Source code for pwem.convert.atom_struct

# **************************************************************************
# *
# * Authors:     Roberto Marabini (
# *              Marta Martinez (
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# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
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# * This program is free software; you can redistribute it and/or modify
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# * This program is distributed in the hope that it will be useful,
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# cif to pdb conversion is based on by Spencer Bliven
# <>
# see for a description
# on the object "structure" and other Bio.xxxx modules

from Bio.PDB.Dice import ChainSelector
from Bio.PDB.MMCIFParser import MMCIFParser
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB import PDBIO, MMCIFIO
from Bio.PDB.mmcifio import mmcif_order
from Bio.PDB import Superimposer
from Bio.PDB.MMCIF2Dict import MMCIF2Dict
from Bio.PDB import Entity
from Bio.PDB import PDBList
from collections import OrderedDict
from Bio.PDB.Polypeptide import is_aa
from Bio.PDB.Polypeptide import three_to_one
from Bio.Seq import Seq
from pwem import Plugin, MAXIT_HOME
from pwem.convert.transformations import translation_from_matrix
import mmap
import re
import os
import numpy
import pyworkflow.utils as pwutils
import shutil

from import Alphabet

SECTION = '_scipion_attributes'
NAME, RECIP, SPEC, VALUE = SECTION + '.name', SECTION + '.recipient', SECTION + '.specifier', SECTION + '.value'

[docs]class OutOfChainsError(Exception): pass
[docs]class scipionMMCIFIO(MMCIFIO): # this class was needed before including maxit # as converter. # TODO: Delete it after a more extensive testing period # DATE mar feb 18 17:48:57 CET 2020 def _save_dict_delete(self, out_file): # Form dictionary where key is first part of mmCIF key and value is list # of corresponding second parts key_lists = {} for key in self.dic: if key == "data_": data_val = self.dic[key] else: s = re.split(r"\.", key) if len(s) == 2: if s[0] in key_lists: key_lists[s[0]].append(s[1]) else: key_lists[s[0]] = [s[1]] else: raise ValueError("Invalid key in mmCIF dictionary: " + key) # Re-order lists if an order has been specified # Not all elements from the specified order are necessarily present for key, key_list in key_lists.items(): # P3 # for key, key_list in list(key_lists.items()): if key in mmcif_order: inds = [] for i in key_list: try: inds.append(mmcif_order[key].index(i)) # Unrecognised key - add at end except ValueError: inds.append(len(mmcif_order[key])) key_lists[key] = [k for _, k in sorted(zip(inds, key_list))] # Write out top data_ line if data_val: out_file.write("data_" + data_val + "\n#\n") # ESCRIBIR POLYSEQTABLE out_file.write("""loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero\n#\n""") total_seqs = [] counter_chain = 1 for model in self.structure: for chain in model: min_val = int(chain.get_unpacked_list()[0].id[1]) # max_val = min_val + len(chain.get_unpacked_list()) # not_are = range(1, min_val-1) # for i in range(min_val)[:-1]: # not_are.append(i + 1) counter = 1 if min_val > 1: for counter in range(1, min_val): if len(chain.get_unpacked_list()[0].resname.strip()) == 3: total_seqs.append((counter_chain, str(counter), "XAA", "n")) elif len(chain.get_unpacked_list()[0].resname.strip()) == 2: total_seqs.append((counter_chain, str(counter), "DX", "n")) elif len(chain.get_unpacked_list()[0].resname.strip()) == 1: total_seqs.append((counter_chain, str(counter), "X", "n")) counter += 1 for residue in chain: if len(chain.get_unpacked_list()[0].resname.strip()) == 3 and \ is_aa(residue.get_resname(), standard=True): # aminoacids total_seqs.append((counter_chain,[1], residue.get_resname(), "n")) elif len(chain.get_unpacked_list()[0].resname.strip()) == 2 and \ residue.get_resname()[1] in ['A', 'C', 'G', 'T']: