Index

A

aa_matching() (in module cyclicpeptide.Structure2Sequence) aa_side_chain_extend() (in module cyclicpeptide.Structure2Sequence)

aa_xyz() (in module cyclicpeptide.Structure2Sequence) amino_acid_composition_freq() (in module cyclicpeptide.GraphAlignment)

B

blend_colors() (in module cyclicpeptide.Structure2Sequence)

C

cal_chemial_physical_properties() (in module cyclicpeptide.PropertyAnalysis) cal_daylight_like_fingerprint() (in module cyclicpeptide.PropertyAnalysis) cal_MACCS_keys() (in module cyclicpeptide.PropertyAnalysis) cal_morgan_fingerprint() (in module cyclicpeptide.PropertyAnalysis) cal_RDKit_fingerprint() (in module cyclicpeptide.PropertyAnalysis) cal_rules() (in module cyclicpeptide.PropertyAnalysis) calculate_amino_acid_composition() (in module cyclicpeptide.PropertyAnalysis) chemial_physical_properties_from_smiles() (in module cyclicpeptide.PropertyAnalysis) code2symbol() (in module cyclicpeptide.Sequence2Structure) connect_two_aa_with_peptide_bond() (in module cyclicpeptide.Sequence2Structure) create_amino_acid_chain() (in module cyclicpeptide.SequenceTransformer) create_graph() (in module cyclicpeptide.GraphAlignment) create_graph_presentation() (in module cyclicpeptide.SequenceTransformer) create_iupac_condensed() (in module cyclicpeptide.SequenceTransformer) create_one_letter_peptide() (in module cyclicpeptide.SequenceTransformer) create_peptide_of_essentialAA() (in module cyclicpeptide.Sequence2Structure) create_peptide_of_no_essentialAA() (in module cyclicpeptide.Sequence2Structure)

create_sequence() (in module cyclicpeptide.SequenceTransformer) cyclicpeptide.GraphAlignment module cyclicpeptide.IOManager module cyclicpeptide.PropertyAnalysis module cyclicpeptide.Sequence2Structure module cyclicpeptide.SequenceGeneration module cyclicpeptide.SequenceTransformer module cyclicpeptide.Structure2Sequence module cyclicpeptide.StructureTransformer module

D

detect_backbone() (in module cyclicpeptide.Sequence2Structure) (in module cyclicpeptide.Structure2Sequence)

F

find_max_match_subgraph() (in module cyclicpeptide.GraphAlignment)

G

generate_similar_sequences() (in module cyclicpeptide.SequenceGeneration) generate_subgraphs_from_edges() (in module cyclicpeptide.GraphAlignment) get_complete_aas() (in module cyclicpeptide.Structure2Sequence) get_connected_chain() (in module cyclicpeptide.Structure2Sequence)

get_connected_pairs() (in module cyclicpeptide.Structure2Sequence) get_molblock() (in module cyclicpeptide.Sequence2Structure) get_molblock_from_smiles() (in module cyclicpeptide.Sequence2Structure) graph2svg() (in module cyclicpeptide.IOManager) graph_similarity() (in module cyclicpeptide.GraphAlignment)

H

highlight_atom() (in module cyclicpeptide.Structure2Sequence)

I

is_subgraph_of() (in module cyclicpeptide.GraphAlignment)

L

link_aa_by_peptide_bond() (in module cyclicpeptide.Sequence2Structure)

M

mcs2similarity() (in module cyclicpeptide.GraphAlignment) mcs_similarity() (in module cyclicpeptide.GraphAlignment) module cyclicpeptide.GraphAlignment cyclicpeptide.IOManager cyclicpeptide.PropertyAnalysis cyclicpeptide.Sequence2Structure cyclicpeptide.SequenceGeneration cyclicpeptide.SequenceTransformer cyclicpeptide.Structure2Sequence cyclicpeptide.StructureTransformer

mol2molblock() (in module cyclicpeptide.StructureTransformer) mol2pdbblock() (in module cyclicpeptide.StructureTransformer) mol2seq_for_essentialAA() (in module cyclicpeptide.Structure2Sequence) mol_optimize() (in module cyclicpeptide.StructureTransformer)

N

node_match() (in module cyclicpeptide.GraphAlignment)

O

order_backbone() (in module cyclicpeptide.Structure2Sequence)

output_molecule() (in module cyclicpeptide.StructureTransformer)

P

plot_graph() (in module cyclicpeptide.IOManager)

plot_smiles() (in module cyclicpeptide.IOManager) predict_3d_conformation() (in module cyclicpeptide.StructureTransformer)

R

read_graph_representation() (in module cyclicpeptide.SequenceTransformer) read_iupac_condensed() (in module cyclicpeptide.SequenceTransformer) read_one_letter_sequence() (in module cyclicpeptide.SequenceTransformer) read_replacement_rules_from_file() (in module cyclicpeptide.SequenceGeneration)

read_sequence() (in module cyclicpeptide.SequenceTransformer) reference_aa_monomer() (in module cyclicpeptide.Sequence2Structure) (in module cyclicpeptide.Structure2Sequence) reorder_result() (in module cyclicpeptide.Structure2Sequence) replace_hyphen() (in module cyclicpeptide.SequenceTransformer)

S

save_mol() (in module cyclicpeptide.IOManager) save_pdb() (in module cyclicpeptide.IOManager) save_sequences_to_csv() (in module cyclicpeptide.SequenceGeneration) save_svg() (in module cyclicpeptide.IOManager) search_one_chain() (in module cyclicpeptide.Structure2Sequence) seq2stru_essentialAA() (in module cyclicpeptide.Sequence2Structure)

seq2stru_no_essentialAA() (in module cyclicpeptide.Sequence2Structure) sequence_map() (in module cyclicpeptide.Structure2Sequence) sequence_str() (in module cyclicpeptide.Structure2Sequence) sequence_to_node_edge() (in module cyclicpeptide.GraphAlignment) side_chain_neighbor() (in module cyclicpeptide.Structure2Sequence) split_aa_unit() (in module cyclicpeptide.Structure2Sequence)

T

transform() (in module cyclicpeptide.Structure2Sequence)