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#!/usr/bin/env python
import sys,math,random
version = "---"
previous = "20140603.11.TAW"
# Modify insane to take in arbitary lipid definition strings and use them as a template for lipids
# Also take in lipid name
# Edits: by Helgi I. Ingolfsson (all edits are marked with: # HII edit - lipid definition )
# PROTOLIPID (diacylglycerol), 18 beads
#
# 1-3-4-6-7--9-10-11-12-13-14
# \| |/ |
# 2 5 8-15-16-17-18-19-20
#
lipidsx = {}
lipidsy = {}
lipidsz = {}
lipidsa = {}
#
## Diacyl glycerols
moltype = "lipid"
lipidsx[moltype] = ( 0, .5, 0, 0, .5, 0, 0, .5, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
lipidsy[moltype] = ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
lipidsz[moltype] = ( 10, 9, 9, 8, 8, 7, 6, 6, 5, 4, 3, 2, 1, 0, 5, 4, 3, 2, 1, 0)
lipidsa.update({ # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
## Phospholipids
"DTPC": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A - - - - C1B C2B - - - - "),
"DLPC": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A C3A - - - C1B C2B C3B - - - "),
"DPPC": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A C3A C4A - - C1B C2B C3B C4B - - "),
"DBPC": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A C3A C4A C5A - C1B C2B C3B C4B C5B - "),
"POPC": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
"DOPC": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A D2A C3A C4A - - C1B D2B C3B C4B - - "),
"DAPC": (moltype, " - - - NC3 - PO4 GL1 GL2 D1A D2A D3A D4A C5A - D1B D2B D3B D4B C5B - "),
"DIPC": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A D2A D3A C4A - - C1B D2B D3B C4B - - "),
"DGPC": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A D3A C4A C5A - C1B C2B D3B C4B C5B - "),
"DNPC": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A C3A D4A C5A C6A C1B C2B C3B D4B C5B C6B"),
"DTPE": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A C2A - - - - C1B C2B - - - - "),
"DLPE": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A C2A C3A - - - C1B C2B C3B - - - "),
"DPPE": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A C2A C3A C4A - - C1B C2B C3B C4B - - "),
"DBPE": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A C2A C3A C4A C5A - C1B C2B C3B C4B C5B - "),
"POPE": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
"DOPE": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A D2A C3A C4A - - C1B D2B C3B C4B - - "),
"POPG": (moltype, " - - - GL0 - PO4 GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
"DOPG": (moltype, " - - - GL0 - PO4 GL1 GL2 C1A D2A C3A C4A - - C1B D2B C3B C4B - - "),
"POPS": (moltype, " - - - CN0 - PO4 GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
"DOPS": (moltype, " - - - CN0 - PO4 GL1 GL2 C1A D2A C3A C4A - - C1B D2B C3B C4B - - "),
"DPSM": (moltype, " - - - NC3 - PO4 AM1 AM2 T1A C2A C3A - - - C1B C2B C3B C4B - - "),
"DBSM": (moltype, " - - - NC3 - PO4 AM1 AM2 T1A C2A C3A C4A - - C1B C2B C3B C4B C5B - "),
"BNSM": (moltype, " - - - NC3 - PO4 AM1 AM2 T1A C2A C3A C4A - - C1B C2B C3B C4B C5B C6B"),
# PG for thylakoid membrane
"OPPG": (moltype, " - - - GL0 - PO4 GL1 GL2 C1A C2A C3A C4A - - C1B D2B C3B C4B - - "),
# PG for thylakoid membrane of spinach (PPT with a trans-unsaturated bond at sn1 and a triple-unsaturated bond at sn2,
# and PPG with a transunsaturated bond at sn1 and a palmitoyl tail at sn2)
"JPPG": (moltype, " - - - GL0 - PO4 GL1 GL2 C1A C2A C3A C4A - - D1B C2B C3B C4B - - "),
"JFPG": (moltype, " - - - GL0 - PO4 GL1 GL2 C1A D2A D3A D4A - - D1B C2B C3B C4B - - "),
## Monoacylglycerol
"GMO": (moltype, " - - - - - - GL1 GL2 C1A C2A D3A C4A C5A - - - - - - - "),
## Templates using the old lipid names and definitions
"DHPC.o": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A - - - - C1B C2B - - - - "),
"DMPC.o": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A C3A - - - C1B C2B C3B - - - "),
"DSPC.o": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A C3A C4A C5A - C1B C2B C3B C4B C5B - "),
"POPC.o": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A C3A C4A - - C1B C2B D3B C4B C5B - "),
"DOPC.o": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A D3A C4A C5A - C1B C2B D3B C4B C5B - "),
"DUPC.o": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A D2A D3A C4A - - C1B D2B D3B C4B - - "),
"DEPC.o": (moltype, " - - - NC3 - PO4 GL1 GL2 C1A C2A C3A D4A C5A C6A C1B C2B C3B D4B C5B C6B"),
"DHPE.o": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A C2A - - - - C1B C2B - - - - "),
"DLPE.o": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A C2A C3A - - - C1B C2B C3B - - - "),
"DMPE.o": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A C2A C3A - - - C1B C2B C3B - - - "),
"DSPE.o": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A C2A C3A C4A C5A - C1B C2B C3B C4B C5B - "),
"POPE.o": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A C2A C3A C4A - - C1B C2B D3B C4B C5B - "),
"DOPE.o": (moltype, " - - - NH3 - PO4 GL1 GL2 C1A C2A D3A C4A C5A - C1B C2B D3B C4B C5B - "),
"PPCS.o": (moltype, " - - - NC3 - PO4 AM1 AM2 C1A C2A C3A C4A - - D1B C2B C3B C4B - - "),
"DOPG.o": (moltype, " - - - GL0 - PO4 GL1 GL2 C1A C2A D3A C4A C5A - C1B C2B D3B C4B C5B - "),
"POPG.o": (moltype, " - - - GL0 - PO4 GL1 GL2 C1A C2A C3A C4A - - C1B C2B D3B C4B C5B - "),
"DOPS.o": (moltype, " - - - CN0 - PO4 GL1 GL2 C1A C2A D3A C4A C5A - C1B C2B D3B C4B C5B - "),
"POPS.o": (moltype, " - - - CN0 - PO4 GL1 GL2 C1A C2A C3A C4A - - C1B C2B D3B C4B C5B - "),
"CPG.o": (moltype, " - - - GL0 - PO4 GL1 GL2 C1A C2A C3A C4A - - C1B C2B D3B C4B - - "),
"PPG.o": (moltype, " - - - GL0 - PO4 GL1 GL2 C1A C2A C3A C4A - - D1B C2B C3B C4B - - "),
"PPT.o": (moltype, " - - - GL0 - PO4 GL1 GL2 C1A D2A D3A D4A - - D1B C2B C3B C4B - - "),
"DSMG.o": (moltype, " - - - C6 C4 C1 GL1 GL2 C1A C2A C3A C4A C5A - C1B C2B C3B C4B C5B - "),
"DSDG.o": (moltype, "C61 C41 C11 C62 C42 C12 GL1 GL2 C1A C2A C3A C4A C5A - C1B C2B C3B C4B C5B - "),
"DSSQ.o": (moltype, " - - S6 C6 C4 C1 GL1 GL2 C1A C2A C3A C4A C5A - C1B C2B C3B C4B C5B - "),
})
# HII fix for PI templates and new templates PI(s) with diffrent tails, PO-PIP1(3) and POPIP2(4,5)
#Prototopology for phosphatidylinositol type lipids 5,6,7 are potentail phosphates (PIP1,PIP2 and PIP3)
