = nullptr;
- ap->residueName[i] = nullptr;
- ap->value[i] = 0;
- ap->isAvailable[i] = FALSE;
- }
- }
- ap->atomName[ap->nprop] = gmx_strdup(atomName);
- ap->residueName[ap->nprop] = gmx_strdup(residueName);
- j = ap->nprop;
- ap->nprop++;
+ ap->entry.emplace_back(BaseEntry(atomName, residueName));
+
+ j = ap->entry.size() - 1;
}
- if (ap->isAvailable[j])
+ if (ap->entry[j].isAvailable)
{
- if (ap->value[j] == propValue)
+ if (ap->entry[j].value == propValue)
{
fprintf(stderr, "Warning double identical entries for %s %s %g on line %d in file %s\n",
- residueName, atomName, propValue, line, ap->db);
+ residueName.c_str(), atomName.c_str(), propValue, line, ap->db.c_str());
}
else
{
fprintf(stderr, "Warning double different entries %s %s %g and %g on line %d in file %s\n"
"Using last entry (%g)\n",
- residueName, atomName, propValue, ap->value[j], line, ap->db, propValue);
- ap->value[j] = propValue;
+ residueName.c_str(), atomName.c_str(),
+ propValue, ap->entry[j].value, line, ap->db.c_str(), propValue);
+ ap->entry[j].value = propValue;
}
}
else
{
- ap->isAvailable[j] = TRUE;
- ap->value[j] = propValue;
+ ap->entry[j].isAvailable = TRUE;
+ ap->entry[j].value = propValue;
}
}
else
{
fprintf(stderr, "WARNING: Error in file %s at line %d ignored\n",
- ap->db, line_no);
+ ap->db.c_str(), line_no);
}
}
ap->isSet = TRUE;
bool printWarning = false;
if (!ap->isSet)
{
- ap->db = gmx_strdup(fns[eprop]);
+ ap->db = fns[eprop];
ap->def = def[eprop];
readProperty(ap, restype, fac[eprop]);
if (debug)
{
- fprintf(debug, "Entries in %s: %d\n", ap->db, ap->nprop);
+ fprintf(debug, "Entries in %s: %zu\n", ap->db.c_str(), ap->entry.size());
}
if ( (!haveBeenWarned && (eprop == epropMass) ) || (eprop == epropVDW))
gmx_residuetype_init(&impl_->restype);
}
-static void destroy_prop(AtomProperty *ap)
-{
- if (ap->isSet)
- {
- sfree(ap->db);
-
- for (int i = 0; i < ap->nprop; i++)
- {
- sfree(ap->atomName[i]);
- sfree(ap->residueName[i]);
- }
- sfree(ap->atomName);
- sfree(ap->residueName);
- sfree(ap->isAvailable);
- sfree(ap->value);
- }
-}
-
AtomProperties::~AtomProperties()
{
- for (int p = 0; p < epropNR; p++)
- {
- destroy_prop(&impl_->prop[p]);
- }
gmx_residuetype_destroy(impl_->restype);
}
return impl_->restype;
}
-//! Print warning about vdW to terminal.
+//! Print warning that vdW radii and masses are guessed.
static void printWarning()
{
printf("\n"
}
}
-bool AtomProperties::setAtomProperty(int eprop,
- const char *residueName,
- const char *atomName,
- real *value)
+bool AtomProperties::setAtomProperty(int eprop,
+ const std::string &residueName,
+ const std::string &atomName,
+ real *value)
{
- int j;
-#define MAXQ 32
- char atomname[MAXQ], resname[MAXQ];
- bool bExact;
+ int j;
+ std::string tmpAtomName, tmpResidueName;
+ gmx_bool bExact;
if (setProperties(prop(eprop), restype(), eprop, impl_->bWarned))
{
printWarning();
impl_->bWarned = true;
}
- if ((strlen(atomName) > MAXQ-1) || (strlen(residueName) > MAXQ-1))
- {
- if (debug)
- {
- fprintf(debug, "WARNING: will only compare first %d characters\n",
- MAXQ-1);
- }
- }
if (isdigit(atomName[0]))
{
- int i;
/* put digit after atomname */
- for (i = 1; i < MAXQ-1 && atomName[i] != '\0'; i++)
- {
- atomname[i-1] = atomName[i];
- }
- atomname[i-1] = atomName[0];
- atomname[i] = '\0';
+ tmpAtomName.append(atomName.substr(1));
+ tmpAtomName.append(1, atomName[0]);
}
else
{
- strncpy(atomname, atomName, MAXQ-1);
+ tmpAtomName = atomName;
}
- strncpy(resname, residueName, MAXQ-1);
-
- j = findPropertyIndex(&(impl_->prop[eprop]), impl_->restype, resname,
- atomname, &bExact);
+ j = findPropertyIndex(&(impl_->prop[eprop]), impl_->restype, residueName,
+ tmpAtomName, &bExact);
if (eprop == epropVDW && !impl_->bWarnVDW)
{
}
if (j >= 0)
{
- *value = impl_->prop[eprop].value[j];
+ *value = impl_->prop[eprop].entry[j].value;
return true;
}
else
}
-const char *AtomProperties::elementFromAtomNumber(int atomNumber)
+const std::string AtomProperties::elementFromAtomNumber(int atomNumber)
{
if (setProperties(prop(epropElement), restype(), epropElement, impl_->bWarned))
{
printWarning();
impl_->bWarned = true;
}
- for (int i = 0; (i < impl_->prop[epropElement].nprop); i++)
+ for (const auto &e : prop(epropElement)->entry)
{
- if (std::round(impl_->prop[epropElement].value[i]) == atomNumber)
+ if (std::round(e.value) == atomNumber)
{
- return impl_->prop[epropElement].atomName[i];
+ return e.atomName;
}
}
- return nullptr;
+ return "";
}
int AtomProperties::atomNumberFromElement(const char *element)
printWarning();
impl_->bWarned = true;
}
- for (int i = 0; (i < impl_->prop[epropElement].nprop); i++)
+ for (const auto &e : prop(epropElement)->entry)
{
- if (gmx_strcasecmp(impl_->prop[epropElement].atomName[i], element) == 0)
+ if (gmx_strcasecmp(e.atomName.c_str(), element) == 0)
{
- return gmx::roundToInt(impl_->prop[epropElement].value[i]);
+ return gmx::roundToInt(e.value);
}
}
return -1;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff