date version compatible with Python 3 is currently in the
making and will be released soon, and will be compatible
with the most recent MDAnalysis currently released (1.0.0).
2. PyInteraph is compatible with all the trajectory formats supported by MDAnalysis, the most popular being XTC,
NETCDF, and DCD. It is also compatible with many topology
formats, with PDB being the most widespread and
commonly used.
3. PyInteraph also supports as input a reference structure file.
This is useful for cases in which we want chain definition and
residue numbering in the output files to be different from the
ones in the topology. This can be useful for instance for cases
in which the MD software has changed the residue numbering
in the topology with respect to the experimental structure or
no chain definition is present in the topology file (as happens
in GRO files). A reference file needs to have the same number
of residues in the same order as topology file, but the number
of atoms can differ – so that an experimentally solved structure
can be used. When no reference file is provided, the topology
is used as the reference instead – as we did in this case
for CypA.
4. The default configuration files for PyInteraph are located in the
PyInteraph installation directory and allow to set which atom
groups constitute charged groups (charged_groups.ini) as well
as to set which atom types can act as acceptor or donor for
hydrogen bonds (hydrogen_bonds.ini). The files are read by
default from the main installation directory, but the user can
specify their specific versions with the command-line options -sb-cg-file and --hb-ad-file. The file formats are straightforward:
for charged groups, the user defines specific charged groups
under the [CHARGED_GROUPS] section. Charged groups
can have any name but must end either with “p” or “n,”
respectively, for positively and negatively charged. Each group
is defined as a list of atom names; if an atom needs not to present
for the group to be considered as charged, its name is prefixed
by an exclamation mark. The default_charged_groups entry is a
list of charged groups that any residue might have. Charged
groups are finally assigned to residues, defined as residue names,
in the [RESIDUES] section. The hydrogen_bonds.ini file just
contains lists of acceptor and donor atoms. By following these
conventions, it is possible to include in the analysis even
non-natural amino acids or small molecules. Further customization is possible through command-line options. It is possible
to calculate electrostatic interactions between residues of the
same charge using the --sb-mode option (--sb-mode
Interaction Networks with PyInteraph
169
making and will be released soon, and will be compatible
with the most recent MDAnalysis currently released (1.0.0).
2. PyInteraph is compatible with all the trajectory formats supported by MDAnalysis, the most popular being XTC,
NETCDF, and DCD. It is also compatible with many topology
formats, with PDB being the most widespread and
commonly used.
3. PyInteraph also supports as input a reference structure file.
This is useful for cases in which we want chain definition and
residue numbering in the output files to be different from the
ones in the topology. This can be useful for instance for cases
in which the MD software has changed the residue numbering
in the topology with respect to the experimental structure or
no chain definition is present in the topology file (as happens
in GRO files). A reference file needs to have the same number
of residues in the same order as topology file, but the number
of atoms can differ – so that an experimentally solved structure
can be used. When no reference file is provided, the topology
is used as the reference instead – as we did in this case
for CypA.
4. The default configuration files for PyInteraph are located in the
PyInteraph installation directory and allow to set which atom
groups constitute charged groups (charged_groups.ini) as well
as to set which atom types can act as acceptor or donor for
hydrogen bonds (hydrogen_bonds.ini). The files are read by
default from the main installation directory, but the user can
specify their specific versions with the command-line options -sb-cg-file and --hb-ad-file. The file formats are straightforward:
for charged groups, the user defines specific charged groups
under the [CHARGED_GROUPS] section. Charged groups
can have any name but must end either with “p” or “n,”
respectively, for positively and negatively charged. Each group
is defined as a list of atom names; if an atom needs not to present
for the group to be considered as charged, its name is prefixed
by an exclamation mark. The default_charged_groups entry is a
list of charged groups that any residue might have. Charged
groups are finally assigned to residues, defined as residue names,
in the [RESIDUES] section. The hydrogen_bonds.ini file just
contains lists of acceptor and donor atoms. By following these
conventions, it is possible to include in the analysis even
non-natural amino acids or small molecules. Further customization is possible through command-line options. It is possible
to calculate electrostatic interactions between residues of the
same charge using the --sb-mode option (--sb-mode
Interaction Networks with PyInteraph
169