# 1,2,3 - is the inositol and 4 is the phosphate that links to the tail part.
# 5
# \
# 6-2-1-4-8--10-11-12-13-14-15
# |/ |
# 7-3 9--16-17-18-19-20-21
moltype = "INOSITOLLIPIDS"
lipidsx[moltype] = ( .5, .5, 0, 0, 1, .5, 0, 0, .5, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
lipidsy[moltype] = ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
lipidsz[moltype] = ( 8, 9, 9, 7, 10, 10, 10, 6, 6, 5, 4, 3, 2, 1, 0, 5, 4, 3, 2, 1, 0)
lipidsa.update({ # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
"DPPI": (moltype, " C1 C2 C3 CP - - - GL1 GL2 C1A C2A C3A C4A - - C1B C2B C3B C4B - - "),
"POPI": (moltype, " C1 C2 C3 CP - - - GL1 GL2 C1A D2A C3A C4A - - C1B C2B C3B C4B - - "),
"PIPI": (moltype, " C1 C2 C3 CP - - - GL1 GL2 C1A D2A D3A C4A - - C1B C2B C3B C4B - - "),
"PAPI": (moltype, " C1 C2 C3 CP - - - GL1 GL2 D1A D2A D3A D4A C5A - C1B C2B C3B C4B - - "),
"PUPI": (moltype, " C1 C2 C3 CP - - - GL1 GL2 D1A D2A D3A D4A D5A - C1B C2B C3B C4B - - "),
"POP1": (moltype, " C1 C2 C3 CP P1 - - GL1 GL2 C1A C2A D3A C4A - - C1B C2B C3B C4B - - "),
"POP2": (moltype, " C1 C2 C3 CP P1 P2 - GL1 GL2 C1A C2A D3A C4A - - C1B C2B C3B C4B - - "),
"POP3": (moltype, " C1 C2 C3 CP P1 P2 P3 GL1 GL2 C1A C2A D3A C4A - - C1B C2B C3B C4B - - "),
## Templates using the old lipid names and definitions
"PI.o" : (moltype, " C1 C2 C3 CP - - - GL1 GL2 C1A C2A C3A C4A - - CU1 CU2 CU3 CU4 CU5 - "),
"PI34.o": (moltype, " C1 C2 C3 CP PO1 PO2 - GL1 GL2 C1A C2A C3A C4A - - CU1 CU2 CU3 CU4 CU5 - "),
})
#Prototopology for longer and branched glycosil and ceramide based glycolipids
#
# 17-15-14-16
# |/
# 13
# |
# 12-10-9-7-6-4-3-1--18--20-21-22-23-24
# |/ |/ |/ |/ |
# 11 8 5 2 19--25-26-27-28-29
moltype = "GLYCOLIPIDS"
lipidsx[moltype] = ( 0, .5, 0, 0, .5, 0, 0, .5, 0, 0, .5, 0, 0, 0, 0, 0, 0, 0, .5, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
lipidsy[moltype] = ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, .5, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
lipidsz[moltype] = ( 6, 7, 7, 8, 9, 9, 10, 11, 11, 12, 13, 13, 10, 9, 10, 8, 11, 5, 5, 4, 3, 2, 1, 0, 4, 3, 2, 1, 0)
lipidsa.update({ # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29
"DPG1": (moltype, "GM1 GM2 GM3 GM4 GM5 GM6 GM7 GM8 GM9 GM10 GM11 GM12 GM13 GM14 GM15 GM16 GM17 AM1 AM2 T1A C2A C3A - - - C1B C2B C3B C4B - - "),
"DXG1": (moltype, "GM1 GM2 GM3 GM4 GM5 GM6 GM7 GM8 GM9 GM10 GM11 GM12 GM13 GM14 GM15 GM16 GM17 AM1 AM2 T1A C2A C3A C4A C5A - C1B C2B C3B C4B C5B C6B"),
"PNG1": (moltype, "GM1 GM2 GM3 GM4 GM5 GM6 GM7 GM8 GM9 GM10 GM11 GM12 GM13 GM14 GM15 GM16 GM17 AM1 AM2 T1A C2A C3A - - - C1B C2B C3B D4B C5B C6B"),
"XNG1": (moltype, "GM1 GM2 GM3 GM4 GM5 GM6 GM7 GM8 GM9 GM10 GM11 GM12 GM13 GM14 GM15 GM16 GM17 AM1 AM2 T1A C2A C3A C4A C5A - C1B C2B C3B D4B C5B C6B"),
"DPG3": (moltype, "GM1 GM2 GM3 GM4 GM5 GM6 - - - - - - GM13 GM14 GM15 GM16 GM17 AM1 AM2 T1A C2A C3A - - - C1B C2B C3B C4B - - "),
"DXG3": (moltype, "GM1 GM2 GM3 GM4 GM5 GM6 - - - - - - GM13 GM14 GM15 GM16 GM17 AM1 AM2 T1A C2A C3A C4A C5A - C1B C2B C3B C4B C5B C6B"),
"PNG3": (moltype, "GM1 GM2 GM3 GM4 GM5 GM6 - - - - - - GM13 GM14 GM15 GM16 GM17 AM1 AM2 T1A C2A C3A - - - C1B C2B C3B D4B C5B C6B"),
"XNG3": (moltype, "GM1 GM2 GM3 GM4 GM5 GM6 - - - - - - GM13 GM14 GM15 GM16 GM17 AM1 AM2 T1A C2A C3A C4A C5A - C1B C2B C3B D4B C5B C6B"),
"DPCE": (moltype, " - - - - - - - - - - - - - - - - - AM1 AM2 T1A C2A C3A - - C1B C2B C3B C4B - "),
"DPGS": (moltype, " C1 C2 C3 - - - - - - - - - - - - - - AM1 AM2 T1A C2A C3A - - C1B C2B C3B C4B - "),
"DPMG": (moltype, " C1 C2 C3 - - - - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B C2B C3B C4B - "),
"DPSG": (moltype, " S1 C1 C2 C3 - - - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B C2B C3B C4B - "),
"DPGG": (moltype, "GB2 GB3 GB1 GA1 GA2 GA3 - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B C2B C3B C4B - "),
#lipids for thylakoid membrane of cyanobacteria: oleoyl tail at sn1 and palmiotyl chain at sn2. SQDG no double bonds
"OPMG": (moltype, " C1 C2 C3 - - - - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B D2B C3B C4B - "),
"OPSG": (moltype, " S1 C1 C2 C3 - - - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B D2B C3B C4B - "),
"OPGG": (moltype, "GB2 GB3 GB1 GA1 GA2 GA3 - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B D2B C3B C4B - "),
#lipids for thylakoid membrane of spinach: for the *T both chains are triple unsaturated and the *G have a triple unsaturated chain at sn1 and a palmitoyl chain at sn2.
