B b5@sdZddlmZmZmZddlZy ddlZWne k rDdZYnXddl m Z ddl m Z ddlmZddlZddZd d ZdS) z7 A collection of utilities for use with Pandas objects )absolute_importdivisionprint_functionN)ParameterWarning)zip) iteritemsc Cs tdkrtdt}|j}dd|D|d<dd|D|d<dd|D|d <d d|D|d <d d|D|d <dd|D|d<dd|D|d<dd|D|d<dd|D|d<dd|D|d<dd|D|d<dd|D|d<dd|D|d<dd|D|d<d d|D|d!<d"d|D|d#<d$d|D|d%<d&d|D|d'<d(d|D|d)<d*d|D|d+<d,d|D|d-<d.d|D|d/<d0d|D|d1<d2d|D|d3<y"tjd4d|Dd5d6d7gd8}Wntk rYn X||}y"tjd9d|Dd:d;d<Wntk rYnXyd?d|D|d@<Wntk rYnXy0tjdAd|DdBdCdDdEdFdGdHdIdJdKg d8}Wntk rYn X||}ydLd|D|dM<Wntk r0YnXydNd|D|dO<Wntk r^YnXdgdP}dQd|D}x.t|D]"\}} t| dRr| ||<qWdS} x4t|D](\}} | dkr|||<n | rdT} qW| s|tj|dUdVdWdXdYdZgd8}|S)[a# Creates a pandas.DataFrame object from the current instance Returns ------- dataframe : :class:`pandas.DataFrame` Notes ----- The DataFrame will be over all atoms. The columns will be the attributes of the atom (as well as its containing residue). Some columns will *always* exist. Others will only exist if those attributes have been set on the Atom instances (see the :class:`Atom` docs for possible attributes and their meaning). The columns that will always be present are: - number : int - name : str - type : str - atomic_number : int - charge : float - mass : float - nb_idx : int - solvent_radius : float - screen : float - occupancy : float - bfactor : float - altloc : str - tree : str - join : int - irotat : int - rmin : float - epsilon : float - rmin_14 : float - epsilon_14 : float - resname : str (name of the containing residue) - resid : int (Sequential index of the containing residue) - resnum : int (original residue number in the input structure) - chain : str (chain ID that the containing residue belongs to) The following attributes are optionally present if they were present in the original file defining the structure: - xx : float (x-coordinate position) - xy : float (y-coordinate position) - xz : float (z-coordinate position) - vx : float (x-coordinate velocity) - vy : float (y-coordinate velocity) - vz : float (z-coordinate velocity) - type_idx : int (integer type index for AMOEBA) - class_idx : int (integer class type index for AMOEBA) - multipole_111 : float (Monopole) - multipole_211 : float (1,1 Dipole component) - multipole_212 : float (1,2 Dipole component) - multipole_222 : float (2,2 Dipole component) - multipole_411 : float (1,1 Quadrupole component) - multipole_412 : float (1,2 Quadrupole component) - multipole_422 : float (2,2 Quadrupole component) - multipole_413 : float (1,3 Quadrupole component) - multipole_423 : float (2,3 Quadrupole component) - multipole_433 : float (3,3 Quadrupole component) - polarizability : float (dipole polarizability) - vdw_parent : int (index of the vdW parent atom of this atom) - U11 : float (U[1][1] of anisotropic b-factor tensor) - U22 : float (U[2][2] of anisotropic b-factor tensor) - U33 : float (U[3][3] of anisotropic b-factor tensor) - U12 : float (U[1][2] of anisotropic b-factor tensor) - U13 : float (U[1][3] of anisotropic b-factor tensor) - U23 : float (U[2][3] of anisotropic b-factor tensor) NzMpandas is not available; cannot create a pandas DataFrame from this StructurecSsg|] }|jqS)number).0atomrr6lib/python3.7/site-packages/parmed/utils/pandautils.py ^sz$create_dataframe..r cSsg|] }|jqSr)name)r r rrr r _srcSsg|] }|jqSr)type)r r rrr r `srcSsg|] }|jqSr) atomic_number)r r rrr r asrcSsg|] }|jqSr)charge)r r rrr r bsrcSsg|] }|jqSr)mass)r r rrr r csrcSsg|] }|jqSr)nb_idx)r r rrr r dsrcSsg|] }|jqSr)solvent_radius)r r rrr r esrcSsg|] }|jqSr)screen)r r rrr r fsrcSsg|] }|jqSr) occupancy)r r rrr r gsrcSsg|] }|jqSr)bfactor)r r rrr r hsrcSsg|] }|jqSr)altloc)r r rrr r isrcSsg|] }|jqSr)tree)r r rrr r jsrcSsg|] }|jqSr)join)r r rrr r ksrcSsg|] }|jqSr)irotat)r r rrr r lsrcSsg|] }|jqSr)rmin)r r rrr r msrcSsg|] }|jqSr)epsilon)r r rrr r nsrcSsg|] }|jqSr)rmin_14)r r rrr r osrcSsg|] }|jqSr) epsilon_14)r r rrr r psrcSsg|] }|jjqSr)residuer)r r rrr r qsresnamecSsg|] }|jjqSr)r idx)r r rrr r rsresidcSsg|] }|jjqSr)r r )r r rrr r ssresnumcSsg|] }|jjqSr)r chain)r r rrr r