Merge pull request #47 from Electrostatics/nathan/fix-run
Add missing option to lib.loadOptions()
This commit is contained in:
Nathan Baker
GitHub
2
.gitignore
vendored
2
.gitignore
vendored
@@ -3,3 +3,5 @@
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*.py[cod]
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*.py[cod]
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# PIP stuff
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# PIP stuff
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*.egg-info
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*.egg-info
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# Visual studio code
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.vscode
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398
propka.cfg
398
propka.cfg
@@ -1,398 +0,0 @@
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# PropKa configuration file
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version version_A
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# Model pKa values
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model_pkas C- 3.20
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model_pkas ASP 3.80
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model_pkas GLU 4.50
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model_pkas HIS 6.50
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model_pkas CYS 9.00
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model_pkas TYR 10.00
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model_pkas LYS 10.50
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model_pkas ARG 12.50
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#model_pkas SER 14.20 Jack Kyte: Structure in Protein Chemistry, 1995, Garland Publishing, Inc New York and London
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model_pkas N+ 8.00
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model_pkas CG 11.50
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model_pkas C2N 11.50
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model_pkas N30 10.00
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model_pkas N31 10.00
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model_pkas N32 10.00
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model_pkas N33 10.00
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model_pkas NAR 5.00
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model_pkas OCO 4.50
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model_pkas SH 10.00
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model_pkas OP 6.00
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# Custom ligand pKa values
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# P. Acharya, P. Cheruku, S. Chatterjee, S. Acharya, and, J. Chattopadhyaya:
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# Measurement of Nucleobase pKa Values in Model Mononucleotides
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# Shows RNA-RNA Duplexes To Be More Stable than DNA-DNA Duplexes
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# Journal of the American Chemical Society 2004 126 (9), 2862-2869
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#
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custom_model_pkas DA-N1 3.82
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custom_model_pkas DA-N3 3.82
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custom_model_pkas DA-N7 3.82
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custom_model_pkas DA-OP1 1.00
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custom_model_pkas DA-OP2 1.00
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custom_model_pkas DG-N1 9.59
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custom_model_pkas DG-N3 9.59
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custom_model_pkas DG-N7 9.59
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custom_model_pkas DG-OP1 1.00
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custom_model_pkas DG-OP2 1.00
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custom_model_pkas DC-N3 4.34
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custom_model_pkas DC-OP1 1.00
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custom_model_pkas DC-OP2 1.00
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custom_model_pkas DT-N3 10.12
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custom_model_pkas DT-OP1 1.00
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custom_model_pkas DT-OP2 1.00
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# protein group mapping
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protein_group_mapping ASP-CG COO
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protein_group_mapping GLU-CD COO
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protein_group_mapping HIS-CG HIS
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protein_group_mapping CYS-SG CYS
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protein_group_mapping TYR-OH TYR
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protein_group_mapping LYS-NZ LYS
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protein_group_mapping ARG-CZ ARG
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#protein_group_mapping SER-OG SER
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protein_group_mapping THR-OG1 ROH
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protein_group_mapping SER-OG ROH#
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protein_group_mapping ASN-CG AMD
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protein_group_mapping GLN-CD AMD
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protein_group_mapping TRP-NE1 TRP
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# matrix for propka interactions
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# 'N' non-iterative interaction
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# 'I' iterative interaction
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# '-' no interaction
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#CYS