"FPMG": (moltype, " C1 C2 C3 - - - - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B D2B D3B D4B - "),
"DFMG": (moltype, " C1 C2 C3 - - - - - - - - - - - - - - GL1 GL2 C1A D2A D3A D4A - C1B D2B D3B D4B - "),
"FPSG": (moltype, " S1 C1 C2 C3 - - - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B D2B D3B D4B - "),
"FPGG": (moltype, "GB2 GB3 GB1 GA1 GA2 GA3 - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B D2B D3B D4B - "),
"DFGG": (moltype, "GB2 GB3 GB1 GA1 GA2 GA3 - - - - - - - - - - - GL1 GL2 C1A D2A D3A D4A - C1B D2B D3B D4B - "),
## Templates using the old lipid names and definitions
"GM1.o" : (moltype, "GM1 GM2 GM3 GM4 GM5 GM6 GM7 GM8 GM9 GM10 GM11 GM12 GM13 GM14 GM15 GM16 GM17 AM1 AM2 C1A C2A C3A C4A C5A C1B C2B C3B C4B - "),
"DGDG.o": (moltype, "GB2 GB3 GB1 GA1 GA2 GA3 - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B C2B C3B C4B - "),
"MGDG.o": (moltype, " C1 C2 C3 - - - - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B C2B C3B C4B - "),
"SQDG.o": (moltype, " S1 C1 C2 C3 - - - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B C2B C3B C4B - "),
"CER.o" : (moltype, " - - - - - - - - - - - - - - - - - AM1 AM2 C1A C2A C3A C4A - C1B C2B C3B C4B - "),
"GCER.o": (moltype, " C1 C2 C3 - - - - - - - - - - - - - - AM1 AM2 C1A C2A C3A C4A - C1B C2B C3B C4B - "),
"DPPI.o": (moltype, " C1 C2 C3 - CP - - - - - - - - - - - - GL1 GL2 C1A C2A C3A C4A - C1B C2B C3B C4B - "),
})
moltype = "QUINONES"
lipidsx[moltype] = ( 0, .5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
lipidsy[moltype] = ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
lipidsz[moltype] = ( 6, 7, 7, 5.5, 5, 4.5, 4, 3.5, 2.5, 2, 1.5, 1)
lipidsa.update({ # 1 2 3 4 5 6 7 8 9 10 11 12
"PLQ": (moltype, " PLQ3 PLQ2 PLQ1 PLQ4 PLQ5 PLQ6 PLQ7 PLQ8 PLQ9 PLQ10 PLQ11 PLQ12"),
})
# Prototopology for cardiolipins
#
# 4-11-12-13-14-15-16
# |
# 2---3--5--6--7--8--9-10
# /
# 1
# \
# 17-18-20-21-22-23-24-25
# |
# 19-26-27-28-29-30-31
#
moltype = "CARDIOLIPINS"
lipidsx[moltype] = ( 0.5, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)
lipidsy[moltype] = ( 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
lipidsz[moltype] = ( 8, 7, 6, 6, 5, 4, 3, 2, 1, 0, 5, 4, 3, 2, 1, 0, 7, 6, 6, 5, 4, 3, 2, 1, 0, 5, 4, 3, 2, 1, 0)
lipidsa.update({ # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31
"CDL0": (moltype, "GL5 PO41 GL1 GL2 C1A C2A D3A C4A C5A - C1B C2B D3B C4B C5B - PO42 GL3 GL4 C1C C2C D3C C4C C5C - C1D C2D D3D C4D C5D -"), # Warning not the same names is in .itp
"CDL1": (moltype, "GL5 PO41 GL1 GL2 C1A C2A D3A C4A C5A - C1B C2B D3B C4B C5B - PO42 GL3 GL4 C1C C2C D3C C4C C5C - C1D C2D D3D C4D C5D -"), # Warning not the same names is in .itp
"CDL2": (moltype, "GL5 PO41 GL1 GL2 C1A C2A D3A C4A C5A - C1B C2B D3B C4B C5B - PO42 GL3 GL4 C1C C2C D3C C4C C5C - C1D C2D D3D C4D C5D -"), # Warning not the same names is in .itp
"CL4P": (moltype, "GL5 PO41 GL1 GL2 C1A C2A C3A C4A C5A - C1B C2B C3B C4B C5B - PO42 GL3 GL4 C1C C2C C3C C4C C5C - C1D C2D C3D C4D C5D -"),
"CL4M": (moltype, "GL5 PO41 GL1 GL2 C1A C2A C3A - - - C1B C2B C3B - - - PO42 GL3 GL4 C1C C2C C3C - - - C1D C2D C3D - - -"),
## Templates using the old lipid names and definitions
"CL4.o" : (moltype, "GL5 PO41 GL1 GL2 C1A C2A D3A C4A C5A - C1B C2B D3B C4B C5B - PO42 GL3 GL4 C1C C2C D3C C4C C5C - C1D C2D D3D C4D C5D -"),
"CL4O.o": (moltype, "GL5 PO41 GL1 GL2 C1A C2A D3A C4A C5A - C1B C2B D3B C4B C5B - PO42 GL3 GL4 C1C C2C D3C C4C C5C - C1D C2D D3D C4D C5D -"),
})
# Prototopology for mycolic acid(s)
#
# 1--2--3--4--5--6--7--8
# |
# 16-15-14-13-12-11-10--9
# |
# 17-18-19-20-21-22-23-24
# /
# 32-31-30-29-28-27-25-26
#
moltype = "MYCOLIC ACIDS"
lipidsx[moltype] = ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)
lipidsy[moltype] = ( 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0)
lipidsz[moltype] = ( 7, 6, 5, 4, 3, 2, 1, 0, 0, 1, 2, 3, 4, 5, 6, 7, 7, 6, 5, 4, 3, 2, 1, 0, 1, 0, 2, 3, 4, 5, 6, 7)
lipidsa.update({ # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
"AMA": (moltype, " - - - C1A C2A C3A C4A C5A M1A C1B C2B C3B C4B - - - - - M1B C1C C2C C3C - - COH OOH C1D C2D C3D C4D C5D C6D"),
"AMA.w": (moltype, " - - - C1A C2A C3A C4A C5A M1A C1B C2B C3B C4B - - - - - M1B C1C C2C C3C - - COH OOH C1D C2D C3D C4D C5D C6D"),
"KMA": (moltype, " - - - C1A C2A C3A C4A C5A M1A C1B C2B C3B C4B - - - - - M1B C1C C2C C3C - - COH OOH C1D C2D C3D C4D C5D C6D"),