total_seqs.append((counter_chain, counter, residue.get_resname(), "n")) elif len(chain.get_unpacked_list()[0].resname.strip()) == 1 and \ residue.get_resname() in ['A', 'C', 'G', 'U']: total_seqs.append((counter_chain, counter, residue.get_resname(), "n")) counter += 1 counter_chain += 1 for item in total_seqs: item = list(item) out_file.write("""%s %s %s %s\n""" % (str(item[0]), item[1], item[2], item[3])) for key, key_list in key_lists.items(): # for key, key_list in list(key_lists.items()): # Pick a sample mmCIF value, which can be a list or a single value sample_val = self.dic[key + "." + key_list[0]] n_vals = len(sample_val) # Check the mmCIF dictionary has consistent list sizes for i in key_list: val = self.dic[key + "." + i] if (isinstance(sample_val, list) and (isinstance(val, str) or len(val) != n_vals)) or ( isinstance(sample_val, str) and isinstance(val, list)): raise ValueError("Inconsistent list sizes in mmCIF dictionary: " + key + "." + i) # If the value is a single value, write as key-value pairs if isinstance(sample_val, str): m = 0 # Find the maximum key length for i in key_list: if len(i) > m: m = len(i) for i in key_list: out_file.write( "{k: <{width}}".format(k=key + "." + i, width=len(key) + m + 4) + self._format_mmcif_col( self.dic[key + "." + i], len(self.dic[key + "." + i])) + "\n") # If the value is a list, write as keys then a value table elif isinstance(sample_val, list): out_file.write("loop_\n") col_widths = {} # Write keys and find max widths for each set of values for i in key_list: out_file.write(key + "." + i + "\n") col_widths[i] = 0 for val in self.dic[key + "." + i]: len_val = len(val) # If the value requires quoting it will add 2 characters if self._requires_quote(val) and not self._requires_newline(val): len_val += 2 if len_val > col_widths[i]: col_widths[i] = len_val # Technically the max of the sum of the column widths is 2048 # Write the values as rows for i in range(n_vals): for col in key_list: out_file.write(self._format_mmcif_col(self.dic[key + "." + col][i], col_widths[col] + 1)) out_file.write("\n") else: raise ValueError("Invalid type in mmCIF dictionary: " + str(type(sample_val))) out_file.write("#\n")
[docs]class AtomicStructHandler: """ Class that contain utilities to handle pdb/cif files""" PDB = 0 CIF = 1 def __init__(self, fileName=None, permissive=1): # The PERMISSIVE flag indicates that a number of common problems # associated with PDB files will be ignored self.permissive = permissive self.pdbParser = None self.cifParser = None self.ioPDB = None self.ioCIF = None self.structure = None self._readDone = False if fileName is not None:
[docs] def readFromPDBDatabase(self, pdbID, dir=None, type='mmCif'): """ Retrieve structure from PDB :param pdbID: :param dir: save structure in this directory :param type: mmCif or pdb :return: filename with pdb file """ if dir is None: dir = os.getcwd() pdbl = PDBList(pdb=dir) for counter in range(5): try: fileName = pdbl.retrieve_pdb_file(pdbID, pdir=dir, file_format=type) except Exception as error: print("Error: ", error) print("Retry connection", counter) if counter == 4: raise return os.path.abspath(fileName)
[docs] def checkLabelInFile(self, fileName, label): with open(fileName, "r") as f: s = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ) if s.find(label) != -1: return True else: return False
[docs] def getStructure(self): """return structure information, model, chain, residues, atoms...""" return self.structure
[docs] def read(self, fileName): """ Read and parse file.""" # biopython assigns an ID to any read structure structure_id = os.path.basename(fileName) structure_id = structure_id[:4] if len(structure_id) > 4 else "1xxx" if fileName.endswith(".pdb") or fileName.endswith(".ent"): if self.pdbParser is None: self.pdbParser = PDBParser(PERMISSIVE=self.permissive) parser = self.pdbParser self.type = self.PDB else: if self.cifParser is None: self.cifParser = MMCIFParser() parser = self.cifParser self.type = self.CIF self.structure = parser.get_structure(structure_id, fileName) self._readDone = True
