ó Ê™xTc@ s±dZddlmZyddlZWnek r?dZnXddlmZddl m Z ddl m Z ddl m Z edd„Zed „Zd „Zd „ZdS( s, Utility functions used within this module. iÿÿÿÿ(tdivisionN(tAuto(tserver(thalides(tcolc c s x|jƒD]ô}xë|jƒD]Ý}xÔ|jƒD]Æ}x½|jƒD]¯}|jjƒjƒ}|jjƒdkrƒ| rƒqFn|dks›||krF|j ƒ}t |ƒdkrõ|d} | j jƒjƒ} | dkrêqFn| VqõqFqFWq3Wq Wq WdS(s! Returns a generator iterating over all atoms in pdb_hierarchy. Optionally skips sites with alternate conformations and can filter by residue name. Parameters ---------- pdb_hierarchy: iotbx.pdb.hierarchy.root split_sites: bool, optional Indicates whether to iterate over sites with alternate conformations, by default they are not included. res_filter: list of str, optional List of residue names to include, by default, all residues are examined. Returns ------- generator of iotbx.pdb.hierarchy.atom tiitHtDN(RR( tmodelstchainstresidue_groupst atom_groupstresnametstriptuppertaltloctNonetatomstlentelement( t pdb_hierarchyt split_sitest res_filtertmodeltchaint residue_groupt atom_groupR RtatomR((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/svm/utils.pyt iterate_sitess   cC sÍt}|j}t}t}t}t}t|jƒ}d} | } xê|jD]ß} | j} | jƒ} | jƒ}| j }t | ƒ}|dkr˜tS|dkrt j |ƒ}|dkrÏ|dkrÏtS|dkr+|dkr+t}| dks|| kr|} qq+qL|dkrb| dkrb|dkrbt}| dksV|| kr+|} q+qL|dkrÎ| d krÎ|sŒ| dkrÎ|dkrÎt}| dkr+| dksÂ|| kr+|} q+qL|d!kr| d"kr|dkrt}|| kr+|} q+qL|d#krL|rLt}qLqLWx‹|jD]€} | j ƒd$krWq9n| jƒ} | jƒ}t | ƒ}|dkr9| dk r9|| dkr9tj|| ƒr9tSq9W|pÌ|pÌ|S(%Ng@tCtNRtOtSig @tNZtLYStNH1tNH2tND2tNE2tARGtASNtGLNtOG1tOG2tOH1tSERtTHRtTYRRtAgš™™™™™ @gš™™™™™É?(RRRRR (R!(R"(R!R#R$R%R&(R'R(R)(R*R+R,(R-R.R/(R(RR0(tTrueRtFalseRtxyzRtcontactsR t atom_nameRtabsRt get_chargeRRtis_negatively_charged_oxygen(tchem_envt scatter_envtassume_hydrogens_all_missingRtbinds_amide_hydrogent near_cationtnear_lyst near_hydroxylR3tmin_distance_to_cationtmin_distance_to_hydroxyltcontacttotherR R5Rtdistancetcharge((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/svm/utils.pyt _is_favorable_halide_environment4s|                                  c C s=d}d}g}x$|D]}|dkr(|jddkrDqn|d krl|jddkrlqqln|j|ƒ\}}|dkrßtj|ƒ} |d|t| ƒkr¼qn|d|t| ƒkrôqqônt||ƒsôqn||krqntd „|j Dƒƒr(qq(n|j |ƒqW|S(s| Applies a simple set of filters to the accepted ions that might match a given chemical and scattering environment to help catch corner cases where the SVM might fail. Parameters ---------- chem_env : mmtbx.ions.environment.ChemicalEnvironment scatter_env : mmtbx.ions.environment.ScatteringEnvironment elements : list of str Returns ------- list of str gà?g333333ã?tHOHiitNAtMGtFtCLtBRtIcs s$|]}t|jƒdkVqdS(gÍÌÌÌÌÌü?N(R6tvector(t.0ti((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/svm/utils.pys Äs(RHRI(RJRKRLRM( t fo_densityt fofc_densityt get_valenceRt get_chargestmintmaxRFtanyR4tappend( R9R:telementst bvs_ratiot vecsum_cutofft ok_elementsRtbvstvecsumtcharges((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/svm/utils.pytfilter_svm_outputs—s2        cC s‰tj|ƒ}|d|dk}|dd…|f}|d||d|f}||d|d|d|d|d|dS(s› Given an upper and lower bound for each row of matrix, scales the values to be within the range specified by target. Parameters ---------- matrix : numpy.array of float The matrix to be scaled. source : tuple of numpy.array of float The upper and lower bound on the values of each row in the original matrix. target : tuple of float The target range to scale to. Returns ------- matrix : numpy.array of float The matrix with scaled values. Examples -------- >>> from mmtbx.ions.svm.utils import scale_to >>> import numpy as np >>> matrix = np.array([[0, 1, 2], [2, 3, 4], [1, 2, 3]]) >>> source = (np.array([2, 3, 4]), np.array([0, 1, 2])) >>> target = (0, 1) >>> scale_to(matrix, source, target) array([[ 1. , 1. , 1. ], [ 0. , 0. , 0. ], [ 0.5, 0.5, 0.5]]) iiN(tnptarray(tmatrixtsourcettargett keep_rows((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/svm/utils.pytscale_toÉs #(t__doc__t __future__RtnumpyRat ImportErrorRtlibtbxRt mmtbx.ionsRRt scitbx.matrixRR2RRFR`Rg(((sB/public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/mmtbx/ions/svm/utils.pyts  $ b 2