コード例 #1
0
def update_graph(gene2graph, cog, signif_struct_info, struct, radius):
    """Updates the residue neighbor graph based on the current structure.

    Residues are linked by edges if they are within the provided radius
    and are on the same gene.

    Parameters
    ----------
    gene2graph : dict
        dictionary with genes as keys pointing to significant hotspot residue
        neighbor graph
    signif_struct_info : dict
        identifies which residues are significant hotspots
    struct : Bio.PDB structure
        structure under consideration when populating the graph
    radius : float
        radius deemed close enough to add an edge between two residues

    Returns
    -------
    gene2graph : dict
        updated graph based on the provided structure
    """
    # get which residues are significant
    signif_pdb_pos = signif_struct_info.keys()
    possible_res = set(signif_pdb_pos)

    # find neighbor residues
    cog = {k: cog[k] for k in cog
           if (k[2], k[3][1]) in signif_pdb_pos}
    neighbors = pstruct.find_neighbors_1D(cog, radius)

    #struct_info = struct_chain[pdb_id]

    # add edge if residues are neighbors
    avail_models = [m.id for m in struct]
    for s in signif_pdb_pos:
        tmp_chain, tmp_res = s
        cur_res = signif_struct_info[s]
        cur_gene = cur_res[0]

        # update gene2graph
        gene2graph.setdefault(cur_gene, {})
        gene2graph[cur_gene].setdefault(cur_res, set())

        for m in avail_models:

            try:
                # get neighbors
                tmp_id = struct[m][tmp_chain][int(tmp_res)].get_full_id()
                tmp_neighbors = set([(n[2], n[3][1]) for n in neighbors[tmp_id]])

                # get only neighbors that are significant and in the
                # same gene
                signif_neighbors = set([signif_struct_info[o]
                                        for o in (tmp_neighbors & possible_res)])
                signif_neighbors_gene = set([s for s in signif_neighbors
                                             if s[0] == cur_gene])

                # add result to the graph
                gene2graph[cur_gene][cur_res] = gene2graph[cur_gene][cur_res] | signif_neighbors_gene
            except KeyError:
                # skip deleted chains, or models without a chain
                # be careful this catches all keyerrors
                pass
    return gene2graph
コード例 #2
0
def update_graph(struct2graph, all_cogs, signif_struct_info, non_signif_struct_info, struct, radius):
    """Updates the residue neighbor graph based on the current structure.

    Residues are linked by edges if they are within the provided radius
    and are on the same gene.

    Parameters
    ----------
    gene2graph : dict
        dictionary with genes as keys pointing to significant hotspot residue
        neighbor graph
    signif_struct_info : dict
        identifies which residues are significant hotspots
    struct : Bio.PDB structure
        structure under consideration when populating the graph
    radius : float
        radius deemed close enough to add an edge between two residues

    Returns
    -------
    gene2graph : dict
        updated graph based on the provided structure
    """

    # get which residues are significant
    signif_pdb_pos = signif_struct_info.keys()
    non_signif_pdb_pos = non_signif_struct_info.keys()
    possible_signif_res = set(signif_pdb_pos)
    possible_non_signif_res = set(non_signif_pdb_pos)

    # find neighbor residues
    signif_cogs = {k: all_cogs[k] for k in all_cogs
           if (k[2], k[3][1]) in signif_pdb_pos}
    neighbors = pstruct.find_neighbors_1D(signif_cogs, radius)
    all_neighbors = pstruct.find_neighbors_for_1D(all_cogs, signif_cogs.keys(), radius)

    #struct_info = struct_chain[pdb_id]

    # add edge if residues are neighbors
    avail_models = [m.id for m in struct]
    signif_res_neighbors = {}
    for s in signif_pdb_pos:
        tmp_chain, tmp_res = s
        cur_res = signif_struct_info[s]
        cur_pdb = cur_res[0]

        # update struct2graph
        struct2graph.setdefault(cur_pdb, {})

        for m in avail_models:
            cur_res = (m, tmp_chain, int(tmp_res))
            struct2graph[cur_pdb].setdefault(cur_res, set())

            try:
                # get neighbors
                tmp_id = struct[m][tmp_chain][int(tmp_res)].get_full_id()
                tmp_neighbors = set([(n[2], n[3][1]) for n in neighbors[tmp_id]])
                all_tmp_neighbors = set([(n[2], n[3][1]) for n in all_neighbors[tmp_id]])

                signif_neighbors = set(tmp_neighbors & possible_signif_res)
                signif_neighbors_struct = set([(m, o[0], o[1]) for o in signif_neighbors])
                non_signif_neighbors = set(all_tmp_neighbors & possible_non_signif_res)
                non_signif_neighbors_struct = set([(m, o[0], o[1]) for o in non_signif_neighbors])

                signif_res_neighbors[cur_res] = non_signif_neighbors_struct
                # add result to the graphs

                struct2graph[cur_pdb][cur_res] = struct2graph[cur_pdb][cur_res] | signif_neighbors_struct
            except KeyError:
                # skip deleted chains, or models without a chain
                # be careful this catches all keyerrors
                print cur_pdb
                pass

    return struct2graph, signif_res_neighbors
コード例 #3
0
def update_graph(gene2graph, cog, signif_struct_info, struct, radius):
    """Updates the residue neighbor graph based on the current structure.

    Residues are linked by edges if they are within the provided radius
    and are on the same gene.

    Parameters
    ----------
    gene2graph : dict
        dictionary with genes as keys pointing to significant hotspot residue
        neighbor graph
    signif_struct_info : dict
        identifies which residues are significant hotspots
    struct : Bio.PDB structure
        structure under consideration when populating the graph
    radius : float
        radius deemed close enough to add an edge between two residues

    Returns
    -------
    gene2graph : dict
        updated graph based on the provided structure
    """
    # get which residues are significant
    signif_pdb_pos = signif_struct_info.keys()
    possible_res = set(signif_pdb_pos)

    # find neighbor residues
    cog = {k: cog[k] for k in cog if (k[2], k[3][1]) in signif_pdb_pos}
    neighbors = pstruct.find_neighbors_1D(cog, radius)

    #struct_info = struct_chain[pdb_id]

    # add edge if residues are neighbors
    avail_models = [m.id for m in struct]
    for s in signif_pdb_pos:
        tmp_chain, tmp_res = s
        cur_res = signif_struct_info[s]
        cur_gene = cur_res[0]

        # update gene2graph
        gene2graph.setdefault(cur_gene, {})
        gene2graph[cur_gene].setdefault(cur_res, set())

        for m in avail_models:

            try:
                # get neighbors
                tmp_id = struct[m][tmp_chain][int(tmp_res)].get_full_id()
                tmp_neighbors = set([(n[2], n[3][1])
                                     for n in neighbors[tmp_id]])

                # get only neighbors that are significant and in the
                # same gene
                signif_neighbors = set([
                    signif_struct_info[o]
                    for o in (tmp_neighbors & possible_res)
                ])
                signif_neighbors_gene = set(
                    [s for s in signif_neighbors if s[0] == cur_gene])

                # add result to the graph
                gene2graph[cur_gene][cur_res] = gene2graph[cur_gene][
                    cur_res] | signif_neighbors_gene
            except KeyError:
                # skip deleted chains, or models without a chain
                # be careful this catches all keyerrors
                pass
    return gene2graph