Split lines with many copyright years

[gromacs.git] / src / gromacs / gmxpreprocess / ter_db.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015,2017,2018 by the GROMACS development team.
 * Copyright (c) 2019,2020, 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.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */
#include "gmxpre.h"

#include "ter_db.h"

#include <cctype>
#include <cstring>

#include <algorithm>
#include <string>
#include <vector>

#include "gromacs/fileio/gmxfio.h"
#include "gromacs/gmxpreprocess/fflibutil.h"
#include "gromacs/gmxpreprocess/gpp_atomtype.h"
#include "gromacs/gmxpreprocess/grompp_impl.h"
#include "gromacs/gmxpreprocess/h_db.h"
#include "gromacs/gmxpreprocess/notset.h"
#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strdb.h"

#include "hackblock.h"
#include "resall.h"

/* use bonded types definitions in hackblock.h */
#define ekwRepl (ebtsNR + 1)
#define ekwAdd (ebtsNR + 2)
#define ekwDel (ebtsNR + 3)
#define ekwNR 3
static const char* kw_names[ekwNR] = { "replace", "add", "delete" };

static int find_kw(char* keyw)
{
    int i;

    for (i = 0; i < ebtsNR; i++)
    {
        if (gmx_strcasecmp(btsNames[i], keyw) == 0)
        {
            return i;
        }
    }
    for (i = 0; i < ekwNR; i++)
    {
        if (gmx_strcasecmp(kw_names[i], keyw) == 0)
        {
            return ebtsNR + 1 + i;
        }
    }

    return NOTSET;
}

#define FATAL() gmx_fatal(FARGS, "Reading Termini Database: not enough items on line\n%s", line)

static void read_atom(char* line, bool bAdd, std::string* nname, t_atom* a, PreprocessingAtomTypes* atype, int* cgnr)
{
    int    nr, i;
    char   buf[5][30];
    double m, q;

    /* This code is messy, because of support for different formats:
     * for replace: [new name] <atom type> <m> <q> [cgnr (old format)]
     * for add:                <atom type> <m> <q> [cgnr]
     */
    nr = sscanf(line, "%s %s %s %s %s", buf[0], buf[1], buf[2], buf[3], buf[4]);

    /* Here there an ambiguity due to the old replace format with cgnr,
     * which was read for years, but ignored in the rest of the code.
     * We have to assume that the atom type does not start with a digit
     * to make a line with 4 entries uniquely interpretable.
     */
    if (!bAdd && nr == 4 && isdigit(buf[1][0]))
    {
        nr = 3;
    }

    if (nr < 3 || nr > 4)
    {
        gmx_fatal(FARGS,
                  "Reading Termini Database: expected %d or %d items of atom data in stead of %d "
                  "on line\n%s",
                  3, 4, nr, line);
    }
    i = 0;
    if (!bAdd)
    {
        if (nr == 4)
        {
            *nname = buf[i++];
        }
        else
        {
            *nname = "";
        }
    }
    a->type = atype->atomTypeFromName(buf[i++]);
    sscanf(buf[i++], "%lf", &m);
    a->m = m;
    sscanf(buf[i++], "%lf", &q);
    a->q = q;
    if (bAdd && nr == 4)
    {
        sscanf(buf[i++], "%d", cgnr);
    }
    else
    {
        *cgnr = NOTSET;
    }
}

static void print_atom(FILE* out, const t_atom& a, PreprocessingAtomTypes* atype)
{
    fprintf(out, "\t%s\t%g\t%g\n", atype->atomNameFromAtomType(a.type), a.m, a.q);
}

static void print_ter_db(const char*                                ff,
                         char                                       C,
                         gmx::ArrayRef<const MoleculePatchDatabase> tb,
                         PreprocessingAtomTypes*                    atype)
{
    std::string buf = gmx::formatString("%s-%c.tdb", ff, C);
    FILE*       out = gmx_fio_fopen(buf.c_str(), "w");

    for (const auto& modification : tb)
    {
        fprintf(out, "[ %s ]\n", modification.name.c_str());

