chainmapper 1.0.2

Tool to map chains of two structures

ChainMapper

Install

pip install chainmapper

Usage

Run simple mapping on samples

chainmapper \
      -r samples/sample1.pdb \
      -q samples/sample2.pdb \
      -o results \
      --n_outputs 1 \
      --unique \
      --verbose

Modules

Reduction Modules: Clustering-based or Heuristic:

Module Name	Id	Method	Description
Sequence Clustering	S	Clustering	Chain sequences are aligned and cluster according to identity score
Minimal Distance Clustering	M	Clustering	Minimal distance vector of the chains are compared using RMSE
Barycentre Distance Clustering	B	Clustering	Barycentre distance vector of the chains are compared using RMSE
Conformation Clustering	C	Clustering	Chain are clustered according to their conformation (chain-chain RMSD)
Pivot	P	Clustering with constraints	One chain of each model is used as pivot to guide minimal distance clustering. Multiple pivots are tested. This module should be used after other clustering modules. If it does not fall below the enumeration threshold, it has no impact on the clustering.
Simulated Annealing	A	Heuristic	Fall back module used to force finding a mapping using simulated annealing search. Need to be used at the end of the module sequence.

Scoring modules:

Module Name	Id	Description
Root Mean Square Deviation (RMSD)	R	RMSD computed on$C_\alpha$ of all residues after alignment.
RMSD on chain PCA points	r	Fast RMSD used in simulated annealing or to fliter out off mappings.

Input arguments, options and flags

Name	Required	Default	Description
Arguments
-r, --ref_file_path	✔️		Path to reference PDB file (mmCIF allowed)
-q, --query_file_path	✔️		Path to query PDB file (mmCIF allowed)
-o, --out_path	✔️		Path of output folder.
Options
-m, --modules		SMBPAR	Modules to launch in order.
--ignore_chains_ref		""	Chains to ignore in the reference structure.
--ignore_chains_query		""	Chains to ignore in the query structure.
-e --max_enum		1000	Maximum number of mappings to enumerate.
--n_siman		1	Number of simulated annealing runs.
--clustering_threshold		0	Minimum threshold for clustering (escept S).
--sequence_clustering_threshold		0.3	Threshold used for sequence clustering.
--ref_name		file_name	Name of the reference structure.
--query_name		file_name	Name of the query structure.
--n_outputs		1	Maximum number of mapped files to return.
--n_print_score		5	Number of final scores to print.
Option flags
--fitted_output			Output the model aligned on ref.
--no_change_chain_ids			Disable the replacement of chain ids in the output file by the respective ids in the ref file.
--no_change_chain_order			Disable the change of chain order in the output file according ot the ref file.
--unique			Enable to have unique ids in the output file names.
--all			Enable to save all mappings scored in csv file.
--stats			Enable to save stats like time and number of mappings in a csv file.
--verbose			Enable logs during processing.