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Merge pull request #426 from ExcitedStates/new_qfit_ligand
New qfit ligand
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@@ -12,3 +12,4 @@ dependencies: | |
| - pyparsing>=2.2.0 | ||
| - cvxopt | ||
| - tqdm | ||
| - rdkit | ||
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@@ -3,3 +3,4 @@ cvxpy | |
| pyscipopt | ||
| scipy | ||
| scikit-learn | ||
| rdkit | ||
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| #!/bin/bash | ||
| # This script works with Phenix version 1.20. | ||
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| qfit_usage() { | ||
| echo >&2 "Usage:"; | ||
| echo >&2 " $0 mapfile.mtz [multiconformer_ligand_bound_with_protein.pdb] [multiconformer_ligand_only.pdb]"; | ||
| echo >&2 ""; | ||
| echo >&2 "mapfile.mtz, multiconformer_ligand_bound_with_protein.pdb, and multiconformer_ligand_only.pdb MUST exist in this directory."; | ||
| echo >&2 "Outputs will be written to mapfile_qFit.{pdb|mtz|log}."; | ||
| exit 1; | ||
| } | ||
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| #___________________________SOURCE__________________________________ | ||
| # Check that Phenix is loaded | ||
| if [ -z "${PHENIX}" ]; then | ||
| echo >&2 "I require PHENIX but it's not loaded."; | ||
| echo >&2 "Please \`source phenix_env.sh\` from where it is installed."; | ||
| exit 1; | ||
| else | ||
| export PHENIX_OVERWRITE_ALL=true; | ||
| fi | ||
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| # Check that qFit is loaded. | ||
| command -v remove_duplicates >/dev/null 2>&1 || { | ||
| echo >&2 "I require qFit (remove_duplicates) but it's not loaded."; | ||
| echo >&2 "Please activate the environment where qFit is installed."; | ||
| echo >&2 " e.g. conda activate qfit" | ||
| exit 1; | ||
| } | ||
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| # Assert required files exist | ||
| mapfile=$1 | ||
| multiconf=${2:-multiconformer_ligand_bound_with_protein.pdb} | ||
| multiconf_lig=${2:-multiconformer_ligand_only.pdb} | ||
| echo "mapfile : ${mapfile} $([[ -f ${mapfile} ]] || echo '[NOT FOUND]')"; | ||
| echo "qfit unrefined model : ${multiconf} $([[ -f ${multiconf} ]] || echo '[NOT FOUND]')"; | ||
| echo "qfit unrefined ligand model : ${multiconf_lig} $([[ -f ${multiconf_lig} ]] || echo '[NOT FOUND]')"; | ||
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| echo ""; | ||
| if [[ ! -f "${mapfile}" ]] || [[ ! -f "${multiconf}" ]]; then | ||
| qfit_usage; | ||
| fi | ||
| pdb_name="${mapfile%.mtz}" | ||
| echo >&2 "PDB name is "${pdb_name}". "; | ||
| echo "${pdb_name}" | ||
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| #__________________________________DETERMINE RESOLUTION AND (AN)ISOTROPIC REFINEMENT__________________________________ | ||
| mtzmetadata=`phenix.mtz.dump "${pdb_name}.mtz"` | ||
| resrange=`grep "Resolution range:" <<< "${mtzmetadata}"` | ||
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| echo "${resrange}" | ||
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| res=`echo "${resrange}" | cut -d " " -f 4 | cut -c 1-5` | ||
| res1000=`echo $res | awk '{tot = $1*1000}{print tot }'` | ||
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| if (( $res1000 < 1550 )); then | ||
| adp='adp.individual.anisotropic="not (water or element H)"' | ||
| else | ||
| adp='adp.individual.isotropic=all' | ||
| fi | ||
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| #__________________________________DETERMINE FOBS v IOBS v FP__________________________________ | ||
| # List of Fo types we will check for | ||
| obstypes=("FP" "FOBS" "F-obs" "I" "IOBS" "I-obs" "F(+)" "I(+)" "FSIM") | ||
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| # Get amplitude fields | ||
| ampfields=`grep -E "amplitude|intensity|F\(\+\)|I\(\+\)" <<< "${mtzmetadata}"` | ||
| ampfields=`echo "${ampfields}" | awk '{$1=$1};1' | cut -d " " -f 1` | ||
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| # Clear xray_data_labels variable | ||
| xray_data_labels="" | ||
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| # Is amplitude an Fo? | ||
| for field in ${ampfields}; do | ||
| # Check field in obstypes | ||
| if [[ " ${obstypes[*]} " =~ " ${field} " ]]; then | ||
| # Check SIGFo is in the mtz too! | ||
| if grep -F -q -w "SIG$field" <<< "${mtzmetadata}"; then | ||
| xray_data_labels="${field},SIG${field}"; | ||
| break | ||
| fi | ||
| fi | ||
| done | ||
| if [ -z "${xray_data_labels}" ]; then | ||
| echo >&2 "Could not determine Fo field name with corresponding SIGFo in .mtz."; | ||
| echo >&2 "Was not among "${obstypes[*]}". Please check .mtz file\!"; | ||
| exit 1; | ||
| else | ||
| echo "data labels: ${xray_data_labels}" | ||
| # Start writing refinement parameters into a parameter file | ||
