Gromacs
2020.4
|
Methods to get residue information during preprocessing.
Functions | |
std::string | searchResidueDatabase (const std::string &key, gmx::ArrayRef< const PreprocessResidue > rtpDBEntry) |
Search for an entry in the rtp database. More... | |
gmx::ArrayRef< const PreprocessResidue > ::const_iterator | getDatabaseEntry (const std::string &rtpname, gmx::ArrayRef< const PreprocessResidue > rtpDBEntry) |
Returns matching entry in database. More... | |
PreprocessingAtomTypes | read_atype (const char *ffdir, t_symtab *tab) |
Read atom types into database. More... | |
void | readResidueDatabase (const std::string &resdb, std::vector< PreprocessResidue > *rtpDBEntry, PreprocessingAtomTypes *atype, t_symtab *tab, bool bAllowOverrideRTP) |
Read in database, append to exisiting. More... | |
void | print_resall (FILE *out, gmx::ArrayRef< const PreprocessResidue > rtpDBEntry, const PreprocessingAtomTypes &atype) |
Print out database. More... | |
gmx::ArrayRef<const PreprocessResidue>::const_iterator getDatabaseEntry | ( | const std::string & | rtpname, |
gmx::ArrayRef< const PreprocessResidue > | rtpDBEntry | ||
) |
Returns matching entry in database.
[in] | rtpname | Name of the entry looked for. |
[in] | rtpDBEntry | Database to search. |
If | the name can not be found in the database. |
void print_resall | ( | FILE * | out, |
gmx::ArrayRef< const PreprocessResidue > | rtpDBEntry, | ||
const PreprocessingAtomTypes & | atype | ||
) |
Print out database.
[in] | out | File to write to. |
[in] | rtpDBEntry | Database to write out. |
[in] | atype | Atom type information. |
PreprocessingAtomTypes read_atype | ( | const char * | ffdir, |
t_symtab * | tab | ||
) |
Read atom types into database.
[in] | ffdir | Force field directory. |
[in] | tab | Symbol table for names. |
void readResidueDatabase | ( | const std::string & | resdb, |
std::vector< PreprocessResidue > * | rtpDBEntry, | ||
PreprocessingAtomTypes * | atype, | ||
t_symtab * | tab, | ||
bool | bAllowOverrideRTP | ||
) |
Read in database, append to exisiting.
[in] | resdb | Name of database file. |
[in,out] | rtpDBEntry | Database to populate. |
[in,out] | atype | Atomtype information. |
[in,out] | tab | Symbol table for names. |
[in] | bAllowOverrideRTP | If entries can be overwritten in the database. |
std::string searchResidueDatabase | ( | const std::string & | key, |
gmx::ArrayRef< const PreprocessResidue > | rtpDBEntry | ||
) |
Search for an entry in the rtp database.
A mismatch of one character is allowed, if there is only one nearly matching entry in the database, a warning will be generated.
[in] | key | The atomname to search for. |
[in] | rtpDBEntry | Database with residue information. |