Refactor preprocessing atom types.

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

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 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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#include "gmxpre.h"

#include "resall.h"

#include <cctype>
#include <cstdlib>
#include <cstring>

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

#include "gromacs/gmxpreprocess/fflibutil.h"
#include "gromacs/gmxpreprocess/gpp_atomtype.h"
#include "gromacs/gmxpreprocess/grompp_impl.h"
#include "gromacs/gmxpreprocess/notset.h"
#include "gromacs/gmxpreprocess/pgutil.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/symtab.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"

PreprocessingAtomTypes read_atype(const char *ffdir, t_symtab *tab)
{
    FILE                    *in;
    char                     buf[STRLEN], name[STRLEN];
    double                   m;
    int                      nratt = 0;
    t_atom                  *a;
    t_param                 *nb;

    std::vector<std::string> files = fflib_search_file_end(ffdir, ".atp", TRUE);
    snew(a, 1);
    snew(nb, 1);
    PreprocessingAtomTypes at;

    for (const auto &filename : files)
    {
        in = fflib_open(filename);
        while (!feof(in))
        {
            /* Skip blank or comment-only lines */
            do
            {
                if (fgets2(buf, STRLEN, in) != nullptr)
                {
                    strip_comment(buf);
                    trim(buf);
                }
            }
            while ((feof(in) == 0) && strlen(buf) == 0);

            if (sscanf(buf, "%s%lf", name, &m) == 2)
            {
                a->m = m;
                at.addType(tab, *a, name, nb, 0, 0);
                fprintf(stderr, "\rAtomtype %d", ++nratt);
                fflush(stderr);
            }
            else
            {
                fprintf(stderr, "\nInvalid format: %s\n", buf);
            }
        }
        gmx_ffclose(in);
    }
    fprintf(stderr, "\n");
    sfree(a);
    return at;
}

static void print_resatoms(FILE *out, const PreprocessingAtomTypes &atype, const PreprocessResidue &rtpDBEntry)
{
    fprintf(out, "[ %s ]\n", rtpDBEntry.resname.c_str());
    fprintf(out, " [ atoms ]\n");

    for (int j = 0; (j < rtpDBEntry.natom()); j++)
    {
        int         tp   = rtpDBEntry.atom[j].type;
        const char *tpnm = atype.atomNameFromAtomType(tp);
        if (tpnm == nullptr)
        {
            gmx_fatal(FARGS, "Incorrect atomtype (%d)", tp);
        }
        fprintf(out, "%6s  %6s  %8.3f  %6d\n",
                *(rtpDBEntry.atomname[j]), tpnm, rtpDBEntry.atom[j].q, rtpDBEntry.cgnr[j]);
    }
}

static bool read_atoms(FILE *in, char *line,
                       PreprocessResidue *r0, t_symtab *tab, PreprocessingAtomTypes *atype)
{
    int    cg;
    char   buf[256], buf1[256];
    double q;

    /* Read Atoms */
    r0->atom.clear();
    r0->atomname.clear();
    r0->cgnr.clear();
    while (get_a_line(in, line, STRLEN) && (strchr(line, '[') == nullptr))
    {
        if (sscanf(line, "%s%s%lf%d", buf, buf1, &q, &cg) != 4)
        {
            return FALSE;
        }
        r0->atomname.push_back(put_symtab(tab, buf));
        r0->atom.emplace_back();
        r0->atom.back().q = q;
        r0->cgnr.push_back(cg);
        int j               = atype->atomTypeFromName(buf1);
        if (j == NOTSET)
        {
            gmx_fatal(FARGS, "Atom type %s (residue %s) not found in atomtype "
                      "database", buf1, r0->resname.c_str());
        }
        r0->atom.back().type = j;
        r0->atom.back().m    = atype->atomMassAFromAtomType(j);
    }

    return TRUE;
}

static bool read_bondeds(int bt, FILE *in, char *line, PreprocessResidue *rtpDBEntry)
{
    char str[STRLEN];

    while (get_a_line(in, line, STRLEN) && (strchr(line, '[') == nullptr))
    {
        int                n = 0;
        int                ni;
        rtpDBEntry->rb[bt].b.emplace_back();
        BondedInteraction *newBond = &rtpDBEntry->rb[bt].b.back();
        for (int j = 0; j < btsNiatoms[bt]; j++)
        {
            if (sscanf(line+n, "%s%n", str, &ni) == 1)
            {
                newBond->a[j]  = str;
            }
            else
            {
                return FALSE;
            }
            n += ni;
        }
        while (isspace(line[n]))
        {
            n++;
        }
        rtrim(line+n);
        newBond->s = line+n;
    }

