Python Module Index
| a | ||
ambertools | Manages execution of AmberTools antechamber, parmchk2. | |
analyze | handles the analyze subcommand | |
| b | ||
banner | Defines the banner method for printing the banner to a logging channel | |
bondlist | Manages bidirectional interatomic bondlists | |
bondtemplate | Manages bond templates (bonds defined by type) and reaction bonds (bonds defined by instances) | |
| c | ||
checkpoint | Implements a simple checkpointing scheme using a wrapper | |
command | Custom handling of calls to subprocess.Popen() | |
configuration | Manages reading and parsing of YAML configuration files | |
coordinates | Class for managing gromacs .gro file data | |
countTime | defines a wrapper implementing method timing | |
curecontroller | Manages execution of the CURE algorithm | |
| d | ||
dataframetools | Some convenient tools for handling pandas dataframes in the context of htpolynet coordinates | |
driver | manages the HTPolyNet application, provides the command-line interface entry point | |
| e | ||
expandreactions | handles expansion of reactions based on chains | |
| g | ||
gromacs | methods for handling the gmx suite of executables | |
| h | ||
HTPolyNet | ||
HTPolyNet.ambertools | ||
HTPolyNet.analyze | ||
HTPolyNet.banner | ||
HTPolyNet.bondlist | ||
HTPolyNet.bondtemplate | ||
HTPolyNet.checkpoint | ||
HTPolyNet.command | ||
HTPolyNet.configuration | ||
HTPolyNet.coordinates | ||
HTPolyNet.countTime | ||
HTPolyNet.curecontroller | ||
HTPolyNet.dataframetools | ||
HTPolyNet.driver | ||
HTPolyNet.expandreactions | ||
HTPolyNet.gromacs | ||
HTPolyNet.inputcheck | ||
HTPolyNet.linkcell | ||
HTPolyNet.matrix4 | ||
HTPolyNet.molecule | ||
HTPolyNet.plot | ||
HTPolyNet.postsim | ||
HTPolyNet.projectfilesystem | ||
HTPolyNet.reaction | ||
HTPolyNet.ring | ||
HTPolyNet.runtime | ||
HTPolyNet.software | ||
HTPolyNet.stringthings | ||
HTPolyNet.topocoord | ||
HTPolyNet.topology | ||
HTPolyNet.unused_symmetry_stuff | ||
HTPolyNet.utils | ||
| i | ||
inputcheck | manages the inputcheck subcommand | |
| l | ||
linkcell | manages the link-cell structure used for searching for pierced rings | |
| m | ||
molecule | manages generation of molecular templates | |
| p | ||
plot | provides plotting functionality | |
postsim | handles the postsim subcommand | |
projectfilesystem | handles project filesystems | |
| r | ||
reaction | handles Reaction objects | |
ring | handles ring-piercing determinations | |
runtime | handles the HTPolyNet runtime workflow | |
| s | ||
software | handles identification of available software needed by HTPolyNet | |
stringthings | defines a specially-formatted logging method (silly) | |
| t | ||
topocoords | Class for jointly handling Topology and Coordinate objects | |
topology | Class for managing gromacs .top file data | |
| u | ||
unused_symmetry_stuff | tools for automated detection of molecular symmetry; as the name implies, HTPolyNet does not use these routines currently. In pre-release versions, we attempted to use these routines along with very high-T MD simulations of flexible molecules to identify symmetry-equivalent atoms using a distance-matrix approach. Now since we force the user to explicitly declare symmetry-sets, these routines are defunct. They didn't work reliably anyway, but they're kept here to stimulate future efforts to make this feature work. I've also included a couple of methods used for enumeration of angles and dihedrals that have not proven necessary. | |
utils | various utility methods for plotting and postprocessing |
