Dear Christian, Thanks for the information about your use of the RDKit. I'm always very happy to hear how people are using the code.
I'm on vacation now, so I don't have the time to answer your questions, I will try to remember to get to them when I'm back in Basel next week. If you have not heard from me by the middle of next week, please send another email to remind me. -greg 2010/3/29 Christian de Bouillé <[email protected]>: > Dear Greg > > To inform you that on our web server > http://www.ambinter.com > approx 11 million chemicals have now the descriptors > calculated by RDkit > > On the first page "Click here to search the Chemical Database" > On the next page is written > The Ambinter database uses ChemAxon software. All descriptors (Mass, LogP, > TPSA, Hacc, Hdon, Rotatable Bonds) have been calculated using RDKit; open > source software developed by Greg Landrum. > > Go further and you will find the descriptors > > Questions > > - I have difficulties to use your cluster scripts > and found 2 scripts below > My idea is to search structures with the help of the descriptors > Regarding how I set the cut, I do not see > any correlation beetween the display and the > print hc.cut(0.25) > > The database includes the fingerprints > perhaps it would be better to use your scripts > > > - the display of the structures with SDFview > is not so good > Could you display the structures as Jchem ? > > Best Regards > > Christian de Bouillé > Ambinter SARL > 50 avenue de Versailles > 75016 Paris > [email protected] > tél: 014524 4860 > fax: 014524 6241 > http://www.ambinter.com (5 millions de structures chimiques, accès libre) > > <<<<<<<<<<<<<< > >> import numpy as np >> from hcluster import * >> import mlpy >> import pylab >> >> x = np.array([[ 1. , 1.5], >> [ 1.1, 1.8], >> [ 2. , 2.8], >> [ 3.2, 3.1], >> [ 3.4, 3.2]]) >> hc = mlpy.HCluster() >> hc.compute(x) >> print hc.ia >> >> print hc.ib >> >> print hc.heights >> >> print hc.cut(0.25) >> >> >> Y = pdist(x,'seuclidean') >> Z = linkage(Y, method='average') >> #dendrogram(Z, color_threshold=0.75, truncate_mode='level', p=10, >> show_contracted=True) >> # lastp 0.75 >> dendrogram(Z, p=5, truncate_mode='lastp', color_threshold=2.75, >> get_leaves=True, orientation='top', labels=None, >> count_sort=False, distance_sort=False, >> show_leaf_counts=True, >> no_plot=False, no_labels=False, color_list=None, >> leaf_font_size=None, leaf_rotation=None, >> leaf_label_func=None, >> no_leaves=False, show_contracted=False, >> link_color_func=None) >> >> >> pylab.show() >> > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
