IMP Reference Guide
develop.7cb8855c60,2024/10/08
The Integrative Modeling Platform
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Set of Python classes to create a multi-state, multi-resolution IMP hierarchy. More...
Set of Python classes to create a multi-state, multi-resolution IMP hierarchy.
model = IMP.Model(); s = IMP.pmi.topology.System(model)
. The System will store all the states.See a comprehensive example for using these classes.
Alternatively one can construct the entire topology and degrees of freedom via formatted text file with TopologyReader and IMP::pmi::macros::BuildSystem(). This is used in the PMI tutorial. Note that this only allows a limited set of the full options available to PMI users (rigid bodies only, fixed resolutions).
Classes | |
class | Molecule |
Stores a named protein chain. More... | |
class | PDBSequences |
Data structure for reading and storing sequence data from PDBs. More... | |
class | PMIMoleculeHierarchy |
Extends the functionality of IMP.atom.Molecule. More... | |
class | Sequences |
A dictionary-like wrapper for reading and storing sequence data. More... | |
class | State |
Stores a list of Molecules all with the same State index. More... | |
class | System |
Represent the root node of the global IMP.atom.Hierarchy. More... | |
class | TempResidue |
Temporarily stores residue information, even without structure available. More... | |
class | TopologyReader |
Automatically setup System and Degrees of Freedom with a formatted text file. More... | |
Functions | |
def | fasta_pdb_alignments |
This function computes and prints the alignment between the fasta file and the pdb sequence, computes the offsets for each contiguous fragment in the PDB. More... | |
def IMP.pmi.topology.fasta_pdb_alignments | ( | fasta_sequences, | |
pdb_sequences, | |||
show = False |
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) |
This function computes and prints the alignment between the fasta file and the pdb sequence, computes the offsets for each contiguous fragment in the PDB.
fasta_sequences | IMP.pmi.topology.Sequences object |
pdb_sequences | IMP.pmi.topology.PDBSequences object |
show | boolean default False, if True prints the alignments. The input objects should be generated using map_name dictionaries such that fasta_id and pdb_chain_id are mapping to the same protein name. It needs BioPython. Returns a dictionary of offsets, organized by peptide range (group): example: offsets={"ProtA":{(1,10):1,(20,30):10}} |
Definition at line 1186 of file pmi/topology/__init__.py.