same_charge) or all of them (--sb-mode all). pyinteraph also
allows to analyze main chain-main chain (--hb-class mc-mc),
main chain-side chains (--hb-class mc-sc), all (--hb-class all), or
hydrogen bonds between custom groups (--hb-class custom).
Custom groups of atoms are defined using MDAnalysis selection format through options --hb-custom-group-1 and --hb-custom-group-2. As far as hydrophobic contacts are considered, the
user can decide which residue needs to be included in the
analysis using the --hc-residues option.
5. pyinteraph supports assigning different masses to atoms
depending on the force field, which is especially important for
the calculation of the correct centers of mass. This is relevant
when considering united-atom force fields, such as GROMOS,
or even coarse-grained systems. PyInteraph supports the GROMOS, AMBER, CHARMM, ENCAD, and OPLS force-field
families, but more can be added in the form of JSONformatted files. In the case of CypA, whose simulations use
the CHARMM22* force field, we used atomic mass from
CHARMM27 after checking that they were identical in the
force-field definition files of GROMACS. Masses files are
found in the ff_masses directory in the PyInteraph installation
directory.
6. interaction_plotter is a second PyMOL plug-in designed to plot
on the 3D structures single interactions between residues
groups encoded in single interaction files (see Note 7). These
include side-chain and main-chain atoms, and each residue can
interact through different groups, depending on the interaction definitions. As the xPyder plug-in supports only one node
per residue, while intramolecular interactions can involve more
than one group per residue, the two formats are not
intercompatible.
7. Interaction networks are written by PyInteraph into two different text formats. One details every single interaction found in
the ensemble and lists the groups of the two residues that are
interacting together with the associated persistence value. The
other is a graph adjacency matrix, which is simply an ASCII
square symmetric matrix in which every line and every column
represents a residue, ordered as the residues in the protein
under study. Each position of the matrix represents a single
edge weight, which is 0.0 if no interactions were found in the
ensemble (which means the edge does not exist in the context
of PyInteraph), or a value in the (0.0,100.0] range if they have
been found. The simplicity of this matrix format allows it to be
easily read in most programming languages and it is compatible
with the xPyder PyMOL plug-in.
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allows to analyze main chain-main chain (--hb-class mc-mc),
main chain-side chains (--hb-class mc-sc), all (--hb-class all), or
hydrogen bonds between custom groups (--hb-class custom).
Custom groups of atoms are defined using MDAnalysis selection format through options --hb-custom-group-1 and --hb-custom-group-2. As far as hydrophobic contacts are considered, the
user can decide which residue needs to be included in the
analysis using the --hc-residues option.
5. pyinteraph supports assigning different masses to atoms
depending on the force field, which is especially important for
the calculation of the correct centers of mass. This is relevant
when considering united-atom force fields, such as GROMOS,
or even coarse-grained systems. PyInteraph supports the GROMOS, AMBER, CHARMM, ENCAD, and OPLS force-field
families, but more can be added in the form of JSONformatted files. In the case of CypA, whose simulations use
the CHARMM22* force field, we used atomic mass from
CHARMM27 after checking that they were identical in the
force-field definition files of GROMACS. Masses files are
found in the ff_masses directory in the PyInteraph installation
directory.
6. interaction_plotter is a second PyMOL plug-in designed to plot
on the 3D structures single interactions between residues
groups encoded in single interaction files (see Note 7). These
include side-chain and main-chain atoms, and each residue can
interact through different groups, depending on the interaction definitions. As the xPyder plug-in supports only one node
per residue, while intramolecular interactions can involve more
than one group per residue, the two formats are not
intercompatible.
7. Interaction networks are written by PyInteraph into two different text formats. One details every single interaction found in
the ensemble and lists the groups of the two residues that are
interacting together with the associated persistence value. The
other is a graph adjacency matrix, which is simply an ASCII
square symmetric matrix in which every line and every column
represents a residue, ordered as the residues in the protein
under study. Each position of the matrix represents a single
edge weight, which is 0.0 if no interactions were found in the
ensemble (which means the edge does not exist in the context
of PyInteraph), or a value in the (0.0,100.0] range if they have
been found. The simplicity of this matrix format allows it to be
easily read in most programming languages and it is compatible
with the xPyder PyMOL plug-in.
170
Matteo Lambrughi et al.