diff options
Diffstat (limited to 'plip/basic/remote.py')
| -rw-r--r-- | plip/basic/remote.py | 95 |
1 files changed, 0 insertions, 95 deletions
diff --git a/plip/basic/remote.py b/plip/basic/remote.py deleted file mode 100644 index 0c67f6f..0000000 --- a/plip/basic/remote.py +++ /dev/null @@ -1,95 +0,0 @@ -from collections import namedtuple - -hbonds_info = namedtuple('hbonds_info', 'ldon_id lig_don_id prot_acc_id pdon_id prot_don_id lig_acc_id') -hydrophobic_info = namedtuple('hydrophobic_info', 'bs_ids lig_ids pairs_ids') -halogen_info = namedtuple('halogen_info', 'don_id acc_id') -pistack_info = namedtuple('pistack_info', 'proteinring_atoms, proteinring_center ligandring_atoms ' - 'ligandring_center type') -pication_info = namedtuple('pication_info', 'ring_center charge_center ring_atoms charge_atoms, protcharged') -sbridge_info = namedtuple('sbridge_info', 'positive_atoms negative_atoms positive_center negative_center protispos') -wbridge_info = namedtuple('wbridge_info', 'don_id acc_id water_id protisdon') -metal_info = namedtuple('metal_info', 'metal_id, target_id location') - - -class VisualizerData: - """Contains all information on a complex relevant for visualization. Can be pickled""" - - def __init__(self, mol, site): - pcomp = mol - pli = mol.interaction_sets[site] - ligand = pli.ligand - - # General Information - self.lig_members = sorted(pli.ligand.members) - self.sourcefile = pcomp.sourcefiles['pdbcomplex'] - self.corrected_pdb = pcomp.corrected_pdb - self.pdbid = mol.pymol_name - self.hetid = ligand.hetid - self.ligandtype = ligand.type - self.chain = ligand.chain if not ligand.chain == "0" else "" # #@todo Fix this - self.position = str(ligand.position) - self.uid = ":".join([self.hetid, self.chain, self.position]) - self.outpath = mol.output_path - self.metal_ids = [x.m_orig_idx for x in pli.ligand.metals] - self.unpaired_hba_idx = pli.unpaired_hba_orig_idx - self.unpaired_hbd_idx = pli.unpaired_hbd_orig_idx - self.unpaired_hal_idx = pli.unpaired_hal_orig_idx - - # Information on Interactions - - # Hydrophobic Contacts - # Contains IDs of contributing binding site, ligand atoms and the pairings - hydroph_pairs_id = [(h.bsatom_orig_idx, h.ligatom_orig_idx) for h in pli.hydrophobic_contacts] - self.hydrophobic_contacts = hydrophobic_info(bs_ids=[hp[0] for hp in hydroph_pairs_id], - lig_ids=[hp[1] for hp in hydroph_pairs_id], - pairs_ids=hydroph_pairs_id) - - # Hydrogen Bonds - # #@todo Don't use indices, simplify this code here - hbonds_ldon, hbonds_pdon = pli.hbonds_ldon, pli.hbonds_pdon - hbonds_ldon_id = [(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_ldon] - hbonds_pdon_id = [(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_pdon] - self.hbonds = hbonds_info(ldon_id=[(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_ldon], - lig_don_id=[hb[1] for hb in hbonds_ldon_id], - prot_acc_id=[hb[0] for hb in hbonds_ldon_id], - pdon_id=[(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_pdon], - prot_don_id=[hb[1] for hb in hbonds_pdon_id], - lig_acc_id=[hb[0] for hb in hbonds_pdon_id]) - - # Halogen Bonds - self.halogen_bonds = [halogen_info(don_id=h.don_orig_idx, acc_id=h.acc_orig_idx) - for h in pli.halogen_bonds] - - # Pistacking - self.pistacking = [pistack_info(proteinring_atoms=pistack.proteinring.atoms_orig_idx, - proteinring_center=pistack.proteinring.center, - ligandring_atoms=pistack.ligandring.atoms_orig_idx, - ligandring_center=pistack.ligandring.center, - type=pistack.type) for pistack in pli.pistacking] - - # Pi-cation interactions - self.pication = [pication_info(ring_center=picat.ring.center, - charge_center=picat.charge.center, - ring_atoms=picat.ring.atoms_orig_idx, - charge_atoms=picat.charge.atoms_orig_idx, - protcharged=picat.protcharged) - for picat in pli.pication_paro + pli.pication_laro] - - # Salt Bridges - self.saltbridges = [sbridge_info(positive_atoms=sbridge.positive.atoms_orig_idx, - negative_atoms=sbridge.negative.atoms_orig_idx, - positive_center=sbridge.positive.center, - negative_center=sbridge.negative.center, - protispos=sbridge.protispos) - for sbridge in pli.saltbridge_lneg + pli.saltbridge_pneg] - - # Water Bridgese('wbridge_info', 'don_id acc_id water_id protisdon') - self.waterbridges = [wbridge_info(don_id=wbridge.d_orig_idx, - acc_id=wbridge.a_orig_idx, - water_id=wbridge.water_orig_idx, - protisdon=wbridge.protisdon) for wbridge in pli.water_bridges] - - # Metal Complexes - self.metal_complexes = [metal_info(metal_id=metalc.metal_orig_idx, - target_id=metalc.target_orig_idx, - location=metalc.location) for metalc in pli.metal_complexes] |