KarrLab/wc_rules

from ..schema.molecules import *
from ..schema.sites import *
from wc_rules.modeling.pattern import GraphContainer

def build_ligand(n_fc=2):
    assert n_fc in [1,2]
    if n_fc == 2:
        classes = [Ligand,FcBind,FcBind]
        names = 'ligand fc_1 fc_2'.split()
        edges = [x.split() for x in ['ligand sites fc_1', 'ligand sites fc_2']]
    elif n_fc == 1:
        classes = [Ligand,FcBind]
        names = 'ligand fc'.split()
        edges = ['ligand sites fc'.split()]
    return GraphContainer.initialize_from(classes,names,edges)

def build_receptor(contents=['alpha', 'beta', 'gamma']):
    classes, names, edges = [Receptor], ['receptor'], []
    if 'alpha' in contents:
        classes.append(Alpha)
        names.append('alpha')
        edges.append('receptor sites alpha'.split())
    if 'beta' in contents:
        classes.append(Beta)
        names.append('beta')
        edges.append('receptor sites beta'.split())
    if 'gamma'  in contents:
        classes.append(Gamma)
        names.append('gamma')
        edges.append('receptor sites gamma'.split())
    return GraphContainer.initialize_from(classes,names,edges)

def build_Lyn():
    return GraphContainer.initialize_from([Lyn, SH2],['lyn','sh2'],['lyn sites sh2'.split()])

def build_Syk(contents=['tsh2','linker','aloop']):
    classes, names, edges = [Syk], ['syk'], []
    if 'tsh2' in contents:
        classes.append(TandemSH2)
        names.append('tsh2')
        edges.append('syk sites tsh2'.split())
    if 'linker' in contents:
        classes.append(LinkerRegion)
        names.append('linker')
        edges.append('syk sites linker'.split())
    if 'aloop' in contents:
        classes.append(ActivationLoop)
        names.append('aloop')
        edges.append('syk sites aloop'.split())
    return GraphContainer.initialize_from(classes,names,edges)

def recruit_to_receptor(gReceptor,gRecruit):
    if 'lyn' in gRecruit._dict:
        gReceptor['beta'].bond = gRecruit['sh2']
    if 'syk' in gRecruit._dict:
        gReceptor['gamma'].bond = gRecruit['tsh2']
    return gReceptor + gRecruit

def recruit_to_ligand(n_fc,g1,g2=None):
    g = build_ligand(n_fc)
    if n_fc==1:
        assert g2 is None
        g['fc'].bond = g1['alpha']
    if n_fc==2:
        g1 = g1.add_suffix('1')
        g['fc_1'].bond = g1['alpha_1']
        if g2:
            g2 = g2.add_suffix('2')
            g['fc_2'].bond = g2['alpha_2']
    return GraphContainer(g['ligand'].get_connected())

def add_phosphosite_to_molecule(g,molname):
    g[molname].sites.add(PhosphoSite('phosphosite'))
    return GraphContainer(g[molname].get_connected())