[docs] def checkRead(self): if self._readDone: return True else: print("you must read the pdb file first") exit(0)
[docs] def getModelsChains(self): """ given an atomic structure returns two dictionaries: (1) for all models and respective chains (chainID and length of residues) (2) for each chain list of residues """ self.checkRead() listOfChains = OrderedDict() listOfResidues = OrderedDict() for model in self.structure: chainDicLength = OrderedDict() chainDicFirstResidue = OrderedDict() for chain in model: if len(chain.get_unpacked_list()[0].resname.strip()) == 1: # RNA seq = list() seq_number = list() for residue in chain: if residue.get_resname() in ['A', 'C', 'G', 'U']: seq.append(residue.get_resname()) else: seq.append("X") seq_number.append((residue.get_id()[1], residue.get_resname())) elif len(chain.get_unpacked_list()[0].resname.strip()) == 2: # DNA seq = list() seq_number = list() for residue in chain: if residue.get_resname()[1] in ['A', 'C', 'G', 'T']: seq.append(residue.get_resname()[1]) else: seq.append("X") seq_number.append((residue.get_id()[1], residue.get_resname())) elif len(chain.get_unpacked_list()[0].resname.strip()) == 3: # Protein seq = list() seq_number = list() counter = 0 for residue in chain: if is_aa(residue.get_resname(), standard=True): # aminoacids seq.append(three_to_one(residue.get_resname())) counter += 1 else: seq.append("X") seq_number.append((residue.get_id()[1], residue.get_resname())) if counter == 0: # HETAM for residue in chain: seq.append(residue.get_resname()) while seq[-1] == "X": del seq[-1] while seq[0] == "X": del seq[0] chainDicLength[] = len(seq) chainDicFirstResidue[] = seq_number listOfChains[] = chainDicLength listOfResidues[] = chainDicFirstResidue return listOfChains, listOfResidues
[docs] def getSequenceFromChain(self, modelID, chainID, returnAlphabet=False): self.checkRead() seq = list() for model in self.structure: if == modelID: for chain in model: if str( == chainID: if len(chain.get_unpacked_list()[0].resname) == 1: print("Your sequence is a nucleotide sequence (" "RNA)\n") alphabet = Alphabet.UNAMBIGOUS_RNA_ALPHABET for residue in chain: # Check if the residue belongs to the # standard RNA and add those residues to the # seq if residue.get_resname() in ['A', 'C', 'G', 'U']: seq.append(residue.get_resname()) else: seq.append("X") elif len(chain.get_unpacked_list()[0].resname) == 2: print("Your sequence is a nucleotide sequence (" "DNA)\n") alphabet = Alphabet.UNAMBIGOUS_DNA_ALPHABET for residue in chain: # Check if the residue belongs to the # standard DNA and add those residues to the # seq if residue.get_resname()[1] in ['A', 'C', 'G', 'T']: seq.append(residue.get_resname()[1]) else: seq.append("X") elif len(chain.get_unpacked_list()[0].resname) == 3: counter = 0 for residue in chain: if is_aa(residue.get_resname(), standard=True): alphabet = Alphabet.EXTENDED_PROTEIN_ALPHABET # The test checks if the amino acid # is one of the 20 standard amino acids # Some proteins have "UNK" or "XXX", or other symbols # for missing or unknown residues seq.append(three_to_one(residue.get_resname())) counter += 1 else: seq.append("X") if counter != 0: # aminoacids print("Your sequence is an aminoacid sequence") else: # HETAM print("Your sequence is a HETAM sequence") for residue in chain: seq.append(residue.get_resname()) while seq[-1] == "X": del seq[-1] while seq[0] == "X": del seq[0] # return Seq(str(''.join(seq)), alphabet=alphabet) if returnAlphabet: return Seq(str(''.join(seq))), alphabet else: return Seq(str(''.join(seq)))
[docs] def getFullID(self, model_id='0', chain_id=None): """ assign a label to a sequence obtained from a PDB file :parameter model_id chain_id :return: string with label """ self.checkRead() # cehck we have read the structure label = "%s" % self.structure.get_id() # PDB_ID # check how many model are in sequence if > 1 add to id models = self.getModelsChains() if len(models) > 1: label = label + "__%s" % str(model_id) # if chain_id is None do not add it to te name if chain_id is not None: label = label + "_%s" % str(chain_id) return label
