apocharmm.charmm_crd.CharmmCrd Class Reference

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Inherits _ApoObject.

Public Member Functions
None	__init__ (self, FilePath path)
	Constructs an owning wrapper from one CHARMM coordinate file.
int	getNumAtoms (self)
	Returns the parsed atom count.
list[list[float]]	getCoordinates (self)
	Returns a copied nested list of Cartesian coordinates.

Detailed Description

Owns coordinates parsed from one CHARMM CRD or COR file.

Construct the wrapper from a str, bytes, os.PathLike[str], or os.PathLike[bytes] path. The path is converted with os.fsencode, copied through the C ABI, and not retained. Native parsing completes synchronously before construction returns.

getCoordinates() returns a newly allocated nested Python list in atom-major [x, y, z] order. Returned values never alias native storage. The wrapper owns one C handle. close(), destroy(), and context-manager exit release it idempotently. Accessing a getter after closure raises RuntimeError.

The wrapper provides no internal synchronization. Do not overlap close() with another method call from a different thread.

See also

coordinates

Constructor & Destructor Documentation

__init__()

None apocharmm.charmm_crd.CharmmCrd.__init__	(		self,
		FilePath	path
	)

Constructs an owning wrapper from one CHARMM coordinate file.

Standard and extended CHARMM fixed-width coordinate records are supported. File-name extensions are not validated. The encoded path and file contents are not retained after native construction finishes.

Parameters

[in]

path

Path supplied as str, bytes, os.PathLike[str], or os.PathLike[bytes]. Its encoded representation must be nonempty.

Exceptions

TypeError	If path cannot be converted by os.fsencode.
ApoCharmmError	If the encoded path is empty, the file cannot be read, the atom count or a coordinate record is malformed, a coordinate is non-finite, or native host allocation fails.
RuntimeError	If APOCHARMM_LIBRARY_PATH is unset or empty, or native construction reports success but produces a NULL handle.
OSError	If the configured apoCHARMM C ABI shared library cannot be loaded.

Postcondition

On success, this wrapper owns a live coordinate handle.

Warning

An encoded path containing an embedded null byte is truncated at that byte by the C-string boundary instead of being rejected.

Member Function Documentation

getCoordinates()

list[list[float]] apocharmm.charmm_crd.CharmmCrd.getCoordinates

(

self

)

Returns a copied nested list of Cartesian coordinates.

The result contains one three-element list per atom in [x, y, z] order. Values are Python float objects copied from native double-precision host storage and use angstroms. An empty coordinate set returns an empty list.

Returns

Newly allocated list[list[float]] with exact shape (N, 3).

Exceptions

RuntimeError	If this wrapper is closed.
ApoCharmmError	If the native count or coordinate getter rejects the handle or output buffer.
OverflowError	If 3 * N cannot be represented as a ctypes array length.
MemoryError	If the temporary C buffer or returned Python lists cannot be allocated.

Postcondition

Mutating the returned lists does not modify native coordinates.

getNumAtoms()

int apocharmm.charmm_crd.CharmmCrd.getNumAtoms

(

self

)

Returns the parsed atom count.

Returns

Non-negative dimensionless Python int.

Exceptions

RuntimeError	If this wrapper is closed.
ApoCharmmError	If the native handle is invalid or reports a negative atom count.