| echo "refinement.input.xray_data.labels=$xray_data_labels" > ${pdb_name}_refine.params | ||
| fi | ||
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| #_____________________________DETERMINE R FREE FLAGS______________________________ | ||
| gen_Rfree=True | ||
| rfreetypes="FREE R-free-flags" | ||
| for field in ${rfreetypes}; do | ||
| if grep -F -q -w $field <<< "${mtzmetadata}"; then | ||
| gen_Rfree=False; | ||
| echo "Rfree column: ${field}"; | ||
| echo "refinement.input.xray_data.r_free_flags.label=${field}" >> ${pdb_name}_refine.params | ||
| break | ||
| fi | ||
| done | ||
| echo "refinement.input.xray_data.r_free_flags.generate=${gen_Rfree}" >> ${pdb_name}_refine.params | ||
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| #__________________________________REMOVE DUPLICATE HET ATOMS__________________________________ | ||
| remove_duplicates "${multiconf}" | ||
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| #__________________________________NORMALIZE OCCUPANCIES________________________________________ | ||
| echo "Normalizing occupancies, before refinement " | ||
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| redistribute_cull_low_occupancies -occ 0.09 "${multiconf}.fixed" | ||
| mv -v "${multiconf}.f_norm.pdb" "${multiconf}.fixed" | ||
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| #________________________________REMOVE TRAILING HYDROGENS___________________________________ | ||
| phenix.pdbtools remove="element H" "${multiconf}.fixed" | ||
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| #__________________________________GET CIF FILE__________________________________ | ||
| echo "Getting the cif file with ready_set/elbow" | ||
| phenix.ready_set hydrogens=false \ | ||
| trust_residue_code_is_chemical_components_code=true \ | ||
| pdb_file_name="${multiconf}.f_modified.pdb" | ||
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| # If ready_set doesn't generate a ligand cif file, use elbow | ||
| if [ ! -f "${multiconf}.f_modified.ligands.cif" ]; then | ||
| phenix.elbow multiconformer_ligand_only.pdb --output ${multiconf}.f_modified.ligands | ||
| fi | ||
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| if [ ! -f "${multiconf}.f_modified.ligands.cif" ]; then | ||
| echo "Ligand CIF generation failed" | ||
| fi | ||
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| #__________________________________FINAL REFINEMENT__________________________________ | ||
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| # Write refinement parameters into parameters file | ||
| echo "refinement.refine.strategy=*individual_sites *individual_adp *occupancies" >> ${pdb_name}_refine.params | ||
| echo "refinement.output.prefix=${pdb_name}" >> ${pdb_name}_refine.params | ||
| echo "refinement.output.serial=2" >> ${pdb_name}_refine.params | ||
| echo "refinement.main.number_of_macro_cycles=5" >> ${pdb_name}_refine.params | ||
| echo "refinement.main.nqh_flips=True" >> ${pdb_name}_refine.params | ||
| echo "refinement.refine.${adp}" >> ${pdb_name}_refine.params | ||
| echo "refinement.output.write_maps=False" >> ${pdb_name}_refine.params | ||
| echo "refinement.hydrogens.refine=riding" >> ${pdb_name}_refine.params | ||
| echo "refinement.main.ordered_solvent=True" >> ${pdb_name}_refine.params | ||
| echo "refinement.target_weights.optimize_xyz_weight=true" >> ${pdb_name}_refine.params | ||
| echo "refinement.target_weights.optimize_adp_weight=true" >> ${pdb_name}_refine.params | ||
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| echo "refinement.input.monomers.file_name='${multiconf}.f_modified.ligands.cif'" >> ${pdb_name}_refine.params | ||
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| phenix.refine "${multiconf}.f_modified.pdb" \ | ||
| "${pdb_name}.mtz" \ | ||
| "${pdb_name}_refine.params" \ | ||
| --overwrite | ||
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| #__________________________________NAME FINAL FILES__________________________________ | ||
| cp -v "${pdb_name}_002.pdb" "${pdb_name}_qFit_ligand.pdb" | ||
| cp -v "${pdb_name}_002.mtz" "${pdb_name}_qFit_ligand.mtz" | ||
| cp -v "${pdb_name}_002.log" "${pdb_name}_qFit_ligand.log" | ||
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| #__________________________COMMENTARY FOR USER_______________________________________ | ||
| if [ -f "${pdb_name}_002.pdb" ]; then | ||
| echo "" | ||
| echo "[qfit_final_refine_ligand] Refinement is complete." | ||
| echo " Please be sure to INSPECT your refined structure, especially all new altconfs." | ||
| echo " The output can be found at ${pdb_name}_qFit_ligand.(pdb|mtz|log) ." | ||
| else | ||
| echo "Refinement did not complete." | ||
| echo "Please check for failure reports by examining log files." | ||
| fi |
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