        if (std::any_of(modification.hack.begin(), modification.hack.end(),
                        [](const auto& mod) { return mod.type() == MoleculePatchType::Replace; }))
        {
            fprintf(out, "[ %s ]\n", kw_names[ekwRepl - ebtsNR - 1]);
            for (const auto& hack : modification.hack)
            {
                if (hack.type() == MoleculePatchType::Replace)
                {
                    fprintf(out, "%s\t", hack.oname.c_str());
                    print_atom(out, hack.atom.back(), atype);
                }
            }
        }
        if (std::any_of(modification.hack.begin(), modification.hack.end(),
                        [](const auto& mod) { return mod.type() == MoleculePatchType::Add; }))
        {
            fprintf(out, "[ %s ]\n", kw_names[ekwAdd - ebtsNR - 1]);
            for (const auto& hack : modification.hack)
            {
                if (hack.type() == MoleculePatchType::Add)
                {
                    print_ab(out, hack, hack.nname.c_str());
                    print_atom(out, hack.atom.back(), atype);
                }
            }
        }
        if (std::any_of(modification.hack.begin(), modification.hack.end(),
                        [](const auto& mod) { return mod.type() == MoleculePatchType::Delete; }))
        {
            fprintf(out, "[ %s ]\n", kw_names[ekwDel - ebtsNR - 1]);
            for (const auto& hack : modification.hack)
            {
                if (hack.type() == MoleculePatchType::Delete)
                {
                    fprintf(out, "%s\n", hack.oname.c_str());
                }
            }
        }
        for (int bt = 0; bt < ebtsNR; bt++)
        {
            if (!modification.rb[bt].b.empty())
            {
                fprintf(out, "[ %s ]\n", btsNames[bt]);
                for (const auto& b : modification.rb[bt].b)
                {
                    for (int k = 0; k < btsNiatoms[bt]; k++)
                    {
                        fprintf(out, "%s%s", k ? "\t" : "", b.a[k].c_str());
                    }
                    if (!b.s.empty())
                    {
                        fprintf(out, "\t%s", b.s.c_str());
                    }
                    fprintf(out, "\n");
                }
            }
        }
        fprintf(out, "\n");
    }
    gmx_fio_fclose(out);
}

static void read_ter_db_file(const char*                         fn,
                             std::vector<MoleculePatchDatabase>* tbptr,
                             PreprocessingAtomTypes*             atype)
{
    char filebase[STRLEN];
    char header[STRLEN], buf[STRLEN], line[STRLEN];

    fflib_filename_base(fn, filebase, STRLEN);
    /* Remove the C/N termini extension */
    char* ptr = strrchr(filebase, '.');
    if (ptr != nullptr)
    {
        ptr[0] = '\0';
    }

    FILE* in = fflib_open(fn);

    int kwnr = NOTSET;
    get_a_line(in, line, STRLEN);
    MoleculePatchDatabase* block = nullptr;
    while (!feof(in))
    {
        if (get_header(line, header))
        {
            /* this is a new block, or a new keyword */
            kwnr = find_kw(header);

            if (kwnr == NOTSET)
            {
                tbptr->emplace_back(MoleculePatchDatabase());
                block = &tbptr->back();
                clearModificationBlock(block);
                block->name     = header;
                block->filebase = filebase;
            }
        }
        else
        {
            if (block == nullptr)
            {
                gmx_fatal(FARGS,
                          "reading termini database: "
                          "directive expected before line:\n%s\n"
                          "This might be a file in an old format.",
                          line);
            }
            /* this is not a header, so it must be data */
            if (kwnr >= ebtsNR)
            {
                /* this is a hack: add/rename/delete atoms */
                /* make space for hacks */
                block->hack.emplace_back(MoleculePatch());
                MoleculePatch* hack = &block->hack.back();

                /* get data */
                int n = 0;
                if (kwnr == ekwRepl || kwnr == ekwDel)
                {
                    if (sscanf(line, "%s%n", buf, &n) != 1)
                    {
                        gmx_fatal(FARGS,
                                  "Reading Termini Database '%s': "
                                  "expected atom name on line\n%s",
                                  fn, line);
                    }
                    hack->oname = buf;
                    /* we only replace or delete one atom at a time */
                    hack->nr = 1;
                }
                else if (kwnr == ekwAdd)
                {
                    read_ab(line, fn, hack);
                    get_a_line(in, line, STRLEN);
                }
                else
                {
                    gmx_fatal(FARGS, "unimplemented keyword number %d (%s:%d)", kwnr, __FILE__, __LINE__);
                }
                if (kwnr == ekwRepl || kwnr == ekwAdd)
                {
                    hack->atom.emplace_back();
                    read_atom(line + n, kwnr == ekwAdd, &hack->nname, &hack->atom.back(), atype,
                              &hack->cgnr);
                    if (hack->nname.empty())
                    {
                        if (!hack->oname.empty())
                        {
                            hack->nname = hack->oname;
                        }
                        else
                        {
                            gmx_fatal(FARGS,
                                      "Reading Termini Database '%s': don't know which name the "
                                      "new atom should have on line\n%s",
                                      fn, line);
                        }
                    }
                }
            }
            else if (kwnr >= 0 && kwnr < ebtsNR)
            {
                /* this is bonded data: bonds, angles, dihedrals or impropers */
                int n = 0;
                block->rb[kwnr].b.emplace_back();
                BondedInteraction* newBond = &block->rb[kwnr].b.back();
                for (int j = 0; j < btsNiatoms[kwnr]; j++)
                {
                    int ni;
                    if (sscanf(line + n, "%s%n", buf, &ni) == 1)
                    {
                        newBond->a[j] = buf;
                    }
                    else
                    {
                        gmx_fatal(FARGS,
                                  "Reading Termini Database '%s': expected %d atom names (found "
                                  "%d) on line\n%s",
                                  fn, btsNiatoms[kwnr], j - 1, line);
                    }
                    n += ni;
                }
                strcpy(buf, "");
                sscanf(line + n, "%s", buf);
                newBond->s = buf;
            }
            else
            {
                gmx_fatal(FARGS,
                          "Reading Termini Database: Expecting a header at line\n"
                          "%s",
                          line);
            }
        }
        get_a_line(in, line, STRLEN);
    }

    gmx_ffclose(in);
}

int read_ter_db(const char* ffdir, char ter, std::vector<MoleculePatchDatabase>* tbptr, PreprocessingAtomTypes* atype)
{
    std::string ext = gmx::formatString(".%c.tdb", ter);

    /* Search for termini database files.
     * Do not generate an error when none are found.
     */
    std::vector<std::string> tdbf = fflib_search_file_end(ffdir, ext.c_str(), FALSE);
    tbptr->clear();
    for (const auto& filename : tdbf)
    {
        read_ter_db_file(filename.c_str(), tbptr, atype);
    }

    if (debug)
    {
        print_ter_db("new", ter, *tbptr, atype);
    }

    return tbptr->size();
}

std::vector<MoleculePatchDatabase*> filter_ter(gmx::ArrayRef<MoleculePatchDatabase> tb, const char* resname)
{
    // TODO Four years later, no force fields have ever used this, so decide status of this feature
    /* Since some force fields (e.g. OPLS) needs different
     * atomtypes for different residues there could be a lot
     * of entries in the databases for specific residues
     * (e.g. GLY-NH3+, SER-NH3+, ALA-NH3+).
     *
     * To reduce the database size, we assume that a terminus specifier liker
     *
     * [ GLY|SER|ALA-NH3+ ]
     *
     * would cover all of the three residue types above.
     * Wildcards (*,?) are not OK. Don't worry about e.g. GLU vs. GLUH since
     * pdb2gmx only uses the first 3 letters when calling this routine.
     *
     * To automate this, this routines scans a list of termini
     * for the residue name "resname" and returns an allocated list of
     * pointers to the termini that could be applied to the
     * residue in question. The variable pointed to by nret will
     * contain the number of valid pointers in the list.
     * Remember to free the list when you are done with it...
     */

    auto                                none_idx = tb.end();
    std::vector<MoleculePatchDatabase*> list;

    for (auto it = tb.begin(); it != tb.end(); it++)
    {
        const char* s     = it->name.c_str();
        bool        found = false;
        do
        {
            if (gmx::equalCaseInsensitive(resname, s, 3))
            {
                found = true;
                list.push_back(it);
            }
            else
            {
                /* advance to next |-separated field */
                s = strchr(s, '|');
                if (s != nullptr)
                {
                    s++;
                }
            }
        } while (!found && s != nullptr);
    }

    /* All residue-specific termini have been added. We might have to fall
     * back on generic termini, which are characterized by not having
     * '-' in the name prior to the last position (which indicates charge).
     * The [ None ] alternative is special since we don't want that
     * to be the default, so we put it last in the list we return.
     */
    for (auto it = tb.begin(); it != tb.end(); it++)
    {
        const char* s = it->name.c_str();
        if (gmx::equalCaseInsensitive("None", it->name))
        {
            none_idx = it;
        }
        else
        {
            /* Time to see if there's a generic terminus that matches.
               Is there a hyphen? */
            const char* c = strchr(s, '-');

            /* A conjunction hyphen normally indicates a residue-specific
               terminus, which is named like "GLY-COOH". A generic terminus
               won't have a hyphen. */
            bool bFoundAnyHyphen = (c != nullptr);
            /* '-' as the last character indicates charge, so if that's
               the only one found e.g. "COO-", then it was not a conjunction
               hyphen, so this is a generic terminus */
            bool bOnlyFoundChargeHyphen = (bFoundAnyHyphen && *(c + 1) == '\0');
            /* Thus, "GLY-COO-" is not recognized as a generic terminus. */
            bool bFoundGenericTerminus = !bFoundAnyHyphen || bOnlyFoundChargeHyphen;
            if (bFoundGenericTerminus)
            {
                /* Check that we haven't already added a residue-specific version
                 * of this terminus.
                 */
                auto found = std::find_if(list.begin(), list.end(), [&s](const MoleculePatchDatabase* b) {
                    return strstr(b->name.c_str(), s) != nullptr;
                });
                if (found == list.end())
                {
                    list.push_back(it);
                }
            }
        }
    }
    if (none_idx != tb.end())
    {
        list.push_back(none_idx);
    }

    return list;
}


MoleculePatchDatabase* choose_ter(gmx::ArrayRef<MoleculePatchDatabase*> tb, const char* title)
{
    int sel, ret;

    printf("%s\n", title);
    int i = 0;
    for (const auto& modification : tb)
    {
        bool bIsZwitterion = (0 == gmx_wcmatch("*ZWITTERION*", modification->name.c_str()));
        printf("%2d: %s%s\n", i, modification->name.c_str(),
               bIsZwitterion ? " (only use with zwitterions containing exactly one residue)" : "");
        i++;
    }
    do
    {
        ret = fscanf(stdin, "%d", &sel);
    } while ((ret != 1) || (sel < 0) || (sel >= tb.ssize()));

    return tb[sel];
}