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Pedro Lacerda edited this page Feb 23, 2021 · 4 revisions

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Command list

fo

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

fo2

Compute the fractional overlap.


SEE:
    fo

fetch_similar_shape3d

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

fetch_similar_blast_update

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_similar_blast

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_ftmap

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

load_atlas

Load an Atlas PDB file. See `help load_ftmap`.

kozakov2015

Calculate a hotspot following Kozakov et al (2015).


USAGE
    calculate_kozakov2015 sel1, ...

EXAMPLES
    calculate_kozakov2015 *CS.000_*, *CS.002_*
    calculate_kozakov2015 *.000_*, *.001_*
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