[docs] def getStructureBFactorValues(self): """Using an atomic structure as input, this method returns two list: * List 1: B-factor field values for each atom of the structure. * List 2 is a list of lists. For each residue of the structure a list with the model, chain, order number of residue, name of residue and average of B-factor field values (atoms) is returned. An example of each list item is: [0, 'A', 103, 'PHE', 96.01]""" self.checkRead() listOfBFactors = [] listOfResiduesBFactors = [] for model in self.structure: for chain in model: for residue in chain: residue_list = [] residue_list.append( residue_list.append( residue_list.append([1]) residue_list.append(residue.get_resname()) sum_list = 0.00 residue_atom_b_factor_list = [] for atom in residue: listOfBFactors.append(atom.get_bfactor()) residue_atom_b_factor_list.append(atom.get_bfactor()) for item in residue_atom_b_factor_list: sum_list += item avg = sum_list / len(residue_atom_b_factor_list) residue_list.append(round(avg, 2)) listOfResiduesBFactors.append(residue_list) return listOfBFactors, listOfResiduesBFactors
[docs] def readLowLevel(self, fileName): """ Return a dictionary with all mmcif fields. you should parse them Example: get the list of the y coordinates of all atoms dict = readLowLevel("kk.pdb") y_list = dict['_atom_site.Cartn_y'] """ if fileName.endswith(".pdb"): print("Low level access to PDB is not implemented") else: dict = MMCIF2Dict(fileName) return dict
def _write(self, fileName): """ Do not use this function use toPDB or toCIF, they take care of some compatibiity issues""" if fileName.endswith(".pdb") or fileName.endswith(".ent"): if self.ioPDB is None: self.ioPDB = PDBIO() io = self.ioPDB else: if self.ioCIF is None: self.ioCIF = scipionMMCIFIO() # self.ioCIF = MMCIFIO() io = self.ioCIF io.set_structure(self.structure) def _writeLowLevel(self, fileName, dict): """ write a dictionary as cif file """ if fileName.endswith(".pdb"): print("Low level access to PDB is not implemented") else: if self.ioCIF is None: self.ioCIF = MMCIFIO() io = self.ioCIF io.set_dict(dict) def _intToChain(self, i, base=62): """ int_to_chain(int,int) -> str Converts a positive integer to a chain ID. Chain IDs include uppercase characters, numbers, and optionally lowercase letters. i = a positive integer to convert base = the alphabet size to include. Typically 36 or 62. """ if i < 0: raise ValueError("positive integers only") if base < 0 or 62 < base: raise ValueError("Invalid base") quot = int(i) // base rem = i % base if rem < 26: letter = chr(ord("A") + rem) elif rem < 36: letter = str(rem - 26) else: letter = chr(ord("a") + rem - 36) if quot == 0: return letter else: return self._intToChain(quot - 1, base) + letter
[docs] def renameChains(self, structure): """Renames chains to be one-letter chains Existing one-letter chains will be kept. Multi-letter chains will be truncated or renamed to the next available letter of the alphabet. If more than 62 chains are present in the structure, raises an OutOfChainsError Returns a map between new and old chain IDs, as well as modifying the input structure """ next_chain = 0 # # single-letters stay the same chainmap = { for c in structure.get_chains() if len( == 1} for o in structure.get_chains(): if len( != 1: if[0] not in chainmap: chainmap[[0]] = =[0] else: c = self._intToChain(next_chain) while c in chainmap: next_chain += 1 c = self._intToChain(next_chain) if next_chain >= 62: raise OutOfChainsError() chainmap[c] = = c return chainmap
[docs] def write(self, fileName): if fileName.endswith(".pdb") or fileName.endswith(".ent"): self.writeAsPdb(fileName) else: self.writeAsCif(fileName)
