p4ward.tools.classes#

class p4ward.tools.classes.Cluster(clusterer, type)#

Bases: object

attributes added/modified by the functions:

get_all_confs()#
get_centroid(cln)#
get_cl_from_pose(pose_obj)#
get_cl_size(cln)#
class p4ward.tools.classes.LinkerConf(parent, conf_number)#

Bases: object

attributes added/modified by the functions:

linker_sampling.rdkit_sampling() linker_sampling.capture_dock6_scores() linker_sampling.detect_clashes()

  • self.active

linker_scoring.capture_rxdock_scores()

  • self.rx_score

protac_scoring.get_unbound_rmsd()

  • self.unbound_stats

class p4ward.tools.classes.Protac(smiles, name, number)#

Bases: object

Represents a PLV. Each protac smiles code from the input file becomes a Protac obj.

attributes added/modified by the functions:
linker_sampling.rdkit_sampling()

  • self.indices_ligs

  • self.indices_link

structure_tools.get_protac_dist_cuttoff()

  • self.dist_cutoff

self.sample_unbound_confs()

  • self.unbound_confs

  • self.unbound_energy

active_poses()#
get_pose(pose_obj)#
sample_unbound_confs(num_unbound_confs=100)#
write_unbound_confs(num_unbound_confs=100, filename='unbound_protac.sdf')#
class p4ward.tools.classes.ProtacPose(parent, protein_parent)#

Bases: object

attributes added/modified by the functions:
linker_sampling.rdkit_sampling()

  • self.active

  • self.file

linker_scoring.rxdock_rescore()

  • self.scored_file

rank.rescore()

  • self.rescore

active_confs()#
class p4ward.tools.classes.Protein(ptn_type, file, lig_file)#

Bases: object

Represent the main receptor target protein or the main ligase protein.

active_confs()#

Out of all the poses, return only the active ones

get_ligand_struct()#

Use the function load_biopython_structures to get the biopython object for the protein ligand.

get_protein_struct(struct_attr='active_file')#

Use the function load_biopython_structures to get the biopython object for the protein.

get_triad_points()#

Get the three points to represent the protein for clustering

class p4ward.tools.classes.ProteinPose(parent, pose_number)#

Bases: object

Represent a (docked) pose of the ligase protein.

get_rotated_struct(struct_type, struct_attr='active_file')#

Use the rotate_atoms function to return a completely rotated coordinate set for the protein pose.

top_protac(protac_obj)#