From 7a72f9aa782ca1361f817407952cbe1002249b25 Mon Sep 17 00:00:00 2001 From: Ben Webb Date: Wed, 17 Jul 2024 16:17:45 -0700 Subject: [PATCH] Squashed 'modules/pmi/' changes from 37e3ab7a74..bf4a780beb bf4a780beb Add missing docs git-subtree-dir: modules/pmi git-subtree-split: bf4a780beb578b2995e24f5f655df0728d4d57d2 --- modules/pmi/pyext/src/io/__init__.py | 2 ++ modules/pmi/pyext/src/macros.py | 8 ++++++++ 2 files changed, 10 insertions(+) diff --git a/modules/pmi/pyext/src/io/__init__.py b/modules/pmi/pyext/src/io/__init__.py index d6ae3e5b86..9368c72607 100644 --- a/modules/pmi/pyext/src/io/__init__.py +++ b/modules/pmi/pyext/src/io/__init__.py @@ -445,6 +445,7 @@ def read_coordinates_of_rmfs(model, @param alignment_components Tuples to specify what you're aligning on @param rmsd_calculation_components Tuples to specify what components are used for RMSD calc + @param state_number The state to extract from the file """ all_coordinates = [] rmsd_coordinates = [] @@ -516,6 +517,7 @@ def get_bead_sizes(model, rmf_tuple, rmsd_calculation_components=None, @param rmf_tuple score,filename,frame number,original order number, rank @param rmsd_calculation_components Tuples to specify what components are used for RMSD calc + @param state_number The state to extract from the file ''' if rmsd_calculation_components is None: return {} diff --git a/modules/pmi/pyext/src/macros.py b/modules/pmi/pyext/src/macros.py index 1e491de8db..d48df7ce4e 100644 --- a/modules/pmi/pyext/src/macros.py +++ b/modules/pmi/pyext/src/macros.py @@ -686,6 +686,8 @@ def add_state(self, reader, keep_chain_id=False, fasta_name_map=None, IMP::pmi::topology::TopologyReader object. When you are done adding states, call execute_macro() @param reader The TopologyReader object + @param keep_chain_id If True, keep the chain IDs from the + original PDB files, if available @param fasta_name_map dictionary for converting protein names found in the fasta file @param chain_ids A list or string of chain IDs for assigning to @@ -1640,6 +1642,8 @@ def __init__(self, model, stat_files, best_models=None, score_key=None, rmf files names @param best_models Integer. Number of best scoring models, if None: all models will be read + @param score_key Use the provided stat key keyword as the score + (by default, the total score is used) @param alignment boolean (Default=True). Align before computing the rmsd. """ @@ -2400,7 +2404,10 @@ def aggregate(self, idxs, rmsd_cutoff=10, metric=IMP.atom.get_rmsd): def merge_aggregates(self, rmsd_cutoff, metric=IMP.atom.get_rmsd): """ merge the clusters that have close members + @param rmsd_cutoff cutoff distance in Angstorms + @param metric Function to calculate distance between two Selections + (by default, IMP.atom.get_rmsd is used) """ # before merging, clusters are spheres of radius rmsd_cutoff # centered on the 1st element @@ -2540,6 +2547,7 @@ def set_reference(self, reference, cluster): @param reference can be either "Absolute" (cluster center of the first cluster) or Relative (cluster center of the current cluster) + #param cluster the reference IMP.pmi.output.Cluster object """ if reference == "Absolute": _ = self.stath0[0]