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 <array>
  47 #include <string>
  48 #include <vector>
  49
  50 #include "gromacs/gmxpreprocess/notset.h"
  51 #include "gromacs/topology/ifunc.h"
  52
  53 struct t_atom;
  54 struct t_symtab;
  55
  56 namespace gmx
  57 {
  58 template<typename>
  59 class ArrayRef;
  60 }
  61
  62 /*! \brief
  63  * Used for reading .rtp/.tdb
  64  * ebtsBONDS must be the first, new types can be added to the end
  65  * these *MUST* correspond to the arrays in hackblock.cpp
  66  */
  67 enum
  68 {
  69     ebtsBONDS,
  70     ebtsANGLES,
  71     ebtsPDIHS,
  72     ebtsIDIHS,
  73     ebtsEXCLS,
  74     ebtsCMAP,
  75     ebtsNR
  76 };
  77 //! Names for interaction type entries
  78 extern const char* btsNames[ebtsNR];
  79 //! Numbers for atoms in the interactions.
  80 extern const int btsNiatoms[ebtsNR];
  81
  82 /* if changing any of these structs, make sure that all of the
  83    free/clear/copy/merge_t_* functions stay updated */
  84
  85 /*! \libinternal \brief
  86  * Information about single bonded interaction.
  87  */
  88 struct BondedInteraction
  89 {
  90     //! Atom names in the bond.
  91     std::array<std::string, MAXATOMLIST> a;
  92     /*! \brief
  93      * Optional define string which gets copied from
  94      * .rtp/.tdb to .top and will be parsed by cpp
  95      * during grompp.
  96      */
  97     std::string s;
  98     //! Has the entry been found?
  99     bool match = false;
 100     //! Get name of first atom in bonded interaction.
 101     const std::string& ai() const { return a[0]; }
 102     //! Get name of second atom in bonded interaction..
 103     const std::string& aj() const { return a[1]; }
 104     //! Get name of third atom in bonded interaction.
 105     const std::string& ak() const { return a[2]; }
 106     //! Get name of fourth atom in bonded interaction.
 107     const std::string& al() const { return a[3]; }
 108     //! Get name of fifth atom in bonded interaction.
 109     const std::string& am() const { return a[4]; }
 110 };
 111
 112 /*! \libinternal \brief
 113  * Accumulation of different bonded types for preprocessing.
 114  * \todo This should be merged with BondedInteraction.
 115  */
 116 struct BondedInteractionList
 117 {
 118     //! The type of bonded interaction.
 119     int type = -1;
 120     //! The actual bonded interactions.
 121     std::vector<BondedInteraction> b;
 122 };
 123
 124 /*! \libinternal \brief
 125  * Information about preprocessing residues.
 126  */
 127 struct PreprocessResidue
 128 {
 129     //! Name of the residue.
 130     std::string resname;
 131     //! The base file name this rtp entry was read from.
 132     std::string filebase;
 133     //! Atom data.
 134     std::vector<t_atom> atom;
 135     //! Atom names.
 136     std::vector<char**> atomname;
 137     //! Charge group numbers.
 138     std::vector<int> cgnr;
 139     //! Delete autogenerated dihedrals or not.
 140     bool bKeepAllGeneratedDihedrals = false;
 141     //! Number of bonded exclusions.
 142     int nrexcl = -1;
 143     //! If Hydrogen only 1-4 interactions should be generated.
 144     bool bGenerateHH14Interactions = false;
 145     //! Delete dihedrals also defined by impropers.
 146     bool bRemoveDihedralIfWithImproper = false;
 147     //! List of bonded interactions to potentially add.
 148     std::array<BondedInteractionList, ebtsNR> rb;
 149     //! Get number of atoms in residue.
 150     int natom() const { return atom.size(); }
 151 };
 152
 153 //! Declare different types of hacks for later check.
 154 enum class MoleculePatchType
 155 {
 156     //! Hack adds atom to structure/rtp.
 157     Add,
 158     //! Hack deletes atom.
 159     Delete,
 160     //! Hack replaces atom.
 161     Replace
 162 };
 163
 164 /*! \libinternal \brief
 165  * Block to modify individual residues
 166  */
 167 struct MoleculePatch
 168 {
 169     //! Number of new are deleted atoms. NOT always equal to atom.size()!
