parmed.namd.namdbinfiles module¶

This module contains classes for reading and writing (single frame) NAMD binary files. The main functionality is currently aimed at manipulation rather than analysis.

class parmed.namd.namdbinfiles.NamdBinCoor(values=[])[source]¶

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.namdbinfiles.NamdBinFile(values=[])[source]¶

Bases: object

From the NAMD manual:

NAMD uses a trivial double-precision binary file format for coordinates, velocities, and forces … The file consists of the atom count as a 32-bit integer followed by all three position or velocity components for each atom as 64-bit double-precision floating point …

The main attributes are the number of atom entries (natom) and a (flat) numpy array of size 3*natom (values). The meaning of “values” is effectively arbitrary, but for convenience derived classes are provided which alias the values to more descriptive names (e.g. “coordinates”).

See also

NamdBinCoor
NamdBinVel

Attributes

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.

copyatoms(start_index, natoms)[source]¶: Convenience function, same as insertatoms() but set ‘values’ to be the same as the previous natoms’ values (i.e. make a copy of them).

delatoms(indices)[source]¶: Delete entries corresponding to the given atom indices.

insertatoms(start_index, natoms, values=None)[source]¶: Insert space for natom entries beginning at start_index. If specified, give them the provided values, otherwise set them to zero.

property natom¶: The current number of atom entries.

classmethod read(fname)[source]¶: Return an object from the values in a NAMD binary file.

write(fname)[source]¶: Write the current attributes to a file.

class parmed.namd.namdbinfiles.NamdBinVel(values=[])[source]¶

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¶