Compute the fractional overlap of sel1 respective to sel2.
FO = Nc/Nt Nc is the number of atoms of sel1 in contact with sel2. Nt is the number of atoms of sel1. Hydrogen atoms are ignored. If the contact radius is 0 then the VdW radii will be used. The states are for select a single state from a multi-state objects. OPTIONS: sel1 ligand object. sel2 hotspot object. radius the radius so two atoms are in contact (default: 2). state1 state of sel1. state2 state of sel2. EXAMPLES: fo ref_lig, ftmap1234.D.003 fo ref_lig, ftmap1234.CS.000_016
Bind site identity analysis.
Compute the coefficient between aminoacids ids nearby two selections. OPTIONS sel1 Selection or object 1. sel2 Selection or object 2. polymer1 protein of sel1. polymer2 protein of sel2. radius Radius to look for nearby aminoacids. method 'overlap' or 'sorensen–dice' EXAMPLES nearby_aminoacids_similarity *CS.000_*, *CS.002_*, radius=4 nearby_aminoacids_similarity *D.001*, *D.002*, polymer1='obj1', polymer2='obj2' nearby_aminoacids_similarity 6y84.Bs.001, 6y84.B.004, method=sorensen-dice
Fetch similar structures using the 3D-Shape algorithm.
https://search.rcsb.org/ OPTIONS: pdb_id Reference PDB id. min_similarity 3D-Shape score threshold. max_resolution Fetch only structures up to such resolution. ligand Refrence ligand PDB id for apo evaluation. dist Distance cut-off around reference ligand for apo evaluation. Only used when ligand is given. compounds Selection that shold be considered ligands upon apo evaluation. Only used when ligand is given. prosthetic_groups List of ligands to be ignored when evaluating apo. EXAMPLES: fetch_similar_shape3d 2XY9 SEE ALSO: fetch_similar_blast
The cluster database needs to be updated before the first use of the
fetch_similar_blast feature. The database ftp://resources.rcsb.org/sequence/clusters/ is updated weekly, for new data is prudent to run this command weekly.
Fetch sequence similar structures from RCSB PDB and optionally keep only
apo structures. Apo are evaluated respective to a choosen ligand on the reference chain. On the first use update the database with the command `update_cluster_data`. Update the database weekly. OPTIONS chain_id Reference structure chain id. similarity Sequence similarity threshold (one of the available from RCSB PDB). ligand Reference ligand PDB id. dist Distance cut-off around reference ligand for apo evaluation. compounds Selection that should be considered ligands upon apo computation. Only used when ligand is given. prothestic_groups List of ligands to be ignored when evaluating apo. max_resolution Fetch only X-ray structures with up to such resolution. max_structures Fetch at most n structures. 0 for all structures. EXAMPLES fetch_similar_blast 2XY9_A, 100 fetch_similar_blast 2XY9_A, 95, 3ES, 3, organic fetch_similar_blast 6Y2F_A, max_structures=0 SEE ALSO update_cluster_data fetch_similar_shape3d
Load a FTMap PDB file and classify hotspot ensembles in accordance to
Kozakov et al. (2015). https://doi.org/10.1021/acs.jmedchem.5b00586 OPTIONS path PDB file path, glob or server result id. group optional group name to put objects in. max_cs the maximum number of consensus sites to consider. plot plot similarity matrix. plot_annot remove numbers on similarity matrix. plot_class filter to show only a specific hotspot class. plot_method see `help nearby_aminoacids_similarity`. EXAMPLES load_ftmap fftmap.1234.pdb load_ftmap fftmap.1111.pdb, fftmap.2222.pdb, group=GRP, max_cs=4 load_ftmap fftmap_*.pdb, plot_annot=0, plot_class=D
Calculate a hotspot following Kozakov et al (2015).
USAGE calculate_kozakov2015 sel1, ... EXAMPLES calculate_kozakov2015 *CS.000_*, *CS.002_* calculate_kozakov2015 *.000_*, *.001_*