[docs] def writeAsPdb(self, pdbFile): """ Save structure as PDB. Be aware that this is not a lossless conversion Returns False is conversion is not possible. True otherwise """ # check input is not PDB if self.type == self.PDB: pass else: # rename long chains try: chainmap = self.renameChains(self.structure) except OutOfChainsError: print("Too many chains to represent in PDB format") return False for new, old in chainmap.items(): # for new, old in list(chainmap.items()): if new != old: print("Renaming chain {0} to {1}".format(old, new)) self._write(pdbFile) return True
[docs] def writeAsCif(self, cifFile): """ Save structure as CIF. Be aware that this is not a lossless conversion """ self._write(cifFile)
[docs] def getBoundingBox(self, expand=3): """Get bounding box (angstroms) for atom struct. Only alpha carbons are taken into account. parameter: expand.- make box larger addind this factor """ # Use the first model ref_model = self.getStructure()[0] # init bounding box volues xmin = 100000; ymin = xmin; zmin = xmin xmax = -100000; ymax = xmax; zmax = xmax # iterate for all aminoacids for chain in ref_model: for residue in chain: (x,y,z) = residue["CA"].get_coord() if x < xmin: xmin = x if x > xmax: xmax = x if y < ymin: ymin = y if y > ymax: ymax = y if z < zmin: zmin = z if z > zmax: zmax = z # DEBUG # with open("/tmp/kk.bild", "w") as file: # file.write(".transparency 0.8\n" # ".color red\n" # ".box %f %f %f %f %f %f\n" % # (xmin - expand , ymin - expand, zmin - expand, # xmax + expand, ymax + expand, zmax + expand)) return [[xmin - expand, ymin - expand, zmin - expand], [xmax + expand, ymax + expand, zmax + expand]]
[docs] def getTransformMatrix(self, atomStructFn, startId=-1, endId=-1, outFn=None): """find matrix that Superimposes two atom structures. this matrix moves atomStructFn to self """ if endId == -1: endId = 10000000 # load second atom structure aSH = AtomicStructHandler() # Use the first model in the atom struct for alignment ref_model = self.getStructure()[0] sample_model = aSH.getStructure()[0] # Make a list of the atoms (in the structures) you wish to align. # In this case we use CA atoms whose index is in the # specified range (starId, endId) ref_atoms = [] sample_atoms = [] # Now get a list with CA atoms (alpha-carbon) # I assume that both atom structs have the same number of chains # and in the same order. for ref_chain, sample_chain in zip(ref_model, sample_model): # create a set with the id of all residues # for the current chain ref_set_id = set(res.get_id()[1] for res in ref_chain) sample_set_id = set(res.get_id()[1] for res in sample_chain) # keep the intersection as an ordered list (sets are not ordered) ref_set_id.intersection_update(sample_set_id) ref_list_id = sorted(ref_set_id) # delete AA smaller or large than the predefined values ref_list_id[:] = [x for x in ref_list_id if x >= startId and x <= endId] # Iiterate through all residues in each chain a store CA atoms for id in ref_list_id: if id in ref_chain and id in sample_chain: ref_atoms.append(ref_chain[id]['CA']) sample_atoms.append(sample_chain[id]['CA']) # Now we initiate the superimposer: super_imposer = Superimposer() super_imposer.set_atoms(ref_atoms, sample_atoms) # super_imposer.apply(sample_model.get_atoms()) (rot, trans) = super_imposer.rotran # DEBUG, uncomment next two lines to see # transformation applied to atomStructFn if outFn: aSH.getStructure().transform(rot, trans) aSH.write(outFn) # convert 3x3 rotation matrix to homogeneous matrix rot = numpy.transpose(rot) # scipion and biopython use # different conventions tmp = numpy.r_[rot, numpy.zeros((1, 3))] mat = numpy.c_[tmp, numpy.array( [[trans[0]], [trans[1]], [trans[2]], [1]])] return mat, super_imposer.rms
