B b@stdZddlmZddlmZmZddlmZmZddl m Z m Z ddl m Z e rTesXtddd d d gZdd d Zd S)a This module is simply a namespace for all Amber topology-like classes. There are different variants; for instance the standard Amber topology, the chamber-made topology, and the tinker_to_amber-made topology. These classes are all defined in their own private modules, but imported here to simplify the API. Copyright (C) 2010 - 2014 Jason Swails This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. ) AmberFormat) AmberParmRst7) ChamberParmConvertFromPSF) AmoebaParm BeemanRestart) string_typesrrrLoadParmrNcCs,ddlm}ddlm}t|}d|jkr6|t}n d|jkrL|t}n |t }t |t r||}t |dr||j dkrtd||j |_ t |d r|jdk r|dkr|j|_n||_ |dk r||_|jd |dkr|jdkr|jd }t|d d|d|d|dg|_|jdk |_|S) a Loads a topology file using the correct class. Parameters ---------- parmname : ``str`` The name of the topology file to load xyz : str or array, optional If provided, the coordinates and unit cell dimensions from the provided Amber inpcrd/restart file will be loaded into the molecule, or the coordinates will be loaded from the coordinate array box : array, optional If provided, the unit cell information will be set from the provided unit cell dimensions (a, b, c, alpha, beta, and gamma, respectively) Returns ------- parm : :class:`AmberParm` (or subclass) This function parses the topology file, determines if it is an Amber-style (i.e., *traditional* Amber force field), Chamber-style (i.e., CHARMM force field), or Amoeba-style (i.e., Amoeba force field), and then returns an instance of the appropriate type. r) load_file)IFBOXZCTITLEZAMOEBA_FORCEFIELD coordinatesNz%s does not have coordinatesboxZPOINTERSZBOX_DIMENSIONS)Zparmedr Zparmed.constantsr rZ flag_listZview_asrrr isinstancer hasattrr TypeErrorrZ parm_datalistZhasbox)ZparmnameZxyzrr r Zparmfr4lib/python3.7/site-packages/parmed/amber/readparm.pyr &s.            ( )NN)__doc__Zparmed.amber.amberformatrZparmed.amber._amberparmrrZparmed.amber._chamberparmrrZparmed.amber._tinkerparmrrZparmed.utils.sixr AssertionError__all__r rrrrs