src/gromacs/gmxpreprocess/hackblock.h

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  37 /*! \file
  38  * \libinternal \brief
  39  * Methods to modify atoms during preprocessing.
  40  */
  41 #ifndef GMX_GMXPREPROCESS_HACKBLOCK_H
  42 #define GMX_GMXPREPROCESS_HACKBLOCK_H
  43
  44 #include <cstdio>
  45
  46 #include <string>
  47 #include <vector>
  48
  49 #include "gromacs/gmxpreprocess/notset.h"
  50 #include "gromacs/topology/ifunc.h"
  51 #include "gromacs/utility/arrayref.h"
  52
  53 struct t_atom;
  54 struct t_symtab;
  55 /*! \brief
  56  * Used for reading .rtp/.tdb
  57  * ebtsBONDS must be the first, new types can be added to the end
  58  * these *MUST* correspond to the arrays in hackblock.cpp
  59  */
  60 enum {
  61     ebtsBONDS, ebtsANGLES, ebtsPDIHS, ebtsIDIHS, ebtsEXCLS, ebtsCMAP, ebtsNR
  62 };
  63 //! Names for interaction type entries
  64 extern const char *btsNames[ebtsNR];
  65 //! Numbers for atoms in the interactions.
  66 extern const int   btsNiatoms[ebtsNR];
  67
  68 /* if changing any of these structs, make sure that all of the
  69    free/clear/copy/merge_t_* functions stay updated */
  70
  71 /*! \libinternal \brief
  72  * Information about single bonded interaction.
  73  */
  74 struct BondedInteraction
  75 {
  76     //! Atom names in the bond.
  77     std::array<std::string, MAXATOMLIST> a;
  78     /*! \brief
  79      * Optional define string which gets copied from
  80      * .rtp/.tdb to .top and will be parsed by cpp
  81      * during grompp.
  82      */
  83     std::string        s;
  84     //! Has the entry been found?
  85     bool               match = false;
  86     //! Get name of first atom in bonded interaction.
  87     const std::string &ai() const { return a[0]; }
  88     //! Get name of second atom in bonded interaction..
  89     const std::string &aj() const { return a[1]; }
  90     //! Get name of third atom in bonded interaction.
  91     const std::string &ak() const { return a[2]; }
  92     //! Get name of fourth atom in bonded interaction.
  93     const std::string &al() const { return a[3]; }
  94     //! Get name of fifth atom in bonded interaction.
  95     const std::string &am() const { return a[4]; }
  96 };
  97
  98 /*! \libinternal \brief
  99  * Accumulation of different bonded types for preprocessing.
 100  * \todo This should be merged with BondedInteraction.
 101  */
 102 struct BondedInteractionList
 103 {
 104     //! The type of bonded interaction.
 105     int                            type = -1;
 106     //! The actual bonded interactions.
 107     std::vector<BondedInteraction> b;
 108 };
 109
 110 /*! \libinternal \brief
 111  * Information about preprocessing residues.
 112  */
 113 struct PreprocessResidue
 114 {
 115     //! Name of the residue.
 116     std::string                               resname;
 117     //! The base file name this rtp entry was read from.
 118     std::string                               filebase;
 119     //! Atom data.
 120     std::vector<t_atom>                       atom;
 121     //! Atom names.
 122     std::vector<char **>                      atomname;
 123     //! Charge group numbers.
 124     std::vector<int>                          cgnr;
 125     //! Delete autogenerated dihedrals or not.
 126     bool                                      bKeepAllGeneratedDihedrals = false;
 127     //! Number of bonded exclusions.
 128     int                                       nrexcl = -1;
 129     //! If Hydrogen only 1-4 interactions should be generated.
 130     bool                                      bGenerateHH14Interactions = false;
 131     //! Delete dihedrals also defined by impropers.
 132     bool                                      bRemoveDihedralIfWithImproper = false;
 133     //! List of bonded interactions to potentially add.
 134     std::array<BondedInteractionList, ebtsNR> rb;
 135     //! Get number of atoms in residue.
 136     int                                       natom() const { return atom.size(); }
 137 };
 138
 139 //! Declare different types of hacks for later check.
 140 enum class MoleculePatchType
 141 {
 142     //! Hack adds atom to structure/rtp.
 143     Add,
 144     //! Hack deletes atom.
 145     Delete,
 146     //! Hack replaces atom.