[docs] def centerOfMass(self, geometric=False): """ Returns gravity [default] or geometric center of mass of an Entity (anything with a get_atoms function in biopython. Geometric assumes all masses are equal (geometric=True) """ entity = self.structure # Structure, Model, Chain, Residue if isinstance(entity, Entity.Entity): atom_list = entity.get_atoms() # List of Atoms elif hasattr(entity, '__iter__') and \ [x for x in entity if x.level == 'A']: atom_list = entity else: # Some other weirdo object raise ValueError("Center of Mass can only be calculated " "from the following objects:\n" "Structure, Model, Chain, Residue, " "list of Atoms.") masses = [] positions = [[], [], []] for atom in atom_list: masses.append(atom.mass) for i, coord in enumerate(atom.coord.tolist()): positions[i].append(coord) # If there is a single atom with undefined mass complain loudly. if 'ukn' in set(masses) and not geometric: raise ValueError("Some Atoms don't have an element assigned.\n" "Try adding them manually or calculate the " "geometrical center of mass instead.") if geometric: return [sum(coord_list) / len(masses) for coord_list in positions] else: w_pos = [[], [], []] for atom_index, atom_mass in enumerate(masses): w_pos[0].append(positions[0][atom_index] * atom_mass) w_pos[1].append(positions[1][atom_index] * atom_mass) w_pos[2].append(positions[2][atom_index] * atom_mass) return [sum(coord_list) / sum(masses) for coord_list in w_pos]
[docs] def transform(self, transformation_matrix, sampling=1.): """ Geometrical transformation of a PDB structure :param entity: PDB biopython structure :param transformation_matrix -> 4x4 scipion matrix :param sampling: scipion transform matrix is applied to voxels so length must be multiplied by samplingRate internal variables: rotation matrix -> numpy.array( [[ 0.5, -0.809017, 0.309017], [ 0.809017, 0.30917, -0.5 ], [ 0.309017, 0.5, 0.809017]]) translation: translation vector -> numpy.array([1., 0., 0.], 'd') :return: no return, new data overwrites entity """ # bioPhython and Scipion conventions do not match rotation_matrix = numpy.transpose(transformation_matrix[:3, :3]) # from geometry get euler angles and recreate matrix translation = translation_from_matrix(transformation_matrix) translation = [x * sampling for x in translation] self.structure.transform(rotation_matrix, translation)
def _renameChainsIfNeed(self, struct2): """Rename chain, we assume that there is a single model per structure""" repeated = False def RepresentsInt(s): try: int(s) return True except ValueError: return False import uuid chainIDs1 = [ for chain in self.structure.get_chains()] for chain in struct2.get_chains(): counter = 2 if in chainIDs1: repeated = True cId = l = len(cId) if l == 1: while True: try: = "%s%03d" % (cId, counter) break except ValueError: counter +=1 if counter > 1000: raise ValueError('Error in _renameChainsIfNeed.') elif RepresentsInt(cId[1:]): # try to fit a number and increase it by one = "%s%03d" % (cId[0], int(cId[1:]) + 1) else: # generate a 4 byte random string = uuid.uuid4().hex[:4] if repeated: self._renameChainsIfNeed(struct2)
[docs] def addStruct(self, secondPDBfileName, outPDBfileName=None, useModel=False): """ Join the second structure to the first one. If cheon numes are the same rename them. if outPDBfileName id provided then new struct is saved to a file""" # read new structure if outPDBfileName is not None: pdbID = (os.path.splitext(os.path.basename(outPDBfileName))[0])[:4] else: pdbID = (os.path.splitext(os.path.basename(secondPDBfileName))[0])[:4] if secondPDBfileName.endswith(".pdb") or secondPDBfileName.endswith(".ent"): parser = PDBParser(PERMISSIVE=self.permissive) else: parser = MMCIFParser() struct2 = parser.get_structure(pdbID, secondPDBfileName) if useModel: modelNumber = 0 modelID = 0 # = model.serial_num = len(self.structure)? # not sure this # is valid always for model in self.structure: pass modelNumber = model.serial_num modelID = for model in struct2: modelNumber += 1 modelID += 1 model.detach_parent() model.serial_num = modelNumber = modelID self.structure.add(model) else: self._renameChainsIfNeed(struct2) for model in struct2: for chain in model: chain.detach_parent() self.structure[0].add(chain) # create new output file if outPDBfileName is not None: self.write(outPDBfileName)
