Implementations of 2 new cvs: native contact fraction Q and angles between two vectors #327
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update the examples, this is simply a better choice of the contacts. Otherwise it contains bonded pairs which will always be there.
pabloferz
reviewed
Aug 8, 2024
pysages/colvars/contacts.py
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| return remapped_contacts | ||
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| @multicomponent |
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Is @multicomponent really needed here? AFAICT, this returns a scalar?
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good catch, I think perhaps I copied some other code with the multicomponent. I'll fix it!
pysages/colvars/angles.py
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| return vector_angle | ||
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| def vector_angle(p1, p2, p3, p4): |
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I think we should be able to reduce some code duplication by having our angle function taking four arguments and then change the Angle class call a lambda that calls angle with one of the arguments repeated.
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I see, that sounds cool
pysages/colvars/contacts.py
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| def remap_indices(contacts, sorted_unique_indices): | ||
| # create the mapping from old indices to new indices | ||
| old_indices = np.array(sorted_unique_indices) | ||
| new_indices = np.arange(len(sorted_unique_indices)) | ||
| index_mapping = np.zeros(old_indices.max() + 1, dtype=new_indices.dtype) | ||
| index_mapping = index_mapping.at[old_indices].set(new_indices) | ||
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| contacts = np.array(contacts) | ||
| remapped_contacts = index_mapping[contacts] | ||
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| return remapped_contacts |
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I need to check, but this looks like something that could be accomplished, by using argsort
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Hi I've implemented two new cvs: 1. angle between two vectors 2. native contact fraction Q. Please let me know if anything needs to be modified! I've added another python script under colvars
contacts.pyfor Q, but the vector angles are added inangles.py. I've implemented testing for Q and its derivatives inexample/openmm/cv_Q.