src/gromacs/gmxpreprocess/genhydro.h

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  37
  38 #ifndef GMX_GMXPREPROCESS_GENHYDRO_H
  39 #define GMX_GMXPREPROCESS_GENHYDRO_H
  40
  41 #include "gromacs/fileio/pdbio.h"
  42 #include "gromacs/gmxpreprocess/hackblock.h"
  43
  44 int add_h(t_atoms **pdbaptr, rvec *xptr[],
  45           int nah, t_hackblock ah[],
  46           int nterpairs,
  47           t_hackblock **ntdb, t_hackblock **ctdb,
  48           int *rN, int *rC, gmx_bool bMissing,
  49           int **nabptr, t_hack ***abptr,
  50           gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba);
  51 /* Generate hydrogen atoms and N and C terminal patches.
  52  * int nterpairs is the number of termini pairs in the molecule
  53  * ntdb[i] and ctdb[i] may be NULL, no replacement will be done then.
  54  * rN[i] is the residue number of the N-terminus of chain i,
  55  * rC[i] is the residue number of the C-terminus of chain i
  56  * if bMissing==TRUE, continue when atoms are not found
  57  * if nabptr && abptrb, the hack array will be returned in them to be used
  58  * a second time
  59  * if bUpdate_pdba, hydrogens are added to *pdbaptr, else it is unchanged
  60  * return the New total number of atoms
  61  */
  62
  63 int protonate(t_atoms **atoms, rvec **x, t_protonate *protdata);
  64 /* Protonate molecule according to oplsaa.ff/aminoacids.hdb
  65  * when called the first time, new atoms are added to atoms,
  66  * second time only coordinates are generated
  67  * return the new total number of atoms
  68  */
  69
  70 void deprotonate(t_atoms *atoms, rvec *x);
  71 /* Deprotonate any molecule: all atoms whose name begins with H will be
  72  * removed
  73  */
  74
  75 #endif