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Fixed biopython bug and fpocket version updated
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@gbayarri
gbayarri committed May 8, 2024
1 parent 583f850 commit 26f7735
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6 changes: 3 additions & 3 deletions biobb_vs/docs/source/command_line.md
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Expand Up @@ -140,7 +140,7 @@ Config parameters for this building block:
* **ligand** (*string*): (None) Ligand to be found in the protein structure. If no ligand provided, the largest one will be selected, if more than one..
* **radius** (*number*): (5.0) Cut-off distance (Ångstroms) around ligand atoms to consider a protein atom as a binding site atom..
* **max_num_ligands** (*integer*): (15) Total number of superimposed ligands to be extracted from the identity cluster. For populated clusters, the restriction avoids to superimpose redundant structures. If 0, all ligands extracted will be considered..
* **matrix_name** (*string*): (blosum62) Substitution matrices for use in alignments. .
* **matrix_name** (*string*): (BLOSUM62) Substitution matrices for use in alignments. .
* **gap_open** (*number*): (-10.0) Gap open penalty..
* **gap_extend** (*number*): (-0.5) Gap extend penalty..
* **remove_tmp** (*boolean*): (True) Remove temporal files..
Expand All @@ -152,7 +152,7 @@ properties:
gap_extend: -0.5
gap_open: -10.0
ligand: PGA
matrix_name: blosum62
matrix_name: BLOSUM62
max_num_ligands: 15
radius: 5