[docs] def extractChain(self, chainID, start=0, end=-1, modelID='0', filename="output.mmcif"): """Code for chopping a structure. This module is used internally by the Bio.PDB.extract() function. """ sel = ChainSelector(chain_id=chainID, start=start, end=end, model_id=int(modelID)) io = scipionMMCIFIO() io.set_structure(self.structure), sel)
[docs] def renameChain(self, chainID, newChainName, modelID='0', filename="output.mmcif"): self.structure[modelID][chainID].id = newChainName self.write(filename)
[docs] def renumberChain(self, chainID, offset=0, modelID='0', filename="output.mmcif"): # get chain object chain = self.structure[modelID][chainID] # remove chain from model self.structure[modelID].detach_child(chainID) from Bio.PDB.Chain import Chain # create new chain newChain = Chain(chainID) for residue in chain: # remove residue, otherwise we cannot renumber it residue.detach_parent() rId = res_id = list(rId) res_id[1] = res_id[1] + offset if res_id[1] < 0: raise ValueError('Residue number cant be <= 0') = tuple(res_id) newChain.add(residue) self.structure[modelID].add(newChain) self.write(filename)
[docs]def cifToPdb(fnCif, fnPdb): h = AtomicStructHandler() h.writeAsPdb(fnPdb)
[docs]def pdbToCif(fnPdb, fnCif): h = AtomicStructHandler() h.writeAsCif(fnCif)
[docs]def toPdb(inFileName, outPDBFile): if inFileName.endswith(".pdb") or inFileName.endswith(".ent"): return inFileName elif inFileName.endswith(".cif") or inFileName.endswith(".mmcif"): cifToPdb(inFileName, outPDBFile) return outPDBFile else: print("ERROR (toPdb), Unknown file type for file = %s" % inFileName)
[docs]def toCIF(inFileName, outCIFFile): if inFileName.endswith(".cif") or inFileName.endswith(".mmcif"): return inFileName elif inFileName.endswith(".pdb") or inFileName.endswith(".ent"): pdbToCif(inFileName, outCIFFile) return outCIFFile else: print("ERROR (toCIF), Unknown file type for file = %s" % inFileName)
[docs]def getEnviron(): environ = pwutils.Environ(os.environ) environ.update({'RCSBROOT': os.path.join(Plugin.getMaxitHome()) }, position=pwutils.Environ.REPLACE) environ.update({'PATH': os.path.join(Plugin.getMaxitHome(), 'bin') }, position=pwutils.Environ.BEGIN) return environ
def _frombase(inFileName, outFileName, log, oParam=1): # check if maxit exists, # if it does not then complain # convert pdb to cif using maxit global maxitAvailable try: maxitAvailable except: if not os.path.exists(Plugin.getMaxitBin()): maxitAvailable = False # show error message else: maxitAvailable = True if maxitAvailable: args = ' -input "' + inFileName + '" -output "' + outFileName + \ '" -o %d' % oParam'Launching: ' + Plugin.getMaxitBin() + args) # run in the background env = getEnviron() pwutils.runJob(None, Plugin.getMaxitBin(), args, env=env) else: # this is not the ideal conversion but it is better # than nothing aSH = AtomicStructHandler() aSH.write(outFileName) # show error message print(pwutils.redStr("Please, install maxit with the command 'scipion installb maxit'")) print(pwutils.redStr("and restart scipion. Packages bison and flex are needed.")) print(pwutils.redStr("If maxit is installed check %s in scipion.conf" % MAXIT_HOME))
[docs]def fromPDBToCIF(inFileName, outFileName, log): _frombase(inFileName, outFileName, log, 1)
[docs]def fromCIFToPDB(inFileName, outFileName, log): _frombase(inFileName, outFileName, log, 2)
[docs]def fromCIFTommCIF(inFileName, outFileName, log): _frombase(inFileName, outFileName, log, 8)
[docs]def testLog(log, messages= None, sdterrLog = None): # Method to capture exceptions like error messages from Phenix when map and model are far apart if sdterrLog is None or messages is None: return # read all content of a file for line in sdterrLog(logFile=1): # check if string present in a file for message in messages: if message[0] in line:"Error: Protocol aborted "))"Error: {message[1]}")) raise Exception(pwutils.redStr("Error: %s" % message[1])) if "Sorry" in line:"WARNING, %s" % line))