 147     Replace
 148 };
 149
 150 /*! \libinternal \brief
 151  * Block to modify individual residues
 152  */
 153 struct MoleculePatch
 154 {
 155     //! Number of new are deleted atoms. NOT always equal to atom.size()!
 156     int                        nr;
 157     //! Old name for entry.
 158     std::string                oname;
 159     //! New name for entry.
 160     std::string                nname;
 161     //! New atom data.
 162     std::vector<t_atom>        atom;
 163     //! Chargegroup number.
 164     int                        cgnr = NOTSET;
 165     //! Type of attachement.
 166     int                        tp = 0;
 167     //! Number of control atoms.
 168     int                        nctl = 0;
 169     //! Name of control atoms.
 170     std::array<std::string, 4> a;
 171     //! Is an atom to be hacked already present?
 172     bool                       bAlreadyPresent = false;
 173     //! Are coordinates for a new atom already set?
 174     bool                       bXSet = false;
 175     //! New position for hacked atom.
 176     rvec                       newx = {NOTSET};
 177     //! New atom index number after additions.
 178     int                        newi = -1;
 179
 180     /*! \brief
 181      * Get type of hack.
 182      *
 183      * This depends on the setting of oname and nname
 184      * for legacy reasons. If oname is empty, we are adding,
 185      * if oname is set and nname is empty, an atom is deleted,
 186      * if both are set replacement is going on. If both are unset,
 187      * an error is thrown.
 188      */
 189     MoleculePatchType type() const;
 190
 191     //! Control atom i name.
 192     const std::string &ai() const { return a[0]; }
 193     //! Control atom j name.
 194     const std::string &aj() const { return a[1]; }
 195     //! Control atom k name.
 196     const std::string &ak() const { return a[2]; }
 197     //! Control atom l name.
 198     const std::string &al() const { return a[3]; }
 199 };
 200 /*! \libinternal \brief
 201  * A set of modifications to apply to atoms.
 202  */
 203 struct MoleculePatchDatabase
 204 {
 205     //! Name of block
 206     std::string                                              name;
 207     //! File that entry was read from.
 208     std::string                                              filebase;
 209     //! List of changes to atoms.
 210     std::vector<MoleculePatch>                               hack;
 211     //! List of bonded interactions to potentially add.
 212     std::array<BondedInteractionList, ebtsNR>                rb;
 213     //! Number of atoms to modify
 214     int                                                      nhack() const { return hack.size(); }
 215 };
 216
 217 /*!\brief
 218  * Reset modification block.
 219  *
 220  * \param[inout] globalPatches Block to reset.
 221  * \todo Remove once constructor/destructor takes care of all of this.
 222  */
 223 void clearModificationBlock(MoleculePatchDatabase *globalPatches);
 224
 225 /*!\brief
 226  * Copy residue information.
 227  *
 228  * \param[in] s Source information.
 229  * \param[in] d Destination to copy to.
 230  * \param[inout] symtab Symbol table for names.
 231  * \todo Remove once copy can be done directly.
 232  */
 233 void copyPreprocessResidues(const PreprocessResidue &s, PreprocessResidue *d, t_symtab *symtab);
 234
 235 /*! \brief
 236  * Add bond information in \p s to \p d.
 237  *
 238  * \param[in] s Source information to copy.
 239  * \param[inout] d Destination to copy to.
 240  * \param[in] bMin don't copy bondeds with atoms starting with '-'.
 241  * \param[in] bPlus don't copy bondeds with atoms starting with '+'.
 242  * \returns if bonds were removed at the termini.
 243  */
 244 bool mergeBondedInteractionList(gmx::ArrayRef<const BondedInteractionList> s,
 245                                 gmx::ArrayRef<BondedInteractionList> d,
 246                                 bool bMin, bool bPlus);
 247
 248 /*! \brief
 249  * Copy all information from datastructure.
 250  *
 251  * \param[in] s Source information.
 252  * \param[inout] d Destination to copy to.
 253  */
 254 void copyModificationBlocks(const MoleculePatchDatabase &s, MoleculePatchDatabase *d);
 255
 256 /*!\brief
 257  * Add the individual modifications in \p s to \p d.
 258  *
 259  * \param[in] s Source information.
 260  * \param[inout] d Destination to copy to.
 261  */
 262 void mergeAtomModifications(const MoleculePatchDatabase &s, MoleculePatchDatabase *d);
 263
 264 //! \copydoc mergeAtomModifications
 265 void mergeAtomAndBondModifications(const MoleculePatchDatabase &s, MoleculePatchDatabase *d);
 266
 267 #endif