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spack/var/spack/repos/builtin/packages/improved-rdock/rdock_python3.patch
otsukay d9f49d7415
add recipe for improved-rdock (#31158) 
* add recipe for improved-rdock

* style: fix format

* style: fix format again

* Fix location of the directory

* Fix copyright

* Fix according to the reviewer's comments.

* Revert "Fix according to the reviewer's comments."

This reverts commit 4877877daf.

* Fix according to the reviewer's comments.

* style: fix format

* Update var/spack/repos/builtin/packages/improved-rdock/package.py

Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>

Co-authored-by: Yuichi Otsuka <otsukay@riken.jp>
Co-authored-by: Tamara Dahlgren <35777542+tldahlgren@users.noreply.github.com>
2022-07-06 09:25:45 -07:00

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diff -u -r -N a/bin/sdrmsd b/bin/sdrmsd
--- a/bin/sdrmsd 2020-10-15 13:34:27.000000000 +0900
+++ b/bin/sdrmsd 2020-10-19 09:21:43.000000000 +0900
@@ -11,7 +11,7 @@
# Date: 08-11-2013
import math
-import pybel
+from openbabel import pybel
import numpy as npy
import optparse
@@ -103,24 +103,24 @@
return mappingpose[0]
def parseArguments():
- optparse.OptionParser.format_epilog = lambda self, formatter: self.epilog
- epilog = """Args:
- reference.sdf SDF file with the reference molecule.
- input.sdf SDF file with the molecules to be compared to reference.\n"""
- parser = optparse.OptionParser("usage: %prog [options] reference.sdf input.sdf", epilog=epilog)
- parser.add_option("-f", "--fit",dest="fit", action="store_true", default=False,
+ optparse.OptionParser.format_epilog = lambda self, formatter: self.epilog
+ epilog = """Args:
+ reference.sdf SDF file with the reference molecule.
+ input.sdf SDF file with the molecules to be compared to reference.\n"""
+ parser = optparse.OptionParser("usage: %prog [options] reference.sdf input.sdf", epilog=epilog)
+ parser.add_option("-f", "--fit",dest="fit", action="store_true", default=False,
help="Superpose molecules before RMSD calculation")
- parser.add_option("--threshold","-t",dest="threshold", action="store", nargs=1,
+ parser.add_option("--threshold","-t",dest="threshold", action="store", nargs=1,
help="Discard poses with RMSD < THRESHOLD with respect previous poses which where not rejected based on same principle. A Population SDField will be added to output SD with the population number.", type=float)
- parser.add_option("-o","--out", dest="outfilename", metavar="FILE", default=False,
+ parser.add_option("-o","--out", dest="outfilename", metavar="FILE", default=False,
help="If declared, write an output SDF file with the input molecules with a new sdfield <RMSD>. If molecule was fitted, the fitted molecule coordinates will be saved.")
- (options, args) = parser.parse_args()
-
- #Check we have two arguments
- if len(args) < 2:
- parser.error("Incorrect number of arguments. Use -h or --help options to print help.")
+ (options, args) = parser.parse_args()
+
+ #Check we have two arguments
+ if len(args) < 2:
+ parser.error("Incorrect number of arguments. Use -h or --help options to print help.")
- return options, args
+ return options, args
def updateCoords(obmol, newcoords):
"Update OBMol coordinates. newcoords is a numpy array"
@@ -133,8 +133,8 @@
for correct RMSD comparison. Only the lowest RMSD will be returned.
Returns:
- If fit=False: bestRMSD (float) RMSD of the best matching mapping.
- If fit=True: (bestRMSD, molecCoordinates) (float, npy.array) RMSD of best match and its molecule fitted coordinates.
+ If fit=False: bestRMSD (float) RMSD of the best matching mapping.
+ If fit=True: (bestRMSD, molecCoordinates) (float, npy.array) RMSD of best match and its molecule fitted coordinates.