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interaction_matrix CYS I#N+
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interaction_matrix N+ N I#HIS
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interaction_matrix HIS I N I#LYS
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interaction_matrix LYS N N N I#AMD
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interaction_matrix AMD N - N - -#COO
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interaction_matrix COO I N I N N I#ARG
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interaction_matrix ARG N N N N - N I#TRP
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interaction_matrix TRP N - - - - N - -#ROH
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interaction_matrix ROH N - - - - N - - -#TYR
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interaction_matrix TYR N I I I N N N N N I#SER
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interaction_matrix SER N N N N N N I N N N I #CG
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interaction_matrix CG N N N N - N I - - N I I#C2N
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interaction_matrix C2N N N N N - N I - - N I I I#N30
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interaction_matrix N30 N I N N - N N - - I N I I I#N31
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interaction_matrix N31 N I N N - N N - - I N I I I I#N32
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interaction_matrix N32 N I N N - N N - - I N I I I I I#N33
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interaction_matrix N33 N I N N - N N - - I N I I I I I I#NAR
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interaction_matrix NAR I N I I N I N - - I N N N N N N N I#OCO
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interaction_matrix OCO I N I N N I N N N N N N N N N N N I I#NP1
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interaction_matrix NP1 N - N - - N - - - N N - - - - - - N N -#OH
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interaction_matrix OH N - - - - N - - - N N - - - - - - - N - -#O3
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interaction_matrix O3 N - N - - N - - - N N - - - - - - N N - - -#CL
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interaction_matrix CL N - N - - N - - - N N - - - - - - N N - - - -#F
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interaction_matrix F N - N - - N - - - N N - - - - - - N N - - - - -#NAM
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interaction_matrix NAM N - N - - N - - - N N - - - - - - N N - - - - - -#N1
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interaction_matrix N1 N - N - - N - - - N N - - - - - - N N - - - - - - -#O2
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interaction_matrix O2 N - N - - N - - - N N - - - - - - N N - - - - - - - -#OP
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interaction_matrix OP I N I N N I N N N N N N N N N N N I I N N N N N N N N I#SH
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interaction_matrix SH I N N N N N N N N N N I I I I I I N N N N N N N N N N N I
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# Cutoff values for side chain interactions
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# default value
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sidechain_cutoffs default 3.0 4.0
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# COO
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sidechain_cutoffs COO COO 2.5 3.5
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Sidechain_cutoffs COO SER 2.65 3.65
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sidechain_cutoffs COO ARG 1.85 2.85
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sidechain_cutoffs COO LYS 2.85 3.85
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sidechain_cutoffs COO HIS 2.0 3.0
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sidechain_cutoffs COO AMD 2.0 3.0
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sidechain_cutoffs COO TRP 2.0 3.0
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sidechain_cutoffs COO ROH 2.65 3.65
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sidechain_cutoffs COO TYR 2.65 3.65
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sidechain_cutoffs COO N+ 2.85 3.85
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sidechain_cutoffs COO CG 1.85 2.85
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sidechain_cutoffs COO C2N 1.85 2.85
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sidechain_cutoffs COO N30 2.85 3.85
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sidechain_cutoffs COO N31 2.85 3.85
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sidechain_cutoffs COO N32 2.85 3.85
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sidechain_cutoffs COO N33 2.85 3.85
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sidechain_cutoffs COO NAR 2.0 3.0
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sidechain_cutoffs COO OCO 2.5 3.5
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sidechain_cutoffs COO OH 2.65 3.65
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sidechain_cutoffs COO NAM 2.0 3.0
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# SER
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sidechain_cutoffs SER SER 3.5 4.5
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sidechain_cutoffs SER ARG 2.5 4.0
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sidechain_cutoffs SER HIS 2.0 3.0
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sidechain_cutoffs SER AMD 2.5 3.5
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sidechain_cutoffs SER CYS 3.5 4.5
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sidechain_cutoffs SER TRP 2.5 3.5
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sidechain_cutoffs SER ROH 3.5 4.5
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sidechain_cutoffs SER CG 2.5 4.0
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sidechain_cutoffs SER C2N 2.5 4.0
