def calcPCA(self, ensemble, logger):
'''
calcPCA:
#ensemble: prody ensmeble with structure information
calculate PCA for a set of structures
return: prody.pca object
'''
logger.info("Calculate PCA")
PCAname = ensemble.getTitle()
pca = prody.PCA(PCAname)
pca.buildCovariance(ensemble)
logger.info("PCA")
pca.calcModes()
logger.info(repr(pca))
outputname = PCAname + "_pca_modes.nmd"
prody.writeNMD(outputname, pca[:10], self.selection_ref_structure)
if self.vmd == True:
prody.viewNMDinVMD(outputname)
logger.info(f"PCA is saved in: {outputname}")
return pca, outputname
def calcANM(self, structure, logger):
'''
calcANM:
#structure: prody PDB-structure
calculate ANM for one specific structure
return: prody.anm object
'''
logger.info("Calculate ANM")
ANMname = structure.getLabel()
anm = prody.ANM(ANMname)
anm.buildHessian(structure, cutoff=15.0)
anm.calcModes()
# write out the three lowest modes as NMD file (visualize with NMWizard in VMD
outputname = ANMname + "_anm_modes.nmd"
prody.writeNMD(outputname, anm[:10], self.selection_ref_structure)
if self.vmd == True:
prody.viewNMDinVMD(outputname)
logger.info(f"ANM is saved in: {outputname}")
return anm