"""
mappings = pybel.ob.vvpairUIntUInt()
bitvec = pybel.ob.OBBitVec()
@@ -148,18 +148,18 @@
posecoords = npy.array([atom.coords for atom in molec])[mappose]
resultrmsd = 999999999999
for mapping in mappings:
- automorph_coords = [None] * len(targetcoords)
- for x, y in mapping:
- automorph_coords[lookup.index(x)] = targetcoords[lookup.index(y)]
- mapping_rmsd = rmsd(posecoords, automorph_coords)
- if mapping_rmsd < resultrmsd:
- resultrmsd = mapping_rmsd
- fitted_result = False
- if fit:
- fitted_pose, fitted_rmsd = superpose3D(npy.array(automorph_coords), npy.array(posecoords))
- if fitted_rmsd < resultrmsd:
- resultrmsd = fitted_rmsd
- fitted_result = fitted_pose
+ automorph_coords = [None] * len(targetcoords)
+ for x, y in mapping:
+ automorph_coords[lookup.index(x)] = targetcoords[lookup.index(y)]
+ mapping_rmsd = rmsd(posecoords, automorph_coords)
+ if mapping_rmsd < resultrmsd:
+ resultrmsd = mapping_rmsd
+ fitted_result = False
+ if fit:
+ fitted_pose, fitted_rmsd = superpose3D(npy.array(automorph_coords), npy.array(posecoords))
+ if fitted_rmsd < resultrmsd:
+ resultrmsd = fitted_rmsd
+ fitted_result = fitted_pose
if fit:
return (resultrmsd, fitted_pose)
@@ -167,16 +167,16 @@
return resultrmsd
def saveMolecWithRMSD(outsdf, molec, rmsd, population=False):
- newData = pybel.ob.OBPairData()
+ newData = pybel.ob.OBPairData()
newData.SetAttribute("RMSD")
newData.SetValue('%.3f'%rmsd)
if population:
- popData = pybel.ob.OBPairData()
- popData.SetAttribute("Population")
- popData.SetValue('%i'%population)
- molec.OBMol.CloneData(popData)
-
+ popData = pybel.ob.OBPairData()
+ popData.SetAttribute("Population")
+ popData.SetValue('%i'%population)
+ molec.OBMol.CloneData(popData)
+
molec.OBMol.CloneData(newData) # Add new data
outsdf.write(molec)
@@ -184,13 +184,13 @@
import sys, os
(opts, args) = parseArguments()
-
+
xtal = args[0]
poses = args[1]
if not os.path.exists(xtal) or not os.path.exists(poses):
- sys.exit("Input files not found. Please check the path given is correct.")
-
+ sys.exit("Input files not found. Please check the path given is correct.")
+
fit = opts.fit
outfname = opts.outfilename
threshold = opts.threshold
@@ -202,71 +202,71 @@
#If outfname is defined, prepare an output SDF sink to write molecules
if outfname:
- outsdf = pybel.Outputfile('sdf', outfname, overwrite=True)
+ outsdf = pybel.Outputfile('sdf', outfname, overwrite=True)
# Find the RMSD between the crystal pose and each docked pose
dockedposes = pybel.readfile("sdf", poses)
- if fit: print "POSE\tRMSD_FIT"
- else: print "POSE\tRMSD_NOFIT"
+ if fit: print ("POSE\tRMSD_FIT")
+ else: print ("POSE\tRMSD_NOFIT")
skipped = []
- moleclist = {} # Save all poses with their dockid
- population = {} # Poses to be written
+ moleclist = {} # Save all poses with their dockid
+ population = {} # Poses to be written
outlist = {}
for docki, dockedpose in enumerate(dockedposes):
dockedpose.removeh()
- natoms = len(dockedpose.atoms)
- if natoms != crystalnumatoms:
- skipped.append(docki+1)
- continue
- if fit:
- resultrmsd, fitted_result = getAutomorphRMSD(crystal, dockedpose, fit=True)
- updateCoords(dockedpose, fitted_result)
- else:
- resultrmsd = getAutomorphRMSD(crystal, dockedpose, fit=False)
-
- if threshold:
- # Calculate RMSD between all previous poses
- # Discard if rmsd < FILTER threshold
- if moleclist:
- match = None
- bestmatchrmsd = 999999
- for did,prevmol in moleclist.iteritems():
- tmprmsd = getAutomorphRMSD(prevmol, dockedpose)
- if tmprmsd < threshold:
- if tmprmsd < bestmatchrmsd:
- bestmatchrmsd = tmprmsd
- match = did
-
- if match != None:
- # Do not write this one
- # sum one up to the matching previous molecule id