Expand All @@ -167,7 +167,7 @@ bindingsite --config config_bindingsite.yml --input_pdb_path bindingsite.pdb --i
{
"properties": {
"ligand": "PGA",
"matrix_name": "blosum62",
"matrix_name": "BLOSUM62",
"gap_open": -10.0,
"gap_extend": -0.5,
"max_num_ligands": 15,
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172 changes: 61 additions & 111 deletions biobb_vs/json_schemas/bindingsite.json
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Expand Up @@ -99,210 +99,160 @@
},
"matrix_name": {
"type": "string",
"default": "blosum62",
"default": "BLOSUM62",
"wf_prop": false,
"description": "Substitution matrices for use in alignments. ",
"enum": [
"benner6",
"benner22",
"benner74",
"blosum100",
"blosum30",
"blosum35",
"blosum40",
"blosum45",
"blosum50",
"blosum55",
"blosum60",
"blosum62",
"blosum65",
"blosum70",
"blosum75",
"blosum80",
"blosum85",
"blosum90",
"blosum95",
"feng",
"fitch",
"genetic",
"gonnet",
"grant",
"ident",
"johnson",
"levin",
"mclach",
"miyata",
"nwsgappep",
"pam120",
"pam180",
"pam250",
"pam30",
"pam300",
"pam60",
"pam90",
"rao",
"risler",
"structure"
"BENNER22",
"BENNER6",
"BENNER74",
"BLASTN",
"BLASTP",
"BLOSUM45",
"BLOSUM50",
"BLOSUM62",
"BLOSUM80",
"BLOSUM90",
"DAYHOFF",
"FENG",
"GENETIC",
"GONNET1992",
"HOXD70",
"JOHNSON",
"JONES",
"LEVIN",
"MCLACHLAN",
"MDM78",
"MEGABLAST",
"NUC.4.4",
"PAM250",
"PAM30",
"PAM70",
"RAO",
"RISLER",
"SCHNEIDER",
"STR",
"TRANS"
],
"property_formats": [
{
"name": "benner6",
"name": "BENNER22",
"description": null
},
{
"name": "benner22",
"name": "BENNER6",
"description": null
},
{
"name": "benner74",
"name": "BENNER74",
"description": null
},
{
"name": "blosum100",
"name": "BLASTN",
"description": null
},
{
"name": "blosum30",
"name": "BLASTP",
"description": null
},
{
"name": "blosum35",
"name": "BLOSUM45",
"description": null
},
{
"name": "blosum40",
"name": "BLOSUM50",
"description": null
},
{
"name": "blosum45",
"name": "BLOSUM62",
"description": null
},
{
"name": "blosum50",
"name": "BLOSUM80",
"description": null
},
{
"name": "blosum55",
"name": "BLOSUM90",
"description": null
},
{
"name": "blosum60",
"name": "DAYHOFF",
"description": null
},
{
"name": "blosum62",
"name": "FENG",
"description": null
},
{
"name": "blosum65",
"name": "GENETIC",
"description": null
},
{
"name": "blosum70",
"name": "GONNET1992",
"description": null
},
{
"name": "blosum75",
"name": "HOXD70",
"description": null
},
{
"name": "blosum80",
"name": "JOHNSON",
"description": null
},
{
"name": "blosum85",
"name": "JONES",
"description": null
},
{
"name": "blosum90",
"name": "LEVIN",
"description": null
},
{
"name": "blosum95",
"name": "MCLACHLAN",
"description": null
},
{
"name": "feng",
"name": "MDM78",
"description": null
},
{
"name": "fitch",
"name": "MEGABLAST",
"description": null
},
{
"name": "genetic",
"name": "NUC.4.4",
"description": null
},
{
"name": "gonnet",
"name": "PAM250",
"description": null
},
{
"name": "grant",
"name": "PAM30",
"description": null
},
{
"name": "ident",
"name": "PAM70",
"description": null
},
{
"name": "johnson",
"name": "RAO",
"description": null
},
{
"name": "levin",
"name": "RISLER",
"description": null
},
{
"name": "mclach",
"name": "SCHNEIDER",
"description": null
},
{
"name": "miyata",
"name": "STR",
"description": null
},
{
"name": "nwsgappep",
"description": null
},
{
"name": "pam120",
"description": null
},
{
"name": "pam180",
"description": null
},
{
"name": "pam250",
"description": null
},
{
"name": "pam30",
"description": null
},
{
"name": "pam300",
"description": null
},
{
"name": "pam60",
"description": null
},
{
"name": "pam90",
"description": null
},
{
"name": "rao",
"description": null
},
{
"name": "risler",
"description": null
},
{
"name": "structure",
"name": "TRANS",
"description": null
}
]
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2 changes: 1 addition & 1 deletion biobb_vs/test/data/config/config_bindingsite.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"properties": {
"ligand": "PGA",
"matrix_name": "blosum62",
"matrix_name": "BLOSUM62",
"gap_open": -10.0,
"gap_extend": -0.5,
"max_num_ligands": 15,
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2 changes: 1 addition & 1 deletion biobb_vs/test/data/config/config_bindingsite.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@ properties:
gap_extend: -0.5
gap_open: -10.0
ligand: PGA
matrix_name: blosum62
matrix_name: BLOSUM62
max_num_ligands: 15
radius: 5
6 changes: 3 additions & 3 deletions biobb_vs/utils/bindingsite.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ class BindingSite(BiobbObject):
* **ligand** (*str*) - (None) Ligand to be found in the protein structure. If no ligand provided, the largest one will be selected, if more than one.
* **radius** (*float*) - (5.0) [0.1~1000|0.1] Cut-off distance (Ångstroms) around ligand atoms to consider a protein atom as a binding site atom.
* **max_num_ligands** (*int*) - (15) [0~1000|1] Total number of superimposed ligands to be extracted from the identity cluster. For populated clusters, the restriction avoids to superimpose redundant structures. If 0, all ligands extracted will be considered.
* **matrix_name** (*str*) - ("blosum62") Substitution matrices for use in alignments. Values: benner6, benner22, benner74, blosum100, blosum30, blosum35, blosum40, blosum45, blosum50, blosum55, blosum60, blosum62, blosum65, blosum70, blosum75, blosum80, blosum85, blosum90, blosum95, feng, fitch, genetic, gonnet, grant, ident, johnson, levin, mclach, miyata, nwsgappep, pam120, pam180, pam250, pam30, pam300, pam60, pam90, rao, risler, structure.
* **matrix_name** (*str*) - ("BLOSUM62") Substitution matrices for use in alignments. Values: BENNER22, BENNER6, BENNER74, BLASTN, BLASTP, BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90, DAYHOFF, FENG, GENETIC, GONNET1992, HOXD70, JOHNSON, JONES, LEVIN, MCLACHLAN, MDM78, MEGABLAST, NUC.4.4, PAM250, PAM30, PAM70, RAO, RISLER, SCHNEIDER, STR, TRANS.
* **gap_open** (*float*) - (-10.0) [-1000~1000|0.1] Gap open penalty.
* **gap_extend** (*float*) - (-0.5) [-1000~1000|0.1] Gap extend penalty.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
Expand All @@ -49,7 +49,7 @@ class BindingSite(BiobbObject):
from biobb_vs.utils.bindingsite import bindingsite
prop = {
'ligand': 'PGA',
'matrix_name': 'blosum62',
'matrix_name': 'BLOSUM62',
'gap_open': -10.0,
'gap_extend': -0.5,
'max_num_ligands': 15,
Expand Down Expand Up @@ -89,7 +89,7 @@ def __init__(self, input_pdb_path, input_clusters_zip, output_pdb_path,
self.ligand = properties.get('ligand', None)
self.radius = float(properties.get('radius', 5.0))
self.max_num_ligands = properties.get('max_num_ligands', 15)
self.matrix_name = properties.get('matrix_name', 'blosum62')
self.matrix_name = properties.get('matrix_name', 'BLOSUM62')
self.gap_open = properties.get('gap_open', -10.0)
self.gap_extend = properties.get('gap_extend', -0.5)
self.properties = properties
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2 changes: 1 addition & 1 deletion biobb_vs/utils/common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ def get_sequence_nucs(structure):
return seq


def align_sequences(seqA, seqB, matrix_name='blosum62', gap_open=-10.0, gap_extend=-0.5):
def align_sequences(seqA, seqB, matrix_name='BLOSUM62', gap_open=-10.0, gap_extend=-0.5):
"""
Performs a global pairwise alignment between two sequences using the Needleman-Wunsch algorithm as implemented in Biopython.
Returns the alignment and the residue mapping between both original sequences.
Expand Down

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