B b_@sdZddlmZmZmZddlmZddlZddl m Z ddl m Z ddl mZddlmZddlmZdd lmZdd lmZmZdd lmZddlZed Zee Gd ddeZGdddeZ dS)z: XML file parsing utilities for OpenMM serialized objects )divisionprint_functionabsolute_import)closingN)Vec3)FileFormatType)!box_vectors_to_lengths_and_angles) needs_openmm)genopen) add_metaclass string_types)StringIOz <(.*?)/?>c@s,eZdZdZeddZeeddZdS)XmlFilez Wrapper for parsing OpenMM-serialized objects. Supports serialized State, System, Integrator, and ForceField objects. c Cstt|dh}x`|D]X}|}|s(qt|}|s:dS|d}|ddkrTq|d}|dkrldSdSWWdQRXdS)a Identifies the file type as an XML file Parameters ---------- filename : str Name of the file to check format for Returns ------- is_fmt : bool True if it is an XML format, False otherwise rFrz?!)ZSystemState ForceFieldZ IntegratorTN)rr strip_xmlrematchgroupssplit)filenameflineZrematchstuffZkindr4lib/python3.7/site-packages/parmed/openmm/xmlfile.py id_formats     zXmlFile.id_formatc Csddlm}ddlm}t|trFtt|d}|}WdQRXn|}d|krzt}| || d| |S|j |}t||jrt|S|S)aB Parses XML file and returns deserialized object. The return value depends on the serialized object, summarized below - System : returns simtk.openmm.System - State : returns simtk.openmm.State - Integrator : returns simtk.openmm.Integrator subclass - ForceField : returns simtk.openmm.app.ForceField Parameters ---------- filename : str or file-like The file name or file object containing the XML-serialized object Returns ------- obj : System, State, Integrator, or ForceField The deserialized object Notes ----- OpenMM requires the entire contents of this file read into memory. As a result, this function may require a significant amount of memory. rN)apprz sz2_OpenMMStateContents.positions..r)r9)r=rrr positionssz_OpenMMStateContents.positions)N) r'r(r)r*r+r4r>propertyrArrrrr#fs  r#)!r*Z __future__rrr contextlibrZnumpyr:Z parmed.vec3rZparmed.formats.registryrZparmed.geometryrZ parmed.unitr1r8Zparmed.utils.decoratorsr Zparmed.utils.ior Zparmed.utils.sixr r Zparmed.utils.six.movesr recompilerobjectrr#rrrrs          Q