"MMA": (moltype, " - - - C1A C2A C3A C4A C5A M1A C1B C2B C3B C4B - - - - - M1B C1C C2C C3C - - COH OOH C1D C2D C3D C4D C5D C6D"),
})
# Sterols
moltype = "sterol"
lipidsx[moltype] = ( 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0)
lipidsy[moltype] = ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
lipidsz[moltype] = ( 0, 0, 0, 0, 0, 0, 5.3,4.5,3.9,3.3, 3 ,2.6,1.4, 0, 0, 0, 0, 0)
lipidsa.update({
"CHOL": (moltype, " - - - - - - ROH R1 R2 R3 R4 R5 C1 C2 - - - - "),
"ERGO": (moltype, " - - - - - - ROH R1 R2 R3 R4 R5 C1 C2 - - - - "),
})
# Hopanoids
moltype = "Hopanoids"
lipidsx[moltype] = ( 0, 0, 0, 0, 0.5,-0.5, 0, 0, 0.5, 0.5, 0, 0, 0, 0, 0, 0, 0, 0)
lipidsy[moltype] = ( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
lipidsz[moltype] = ( 0, 0, 0, 0, 0.5, 1.4, 2.6, 3, 3.3, 3.9, 4.5, 5.0, 5.5, 6.0, 0, 0, 0, 0)
lipidsa.update({
"HOPR": (moltype, " - - - R1 R2 R3 R4 R5 R6 R7 R8 - - - - - - - "),
"HHOP": (moltype, " - - - R1 R2 R3 R4 R5 R6 R7 R8 C1 - - - - - - "),
"HDPT": (moltype, " - - - R1 R2 R3 R4 R5 R6 R7 R8 C1 - - - - - - "),
"HBHT": (moltype, " - - - R1 R2 R3 R4 R5 R6 R7 R8 C1 C2 C3 - - - - "),
})
# Lists for automatic charge determination
charges = {"ARG":1, "LYS":1, "ASP":-1, "GLU":-1, "DOPG":-1, "POPG":-1, "DOPS":-1, "POPS":-1, "DSSQ":-1}
a, b = math.sqrt(2)/20, math.sqrt(2)/60
ct, st = math.cos(math.pi*109.47/180), math.sin(math.pi*109.47/180) # Tetrahedral
# Get a set of coordinates for a solvent particle with a given name
# Dictionary of solvents; First only those with multiple atoms
solventParticles = {
"PW": (("W",(-0.07,0,0)), # Polarizable water
("WP",(0.07,0,0)),
("WM",(0.07,0,0))),
"BMW": (("C",(0,0,0)),
("Q1",(0.12,0,0)),
("Q2",(-0.06,math.cos(math.pi/6)*0.12,0))), # BMW water
"SPC": (("OW",(0,0,0)), # SPC
("HW1",(0.01,0,0)),
("HW2",(0.01*ct,0.01*st,0))),
"SPCM": (("OW",(0,0,0)), # Multiscale/Martini SPC
("HW1",(0.01,0,0)),
("HW2",(0.01*ct,0.01*st,0)),
("vW",(0,0,0))),
"FG4W": (("OW1",(a,a,a)), # Bundled water
("HW11",(a,a-b,a-b)),
("HW12",(a,a+b,a+b)),
("OW2",(a,-a,-a)),
("HW21",(a-b,-a,-a+b)),
("HW22",(a+b,-a,-a-b)),
("OW3",(-a,-a,a)),
("HW31",(-a,-a+b,a-b)),
("HW32",(-a,-a-b,a+b)),
("OW4",(-a,a,-a)),
("HW41",(-a+b,a,-a+b)),
("HW42",(-a-b,a,-a-b))),
"FG4W-MS": (("OW1",(a,a,a)), # Bundled water, multiscaled
("HW11",(a,a-b,a-b)),
("HW12",(a,a+b,a+b)),
("OW2",(a,-a,-a)),
("HW21",(a-b,-a,-a+b)),
("HW22",(a+b,-a,-a-b)),
("OW3",(-a,-a,a)),
("HW31",(-a,-a+b,a-b)),
("HW32",(-a,-a-b,a+b)),
("OW4",(-a,a,-a)),
("HW41",(-a+b,a,-a+b)),
("HW42",(-a-b,a,-a-b)),
("VZ",(0,0,0))),
"GLUC": (("B1",(-0.11, 0, 0)),
("B2",( 0.05, 0.16,0)),
("B3",( 0.05,-0.16,0))),
"FRUC": (("B1",(-0.11, 0, 0)),
("B2",( 0.05, 0.16,0)),
("B3",( 0.05,-0.16,0))),
"SUCR": (("B1",(-0.25, 0.25,0)),
("B2",(-0.25, 0, 0)),
("B3",(-0.25,-0.25,0)),
("B4",( 0.25, 0, 0)),
("B5",( 0.25, 0.25,0)),
("B6",( 0.25,-0.25,0))),
"MALT": (("B1",(-0.25, 0.25,0)),
("B2",(-0.25, 0, 0)),
("B3",(-0.25,-0.25,0)),
("B4",( 0.25, 0, 0)),
("B5",( 0.25, 0.25,0)),
("B6",( 0.25,-0.25,0))),
"CELL": (("B1",(-0.25, 0.25,0)),
("B2",(-0.25, 0, 0)),
("B3",(-0.25,-0.25,0)),
("B4",( 0.25, 0, 0)),
("B5",( 0.25, 0.25,0)),
("B6",( 0.25,-0.25,0))),
"KOJI": (("B1",(-0.25, 0.25,0)),
("B2",(-0.25, 0, 0)),
("B3",(-0.25,-0.25,0)),
("B4",( 0.25, 0, 0)),
("B5",( 0.25, 0.25,0)),
("B6",( 0.25,-0.25,0))),
"SOPH": (("B1",(-0.25, 0.25,0)),
("B2",(-0.25, 0, 0)),
("B3",(-0.25,-0.25,0)),
("B4",( 0.25, 0, 0)),
("B5",( 0.25, 0.25,0)),
("B6",( 0.25,-0.25,0))),
"NIGE": (("B1",(-0.25, 0.25,0)),
("B2",(-0.25, 0, 0)),
("B3",(-0.25,-0.25,0)),
("B4",( 0.25, 0, 0)),
("B5",( 0.25, 0.25,0)),
("B6",( 0.25,-0.25,0))),
"LAMI": (("B1",(-0.25, 0.25,0)),
("B2",(-0.25, 0, 0)),
("B3",(-0.25,-0.25,0)),
("B4",( 0.25, 0, 0)),
("B5",( 0.25, 0.25,0)),
("B6",( 0.25,-0.25,0))),
"TREH": (("B1",(-0.25, 0.25,0)),
("B2",(-0.25, 0, 0)),
("B3",(-0.25,-0.25,0)),
("B4",( 0.25, 0, 0)),
("B5",( 0.25, 0.25,0)),
("B6",( 0.25,-0.25,0))),
# Loose aminoacids
"GLY": (("BB", ( 0, 0, 0)),),
"ALA": (("BB", ( 0, 0, 0)),),
"ASN": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"ASP": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"GLU": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"GLN": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"LEU": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"ILE": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"VAL": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"SER": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"THR": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"CYS": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"MET": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"LYS": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"PRO": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"HYP": (("BB", ( 0.25, 0, 0)),
("SC1",(-0.25, 0, 0))),
"ARG": (("BB", ( 0.25, 0, 0)),
("SC1",( 0, 0, 0)),
("SC2",(-0.25, 0.125, 0))),
"PHE": (("BB", ( 0.25, 0, 0)),
("SC1",( 0, 0, 0)),
("SC2",(-0.25,-0.125, 0)),
("SC3",(-0.25, 0.125, 0))),
"TYR": (("BB", ( 0.25, 0, 0)),
("SC1",( 0, 0, 0)),
("SC2",(-0.25,-0.125, 0)),
("SC3",(-0.25, 0.125, 0))),
"TRP": (("BB", ( 0.25, 0.125, 0)),
("SC1",( 0.25, 0, 0)),
("SC2",( 0, -0.125, 0)),
("SC3",( 0, 0.125, 0)),
("SC4",(-0.25, 0, 0))),
}
# Update the solvents dictionary with single atom ones
for s in ["W","NA","CL","Mg","K","BUT"]:
solventParticles[s] = ((s,(0,0,0)),)
# Apolar amino acids nd stuff for orienting proteins in membrane
apolar = "ALA CYS PHE ILE LEU MET VAL TRP PLM CLR".split()
## PRIVATE PARTS FROM THIS POINT ON ##
S = str
F = float
I = int
R = random.random
def vector(v):
if type(v) == str and "," in v:
return [float(i) for i in v.split(",")]
return float(v)
def vvadd(a,b):
if type(b) in (int,float):
return [i+b for i in a]
return [i+j for i,j in zip(a,b)]
def vvsub(a,b):
if type(b) in (int,float):
return [i-b for i in a]
return [i-j for i,j in zip(a,b)]
def isPDBAtom(l):
return l.startswith("ATOM") or l.startswith("HETATM")
def pdbAtom(a):
##01234567890123456789012345678901234567890123456789012345678901234567890123456789
##ATOM 2155 HH11 ARG C 203 116.140 48.800 6.280 1.00 0.00
## ===> atom name, res name, res id, chain, x, y, z
return (S(a[12:16]),S(a[17:20]),I(a[22:26]),a[21],F(a[30:38])/10,F(a[38:46])/10,F(a[46:54])/10)
d2r = 3.14159265358979323846264338327950288/180
def pdbBoxRead(a):
# Convert a PDB CRYST1 entry to a lattice definition.
# Convert from Angstrom to nanometer
fa, fb, fc, aa, ab, ac = [float(i) for i in a.split()[1:7]]
ca, cb, cg, sg = math.cos(d2r*aa), math.cos(d2r*ab), math.cos(d2r*ac) , math.sin(d2r*ac)
wx, wy = 0.1*fc*cb, 0.1*fc*(ca-cb*cg)/sg
wz = math.sqrt(0.01*fc*fc - wx*wx - wy*wy)
return [0.1*fa, 0, 0, 0.1*fb*cg, 0.1*fb*sg, 0, wx, wy, wz]
def groAtom(a):
#012345678901234567890123456789012345678901234567890
# 1PRN N 1 4.168 11.132 5.291
## ===> atom name, res name, res id, chain, x, y, z
return (S(a[10:15]), S(a[5:10]), I(a[:5]), " ", F(a[20:28]),F(a[28:36]),F(a[36:44]))
def groBoxRead(a):
b = [F(i) for i in a.split()] + 6*[0] # Padding for rectangular boxes
return b[0],b[3],b[4],b[5],b[1],b[6],b[7],b[8],b[2]
def readBox(a):
x = [ float(i) for i in a.split(",") ] + 6*[0]
if len(x) == 12: # PDB format
return pdbBoxRead("CRYST1 "+" ".join([str(i) for i in x]))
else: # GRO format
return x[0],x[3],x[4],x[5],x[1],x[6],x[7],x[8],x[2]
class Structure:
def __init__(self,filename=None):
self.title = ""
self.atoms = []
self.coord = []
self.rest = []
self.box = []
self._center = None
if filename:
lines = open(filename).readlines()
# Try extracting PDB atom/hetatm definitions
self.rest = []
self.atoms = [pdbAtom(i) for i in lines if isPDBAtom(i) or self.rest.append(i)]
if self.atoms:
# This must be a PDB file
self.title = "THIS IS INSANE!\n"
for i in self.rest:
if i.startswith("TITLE"):
self.title = i
self.box = [0,0,0,0,0,0,0,0,0]
for i in self.rest:
if i.startswith("CRYST1"):
self.box = pdbBoxRead(i)
else:
# This should be a GRO file
self.atoms = [groAtom(i) for i in lines[2:-1]]
self.rest = [lines[0],lines[1],lines[-1]]
self.box = groBoxRead(lines[-1])
self.title = lines[0]
self.coord = [i[4:7] for i in self.atoms]
self.center()
def __bool__(self):
return bool(self.atoms)
def __len__(self):
return len(self.atoms)
def __iadd__(self,s):
for i in range(len(self)):
self.coord[i] = vvadd(self.coord[i],s)
return self
def center(self,other=None):
if not self._center:
self._center = [ sum(i)/len(i) for i in zip(*self.coord)]
if other:
s = vvsub(other,self._center)
for i in range(len(self)):
self.coord[i] = vvadd(self.coord[i],s)
self._center = other
return s # return the shift
return self._center
def diam(self):
if self._center != (0,0,0):
self.center((0,0,0))
return 2*math.sqrt(max([i*i+j*j+k*k for i,j,k in self.coord]))
def diamxy(self):
if self._center != (0,0,0):
self.center((0,0,0))
