* 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.
}
}
-void rename_bb(t_atoms* pdba, const char* oldnm, const char* newnm, bool bFullCompare, t_symtab* symtab)
+/*! \brief Rename all residues named \c oldnm to \c newnm
+ *
+ * Search for residues for which the residue name from the input
+ * configuration file matches \c oldnm, and when found choose the rtp
+ * entry and name of \c newnm.
+ *
+ * \todo Refactor this function to accept a lambda that accepts i and
+ * numMatchesFound but always produces \c newnm. Then remove
+ * renameResiduesInteractively by calling this method with suitable
+ * lambdas that capture its parameter \c rr and ignores
+ * numMatchesFound. */
+void renameResidue(const gmx::MDLogger& logger,
+ t_atoms* pdba,
+ const char* oldnm,
+ const char* newnm,
+ bool bFullCompare,
+ t_symtab* symtab)
{
- char* bbnm;
- int i;
-
- for (i = 0; (i < pdba->nres); i++)
+ int numMatchesFound = 0;
+ for (int i = 0; (i < pdba->nres); i++)
{
- /* We have not set the rtp name yes, use the residue name */
- bbnm = *pdba->resinfo[i].name;
- if ((bFullCompare && (gmx::equalCaseInsensitive(bbnm, oldnm)))
- || (!bFullCompare && strstr(bbnm, oldnm) != nullptr))
+ /* We have not set the rtp name yet, use the residue name */
+ const char* residueNameInInputConfiguration = *pdba->resinfo[i].name;
+ if ((bFullCompare && (gmx::equalCaseInsensitive(residueNameInInputConfiguration, oldnm)))
+ || (!bFullCompare && strstr(residueNameInInputConfiguration, oldnm) != nullptr))
{
- /* Change the rtp builing block name */
- pdba->resinfo[i].rtp = put_symtab(symtab, newnm);
+ /* Change the rtp building block name */
+ pdba->resinfo[i].rtp = put_symtab(symtab, newnm);
+ pdba->resinfo[i].name = pdba->resinfo[i].rtp;
+ numMatchesFound++;
}
}
+ if (numMatchesFound > 0)
+ {
+ GMX_LOG(logger.info)
+ .asParagraph()
+ .appendTextFormatted(
+ "Replaced %d residue%s named %s to the default %s. Use interactive "
+ "selection of protonated residues if that is what you need.",
+ numMatchesFound,
+ numMatchesFound > 1 ? "s" : "",
+ oldnm,
+ newnm);
+ }
}
-void rename_bbint(t_atoms* pdba,
- const char* oldnm,
- const char* gettp(int, gmx::ArrayRef<const RtpRename>),
- bool bFullCompare,
- t_symtab* symtab,
- gmx::ArrayRef<const RtpRename> rr)
+/*! \brief Rename all residues named \c oldnm according to the user's
+ * interactive choice
+ *
+ * Search for residues for which the residue name from the input
+ * configuration file matches \c oldnm, and when found choose the rtp
+ * entry and name of the interactive choice from \c gettp.
+ *
+ * \todo Remove this function, per todo in \c renameResidue. */
+void renameResidueInteractively(t_atoms* pdba,
+ const char* oldnm,
+ const char* gettp(int, gmx::ArrayRef<const RtpRename>),
+ bool bFullCompare,
+ t_symtab* symtab,
+ gmx::ArrayRef<const RtpRename> rr)
{
- int i;
- const char* ptr;
- char* bbnm;
-
- for (i = 0; i < pdba->nres; i++)
+ // Search for residues i for which the residue name from the input
+ // configuration file matches oldnm, so it can replaced by the rtp
+ // entry and name of newnm.
+ for (int i = 0; i < pdba->nres; i++)
{
/* We have not set the rtp name yet, use the residue name */
- bbnm = *pdba->resinfo[i].name;
- if ((bFullCompare && (strcmp(bbnm, oldnm) == 0)) || (!bFullCompare && strstr(bbnm, oldnm) != nullptr))
+ char* residueNameInInputConfiguration = *pdba->resinfo[i].name;
+ if ((bFullCompare && (strcmp(residueNameInInputConfiguration, oldnm) == 0))
+ || (!bFullCompare && strstr(residueNameInInputConfiguration, oldnm) != nullptr))
{
- ptr = gettp(i, rr);
- pdba->resinfo[i].rtp = put_symtab(symtab, ptr);
+ const char* interactiveRtpChoice = gettp(i, rr);
+ pdba->resinfo[i].rtp = put_symtab(symtab, interactiveRtpChoice);
+ pdba->resinfo[i].name = pdba->resinfo[i].rtp;
}
}
}
return natom;
}
-void process_chain(t_atoms* pdba,
+void process_chain(const gmx::MDLogger& logger,
+ t_atoms* pdba,
gmx::ArrayRef<gmx::RVec> x,
bool bTrpU,
bool bPheU,
/* Rename aromatics, lys, asp and histidine */
if (bTyrU)
{
- rename_bb(pdba, "TYR", "TYRU", false, symtab);
+ renameResidue(logger, pdba, "TYR", "TYRU", false, symtab);
}
if (bTrpU)
{
- rename_bb(pdba, "TRP", "TRPU", false, symtab);
+ renameResidue(logger, pdba, "TRP", "TRPU", false, symtab);
}
if (bPheU)
{
- rename_bb(pdba, "PHE", "PHEU", false, symtab);
+ renameResidue(logger, pdba, "PHE", "PHEU", false, symtab);
}
if (bLysMan)
{
- rename_bbint(pdba, "LYS", get_lystp, false, symtab, rr);
+ renameResidueInteractively(pdba, "LYS", get_lystp, false, symtab, rr);
}
if (bArgMan)
{
- rename_bbint(pdba, "ARG", get_argtp, false, symtab, rr);
+ renameResidueInteractively(pdba, "ARG", get_argtp, false, symtab, rr);
}
if (bGlnMan)
{
- rename_bbint(pdba, "GLN", get_glntp, false, symtab, rr);
+ renameResidueInteractively(pdba, "GLN", get_glntp, false, symtab, rr);
}
if (bAspMan)
{
- rename_bbint(pdba, "ASP", get_asptp, false, symtab, rr);
+ renameResidueInteractively(pdba, "ASP", get_asptp, false, symtab, rr);
}
else
{
- rename_bb(pdba, "ASPH", "ASP", false, symtab);
+ renameResidue(logger, pdba, "ASPH", "ASP", false, symtab);
}
if (bGluMan)
{
- rename_bbint(pdba, "GLU", get_glutp, false, symtab, rr);
+ renameResidueInteractively(pdba, "GLU", get_glutp, false, symtab, rr);
}
else
{
- rename_bb(pdba, "GLUH", "GLU", false, symtab);
+ renameResidue(logger, pdba, "GLUH", "GLU", false, symtab);
}
if (!bHisMan)
}
else
{
- rename_bbint(pdba, "HIS", get_histp, true, symtab, rr);
+ renameResidueInteractively(pdba, "HIS", get_histp, true, symtab, rr);
}
/* Initialize the rtp builing block names with the residue names
"Processing chain %d (%d atoms, %d residues)", chain + 1, natom, nres);
}
- process_chain(pdba,
+ process_chain(logger,
+ pdba,
x,
bUnA_,
bUnA_,
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff