parmed.namd package

Submodules

• parmed.namd.namdbinfiles module

Module contents

This package contains code for reading, writing, and modifying NAMD files needed to start and/or restart simulations with NAMD. The most common formats are the so-called “namdbin” files heavily utilized by VMD; these are often given the extensions .coor and .vel (coordinates and velocities, respectively).

class parmed.namd.NamdBinCoor(values=[])

Bases: parmed.namd.namdbinfiles.NamdBinFile

Class to read or write NAMD “bincoordinates” files.

Attributes

coordinates

natom

The current number of atom entries.

Methods

copyatoms(start_index, natoms)	Convenience function, same as insertatoms() but set ‘values’ to be the same as the previous natoms’ values (i.e.
delatoms(indices)	Delete entries corresponding to the given atom indices.
insertatoms(start_index, natoms[, values])	Insert space for natom entries beginning at start_index.
read(fname)	Return an object from the values in a NAMD binary file.
write(fname)	Write the current attributes to a file.

property coordinates

class parmed.namd.NamdBinVel(values=[])

Bases: parmed.namd.namdbinfiles.NamdBinFile

Class to read or write NAMD “binvelocities” files.

Attributes

natom

The current number of atom entries.

velocities

Methods

copyatoms(start_index, natoms)	Convenience function, same as insertatoms() but set ‘values’ to be the same as the previous natoms’ values (i.e.
delatoms(indices)	Delete entries corresponding to the given atom indices.
insertatoms(start_index, natoms[, values])	Insert space for natom entries beginning at start_index.
read(fname)	Return an object from the values in a NAMD binary file.
write(fname)	Write the current attributes to a file.

property velocities