return 2*math.sqrt(max([i*i+j*j for i,j,k in self.coord]))
def fun(self,fn):
return [fn(i) for i in zip(*self.coord)]
# Mean of deviations from initial value
def meand(v):
return sum([i-v[0] for i in v])/len(v)
# Sum of squares/crossproducts of deviations
def ssd(u,v):
return sum([(i-u[0])*(j-v[0]) for i,j in zip(u,v)])/(len(u)-1)
# Parse a string for a lipid as given on the command line (LIPID[:NUMBER])
def parse_mol(x):
l = x.split(":")
return l[0], len(l) == 1 and 1 or float(l[1])
## MIJN EIGEN ROUTINE ##
# Quite short piece of code for diagonalizing symmetric 3x3 matrices :)
# Analytic solution for third order polynomial
def solve_p3( a, b, c ):
Q,R,a3 = (3*b-a**2)/9.0, (-27*c+a*(9*b-2*a**2))/54.0, a/3.0
if Q**3 + R**2:
t,R13 = math.acos(R/math.sqrt(-Q**3))/3, 2*math.sqrt(-Q)
u,v,w = math.cos(t), math.sin(t+math.pi/6), math.cos(t+math.pi/3)
return R13*u-a3, -R13*v-a3, -R13*w-a3
else:
R13 = math.sqrt3(R)
return 2*R13-a3, -R13-a3, -R13-a3
# Normalization of 3-vector
def normalize(a):
f = 1.0/math.sqrt(a[0]*a[0]+a[1]*a[1]+a[2]*a[2])
return f*a[0],f*a[1],f*a[2]
# Eigenvectors for a symmetric 3x3 matrix:
# For symmetric matrix A the eigenvector v with root r satisfies
# v.Aw = Av.w = rv.w = v.rw
# v.(A-rI)w = v.Aw - v.rw = 0 for all w
# This means that for any two vectors p,q the eigenvector v follows from:
# (A-rI)p x (A-rI)q
# The input is var(x),var(y),var(z),cov(x,y),cov(x,z),cov(y,z)
# The routine has been checked and yields proper eigenvalues/-vectors
def mijn_eigen_sym_3x3(a,d,f,b,c,e):
a,d,f,b,c,e=1,d/a,f/a,b/a,c/a,e/a
b2, c2, e2, df = b*b, c*c, e*e, d*f
roots = list(solve_p3(-a-d-f, df-b2-c2-e2+a*(f+d), a*e2+d*c2+f*b2-a*df-2*b*c*e))
roots.sort(reverse=True)
ux, uy, uz = b*e-c*d, b*c-a*e, a*d-b*b
u = (ux+roots[0]*c,uy+roots[0]*e,uz+roots[0]*(roots[0]-a-d))
v = (ux+roots[1]*c,uy+roots[1]*e,uz+roots[1]*(roots[1]-a-d))
w = u[1]*v[2]-u[2]*v[1],u[2]*v[0]-u[0]*v[2],u[0]*v[1]-u[1]*v[0] # Cross product
return normalize(u),normalize(v),normalize(w),roots
# Very simple option class
class Option:
def __init__(self,func=str,num=1,default=None,description=""):
self.func = func
self.num = num
self.value = default
self.description = description
def __bool__(self):
return self.value != None
def __str__(self):
return self.value and str(self.value) or ""
def setvalue(self,v):
if len(v) == 1:
self.value = self.func(v[0])
else:
self.value = [ self.func(i) for i in v ]
tm = []
lipL = []
lipU = []
solv = []
# HII edit - lipid definition, for extra lipid definitaions
usrmols = []
usrheads = []
usrlinks = []
usrtails = []
usrLipHeadMapp = { # Define supported lipid head beads. One letter name mapped to atom name
"C": ('NC3'), # NC3 = Choline
"E": ('NH3'), # NH3 = Ethanolamine
"G": ('GL0'), # GL0 = Glycerol
"S": ('CNO'), # CNO = Serine
"P": ('PO4'), # PO4 = Phosphate
"O": ('PO4') # PO4 = Phosphate acid
}
usrIndexToLetter = "A B C D E F G H I J K L M N".split() # For naming lipid tail beads
# Description
desc = ""
# Option list
options = [
# option type number default description
# HII edit - lipid definition (last options are for additional lipid specification)
"""
Input/output related options
""",
("-f", Option(tm.append, 1, None, "Input GRO or PDB file 1: Protein")),
("-o", Option(str, 1, None, "Output GRO file: Membrane with Protein")),
("-p", Option(str, 1, None, "Optional rudimentary topology file")),
"""
Periodic boundary conditions
If -d is given, set up PBC according to -pbc such that no periodic
images are closer than the value given. This will make the numbers
provided for lipids be interpreted as relative numbers. If -d is
omitted, those numbers are interpreted as absolute numbers, and the
PBC are set to fit the given number of lipids in.
""",
("-pbc", Option(str, 1, "hexagonal", "PBC type: hexagonal, rectangular, square, cubic, optimal or keep")),
("-d", Option(float, 1, 0, "Distance between periodic images (nm)")),
("-dz", Option(float, 1, 0, "Z distance between periodic images (nm)")),
("-x", Option(vector, 1, 0, "X dimension or first lattice vector of system (nm)")),
("-y", Option(vector, 1, 0, "Y dimension or first lattice vector of system (nm)")),
("-z", Option(vector, 1, 0, "Z dimension or first lattice vector of system (nm)")),
("-box", Option(readBox, 1, None, "Box in GRO (3 or 9 floats) or PDB (6 floats) format, comma separated")),
("-n", Option(str, 1, None, "Index file --- TO BE IMPLEMENTED")),
"""
Membrane/lipid related options.
