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insane.py
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#!/usr/bin/env python
import sys
import math
import random
import collections
version = "20150920.13.TAW"
previous = "20140814.13.TAW"
# 20150920 - Insane can read lipid definitions from MARTINI repository:
# ;@INSANE alhead=C P, allink=A A, altail=TCC CCCC, alname=DPSM, charge=0.0
# 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 - - - - "),
})
# 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 mean(a):
return sum(a)/len(a)
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 __nonzero__(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)]
headbeads = { # 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
}
linkbeads = { # Define supported lipid link beads. One letter name mapped to atom name
"G": "GL", # Glycerol
"A": "AM", # Amide (Ceramide/Sphingomyelin)
}
class Lipid:
"""Lipid structure"""
def __init__(self,**kwargs):
self.name = kwargs.get("name")
self.head = kwargs.get("head")
self.link = kwargs.get("link")
self.tail = kwargs.get("tail")
self.beads = kwargs.get("beads")
if type(self.beads) == str:
self.beads = self.beads.split()
self.charge = kwargs.get("charge")
self.template = kwargs.get("template")
self.coords = None
if kwargs.get("string"):
self.parse(kwargs["string"])
def parse(self,string):
"""
Parse lipid definition from string:
alhead=C P, allink=A A, altail=TCC CCCC, alname=DPSM, charge=0.0
"""
fields = [i.split("=") for i in string.split(',')]
for what,val in fields:
what = what.strip()
val = val.split()
if what.endswith("head"):
self.head = val
elif what.endswith("link"):
self.link = val
elif what.endswith("tail"):
self.tail = val
elif what == "charge":
self.charge = float(val[0])
elif what.endswith("name") and not self.name:
self.name = val[0]
if self.charge is None:
# Infer charge from head groups
self.charge = sum([headgroup_charges[bead] for bead in self.head])
def build(self):
"""Build/return a list of [(bead,x,y,z),...]"""
if self.coords:
return self.coords
if self.beads and self.template:
stuff = zip(self.beads,self.template)
self.coords = [[i,x,y,z] for i,(x,y,z) in stuff if i != "-"]
minz = min(zip(*self.coords)[3])
for i in self.coords:
i[3] -= minz
return self.coords
# Set beads/structure from head/link/tail
# Set bead names
if self.beads:
beads = list(self.beads)
else:
beads = [ headbeads[i] for i in self.head ]
beads.extend([ linkbeads[n]+str(i+1) for i,n in enumerate(self.link)])
for i,t in enumerate(self.tail):
beads.extend([n+chr(65+i)+str(j+1) for j,n in enumerate(t)])
taillength = max([0]+[len(i) for i in self.tail])
length = len(self.head)+taillength
# Add the pseudocoordinates for the head
rl = range(len(self.head))
struc = [(0,0,length-i) for i in rl]
# Add the linkers
rl = range(len(self.link))
struc.extend([(i%2,i/2,taillength) for i in rl ])
# Add the tails
for j,tail in enumerate(self.tail):
rl = range(len(tail))
struc.extend([(j%2,j/2,taillength-1-i) for i in rl])
# Scale the x/y (magic number -- should be scaling factor)
mx,my,mz = [ (max(i)+min(i))/2 for i in zip(*struc) ]
self.coords = [(i,0.25*(x-mx),0.25*(y-my),z) for i,(x,y,z) in zip(beads,struc)]
return self.coords
def h(self,head):
self.head = head.split()
def l(self,link):
self.link = link.split()
def t(self,tail):
self.tail = tail.split()
def c(self,charge):
self.charge = float(charge)
class Lipid_List(collections.MutableMapping):
"""Container class for lipid definitions"""
def __init__(self):
self.store = dict()
self.last = None
def __getitem__(self,key):
if key == -1:
return self.last
return self.store[key]
def __setitem__(self, key, value):
self.store[key] = value
def __delitem__(self, key):
del self.store[key]
def __iter__(self):
return iter(self.store)
def __len__(self):
return len(self.store)
def add(self,name=None,string=None):
lip = Lipid(name=name,string=string)
self.store[lip.name] = lip
self.last = lip.name
# 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 __nonzero__(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 = []
usrlip = Lipid_List()
mollist = []
usrnames = []
usrheads = []
usrlinks = []
usrtails = []
# Description
desc = ""
# Option list
options = [
# option type number default description
"""
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, 0, 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(usrnames.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")),
("-m", Option(mollist.append, 1, None, "Read molecule definitions from file")),
]
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"]
## I. STRUCTURES
## a. LIPIDS
liplist = Lipid_List()
# First add internal lipids
for name,lip in lipidsa.items():
moltype = lip[0]
template = zip(lipidsx[moltype],lipidsy[moltype],lipidsz[moltype])
liplist[name] = Lipid(name=name,beads=lip[1],template=template)
# Then add lipids from file
for filename in mollist:
stuff = open(filename).read().split("@INSANE")
for group in stuff[1:]:
lines = group.split("\n")
lipdef = lines.pop(0)
beads = None
for line in lines:
if line.startswith('[') or not line.strip():
break
if "@BEADS" in line:
beads = line.split("@BEADS")[1].split()
lip = Lipid(string=lipdef,beads=beads)
liplist[lip.name] = lip
# Last, add lipids from command line
for name, head, link, tail in zip(usrnames,usrheads,usrlinks,usrtails):
heads = head.split()
linkers = link.split()
tails = tail.split()
if len(tails) != len(linkers):
print "Error, Number of tails has to equal number of linkers"
sys.exit(1)
liplist[name] = Lipid(name=name,head=heads,link=linkers,tail=tails)
# 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