[docs]def retry(runEnvirom, program, args, cwd, listAtomStruct=[], log=None, clean_dir=None, messages=[], sdterrLog=None): messages.append(("Sorry: Input map is all zero after boxing", "Sorry: Input map is all zero after boxing")) try: runEnvirom(program, args, cwd=cwd) except: testLog(log, messages,sdterrLog) # first remove every files or directories in the extra folder, # except maps partiallyCleaningFolder(program, cwd) # something went wrong, may be bad atomStruct format'retry with maxit conversion') for i, atomStructName in enumerate(listAtomStruct): if atomStructName.endswith(".pdb.cif"): aSH = AtomicStructHandler() aSH.write(atomStructName) try: runEnvirom(program, args, cwd=cwd) except: testLog(log, messages,sdterrLog) else: try: if atomStructName.endswith(".pdb"): newAtomStructName = os.path.abspath( os.path.join(cwd, "retrypdb%d.cif" % i)) fromPDBToCIF(atomStructName, newAtomStructName, log) _args = args.replace(atomStructName, newAtomStructName) try: runEnvirom(program, _args, cwd=cwd) except: testLog(log, messages,sdterrLog) fromCIFTommCIF(newAtomStructName, newAtomStructName, log) runEnvirom(program, _args, cwd=cwd) elif atomStructName.endswith(".cif"): newAtomStructName = os.path.abspath( os.path.join(cwd, "retrycif%d.cif" % i)) fromCIFTommCIF(atomStructName, newAtomStructName, log) _args = args.replace(atomStructName, newAtomStructName) try: runEnvirom(program, _args, cwd=cwd) except: testLog(log, messages,sdterrLog) newAtomStructName = os.path.abspath( os.path.join(cwd, "retrycif%d.pdb" % i)) fromCIFToPDB(atomStructName, newAtomStructName, log) _args = args.replace(atomStructName, newAtomStructName) runEnvirom(program, _args, cwd=cwd) testLog(log, messages,sdterrLog) except: testLog(log, messages,sdterrLog) # first remove files or directories in the extra folder, # except maps partiallyCleaningFolder(program, cwd) # biopython conversion aSH = AtomicStructHandler() if atomStructName.endswith(".pdb") or atomStructName.endswith(".ent"): newAtomStructName = atomStructName.replace(".pdb", ".cif"). \ replace(".ent", ".cif") else: newAtomStructName = atomStructName try: aSH.write(newAtomStructName) _args = args.replace(atomStructName, newAtomStructName) runEnvirom(program, _args, cwd=cwd) testLog(log, messages,sdterrLog) except: print("CIF file standardisation failed.")
# atomStructName = newAtomStructName # TODO this should no be here, ROB
[docs]def partiallyCleaningFolder(program, cwd): l1 = os.listdir(cwd) l2 = ['molprobity.out', 'molprobity_probe.txt', ''] l3 = ['validation_cryoem.pkl'] l4 = ['placed_model.pdb', 'placed_model.cif'] for item in l1: if (program.endswith('') and (item.endswith('geo') or item.endswith('real_space_refined.log') or item.endswith('real_space_refine.pdb') or item.endswith('real_space_refined.cif'))) or \ (program.endswith('') and item in l2) or \ (program.endswith('') and item in l3) or \ (program.endswith('') and (item.endswith("emringer.csv") or item.endswith("emringer.pkl") or item.endswith("emringer_plots") or item.startswith('emringer_transfer'))) or \ (program.endswith('') and item in l4): path1 = os.path.join(cwd, item) if os.path.exists(path1): if os.path.isfile(path1) or os.path.islink(path1): os.remove(path1) elif os.path.isdir(path1): shutil.rmtree(path1)
[docs]def addScipionAttribute(cifDic, attributeScoresDic, attrName, recipient='residues'): '''Add a scipion attribute in a section of the CIF dictionary "cifDic": must be a cif dictionary parsed by Biopython "attributeScoresDic" a dictionary of the form {spec: value}"''' if not NAME in cifDic: cifDic[NAME], cifDic[RECIP] = [], [] cifDic[SPEC], cifDic[VALUE] = [], [] for spec in attributeScoresDic: value = attributeScoresDic[spec] cifDic[NAME].append(attrName) cifDic[RECIP].append(recipient) cifDic[SPEC].append(spec) cifDic[VALUE].append(str(value)) return cifDic