The options -l and -u can be given multiple times. Option -u can be
used to set the lipid type and abundance for the upper leaflet. Option
-l sets the type and abundance for the lower leaflet if option -u is
also given, or for both leaflets if option -u is not given. The
meaning of the number depends on whether option -d is used to set up
PBC
""",
("-l", Option(lipL.append, 1, None, "Lipid type and relative abundance (NAME[:#])")),
("-u", Option(lipU.append, 1, None, "Lipid type and relative abundance (NAME[:#])")),
("-a", Option(float, 1, 0.60, "Area per lipid (nm*nm)")),
("-au", Option(float, 1, None, "Area per lipid (nm*nm) for upper layer")),
("-asym", Option(int, 1, None, "Membrane asymmetry (number of lipids)")),
("-hole", Option(float, 1, None, "Make a hole in the membrane with specified radius")),
("-disc", Option(float, 1, None, "Make a membrane disc with specified radius")),
("-rand", Option(float, 1, 0.1, "Random kick size (maximum atom displacement)")),
("-bd", Option(float, 1, 0.3, "Bead distance unit for scaling z-coordinates (nm)")),
"""
Protein related options.
""",
("-center", Option(bool, 0, None, "Center the protein on z")),
("-orient", Option(bool, 0, None, "Orient protein in membrane")),
("-rotate", Option(str, 1, None, "Rotate protein (random|princ|angle(float))")),
("-od", Option(float, 1, 1.0, "Grid spacing for determining orientation")),
("-op", Option(float, 1, 4.0, "Hydrophobic ratio power for determining orientation")),
("-fudge", Option(float, 1, 0.1, "Fudge factor for allowing lipid-protein overlap")),
("-ring", Option(bool, 0, None, "Put lipids inside the protein")),
("-dm", Option(float, 1, None, "Shift protein with respect to membrane")),
"""
Solvent related options.
""",
("-sol", Option(solv.append, 1, None, "Solvent type and relative abundance (NAME[:#])")),
("-sold", Option(float, 1, 0.5, "Solvent diameter")),
("-solr", Option(float, 1, 0.1, "Solvent random kick")),
("-excl", Option(float, 1, 1.5, "Exclusion range (nm) for solvent addition relative to membrane center")),
"""
Salt related options.
""",
("-salt", Option(str, 1, None, "Salt concentration")),
("-charge", Option(str, 1, "auto", "Charge of system. Set to auto to infer from residue names")),
"""
Define additional lipid types (same format as in lipid-martini-itp-v01.py)
""",
("-alname", Option(usrmols.append, 1, None, "Additional lipid name, x4 letter")),
("-alhead", Option(usrheads.append, 1, None, "Additional lipid head specification string")),
("-allink", Option(usrlinks.append, 1, None, "Additional lipid linker specification string")),
("-altail", Option(usrtails.append, 1, None, "Additional lipid tail specification string")),
]
args = sys.argv[1:]
if '-h' in args or '--help' in args:
print("\n",__file__)
print(desc or "\nSomeone ought to write a description for this script...\n")
for thing in options:
print(type(thing) != str and "%10s %s"%(thing[0],thing[1].description) or thing)
print()
sys.exit()
# Convert the option list to a dictionary, discarding all comments
options = dict([i for i in options if not type(i) == str])
# Process the command line
while args:
ar = args.pop(0)
options[ar].setvalue([args.pop(0) for i in range(options[ar].num)])
# Read in the structures (if any)
tm = [ Structure(i) for i in tm ]
absoluteNumbers = not options["-d"]
# HII edit - lipid definition
# Add specified lipid definition to insane lipid library
for name, head, link, tail in zip(usrmols,usrheads,usrlinks,usrtails):
moltype = "usr_"+name
lipidsx[moltype] = []
lipidsy[moltype] = []
lipidsz[moltype] = []
headArray = (head).split()
linkArray = (link).split()
tailsArray = (tail).split()
lipidDefString = ""
if len(tailsArray) != len(linkArray):
print("Error, Number of tails has to equal number of linkers")
sys.exit()
# Find longest tail
maxTail = 0
for cTail in tailsArray:
if len(cTail) > maxTail:
maxTail = len(cTail)
cBeadZ = maxTail + len(headArray) # longest tail + linker (always x1) + lengths of all heads - 1 (as it starts on 0)
# Add head beads
for cHead in headArray:
lipidsx[moltype].append(0)
lipidsy[moltype].append(0)
lipidsz[moltype].append(cBeadZ)
cBeadZ -= 1
lipidDefString += usrLipHeadMapp[cHead] + " "
# Add linkers
for i,cLinker in enumerate(linkArray):
lipidsx[moltype].append(max(i-0.5,0))
lipidsy[moltype].append(0)
lipidsz[moltype].append(cBeadZ)
if cLinker == 'G':
lipidDefString += "GL" + str(i+1) + " "
elif cLinker == 'A':
lipidDefString += "AM" + str(i+1) + " "
else:
print("Error, linker type not supported")
sys.exit()
# Add tails
for i,cTail in enumerate(tailsArray):
cBeadZ = maxTail - 1
for j,cTailBead in enumerate(cTail):
lipidsx[moltype].append(i)
lipidsy[moltype].append(0)
lipidsz[moltype].append(cBeadZ)
cBeadZ -= 1
lipidDefString += cTailBead + str(j+1) + usrIndexToLetter[i] + " "
lipidsa[name] = (moltype,lipidDefString)