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sidechain_cutoffs SER NAR 2.0 3.0
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sidechain_cutoffs SER OH 3.5 4.5
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sidechain_cutoffs SER SH 3.5 4.5
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sidechain_cutoffs SER TYR 3.5 4.5
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sidechain_cutoffs SER N+ 3.0 4.5
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sidechain_cutoffs SER NAM 2.5 3.5
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# ARG
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sidechain_cutoffs ARG CYS 2.5 4.0
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sidechain_cutoffs ARG TYR 2.5 4.0
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sidechain_cutoffs ARG OCO 1.85 2.85
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sidechain_cutoffs ARG SH 2.5 4.0
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# HIS
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sidechain_cutoffs HIS AMD 2.0 3.0
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sidechain_cutoffs HIS TYR 2.0 3.0
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sidechain_cutoffs HIS OCO 2.0 3.0
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# CYS
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sidechain_cutoffs CYS CYS 3.0 5.0
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sidechain_cutoffs CYS TRP 2.5 3.5
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sidechain_cutoffs CYS ROH 3.5 4.5
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sidechain_cutoffs CYS AMD 2.5 3.5
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sidechain_cutoffs CYS TYR 3.5 4.5
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sidechain_cutoffs CYS N+ 3.0 4.5
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sidechain_cutoffs CYS CG 2.5 4.0
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sidechain_cutoffs CYS C2N 2.5 4.0
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sidechain_cutoffs CYS N30 3.0 4.5
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sidechain_cutoffs CYS N31 3.0 4.5
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sidechain_cutoffs CYS N32 3.0 4.5
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sidechain_cutoffs CYS N33 3.0 4.5
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sidechain_cutoffs CYS OH 3.5 4.5
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sidechain_cutoffs CYS NAM 2.5 3.5
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sidechain_cutoffs CYS SH 3.0 5.0
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# TYR
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sidechain_cutoffs TYR TYR 3.5 4.5
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sidechain_cutoffs TYR N+ 3.0 4.5
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sidechain_cutoffs TYR AMD 2.5 3.5
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sidechain_cutoffs TYR TRP 2.5 3.5
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sidechain_cutoffs TYR ROH 3.5 4.5
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sidechain_cutoffs TYR CG 2.5 4.0
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sidechain_cutoffs TYR C2N 2.5 4.0
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sidechain_cutoffs TYR OCO 2.65 3.65
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sidechain_cutoffs TYR NAR 2.0 3.0
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sidechain_cutoffs TYR OH 3.5 4.5
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sidechain_cutoffs TYR NAM 2.5 3.5
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sidechain_cutoffs TYR SH 3.5 4.5
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# N+
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sidechain_cutoffs N+ OCO 2.85 3.85
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sidechain_cutoffs N+ SH 3.0 4.5
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# LYS
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sidechain_cutoffs LYS OCO 2.85 3.85
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# OCO
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sidechain_cutoffs OCO OCO 2.5 3.5
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sidechain_cutoffs OCO TRP 2.0 3.0
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sidechain_cutoffs OCO ROH 2.65 3.65
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sidechain_cutoffs OCO AMD 2.0 3.0
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sidechain_cutoffs OCO CG 1.85 2.85
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sidechain_cutoffs OCO C2N 1.85 2.85
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sidechain_cutoffs OCO N30 2.85 3.85
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sidechain_cutoffs OCO N31 2.85 3.85
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sidechain_cutoffs OCO N32 2.85 3.85
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sidechain_cutoffs OCO N33 2.85 3.85
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sidechain_cutoffs OCO NAR 2.0 3.0
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sidechain_cutoffs OCO OH 2.65 3.65
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sidechain_cutoffs OCO NAM 2.0 3.0
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# NAR
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sidechain_cutoffs NAR AMD 2.0 3.0
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# SH
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sidechain_cutoffs SH ROH 3.5 4.5
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sidechain_cutoffs SH TRP 2.5 3.5
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sidechain_cutoffs SH AMD 2.5 3.5
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sidechain_cutoffs SH NAM 2.5 3.5
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sidechain_cutoffs SH CG 2.5 4.0
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sidechain_cutoffs SH C2N 2.5 4.0
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sidechain_cutoffs SH OH 3.5 4.5
