o Rŀg9!@sUdZddlZddlZddlmZddlZddlmZdgZ ddddd d Z e d d Z ee efed <e iddddddddddddddddddd dd!d"d#d$d%d&d'd(d)dd*d+d,d-d.d/d0dd1Gd2ddZdS)3aCalculation of solvent accessible surface areas for Bio.PDB entities. Uses the "rolling ball" algorithm developed by Shrake & Rupley algorithm, which uses a sphere (of equal radius to a solvent molecule) to probe the surface of the molecule. Reference: Shrake, A; Rupley, JA. (1973). J Mol Biol "Environment and exposure to solvent of protein atoms. Lysozyme and insulin". N)MutableMapping)KDTree ShrakeRupley)ARCMScCsdS)N@rrr@/var/www/html/myenv/lib/python3.10/site-packages/Bio/PDB/SASA.py-sr ATOMIC_RADIIHg333333?HEffffff?r g333333?Ng?OgRQ?FgQ?NAg)\(@MGgGz?Pg?r CLg?Kg@CAg{Gz@NIgGz?CUZNg= ףp=?SEgffffff?g?gHzG?gGz?)BRCDIHGc@s,eZdZdZd ddZddZd d d ZdS)rz3Calculates SASAs using the Shrake-Rupley algorithm.rdNcCsj|dkr td|dt||_|dkrtd|||_t|_|dur.|j|||_ dS)a Initialize the class. :param probe_radius: radius of the probe in A. Default is 1.40, roughly the radius of a water molecule. :type probe_radius: float :param n_points: resolution of the surface of each atom. Default is 100. A higher number of points results in more precise measurements, but slows down the calculation. :type n_points: int :param radii_dict: user-provided dictionary of atomic radii to use in the calculation. Values will replace/complement those in the default ATOMIC_RADII dictionary. :type radii_dict: dict >>> sr = ShrakeRupley() >>> sr = ShrakeRupley(n_points=960) >>> sr = ShrakeRupley(radii_dict={"O": 3.1415}) gz(Probe radius must be a positive number: z <= 0rz/Number of sphere points must be larger than 1: N) ValueErrorfloat probe_radiusn_pointsrcopy radii_dictupdate_compute_sphere_sphere)selfr*r+r-rrr__init__Ls    zShrakeRupley.__init__c Cs|j}tjd}d|}d}d|d}tj|dftjd}t|D].}d||d}t||||df<t||||df<|||df<||8}||7}q"|S) aReturn the 3D coordinates of n points on a sphere. Uses the golden spiral algorithm to place points 'evenly' on the sphere surface. We compute this once and then move the sphere to the centroid of each atom as we compute the ASAs. g`-!r?rrrrrdtypeg?) r+nppizerosfloat32rangemathcossin) r1ndldz longitudezcoordskrrrrr/vs     zShrakeRupley._compute_spherer c st|do |jdv}|stdt|d|tvr"td|dt|t|jkr6td|d|jt|}t|}|sFtd tj d d |Dtj d }t |d }|j tj fdd |Dtj d }||j 7}t|d} tj|dftjd } tt|j} t|D]P} || } tj |jdd| || }| }t |d }||| | D]$}|j}| |krq|j| ||kr|dd|||||D8}qt|| | <q||dtj|j}| |ddtjf} t|D] \} }| | df|_q|dkr@t|}t|}t|D] }dd|D}qddt|D|D]}fdd |D}| ||_q*dSdS)a Calculate surface accessibility surface area for an entity. The resulting atomic surface accessibility values are attached to the .sasa attribute of each entity (or atom), depending on the level. For example, if level="R", all residues will have a .sasa attribute. Atoms will always be assigned a .sasa attribute with their individual values. :param entity: input entity. :type entity: Bio.PDB.Entity, e.g. Residue, Chain, ... :param level: the level at which ASA values are assigned, which can be one of "A" (Atom), "R" (Residue), "C" (Chain), "M" (Model), or "S" (Structure). The ASA value of an entity is the sum of all ASA values of its children. Defaults to "A". :type entity: Bio.PDB.Entity >>> from Bio.PDB import PDBParser >>> from Bio.PDB.SASA import ShrakeRupley >>> p = PDBParser(QUIET=1) >>> # This assumes you have a local copy of 1LCD.pdb in a directory called "PDB" >>> struct = p.get_structure("1LCD", "PDB/1LCD.pdb") >>> sr = ShrakeRupley() >>> sr.compute(struct, level="S") >>> print(round(struct.sasa, 2)) 7053.43 >>> print(round(struct[0]["A"][11]["OE1"].sasa, 2)) 9.64 level>r r r r zInvalid entity type 'z.'. Must be Residue, Chain, Model, or StructurezInvalid level 'z'. Must be A, R, C, M, or S.zLevel 'z.' must be equal or smaller than input entity: zEntity has no child atoms.cSsg|]}|jqSr)coord.0arrr z(ShrakeRupley.compute..r3 cg|]}|jqSr)elementrG)r-rrrJrrT)r,cSh|]}|jqSr)index)rHptrrr sz'ShrakeRupley.compute..rNrr cSrPr)parent)rHerrrrSrKcSsi|]\}}|j|qSrfull_id)rHidxrIrrr sz(ShrakeRupley.compute..crMrrVrG)atomdictrrrJrO)hasattrrEr(type_ENTITY_HIERARCHYlist get_atomslenr5arrayfloat64rr-r*maxr7int64setr9r+r0r,searchrQradiusr6newaxis enumeratesasasum)r1entityrEis_validatomsn_atomsrBkdtradiitwice_maxradii asa_arrayptsetir_is_on_i available_set kdt_spherejjjfatomentitiestarget_rUe_atomsr)rZr-rcomputesj       zShrakeRupley.compute)rr'N)r )__name__ __module__ __qualname____doc__r2r/rrrrrrIs  *)r collectionsr:collections.abcrnumpyr5Bio.PDB.kdtreesr__all__r] defaultdictrstrr)__annotations__r.rrrrrsr