- print >> sys.stderr, "Pose %i matches pose %i with %.3f RMSD"%(docki+1, match+1, bestmatchrmsd)
- population[match] += 1
- else:
- # There's no match. Print info for this one and write to outsdf if needed
- # Save this one!
- if outfname: outlist[docki] = (dockedpose, resultrmsd)
- print "%d\t%.2f"%((docki+1),resultrmsd)
- moleclist[docki] = dockedpose
- population[docki] = 1
- else:
- # First molecule in list. Append for sure
- moleclist[docki] = dockedpose
- population[docki] = 1
- if outfname: outlist[docki] = (dockedpose, resultrmsd)
- else:
- # Just write best rmsd found and the molecule to outsdf if demanded
- if outfname: saveMolecWithRMSD(outsdf, dockedpose, resultrmsd)
- print "%d\t%.2f"%((docki+1),resultrmsd)
+ natoms = len(dockedpose.atoms)
+ if natoms != crystalnumatoms:
+ skipped.append(docki+1)
+ continue
+ if fit:
+ resultrmsd, fitted_result = getAutomorphRMSD(crystal, dockedpose, fit=True)
+ updateCoords(dockedpose, fitted_result)
+ else:
+ resultrmsd = getAutomorphRMSD(crystal, dockedpose, fit=False)
+
+ if threshold:
+ # Calculate RMSD between all previous poses
+ # Discard if rmsd < FILTER threshold
+ if moleclist:
+ match = None
+ bestmatchrmsd = 999999
+ for did,prevmol in moleclist.iteritems():
+ tmprmsd = getAutomorphRMSD(prevmol, dockedpose)
+ if tmprmsd < threshold:
+ if tmprmsd < bestmatchrmsd:
+ bestmatchrmsd = tmprmsd
+ match = did
+
+ if match != None:
+ # Do not write this one
+ # sum one up to the matching previous molecule id
+ print >> sys.stderr, "Pose %i matches pose %i with %.3f RMSD"%(docki+1, match+1, bestmatchrmsd)
+ population[match] += 1
+ else:
+ # There's no match. Print info for this one and write to outsdf if needed
+ # Save this one!
+ if outfname: outlist[docki] = (dockedpose, resultrmsd)
+ print ("%d\t%.2f"%((docki+1),resultrmsd))
+ moleclist[docki] = dockedpose
+ population[docki] = 1
+ else:
+ # First molecule in list. Append for sure
+ moleclist[docki] = dockedpose
+ population[docki] = 1
+ if outfname: outlist[docki] = (dockedpose, resultrmsd)
+ else:
+ # Just write best rmsd found and the molecule to outsdf if demanded
+ if outfname: saveMolecWithRMSD(outsdf, dockedpose, resultrmsd)
+ print ("%d\t%.2f"%((docki+1),resultrmsd))
if outlist:
- # Threshold applied and outlist need to be written
- for docki in sorted(outlist.iterkeys()):
- molrmsd = outlist[docki]
- # Get number of matchs in thresholding operation
- pop = population.get(docki)
- if not pop: pop = 1
- # Save molecule
- saveMolecWithRMSD(outsdf, molrmsd[0], molrmsd[1], pop)
-
- if skipped: print >> sys.stderr, "SKIPPED input molecules due to number of atom missmatch: %s"%skipped
+ # Threshold applied and outlist need to be written
+ for docki in sorted(outlist.iterkeys()):
+ molrmsd = outlist[docki]
+ # Get number of matchs in thresholding operation
+ pop = population.get(docki)
+ if not pop: pop = 1
+ # Save molecule
+ saveMolecWithRMSD(outsdf, molrmsd[0], molrmsd[1], pop)
+
+ if skipped: print("SKIPPED input molecules due to number of atom missmatch: %s"%skipped, file=sys.stderr)
diff -u -r -N a/build/test/RBT_HOME/check_test.py b/build/test/RBT_HOME/check_test.py
--- a/build/test/RBT_HOME/check_test.py 2020-10-14 11:48:36.000000000 +0900
+++ b/build/test/RBT_HOME/check_test.py 2020-10-19 09:23:31.000000000 +0900
@@ -21,6 +21,6 @@
error = 1
if error == 1:
- print "The test failed, please check the compilation is OK and no errors were raised."
+ print ("The test failed, please check the compilation is OK and no errors were raised.")
else:
- print "The test succeeded! The results agree with the reference ones.\nHave fun using rDock!!"
+ print ("The test succeeded! The results agree with the reference ones.\nHave fun using rDock!!")
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