diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures index 04958cf84c4d0d95e9894b05d7c9dad0d34ab316..d4d04f94cb036ad58a6e64cd0371f7b6d53bcf0f 100644 --- a/actions/ost-compare-structures +++ b/actions/ost-compare-structures @@ -2,7 +2,64 @@ eg. -ost compare-structures -m 3ia3.pdb -r 3ia3.pdb -o output.json -l -sc -cc -ml -rm oxt hyd -mn + ost compare-structures \ + -m <MODEL> \ + -r <REF> \ + -o output.json \ + -l \ + -sc \ + -cc \ + -ml \ + -rm oxt hyd \ + -mn + +CAMEO calls lddt binary as follows: + + lddt \ + -p <PARAMETER FILE> \ + -f \ + -a 15 \ + -b 15 \ + -r 15 \ + <MODEL> \ + <REF> + +Only model structures are "Molck-ed" in CAMEO. The call to molck is as follows: + + molck \ + --complib=<COMPOUND LIB> \ + --rm=hyd,oxt,unk \ + --fix-ele \ + --map-nonstd <FILEPATH> \ + --out=<OUTPUT> + +To be as much compatible with with CAMEO as possible one should call +compare-structures as follows: + + ost compare-structures \ + # General parameters + #################### + --model <MODEL> \ + --reference <REF> \ + --output output.json \ + # QS-score parameters + ##################### + --qs-score \ + --residue-number-alignment \ + # lDDT parameters + ################# + --lddt \ + --structural-checks \ + --consistency-checks \ + --inclusion-radius 15.0 \ + --bond-tolerance 15.0 \ + --angle-tolerance 15.0 \ + # Molck parameters + ################## + --molck \ + --remove oxt hyd unk \ + --clean-element-column \ + --map-nonstandard-residues """ import os