 170     int nr;
 171     //! Old name for entry.
 172     std::string oname;
 173     //! New name for entry.
 174     std::string nname;
 175     //! New atom data.
 176     std::vector<t_atom> atom;
 177     //! Chargegroup number.
 178     int cgnr = NOTSET;
 179     //! Type of attachement.
 180     int tp = 0;
 181     //! Number of control atoms.
 182     int nctl = 0;
 183     //! Name of control atoms.
 184     std::array<std::string, 4> a;
 185     //! Is an atom to be hacked already present?
 186     bool bAlreadyPresent = false;
 187     //! Are coordinates for a new atom already set?
 188     bool bXSet = false;
 189     //! New position for hacked atom.
 190     rvec newx = { NOTSET };
 191     //! New atom index number after additions.
 192     int newi = -1;
 193
 194     /*! \brief
 195      * Get type of hack.
 196      *
 197      * This depends on the setting of oname and nname
 198      * for legacy reasons. If oname is empty, we are adding,
 199      * if oname is set and nname is empty, an atom is deleted,
 200      * if both are set replacement is going on. If both are unset,
 201      * an error is thrown.
 202      */
 203     MoleculePatchType type() const;
 204
 205     //! Control atom i name.
 206     const std::string& ai() const { return a[0]; }
 207     //! Control atom j name.
 208     const std::string& aj() const { return a[1]; }
 209     //! Control atom k name.
 210     const std::string& ak() const { return a[2]; }
 211     //! Control atom l name.
 212     const std::string& al() const { return a[3]; }
 213 };
 214 /*! \libinternal \brief
 215  * A set of modifications to apply to atoms.
 216  */
 217 struct MoleculePatchDatabase
 218 {
 219     //! Name of block
 220     std::string name;
 221     //! File that entry was read from.
 222     std::string filebase;
 223     //! List of changes to atoms.
 224     std::vector<MoleculePatch> hack;
 225     //! List of bonded interactions to potentially add.
 226     std::array<BondedInteractionList, ebtsNR> rb;
 227     //! Number of atoms to modify
 228     int nhack() const { return hack.size(); }
 229 };
 230
 231 /*!\brief
 232  * Reset modification block.
 233  *
 234  * \param[inout] globalPatches Block to reset.
 235  * \todo Remove once constructor/destructor takes care of all of this.
 236  */
 237 void clearModificationBlock(MoleculePatchDatabase* globalPatches);
 238
 239 /*!\brief
 240  * Copy residue information.
 241  *
 242  * \param[in] s Source information.
 243  * \param[in] d Destination to copy to.
 244  * \param[inout] symtab Symbol table for names.
 245  * \todo Remove once copy can be done directly.
 246  */
 247 void copyPreprocessResidues(const PreprocessResidue& s, PreprocessResidue* d, t_symtab* symtab);
 248
 249 /*! \brief
 250  * Add bond information in \p s to \p d.
 251  *
 252  * \param[in] s Source information to copy.
 253  * \param[inout] d Destination to copy to.
 254  * \param[in] bMin don't copy bondeds with atoms starting with '-'.
 255  * \param[in] bPlus don't copy bondeds with atoms starting with '+'.
 256  * \returns if bonds were removed at the termini.
 257  */
 258 bool mergeBondedInteractionList(gmx::ArrayRef<const BondedInteractionList> s,
 259                                 gmx::ArrayRef<BondedInteractionList>       d,
 260                                 bool                                       bMin,
 261                                 bool                                       bPlus);
 262
 263 /*! \brief
 264  * Copy all information from datastructure.
 265  *
 266  * \param[in] s Source information.
 267  * \param[inout] d Destination to copy to.
 268  */
 269 void copyModificationBlocks(const MoleculePatchDatabase& s, MoleculePatchDatabase* d);
 270
 271 /*!\brief
 272  * Add the individual modifications in \p s to \p d.
 273  *
 274  * \param[in] s Source information.
 275  * \param[inout] d Destination to copy to.
 276  */
 277 void mergeAtomModifications(const MoleculePatchDatabase& s, MoleculePatchDatabase* d);
 278
 279 //! \copydoc mergeAtomModifications
 280 void mergeAtomAndBondModifications(const MoleculePatchDatabase& s, MoleculePatchDatabase* d);
 281
 282 #endif