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sidechain_cutoffs SH SH 3.0 5.0
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# Maximal interaction energies for side chains
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sidechain_interaction 0.85
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# Angular dependent sidechain interactions
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angular_dependent_sidechain_interactions HIS
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angular_dependent_sidechain_interactions ARG
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angular_dependent_sidechain_interactions AMD
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angular_dependent_sidechain_interactions TRP
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# exception interaction values
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COO_HIS_exception 1.60
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OCO_HIS_exception 1.60
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CYS_HIS_exception 1.60
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CYS_CYS_exception 3.60
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# Coulomb interaction parameters
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coulomb_cutoff1 4.0
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coulomb_cutoff2 10.0
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coulomb_diel 80.0
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# Backbone hydrogen bond parameters
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backbone_NH_hydrogen_bond COO -0.85 2.00 3.00
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#backbone_NH_hydrogen_bond C- -0.85 2.00 3.00
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backbone_NH_hydrogen_bond CYS -0.85 3.00 4.00
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backbone_NH_hydrogen_bond TYR -0.85 2.20 3.20
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backbone_NH_hydrogen_bond OCO -0.85 2.00 3.50
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backbone_NH_hydrogen_bond NAR -0.85 2.00 3.50
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backbone_CO_hydrogen_bond HIS 0.85 2.00 3.00
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backbone_CO_hydrogen_bond OCO 0.85 3.00 4.00
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backbone_CO_hydrogen_bond CG 0.85 2.00 4.00
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backbone_CO_hydrogen_bond C2N 0.85 2.00 4.00
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backbone_CO_hydrogen_bond N30 0.85 2.00 4.00
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backbone_CO_hydrogen_bond N31 0.85 2.00 4.00
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backbone_CO_hydrogen_bond N32 0.85 2.00 4.00
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backbone_CO_hydrogen_bond N33 0.85 2.00 4.00
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backbone_CO_hydrogen_bond NAR 0.85 2.00 3.50
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# Group charges
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charge COO -1
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charge HIS +1
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charge CYS -1
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charge TYR -1
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charge LYS +1
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charge ARG +1
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charge N+ +1
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charge C- -1
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charge OCO -1
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charge SER -1
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charge CG +1
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charge C2N +1
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charge N30 +1
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charge N31 +1
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charge N32 +1
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charge N33 +1
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charge NAR +1
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charge SH -1
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charge OP -1
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# list of acids
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acid_list ASP
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acid_list GLU
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acid_list CYS
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acid_list TYR
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acid_list SER
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acid_list C-
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acid_list OCO
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acid_list OP
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acid_list SH
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# list of bases
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base_list ARG
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base_list LYS
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base_list HIS
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base_list N+
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||||||
base_list CG
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base_list C2N
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base_list N30
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||||||
base_list N31
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base_list N32
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base_list N33
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base_list NAR
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# list of groups used in backbone reorganisation calculations
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backbone_reorganisation_list ASP
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backbone_reorganisation_list GLU