    return TRUE;
}

static void print_resbondeds(FILE *out, int bt, const PreprocessResidue &rtpDBEntry)
{
    if (!rtpDBEntry.rb[bt].b.empty())
    {
        fprintf(out, " [ %s ]\n", btsNames[bt]);

        for (const auto &b : rtpDBEntry.rb[bt].b)
        {
            for (int j = 0; j < btsNiatoms[bt]; j++)
            {
                fprintf(out, "%6s ", b.a[j].c_str());
            }
            if (!b.s.empty())
            {
                fprintf(out, "    %s", b.s.c_str());
            }
            fprintf(out, "\n");
        }
    }
}

static void check_rtp(gmx::ArrayRef<const PreprocessResidue> rtpDBEntry, const std::string &libfn)
{
    /* check for double entries, assuming list is already sorted */
    for (auto it = rtpDBEntry.begin() + 1; it != rtpDBEntry.end(); it++)
    {
        auto prev = it-1;
        if (gmx::equalCaseInsensitive(prev->resname, it->resname))
        {
            fprintf(stderr, "WARNING double entry %s in file %s\n",
                    it->resname.c_str(), libfn.c_str());
        }
    }
}

static int get_bt(char* header)
{
    int i;

    for (i = 0; i < ebtsNR; i++)
    {
        if (gmx_strcasecmp(btsNames[i], header) == 0)
        {
            return i;
        }
    }
    return NOTSET;
}

/* print all the ebtsNR type numbers */
static void print_resall_header(FILE *out, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry)
{
    fprintf(out, "[ bondedtypes ]\n");
    fprintf(out, "; bonds  angles  dihedrals  impropers all_dihedrals nr_exclusions  HH14  remove_dih\n");
    fprintf(out, " %5d  %6d  %9d  %9d  %14d  %14d %14d %14d\n\n",
            rtpDBEntry[0].rb[0].type,
            rtpDBEntry[0].rb[1].type,
            rtpDBEntry[0].rb[2].type,
            rtpDBEntry[0].rb[3].type,
            static_cast<int>(rtpDBEntry[0].bKeepAllGeneratedDihedrals),
            rtpDBEntry[0].nrexcl,
            static_cast<int>(rtpDBEntry[0].bGenerateHH14Interactions),
            static_cast<int>(rtpDBEntry[0].bRemoveDihedralIfWithImproper));
}

void print_resall(FILE *out, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry,
                  const PreprocessingAtomTypes &atype)
{
    if (rtpDBEntry.empty())
    {
        return;
    }

    print_resall_header(out, rtpDBEntry);

    for (const auto &r : rtpDBEntry)
    {
        if (r.natom() > 0)
        {
            print_resatoms(out, atype, r);
            for (int bt = 0; bt < ebtsNR; bt++)
            {
                print_resbondeds(out, bt, r);
            }
        }
    }
}

void readResidueDatabase(const std::string &rrdb, std::vector<PreprocessResidue> *rtpDBEntry,
                         PreprocessingAtomTypes *atype, t_symtab *tab,
                         bool bAllowOverrideRTP)
{
    FILE         *in;
    char          filebase[STRLEN], line[STRLEN], header[STRLEN];
    int           bt, nparam;
    int           dum1, dum2, dum3;
    bool          bNextResidue, bError;

    fflib_filename_base(rrdb.c_str(), filebase, STRLEN);

    in = fflib_open(rrdb);

    PreprocessResidue header_settings;

    /* these bonded parameters will overwritten be when  *
     * there is a [ bondedtypes ] entry in the .rtp file */
    header_settings.rb[ebtsBONDS].type  = 1; /* normal bonds     */
    header_settings.rb[ebtsANGLES].type = 1; /* normal angles    */
    header_settings.rb[ebtsPDIHS].type  = 1; /* normal dihedrals */
    header_settings.rb[ebtsIDIHS].type  = 2; /* normal impropers */
    header_settings.rb[ebtsEXCLS].type  = 1; /* normal exclusions */
    header_settings.rb[ebtsCMAP].type   = 1; /* normal cmap torsions */

    header_settings.bKeepAllGeneratedDihedrals    = FALSE;
    header_settings.nrexcl                        = 3;
    header_settings.bGenerateHH14Interactions     = TRUE;
    header_settings.bRemoveDihedralIfWithImproper = TRUE;

    /* Column 5 & 6 aren't really bonded types, but we include
     * them here to avoid introducing a new section:
     * Column 5 : This controls the generation of dihedrals from the bonding.
     *            All possible dihedrals are generated automatically. A value of
     *            1 here means that all these are retained. A value of
     *            0 here requires generated dihedrals be removed if
     *              * there are any dihedrals on the same central atoms
     *                specified in the residue topology, or
     *              * there are other identical generated dihedrals
     *                sharing the same central atoms, or
     *              * there are other generated dihedrals sharing the
     *                same central bond that have fewer hydrogen atoms
     * Column 6: Number of bonded neighbors to exclude.
     * Column 7: Generate 1,4 interactions between two hydrogen atoms
     * Column 8: Remove proper dihedrals if centered on the same bond
     *           as an improper dihedral
     */
    get_a_line(in, line, STRLEN);
    if (!get_header(line, header))
    {
        gmx_fatal(FARGS, "in .rtp file at line:\n%s\n", line);
    }
    if (gmx_strncasecmp("bondedtypes", header, 5) == 0)
    {
        get_a_line(in, line, STRLEN);
        if ((nparam = sscanf(line, "%d %d %d %d %d %d %d %d",
                             &header_settings.rb[ebtsBONDS].type, &header_settings.rb[ebtsANGLES].type,
                             &header_settings.rb[ebtsPDIHS].type, &header_settings.rb[ebtsIDIHS].type,
                             &dum1, &header_settings.nrexcl, &dum2, &dum3)) < 4)
        {
            gmx_fatal(FARGS, "need 4 to 8 parameters in the header of .rtp file %s at line:\n%s\n", rrdb.c_str(), line);
        }
        header_settings.bKeepAllGeneratedDihedrals    = (dum1 != 0);
        header_settings.bGenerateHH14Interactions     = (dum2 != 0);
        header_settings.bRemoveDihedralIfWithImproper = (dum3 != 0);
        get_a_line(in, line, STRLEN);
        if (nparam < 5)
        {
            fprintf(stderr, "Using default: not generating all possible dihedrals\n");
            header_settings.bKeepAllGeneratedDihedrals = FALSE;
        }
        if (nparam < 6)
        {
            fprintf(stderr, "Using default: excluding 3 bonded neighbors\n");
            header_settings.nrexcl = 3;
        }
        if (nparam < 7)
        {
            fprintf(stderr, "Using default: generating 1,4 H--H interactions\n");
            header_settings.bGenerateHH14Interactions = TRUE;
        }
        if (nparam < 8)
        {
            fprintf(stderr, "Using default: removing proper dihedrals found on the same bond as a proper dihedral\n");
            header_settings.bRemoveDihedralIfWithImproper = TRUE;
        }
    }
    else
    {
        fprintf(stderr,
                "Reading .rtp file without '[ bondedtypes ]' directive,\n"
                "Will proceed as if the entry was:\n");
        print_resall_header(stderr, gmx::arrayRefFromArray(&header_settings, 1));
    }
    /* We don't know the current size of rrtp, but simply realloc immediately */
    auto oldArrayEnd = rtpDBEntry->end() - 1;
    while (!feof(in))
    {
        /* Initialise rtp entry structure */
        rtpDBEntry->push_back(header_settings);
        PreprocessResidue *res = &rtpDBEntry->back();
        if (!get_header(line, header))
        {
            gmx_fatal(FARGS, "in .rtp file at line:\n%s\n", line);
        }
        res->resname  = header;
        res->filebase = filebase;

        get_a_line(in, line, STRLEN);
        bError       = FALSE;
        bNextResidue = FALSE;
        do
        {
            if (!get_header(line, header))
            {
                bError = TRUE;
            }
            else
            {
                bt = get_bt(header);
                if (bt != NOTSET)
                {
                    /* header is an bonded directive */
                    bError = !read_bondeds(bt, in, line, res);
                }
                else if (gmx_strncasecmp("atoms", header, 5) == 0)
                {
                    /* header is the atoms directive */
                    bError = !read_atoms(in, line, res, tab, atype);
                }
                else
                {
                    /* else header must be a residue name */
                    bNextResidue = TRUE;
                }
            }
            if (bError)
            {
                gmx_fatal(FARGS, "in .rtp file in residue %s at line:\n%s\n",
                          res->resname.c_str(), line);
            }
        }
        while ((feof(in) == 0) && !bNextResidue);

        if (res->natom() == 0)
        {
            gmx_fatal(FARGS, "No atoms found in .rtp file in residue %s\n",
                      res->resname.c_str());
        }

        auto found = std::find_if(rtpDBEntry->begin(), rtpDBEntry->end()-1,
                                  [&res](const PreprocessResidue &entry)
                                  { return gmx::equalCaseInsensitive(res->resname, entry.resname); });

        if (found == rtpDBEntry->end() - 1)
        {
            int size = rtpDBEntry->size() - 1;
            fprintf(stderr, "\rResidue %d", size);
            fflush(stderr);
        }
        else
        {
            if (found >= oldArrayEnd)
            {
                gmx_fatal(FARGS, "Found a second entry for '%s' in '%s'",
                          res->resname.c_str(), rrdb.c_str());
            }
            if (bAllowOverrideRTP)
            {
                fprintf(stderr, "\n");
                fprintf(stderr, "Found another rtp entry for '%s' in '%s', ignoring this entry and keeping the one from '%s.rtp'\n",
                        res->resname.c_str(), rrdb.c_str(), found->filebase.c_str());
                /* We should free all the data for this entry.
                 * The current code gives a lot of dangling pointers.
                 */
                rtpDBEntry->erase(rtpDBEntry->end() - 1);
            }
            else
            {
                gmx_fatal(FARGS, "Found rtp entries for '%s' in both '%s' and '%s'. If you want the first definition to override the second one, set the -rtpo option of pdb2gmx.", res->resname.c_str(), found->filebase.c_str(), rrdb.c_str());
            }
        }
    }
    gmx_ffclose(in);

    fprintf(stderr, "\nSorting it all out...\n");
    std::sort(rtpDBEntry->begin(), rtpDBEntry->end(), []
                  (const PreprocessResidue &a,
                  const PreprocessResidue &b)
              {return std::lexicographical_compare(
                       a.resname.begin(), a.resname.end(),
                       b.resname.begin(), b.resname.end(),
                       [](const char &c1, const char &c2)
                       { return std::toupper(c1) < std::toupper(c2); }); });

    check_rtp(*rtpDBEntry, rrdb);
}

/************************************************************
 *
 *                  SEARCH   ROUTINES
 *
 ***********************************************************/
static bool is_sign(char c)
{
    return (c == '+' || c == '-');
}

/* Compares if the strins match except for a sign at the end
 * of (only) one of the two.
 */
static int neq_str_sign(const char *a1, const char *a2)
{
    int l1, l2, lm;

    l1 = static_cast<int>(strlen(a1));
    l2 = static_cast<int>(strlen(a2));
    lm = std::min(l1, l2);

    if (lm >= 1 &&
        ((l1 == l2+1 && is_sign(a1[l1-1])) ||
         (l2 == l1+1 && is_sign(a2[l2-1]))) &&
        gmx_strncasecmp(a1, a2, lm) == 0)
    {
        return lm;
    }
    else
    {
        return 0;
    }
}

std::string searchResidueDatabase(const std::string &key, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry)
{
    int         nbest, best, besti;
    std::string bestbuf;

    nbest =  0;
    besti = -1;
    /* We want to match at least one character */
    best  =  1;
    for (auto it = rtpDBEntry.begin(); it != rtpDBEntry.end(); it++)
    {
        if (gmx::equalCaseInsensitive(key, it->resname))
        {
            besti = std::distance(rtpDBEntry.begin(), it);
            nbest = 1;
            break;
        }
        else
        {
            /* Allow a mismatch of at most a sign character (with warning) */
            int n = neq_str_sign(key.c_str(), it->resname.c_str());
            if (n >= best &&
                n+1 >= gmx::index(key.length()) &&
                n+1 >= gmx::index(it->resname.length()))
            {
                if (n == best)
                {
                    if (nbest == 1)
                    {
                        bestbuf = rtpDBEntry[besti].resname;
                    }
                    if (nbest >= 1)
                    {
                        bestbuf.append(" or ");
                        bestbuf.append(it->resname);
                    }
                }
                else
                {
                    nbest = 0;
                }
                besti = std::distance(rtpDBEntry.begin(), it);
                best  = n;
                nbest++;
            }
        }
    }
    if (nbest > 1)
    {
        gmx_fatal(FARGS, "Residue '%s' not found in residue topology database, looks a bit like %s", key.c_str(), bestbuf.c_str());
    }
    else if (besti == -1)
    {
        gmx_fatal(FARGS, "Residue '%s' not found in residue topology database", key.c_str());
    }
    if (!gmx::equalCaseInsensitive(rtpDBEntry[besti].resname, key))
    {
        fprintf(stderr,
                "\nWARNING: '%s' not found in residue topology database, "
                "trying to use '%s'\n\n", key.c_str(), rtpDBEntry[besti].resname.c_str());
    }

    return rtpDBEntry[besti].resname;
}

gmx::ArrayRef<const PreprocessResidue>::const_iterator
getDatabaseEntry(const std::string &rtpname, gmx::ArrayRef<const PreprocessResidue> rtpDBEntry)
{
    auto found = std::find_if(rtpDBEntry.begin(), rtpDBEntry.end(),
                              [&rtpname](const PreprocessResidue &entry)
                              { return gmx::equalCaseInsensitive(rtpname, entry.resname); });
    if (found == rtpDBEntry.end())
    {
        /* This should never happen, since searchResidueDatabase should have been called
         * before calling getDatabaseEntry.
         */
        gmx_fatal(FARGS, "Residue type '%s' not found in residue topology database", rtpname.c_str());
    }

    return found;
}