# End user lipid definition
# HII edit - lipid definition, had to move this one below the user lipid definitions to scale them to.
# First all X/Y coordinates of templates are centered and scaled (magic numbers!)
for i in list(lipidsx.keys()):
cx = (min(lipidsx[i])+max(lipidsx[i]))/2
lipidsx[i] = [0.25*(j-cx) for j in lipidsx[i]]
cy = (min(lipidsy[i])+max(lipidsy[i]))/2
lipidsy[i] = [0.25*(j-cy) for j in lipidsy[i]]
# Periodic boundary conditions
# option -box overrides everything
if options["-box"]:
options["-x"].value = options["-box"].value[:3]
options["-y"].value = options["-box"].value[3:6]
options["-z"].value = options["-box"].value[6:]
# option -pbc keep really overrides everything
if options["-pbc"].value == "keep" and tm:
options["-x"].value = tm[0].box[:3]
options["-y"].value = tm[0].box[3:6]
options["-z"].value = tm[0].box[6:]
# options -x, -y, -z take precedence over automatic determination
pbcSetX = 0
if type(options["-x"].value) in (list,tuple):
pbcSetX = options["-x"].value
elif options["-x"].value:
pbcSetX = [options["-x"].value,0,0]
pbcSetY = 0
if type(options["-y"].value) in (list,tuple):
pbcSetY = options["-y"].value
elif options["-y"].value:
pbcSetY = [0,options["-y"].value,0]
pbcSetZ = 0
if type(options["-z"].value) in (list,tuple):
pbcSetZ = options["-z"].value
elif options["-z"].value:
pbcSetZ = [0,0,options["-z"].value]
lo_lipd = math.sqrt(options["-a"].value)
up_lipd = options["-au"].value or lo_lipd
################
## I. PROTEIN ##
################
protein = Structure()
prot = []
xshifts = [0] # Shift in x direction per protein
## A. NO PROTEIN ---
if not tm:
resi = 0
# Set the box -- If there is a disc/hole, add its radius to the distance
if options["-disc"]:
pbcx = pbcy = pbcz = options["-d"].value + 2*options["-disc"].value
elif options["-hole"]:
pbcx = pbcy = pbcz = options["-d"].value + 2*options["-hole"].value
else:
pbcx = pbcy = pbcz = options["-d"].value
if "hexagonal".startswith(options["-pbc"].value):
# Hexagonal prism -- y derived from x directly
pbcy = math.sqrt(3)*pbcx/2
pbcz = options["-dz"].value or options["-z"].value or options["-d"].value
elif "optimal".startswith(options["-pbc"].value):
# Rhombic dodecahedron with hexagonal XY plane
pbcy = math.sqrt(3)*pbcx/2
pbcz = math.sqrt(6)*options["-d"].value/3
if "rectangular".startswith(options["-pbc"].value):
pbcz = options["-dz"].value or options["-z"].value or options["-d"].value
# Possibly override
pbcx = pbcSetX and pbcSetX[0] or pbcx
pbcy = pbcSetY and pbcSetY[1] or pbcy
pbcz = pbcSetZ and pbcSetZ[2] or pbcz
## B. PROTEIN ---
else:
for prot in tm:
## a. NO MEMBRANE --
if not lipL:
# A protein, but don't add lipids... Just solvate the protein
# Maybe align along principal axes and then build a cell according to PBC
# Set PBC starting from diameter and adding distance
if "cubic".startswith(options["-pbc"].value):
pbcx = pbcy = pbcz = prot.diam()+options["-d"].value
elif "rectangular".startswith(options["-pbc"].value):
pbcx, pbcy, pbcz = vvadd(vvsub(prot.fun(max),prot.fun(min)),options["-d"].value)
else:
# Rhombic dodecahedron
pbcx = pbcy = prot.diam()+options["-d"].value
pbcz = math.sqrt(2)*pbcx/2
# Possibly override
pbcx = pbcSetX and pbcSetX[0] or pbcx
pbcy = pbcSetY and pbcSetY[1] or pbcy
pbcz = pbcSetZ and pbcSetZ[2] or pbcz
# Center coordinates in rectangular brick -- Add solvent next
if len(tm) == 1:
prot.center((0.5*pbcx, 0.5*pbcy, 0.5*pbcz))
# Do not set an exclusion range for solvent
options["-excl"].value = -1
## b. PROTEIN AND MEMBRANE --
else:
# Have to build a membrane around the protein.
# So first put the protein in properly.
# Center the protein and store the shift
shift = prot.center((0,0,0))
## 1. Orient with respect to membrane
# Orient the protein according to the TM region, if requested
# This doesn't actually work very well...
if options["-orient"]:
# Grid spacing (nm)
d = options["-od"].value
pw = options["-op"].value
# Determine grid size
mx,my,mz = prot.fun(min)
rx,ry,rz = prot.fun(lambda x: max(x)-min(x)+1e-8)
# Number of grid cells
nx,ny,nz = int(rx/d+0.5),int(ry/d+0.5),int(rz/d+0.5)
# Initialize grids
atom = [[[0 for i in range(nz+2)] for j in range(ny+2)] for k in range(nx+2)]
phobic = [[[0 for i in range(nz+2)] for j in range(ny+2)] for k in range(nx+2)]
surface = []
for i, (ix, iy, iz) in zip(prot.atoms,prot.coord):
if i[1] != "DUM":
jx,jy,jz = int(nx*(ix-mx)/rx), int(ny*(iy-my)/ry), int(nz*(iz-mz)/rz)
atom[jx][jy][jz] += 1
phobic[jx][jy][jz] += (i[1].strip() in apolar)
# Determine average density
occupd = sum([bool(k) for i in atom for j in i for k in j])
avdens = float(sum([sum(j) for i in atom for j in i]))/occupd
#cgofile = open('density.cgo',"w")
#cgofile.write('[\n')
for i in range(nx):
for j in range(ny):
for k in range(nz):
if atom[i][j][k] > 0.1*avdens:
# Check the neighbouring cells; If one of them is not occupied, count cell as surface
if not (atom[i-1][j][k] and atom[i+1][j][k] and
atom[i][j-1][k] and atom[i][j+1][k] and
atom[i][j][k-1] and atom[i][j][k+1]):
sx,sy,sz = mx+rx*(i+0.5)/nx, my+ry*(j+0.5)/ny, mz+rz*(k+0.5)/nz
sw = (2.0*phobic[i][j][k]/atom[i][j][k])**pw
surface.append((sx,sy,sz,sw))
#cgofile.write(" 7.0, %f, %f, %f, %f,\n"%(10*sx,10*sy,10*sz,0.25*sw))
#cgofile.write(']\n')
#cgofile.close()
sx, sy, sz, w = list(zip(*surface))
W = 1.0/sum(w)
# Weighted center of apolar region; has to go to (0,0,0)
sxm,sym,szm = [sum(p)*W for p in zip(*[(m*i,m*j,m*k) for m,i,j,k in zip(w,sx,sy,sz)])]
# Place apolar center at origin
prot.center((-sxm,-sym,-szm))
sx, sy, sz = list(zip(*[(i-sxm,j-sym,k-szm) for i,j,k in zip(sx,sy,sz)]))
# Determine weighted deviations from centers
dx,dy,dz = list(zip(*[(m*i,m*j,m*k) for m,i,j,k in zip(w,sx,sy,sz)]))
# Covariance matrix for surface
xx,yy,zz,xy,yz,zx = [sum(p)*W for p in zip(*[(i*i,j*j,k*k,i*j,j*k,k*i) for i,j,k in zip(dx,dy,dz)])]
# PCA: u,v,w are a rotation matrix
(ux,uy,uz),(vx,vy,vz),(wx,wy,wz),r = mijn_eigen_sym_3x3(xx,yy,zz,xy,zx,yz)
# Rotate the coordinates
prot.coord = [(ux*i+uy*j+uz*k,vx*i+vy*j+vz*k,wx*i+wy*j+wz*k) for i,j,k in prot.coord]
## 4. Orient the protein in the xy-plane
## i. According to principal axes and unit cell
if options["-rotate"].value == "princ":
x, y, z = list(zip(*prot.coord))
# The rotation matrix in the plane equals the transpose
# of the matrix of eigenvectors from the 2x2 covariance
# matrix of the positions.
# For numerical stability we do
# d_i = x_i - x_0
# mean(x) = x_0 + sum(d_i)/N =