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Extract ligands from original PDB file
This project forked from realbigws/lig_tool
Extract ligands from original PDB file
================= LIG_Tool (v1.03) date: 2019.09.01 ================= Title: LIG_Tool: a tool to extract ligands in PDB file Author: Sheng Wang Contact email: [email protected] -------------------------------------------------------- ======== Install: ======== 1. download the package git clone https://github.com/realbigws/LIG_Tool cd LIG_Tool/ -------------- 2. compile cd source_code/ make cd ../ -------------- 3. update the package git pull -------------- 4. update the ligand library ./update_Ligand_Utility.sh ====== Usage: ====== ========================================================| LIG_Tool (version 1.03) [2019.09.01] | Extract ligands and chains from official PDB file | Usage: ./LIG_Tool <-i input_pdb> [-o out_name] | [-p chain_out_root] [-q ligand_out_root] | [-n length_cut] [-d distance_cut] [-l log] | [-O PC_out] [-T PC_type] [-t LG_type] | --------------------------------------------------------| -i input_pdb : input original PDB file, e.g., 1col.pdb | -o out_name : output file name. [default: input_name] | -p chain_out_root : chain output root [default: ./ ] | -q ligand_out_root: ligand output root [default: ./ ] | -n length_cut : chain length cutoff [default: 25 ] | -d distance_cut : ligand distance cutoff [default: 4.0] | -l log : output log files (1) or not (0) [default: 0] | -O PC_root : binding residues in PC [default:null] | -T PC_type : CA+CB (-1), backbone+CB [0], full atom (1) | -t LG_type : select ligand type. [ default: 'IOPNX'] | ========================================================| ================ Running example: ================ 1. output ligand ./LIG_Tool -i examples/1paz.pdb ---------------------------------- 2. output binding information ./LIG_Tool -i examples/1paz.pdb -l 1 ---------------------------------- 3. output ligand to point-cloud (PC) ./LIG_Tool -i examples/1paz.pdb -O ./ ---------------------------------- 4. generate scPDB-like result ./LIG_Tool -i examples/10mh.pdb -l 1 -d 6.5 -O ./ -T 1 -t 'OPX' ---------------------------------- 5. filter a given ligand ./LIG_Tool -i examples/1paz.pdb -l 1 -f examples/filt ---------------------------------- 6. point-cloud form with ligand label #-> dump ligands ./LIG_Tool -i examples/1paz.pdb -l 1 #-> label point-cloud at ligand-level util/PDB_To_XYZ -i 1pazA.pdb -o 1pazA.xyz -a 1 util/PDB_To_XYZ -i 1paz_CU__0___.pdb -o 1paz_CU__0___.xyz -f 1 util/XYZ_ContResi 1pazA.xyz 1paz_CU__0___.xyz 6.5 1pazA.pc_xyz 1 or, use the util/multi_ligand_dump_chain.sh script #-> alternative approach echo "1pazA" > proc_list util/multi_ligand_dump_chain.sh -i proc_list -o out_root -r ./ -d 6.5 The two files 'out_root/1pazA_atom.xyz' and '1pazA.pc_xyz' shall be the same. Additionaly, we may also keep the additional info in the original point-cloud file: #-> dump ligands in original point-cloud file ./LIG_Tool -i examples/1paz.pdb -l 1 -O ./ -T 1 #-> label point-cloud at ligand-level util/PDB_To_XYZ -i 1paz_CU__0___.pdb -o 1paz_CU__0___.xyz -f 1 util/XYZ_ContResi 1pazA.pc_xyz 1paz_CU__0___.xyz 4.0 1pazA.pcl_xyz 1 ---------------------------------- 7. conversion between PDB and XYZ ./LIG_Tool -i examples/1paz.pdb util/PDB_To_XYZ -i 1pazA.pdb -o 1pazA.xyz -a 1 util/XYZ_To_PDB -i 1pazA.xyz -o 1pazA.pdb_pc -b 7 The two files '1pazA.pdb' and '1pazA.pdb_pc' shall be the same. ---------------------------------- 8. generate residual/atom-level features (according to P2Rank) ./LIG_Tool -i examples/1paz.pdb -l 1 -O ./ -T 1 util/XYZ_Gen_Feature 1pazA.pc_xyz 1pazA.pc_xyz_feat 10 1
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