tsr%cSsg|] }|jjqSr)r segid)r r rrr r usr&cSsg|]}|j|j|jgqSr)xxxyxz)r r rrr r {sr'r(r))columnscSsg|]}|j|j|jgqSr)vxvyvz)r r rrr r sr+r,r-cSsg|] }|jqSr)type_idx)r r rrr r sr.cSsg|] }|jqSr) class_idx)r r rrr r sr/cSsg|] }|jqSr) multipoles)r r rrr r s multipole_111 multipole_211 multipole_212Z multipole_222 multipole_411 multipole_412 multipole_422 multipole_413 multipole_423 multipole_433cSsg|] }|jqSr)polarizability)r r rrr r sr:cSsg|] }|jjqSr) vdw_parentr")r r rrr r sr;cSsg|] }|jqSr)anisou)r r rrr r stolistTFU11U22U33U12U13U23) pd ImportErrorZ DataFrameatomsAttributeErrorr enumeratehasattrr>) objZretrGZcoordsZvelsr0Znone6ZanisosiZanisoZ all_nonesrrr create_dataframesF           rMc s|jfdd}fdd}ddtdD}ddtd D}x"t|D]\}}|d krl|d |qN|d kr|d |qN|d kr|d |qN|d kr|d |qN|dkr|d|qN|dkr|d|qN|dkr|d|qN|dkr|d|qN|dkr|d|qN|dkr&|d|qN|dkr<|d|qN|dkrR|d|qN|dkrh|d|qN|dkr~|d|qN|dkr|d|qN|dkr|d|qN|dkr|d|qN|dkr|d|qN|dkr|d|qN|dkr|d|qN|dkr|d|qN|dkr.|d|qN|d krD|d |qN|d!krZ|d!|qN|d"krp|d"|qN|d#kr|d#|qN|d$kr|d$|qN|d%krt|tkrtd&x"t|D]\}} | |_qWqN|d'kr|d'|qN|d(kr||d)<qN|d*kr$||d+<qN|d,kr8||d-<qN|d.krL||d/<qN|d0kr`||d1<qN|d2krt||d3<qN|d4kr||d <qN|d5kr||d6<qN|d7kr||d8<qN|d9kr||d:<qN|d;kr||d)<qN|dkr||d/<qN|d?kr(||d1<qN|d@kr<||d3<qN|dAkrT|||qNqNtdB|t qNWdC|kr|dDt |j dC|kr|dEt |j dCS)Fa Loads a DataFrame into the current object, setting atomic properties based on the entries of the DataFrame. Supported atomic properties are: - number : int - name : str - type : str - atomic_number : int - charge : float - mass : float - nb_idx : int - solvent_radius : float - screen : float - occupancy : float - bfactor : float - altloc : str - tree : str - join : int - irotat : int - rmin : float - epsilon : float - rmin_14 : float - epsilon_14 : float - xx : float (x-coordinate position) - xy : float (y-coordinate position) - xz : float (z-coordinate position) - vx : float (x-coordinate velocity) - vy : float (y-coordinate velocity) - vz : float (z-coordinate velocity) - type_idx : int (integer type index for AMOEBA) - class_idx : int (integer class type index for AMOEBA) - multipole_111 : float (Monopole) - multipole_211 : float (1,1 Dipole component) - multipole_212 : float (1,2 Dipole component) - multipole_222 : float (2,2 Dipole component) - multipole_411 : float (1,1 Quadrupole component) - multipole_412 : float (1,2 Quadrupole component) - multipole_422 : float (2,2 Quadrupole component) - multipole_413 : float (1,3 Quadrupole component) - multipole_423 : float (2,3 Quadrupole component) - multipole_433 : float (3,3 Quadrupole component) - polarizability : float (dipole polarizability) - vdw_parent : int (index of the vdW parent atom of this atom) - segid : segment ID (similar to chain, but for CHARMM) - U11 : float (U[1][1] of anisotropic b-factor tensor) - U22 : float (U[2][2] of anisotropic b-factor tensor) - U33 : float (U[3][3] of anisotropic b-factor tensor) - U12 : float (U[1][2] of anisotropic b-factor tensor) - U13 : float (U[1][3] of anisotropic b-factor tensor) - U23 : float (U[2][3] of anisotropic b-factor tensor) The resname, resid, chain, and resnum attributes are ignored. Other attributes emit a ParameterWarning cs@t|tkrtdx"t|D]\}}t|||q$WdS)z& Set the attribute list from the data z(Data does not match length of atoms listN)len ValueErrorrsetattr)attrdatar x)rGrr set_attributesz%load_dataframe..set_attributecsBt|tkrtdx$t|D]\}}t|j||q$WdS)Nz(Data does not match length of atoms list)rNrOrrPr )rQrRr rS)rGrr set_residue_attrsz(load_dataframe..set_residue_attrcSsg|]}dqS)Nr)r rLrrr r sz"load_dataframe.. cSsg|]}dqS)Nr)r rLrrr r sr<r rrrrrrrrrrrrrrrrrrr'r(r)r+r,r-r.r/r;z$vdw_parent length not equal to natomr:r1rr2r3Z multipole_213r4r5r6r7r8r9 r?r@rArBrCrD)r!r#r$r%r&z!Atomic property %s not recognizedNr=r0) rGrangerrNrOrr;warningswarnrnpZvstackT) rKZ dataframerTrUr0ZanisouskeyrRr parentr)rGr load_dataframes7                                                                                          rf)__doc__Z __future__rrrZnumpyrbZpandasrErFZparmed.exceptionsrZparmed.utils.six.movesrZparmed.utils.sixrr`rMrfrrrr s     0