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# Residues that should be ignored
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ignore_residues HOH
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ignore_residues H2O
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ignore_residues HOH
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ignore_residues SO4
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ignore_residues PO4
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ignore_residues PEG
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ignore_residues EPE
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||||||
#ignore_residues NAG
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ignore_residues TRS
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||||||
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# Relative Van der Waals volume parameters for the radial volume model
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||||||
# Radii adopted from Bondi, A. (1964). "Van der Waals Volumes and Radii". J. Phys. Chem. 68 (3): 441-51
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||||||
VanDerWaalsVolume C 1.40 # radius: 1.70, volume: 20.58 all 'C' and 'CA' atoms
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||||||
VanDerWaalsVolume C4 2.64 # 38.79 hydrodphobic carbon atoms + unidentified atoms
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||||||
VanDerWaalsVolume N 1.06 # radius: 1.55, volume: 15.60 all nitrogen atoms
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VanDerWaalsVolume O 1.00 # radius: 1.52, volume: 14.71 all oxygen atoms
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VanDerWaalsVolume S 1.66 # radius: 1.80, volume: 24.43 all sulphur atoms
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VanDerWaalsVolume F 0.90 # raidus: 1.47, volume: 13.30 for fluorine
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VanDerWaalsVolume Cl 1.53 # radius: 1.75, volume: 22.44 for chlorine
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||||||
VanDerWaalsVolume P 1.66 # radius: 1.80, volume: 24.42 for phosphorus
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# Other desolvation parameters
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desolvationSurfaceScalingFactor 0.25
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|
||||||
desolvationPrefactor -13.0
|
|
||||||
desolvationAllowance 0.0
|
|
||||||
desolv_cutoff 20.0
|
|
||||||
buried_cutoff 15.0
|
|
||||||
Nmin 280
|
|
||||||
Nmax 560
|
|
||||||
|
|
||||||
# Ligand groups
|
|
||||||
ligand_typing groups
|
|
||||||
min_bond_distance_for_hydrogen_bonds 4
|
|
||||||
|
|
||||||
# covalent coupling
|
|
||||||
coupling_max_number_of_bonds 3
|
|
||||||
shared_determinants 0
|
|
||||||
common_charge_centre 0
|
|
||||||
remove_penalised_group 1
|
|
||||||
|
|
||||||
# non-covalent coupling
|
|
||||||
max_intrinsic_pKa_diff 2.0
|
|
||||||
min_interaction_energy 0.5
|
|
||||||
max_free_energy_diff 1.0
|
|
||||||
min_swap_pka_shift 1.0
|
|
||||||
min_pka 0.0
|
|
||||||
max_pka 10.0
|
|
||||||
pH variable
|
|
||||||
reference neutral
|
|
||||||
|
|
||||||
# ions
|
|
||||||
ions 1P 1 # generic charged atoms
|
|
||||||
ions 2P 2
|
|
||||||
ions 1N -1
|
|
||||||
ions 2N -2
|
|
||||||
|
|
||||||
ions MG 2 #Magnesium Ion
|
|
||||||
ions CA 2 #Calcium Ion
|
|
||||||
ions ZN 2 #Zinc Ion
|
|
||||||
ions NA 1 #Sodium Ion
|
|
||||||
ions CL -1 #Chloride Ion
|
|
||||||
ions MN 2 #Manganese (ii) Ion
|
|
||||||
ions K 1 #Potassium Ion
|
|
||||||
ions CD 2 #Cadmium Ion
|
|
||||||
ions FE 3 #Fe (iii) Ion
|
|
||||||
ions SR 2 #Strontium Ion
|
|
||||||
ions CU 2 #Copper (ii) Ion
|
|
||||||
ions IOD -1 #Iodide Ion
|
|
||||||
ions HG 2 #Mercury (ii) Ion
|
|
||||||
ions BR -1 #Bromide Ion
|
|
||||||
ions CO 2 #Cobalt (ii) Ion
|
|
||||||
ions NI 2 #Nickel (ii) Ion
|
|
||||||
ions FE2 2 #Fe (ii) Ion
|
|
||||||
|
|
||||||
# write out order of residues
|
|
||||||
write_out_order ASP
|
|
||||||
write_out_order GLU
|
|
||||||
write_out_order C-
|
|
||||||
write_out_order HIS
|
|
||||||
write_out_order CYS
|
|
||||||
write_out_order TYR
|
|
||||||
write_out_order LYS
|
|
||||||
write_out_order ARG
|
|
||||||
write_out_order SER
|
|
||||||
write_out_order N+
|
|
||||||
write_out_order CG
|
|
||||||
write_out_order C2N
|
|
||||||
write_out_order N30
|
|
||||||
write_out_order N31
|
|
||||||
write_out_order N32
|
|
||||||
write_out_order N33
|
|
||||||
write_out_order NAR
|
|
||||||
write_out_order OCO
|
|
||||||
write_out_order SH
|
|
||||||
write_out_order OP
|
|
||||||
8
propka/__main__.py
Normal file
8
propka/__main__.py
Normal file
@@ -0,0 +1,8 @@
|
|||||||
|
"""Allow the PROPKA package to be run as a program.
|
||||||
|
|
||||||
|
For example, `python -m propka`
|
||||||
|
"""
|
||||||
|
from .run import main
|
||||||
|
|
||||||
|
if __name__ == "__main__":
|
||||||
|
main()
|
||||||
@@ -222,7 +222,7 @@ def build_parser(parser=None):
|
|||||||
return parser
|
return parser
|
||||||
|
|
||||||
|
|
||||||
def loadOptions(args):
|
def loadOptions(args=None):
|
||||||
"""
|
"""
|
||||||
Load the arguments parser with options. Note that verbosity is set as soon
|
Load the arguments parser with options. Note that verbosity is set as soon
|
||||||
as this function is invoked.
|
as this function is invoked.
|
||||||
@@ -232,17 +232,10 @@ def loadOptions(args):
|
|||||||
Returns:
|
Returns:
|
||||||
argparse namespace
|
argparse namespace
|
||||||
"""
|
"""
|
||||||
# defining a 'usage' message
|
|
||||||
usage = "usage: %prog [options] filename"
|
|
||||||
|
|
||||||
# loading the parser
|
# loading the parser
|
||||||
parser = build_parser()
|
parser = build_parser()
|
||||||
|
|
||||||
# parsing and returning options and arguments
|
# parsing and returning options and arguments
|
||||||
if len(args) == 0:
|
|
||||||
# command line
|
|
||||||
options = parser.parse_args()
|
|
||||||
else:
|
|
||||||
options = parser.parse_args(args)
|
options = parser.parse_args(args)
|
||||||
|
|
||||||
# adding specified filenames to arguments
|
# adding specified filenames to arguments
|
||||||
|
|||||||
Reference in New Issue
Block a user